README
======

Dataset title:
Data for: Persistent and Compartmentalized T cell Immunity in ALS

Recommended Citation:  
https://doi.org/10.48723/cypd-qp27
See the Researchdata.se catalogue entry for this dataset - accessible via the DOI link above - for compete metadata, including the dataset description, contact information and information about how to obtain the dataset. 


Responsible organization:
Karolinska Institutet

Description: 
Human single cell RNA sequencing and TCR sequencing data (fastq file format) from ALS patients and demographic information. See list of variables in meta dataset below: 
sample_id: sample ID number. sample ID number. ID starting with P was taken around diagnosis. ID starting with FU were taken at minimum 1 year after diagnosis.	(PX_csf; PX_pbmc; FUX_csf; FUX_pbmc)
participant: participant's ID; used to link samples taken at diagnose with follow up samples (caseX)
sex: sex of participants M (male), F (female)
age_diagnosis: participant's age at diagnosis
age_sampling: participant's age at sample collection
experiment: information if either scRNA sequencing or TCR sequencing was performed (scRNAseq or TCR seq)
biospeciment: information if the cells were isolated from either blood or CSF (CSF or PBMC)
batch: batch number; samples with the same number were sequenced together (batchX)
fastq_file: name of the deposited fastq file (filename.fastq)


Access restrictions: This dataset contains personal data and is subject to legal protections. This dataset can be requested from the Researchdata.se research data catalog using the link above. In addition, the data use is restricted to research purposes, and the requesting third party require their own local ethical approval.

Essential information for dataset reuse.
----------------------------------------

Provide essential information about the data collection that secondary users will need to know in order to reuse the dataset or understand its contents. This typically includes information about sampling, experiment or survey configurations, which are especially important if different datafiles contain measurements for different times, locations, levels, population samples, etc.

If any special software is needed to read the data files, note how to obtain it.

If the dataset includes code, provide basic instructions for how to run the code. 

Dataset organization
--------------------
The dataset has an approximate size of 1.1 TB. The sequencing files are in .fastq.gz format. The link between file name and participant is found in in the file Metadata_2026-229.xlsx


The documentation folder contains:
- README_2026-229.txt
- variables_2026-229.xlsx
- Method_2026-229.docx

The data folder contains:
- Metadata_2026-229.xlsx
- 14 folders containing the sequencing data:

Folder P28352_GEX:
P28352_1009: 	P28352_1009_S9_L004_R2_001.fastq.gz
		P28352_1009_S9_L004_R1_001.fastq.gz
		P28352_1009_S9_L003_R2_001.fastq.gz
		P28352_1009_S9_L003_R1_001.fastq.gz

P28352_1010:	P28352_1010_S10_L004_R2_001.fastq.gz
		P28352_1010_S10_L004_R1_001.fastq.gz
		P28352_1010_S10_L003_R2_001.fastq.gz
		P28352_1010_S10_L003_R1_001.fastq.gz

P28352_1001	P28352_1001_S1_L004_R2_001.fastq.gz
		P28352_1001_S1_L004_R1_001.fastq.gz
		P28352_1001_S1_L003_R2_001.fastq.gz
		P28352_1001_S1_L003_R1_001.fastq.gz

P28352_1002	P28352_1002_S2_L004_R2_001.fastq.gz
		P28352_1002_S2_L004_R1_001.fastq.gz
		P28352_1002_S2_L003_R2_001.fastq.gz
		P28352_1002_S2_L003_R1_001.fastq.gz

P28352_1014 	P28352_1014_S14_L004_R2_001.fastq.gz
		P28352_1014_S14_L004_R1_001.fastq.gz
		P28352_1014_S14_L003_R2_001.fastq.gz
		P28352_1014_S14_L003_R1_001.fastq.gz

P28352_1003	P28352_1003_S3_L004_R2_001.fastq.gz
		P28352_1003_S3_L004_R1_001.fastq.gz
		P28352_1003_S3_L003_R2_001.fastq.gz
		P28352_1003_S3_L003_R1_001.fastq.gz

P28352_1004	P28352_1004_S4_L004_R2_001.fastq.gz
		P28352_1004_S4_L004_R1_001.fastq.gz
		P28352_1004_S4_L003_R2_001.fastq.gz
		P28352_1004_S4_L003_R1_001.fastq.gz

P28352_1011	P28352_1011_S11_L004_R2_001.fastq.gz
		P28352_1011_S11_L004_R1_001.fastq.gz
		P28352_1011_S11_L003_R2_001.fastq.gz
		P28352_1011_S11_L003_R1_001.fastq.gz

P28352_1012	P28352_1012_S12_L004_R2_001.fastq.gz
		P28352_1012_S12_L004_R1_001.fastq.gz
		P28352_1012_S12_L003_R2_001.fastq.gz
		P28352_1012_S12_L003_R1_001.fastq.gz

P28352_1007	P28352_1007_S7_L004_R2_001.fastq.gz
		P28352_1007_S7_L004_R1_001.fastq.gz
		P28352_1007_S7_L003_R2_001.fastq.gz
		P28352_1007_S7_L003_R1_001.fastq.gz

P28352_1008	P28352_1008_S8_L004_R2_001.fastq.gz
		P28352_1008_S8_L004_R1_001.fastq.gz
		P28352_1008_S8_L003_R2_001.fastq.gz
		P28352_1008_S8_L003_R1_001.fastq.gz

P28353_1013	P28352_1013_S13_L004_R2_001.fastq.gz
		P28352_1013_S13_L004_R1_001.fastq.gz
		P28352_1013_S13_L003_R2_001.fastq.gz
		P28352_1013_S13_L003_R1_001.fastq.gz

Folder P28353_TCR:
P28353_1013	P28353_1013_S13_L002_R2_001.fastq.gz
		P28353_1013_S13_L002_R1_001.fastq.gz
		P28353_1013_S13_L001_R2_001.fastq.gz
		P28353_1013_S13_L001_R1_001.fastq.gz

P28353_1016	P28353_1016_S16_L002_R2_001.fastq.gz
		P28353_1016_S16_L002_R1_001.fastq.gz
		P28353_1016_S16_L001_R2_001.fastq.gz
		P28353_1016_S16_L001_R1_001.fastq.gz

P28353_1001	P28353_1001_S1_L002_R2_001.fastq.gz
		P28353_1001_S1_L002_R1_001.fastq.gz
		P28353_1001_S1_L001_R2_001.fastq.gz
		P28353_1001_S1_L001_R1_001.fastq.gz

P28353_1002	P28353_1002_S2_L002_R2_001.fastq.gz
		P28353_1002_S2_L002_R1_001.fastq.gz
		P28353_1002_S2_L001_R2_001.fastq.gz
		P28353_1002_S2_L001_R1_001.fastq.gz

P28353_1015	P28353_1015_S15_L002_R2_001.fastq.gz
		P28353_1015_S15_L002_R1_001.fastq.gz
		P28353_1015_S15_L001_R2_001.fastq.gz
		P28353_1015_S15_L001_R1_001.fastq.gz

P28353_1018	P28353_1018_S18_L002_R2_001.fastq.gz
		P28353_1018_S18_L002_R1_001.fastq.gz
		P28353_1018_S18_L001_R2_001.fastq.gz
		P28353_1018_S18_L001_R1_001.fastq.gz

P28353_1004	P28353_1004_S4_L002_R2_001.fastq.gz
		P28353_1004_S4_L002_R1_001.fastq.gz
		P28353_1004_S4_L001_R2_001.fastq.gz
		P28353_1004_S4_L001_R1_001.fastq.gz

P28353_1005	P28353_1005_S5_L002_R2_001.fastq.gz
		P28353_1005_S5_L002_R1_001.fastq.gz
		P28353_1005_S5_L001_R2_001.fastq.gz
		P28353_1005_S5_L001_R1_001.fastq.gz

P28353_1014	P28353_1014_S14_L002_R2_001.fastq.gz
		P28353_1014_S14_L002_R1_001.fastq.gz
		P28353_1014_S14_L001_R2_001.fastq.gz
		P28353_1014_S14_L001_R1_001.fastq.gz

P28353_1017	P28353_1017_S17_L002_R2_001.fastq.gz
		P28353_1017_S17_L002_R1_001.fastq.gz
		P28353_1017_S17_L001_R2_001.fastq.gz
		P28353_1017_S17_L001_R1_001.fastq.gz

P28353_1010	P28353_1010_S10_L002_R2_001.fastq.gz
		P28353_1010_S10_L002_R1_001.fastq.gz
		P28353_1010_S10_L001_R2_001.fastq.gz
		P28353_1010_S10_L001_R1_001.fastq.gz

P28353_1011	P28353_1011_S11_L002_R2_001.fastq.gz
		P28353_1011_S11_L002_R1_001.fastq.gz
		P28353_1011_S11_L001_R2_001.fastq.gz
		P28353_1011_S11_L001_R1_001.fastq.gz


Folder P29358_GEX:
P29358_1007	P29358_1007_S7_L002_R2_001.fastq.gz
		P29358_1007_S7_L002_R1_001.fastq.gz
		P29358_1007_S7_L001_R2_001.fastq.gz
		P29358_1007_S7_L001_R1_001.fastq.gz

P29358_1008	P29358_1008_S8_L002_R2_001.fastq.gz
		P29358_1008_S8_L002_R1_001.fastq.gz
		P29358_1008_S8_L001_R2_001.fastq.gz
		P29358_1008_S8_L001_R1_001.fastq.gz

P29358_1005	P29358_1005_S5_L002_R2_001.fastq.gz
		P29358_1005_S5_L002_R1_001.fastq.gz
		P29358_1005_S5_L001_R2_001.fastq.gz
		P29358_1005_S5_L001_R1_001.fastq.gz

P29358_1006	P29358_1006_S6_L002_R2_001.fastq.gz
		P29358_1006_S6_L002_R1_001.fastq.gz
		P29358_1006_S6_L001_R2_001.fastq.gz
		P29358_1006_S6_L001_R1_001.fastq.gz

P29358_1003	P29358_1003_S3_L002_R2_001.fastq.gz
		P29358_1003_S3_L002_R1_001.fastq.gz
		P29358_1003_S3_L001_R2_001.fastq.gz
		P29358_1003_S3_L001_R1_001.fastq.gz

P29358_1004	P29358_1004_S4_L002_R2_001.fastq.gz
		P29358_1004_S4_L002_R1_001.fastq.gz
		P29358_1004_S4_L001_R2_001.fastq.gz
		P29358_1004_S4_L001_R1_001.fastq.gz

P29358_1001	P29358_1001_S1_L002_R2_001.fastq.gz
		P29358_1001_S1_L002_R1_001.fastq.gz
		P29358_1001_S1_L001_R2_001.fastq.gz
		P29358_1001_S1_L001_R1_001.fastq.gz

P29358_1002	P29358_1002_S2_L002_R2_001.fastq.gz
		P29358_1002_S2_L002_R1_001.fastq.gz
		P29358_1002_S2_L001_R2_001.fastq.gz
		P29358_1002_S2_L001_R1_001.fastq.gz


Folder P29359_TCR:
P29359_1010	P29359_1010_S10_L002_R2_001.fastq.gz
		P29359_1010_S10_L002_R1_001.fastq.gz
		P29359_1010_S10_L001_R2_001.fastq.gz
		P29359_1010_S10_L001_R1_001.fastq.gz

P29359_1011	P29359_1011_S11_L002_R2_001.fastq.gz
		P29359_1011_S11_L002_R1_001.fastq.gz
		P29359_1011_S11_L001_R2_001.fastq.gz
		P29359_1011_S11_L001_R1_001.fastq.gz

P29359_1007	P29359_1007_S7_L002_R2_001.fastq.gz
		P29359_1007_S7_L002_R1_001.fastq.gz
		P29359_1007_S7_L001_R2_001.fastq.gz
		P29359_1007_S7_L001_R1_001.fastq.gz

P29359_1008	P29359_1008_S8_L002_R2_001.fastq.gz
		P29359_1008_S8_L002_R1_001.fastq.gz
		P29359_1008_S8_L001_R2_001.fastq.gz
		P29359_1008_S8_L001_R1_001.fastq.gz

P29359_1004	P29359_1004_S4_L002_R2_001.fastq.gz
		P29359_1004_S4_L002_R1_001.fastq.gz
		P29359_1004_S4_L001_R2_001.fastq.gz
		P29359_1004_S4_L001_R1_001.fastq.gz

P29359_1005	P29359_1005_S5_L002_R2_001.fastq.gz
		P29359_1005_S5_L002_R1_001.fastq.gz
		P29359_1005_S5_L001_R2_001.fastq.gz
		P29359_1005_S5_L001_R1_001.fastq.gz

P29359_1001	P29359_1001_S1_L002_R2_001.fastq.gz
		P29359_1001_S1_L002_R1_001.fastq.gz
		P29359_1001_S1_L001_R2_001.fastq.gz
		P29359_1001_S1_L001_R1_001.fastq.gz

P29359_1002	P29359_1002_S2_L002_R2_001.fastq.gz
		P29359_1002_S2_L002_R1_001.fastq.gz
		P29359_1002_S2_L001_R2_001.fastq.gz
		P29359_1002_S2_L001_R1_001.fastq.gz


Folder P29868_GEX:
P29868_1007	P29868_1007_S13_L004_R2_001.fastq.gz
		P29868_1007_S13_L004_R1_001.fastq.gz

P29868_1008	P29868_1008_S14_L004_R2_001.fastq.gz
		P29868_1008_S14_L004_R1_001.fastq.gz

P29868_1003	P29868_1003_S9_L004_R2_001.fastq.gz
		P29868_1003_S9_L004_R1_001.fastq.gz

P29868_1004	P29868_1004_S10_L004_R2_001.fastq.gz
		P29868_1004_S10_L004_R1_001.fastq.gz

P29868_1001	P29868_1001_S7_L004_R2_001.fastq.gz
		P29868_1001_S7_L004_R1_001.fastq.gz

P29868_1002	P29868_1002_S8_L004_R2_001.fastq.gz
		P29868_1002_S8_L004_R1_001.fastq.gz


Folder P29869_TCR:
P29869_1010	P29869_1010_S10_L001_R2_001.fastq.gz
		P29869_1010_S10_L001_R1_001.fastq.gz

P29869_1011	P29869_1011_S11_L001_R2_001.fastq.gz
		P29869_1011_S11_L001_R1_001.fastq.gz

P29869_1004	P29869_1004_S4_L001_R2_001.fastq.gz
		P29869_1004_S4_L001_R1_001.fastq.gz

P29869_1005	P29869_1005_S5_L001_R2_001.fastq.gz
		P29869_1005_S5_L001_R1_001.fastq.gz

P29869_1001	P29869_1001_S1_L001_R2_001.fastq.gz
		P29869_1001_S1_L001_R1_001.fastq.gz

P29869_1002	P29869_1002_S2_L001_R2_001.fastq.gz
		P29869_1002_S2_L001_R1_001.fastq.gz


Folder P32005_GEX:
P32005_1009	P32005_1009_S9_L001_R2_001.fastq.gz
		P32005_1009_S9_L001_R1_001.fastq.gz

P32005_1010	P32005_1010_S10_L001_R2_001.fastq.gz
		P32005_1010_S10_L001_R1_001.fastq.gz

P32005_1005	P32005_1005_S5_L001_R2_001.fastq.gz
		P32005_1005_S5_L001_R1_001.fastq.gz

P32005_1006	P32005_1006_S6_L001_R2_001.fastq.gz
		P32005_1006_S6_L001_R1_001.fastq.gz

P32005_1001	P32005_1001_S1_L001_R2_001.fastq.gz
		P32005_1001_S1_L001_R1_001.fastq.gz

P32005_1002	P32005_1002_S2_L001_R2_001.fastq.gz
		P32005_1002_S2_L001_R1_001.fastq.gz

P32005_1003	P32005_1003_S3_L001_R2_001.fastq.gz
		P32005_1003_S3_L001_R1_001.fastq.gz

P32005_1004	P32005_1004_S4_L001_R2_001.fastq.gz
		P32005_1004_S4_L001_R1_001.fastq.gz

P32005_1007	P32005_1007_S7_L001_R2_001.fastq.gz
		P32005_1007_S7_L001_R1_001.fastq.gz

P32005_1008	P32005_1008_S8_L001_R2_001.fastq.gz
		P32005_1008_S8_L001_R1_001.fastq.gz


Folder P32006_TCR:
P32006_1013	P32006_1013_S13_L002_R2_001.fastq.gz
		P32006_1013_S13_L002_R1_001.fastq.gz

P32006_1014	P32006_1014_S14_L002_R2_001.fastq.gz
		P32006_1014_S14_L002_R1_001.fastq.gz

P32006_1007	P32006_1007_S7_L002_R2_001.fastq.gz
		P32006_1007_S7_L002_R1_001.fastq.gz

P32006_1008	P32006_1008_S8_L002_R2_001.fastq.gz
		P32006_1008_S8_L002_R1_001.fastq.gz

P32006_1001	P32006_1001_S1_L002_R2_001.fastq.gz
		P32006_1001_S1_L002_R1_001.fastq.gz

P32006_1002	P32006_1002_S2_L002_R2_001.fastq.gz
		P32006_1002_S2_L002_R1_001.fastq.gz

P32006_1004	P32006_1004_S4_L002_R2_001.fastq.gz
		P32006_1004_S4_L002_R1_001.fastq.gz

P32006_1005	P32006_1005_S5_L002_R2_001.fastq.gz
		P32006_1005_S5_L002_R1_001.fastq.gz

P32006_1010	P32006_1010_S10_L002_R2_001.fastq.gz
		P32006_1010_S10_L002_R1_001.fastq.gz

P32006_1011	P32006_1011_S11_L002_R2_001.fastq.gz
		P32006_1011_S11_L002_R1_001.fastq.gz


Folder P34113_GEX:
P34113_1001	P34113_1001_S1_L002_R2_001.fastq.gz
		P34113_1001_S1_L002_R1_001.fastq.gz

P34113_1002	P34113_1002_S2_L002_R2_001.fastq.gz
		P34113_1002_S2_L002_R1_001.fastq.gz


Folder P34114_TCR:
P34114_1001	P34114_1001_S1_L001_R2_001.fastq.gz
		P34114_1001_S1_L001_R1_001.fastq.gz

P34114_1002	P34114_1002_S2_L001_R2_001.fastq.gz
		P34114_1002_S2_L001_R1_001.fastq.gz


Folder P36009_TCR:
P36009_1010	P36009_1010_S10_L001_R2_001.fastq.gz
		P36009_1010_S10_L001_R1_001.fastq.gz

P36009_1011	P36009_1011_S11_L001_R1_001.fastq.gz
		P36009_1011_S11_L001_R2_001.fastq.gz


Folder P36010_GEX: 
P36010_1007	P36010_1007_S7_L004_R2_001.fastq.gz
		P36010_1007_S7_L004_R1_001.fastq.gz

P36010_1008	P36010_1008_S8_L004_R1_001.fastq.gz
		P36010_1008_S8_L004_R2_001.fastq.gz


Folder P37355_GEX:
P37355_1003	P37355_1003_S3_L001_R1_001.fastq.gz
		P37355_1003_S3_L001_R2_001.fastq.gz

P37355_1004	P37355_1004_S4_L001_R1_001.fastq.gz
		P37355_1004_S4_L001_R2_001.fastq.gz


Folder P37355_TCR:
P37355_1008	P37355_1008_S8_L002_R2_001.fastq.gz
		P37355_1008_S8_L002_R1_001.fastq.gz

P37355_1009	P37355_1009_S9_L002_R2_001.fastq.gz
		P37355_1009_S9_L002_R1_001.fastq.gz

Datafile descriptions
----------------------

The file Method_2026-229.docx contains information on the experimental protocol used to isolate immune cells from both CSF and blood as wells as the information on the library preparation and sequencing. 

The file metadata_2016-229 contains the following variables:

sample_id: sample ID number. sample ID number. ID starting with P was taken around diagnosis. ID starting with FU were taken at minimum 1 year after diagnosis.	(PX_csf; PX_pbmc; FUX_csf; FUX_pbmc)
participant: participant's ID; used to link samples taken at diagnose with follow up samples (caseX)
sex: sex of participants M (male), F (female)
age_diagnosis: participant's age at diagnosis
age_sampling: participant's age at sample collection
experiment: information if either scRNA sequencing or TCR sequencing was performed (scRNAseq or TCR seq)
biospeciment: information if the cells were isolated from either blood or CSF (CSF or PBMC)
batch: batch number; samples with the same number were sequenced together (batchX)
fastq_file: name of the deposited fastq file (filename.fastq)


These folders contain the scRNA sequencing files:
P28352_GEX
P29358_GEX
P29868_GEX
P32005_GEX
P34113_GEX
P36010_GEX
P37355_GEX

These folders contain the TCR sequencing files:
P28353_TCR
P29359_TCR
P29869_TCR
P32006_TCR
P34114_TCR
P36009_TCR
P37355_TCR

Reference information
---------------------
Abbreviations:
TCR seq: 	T cell receptor sequencing
scRNAseq:	single cell RNA sequencing
CSF:		Cerebrospinal fluid
PBMC:		Peripheral Blood Mononuclear Cell

