title: Feature-2021-04-29-2-4

city: Philadelphia

first: Alexander

middle: C

last: Huang

state: PA

address: 421 Curie Boulevard

department: Department of Hematology/Oncology

institute: University of Pennsylvania

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-29-2-4_barcodes.tsv.gz
2021-04-29-2-4_features.tsv.gz
2021-04-29-2-4_matrix.mtx.gz

data_processing:
CellRanger v7.0.0 count was run on GEX and ADT fastqs together to generate a matrix containing both gene and protein counts, supplying a Feature Reference csv file containing the feature barcode library. CellRanger vdj was run on VDJ reads.
Assembly: GRCh38-2020-A
Supplementary files format and content: CellRanger output files containing both GEX and ADT data: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz (linked to the corresponding GEX sample records)
Supplementary files format and content: CellRanger output files containing VDJ data: airr_rearrangement.tsv, clonotypes.csv, filtered_contig.fasta, filtered_contig_annotations.csv
Library strategy: CITE-seq

source_name: peripheral blood

extract_protocol:
For PBMC samples, 300,000 cells from each sample were sorted on a DAPI negative gate for live cells. Pan T cell samples were additionally gated on CD3+. Non-naïve T cell sorted samples were additionally gated as cells that were not CD45RA+CCR7+. Non-naïve CD4 and CD8 sorted samples were additionally gated on CD4+ and CD8+, respectively.
Cells were with either a panel of 60 or 101 Total-Seq-C antibodies that also labeled samples individually through sample-specific barcodes. Cells were pooled and loaded on the 10x Chromium Next GEM Single Cell 5' Kit (v2) using a superloading strategy, mixing cells from different samples in each 10x lane. TCR sequences were enriched using the human V(D)J B/T cell enrichment. Libraries were prepared according to manufacturer’s protocol (10x Genomics).

value: peripheral blood

value: CD3+ T cells

tag: disease

value: melanoma

value: immune checkpoint blockade

tag: isolate

value: 12-267 Follow Up 3 (hash4), 13-471 Follow Up 1 (hash9), 13-508 Follow Up 1 (hash8), 14-1138 Follow Up 2 (hash10), 14-1319 Follow Up 2 (hash2)

tag: feature panel


title: CTRL_SUNI_PD_03x41xx_X017_S11_L021_B1_T1_P037.pe.q10.sort.rmdup.bam

status: Public on Jul 30 2024

type: SRA

city: Stanford

first: Eloise

last: Berson

address: 291 Campus Drive

country: USA

institute: Stanford University

description: Bulk ATAC-seq CTRL Sustantia Nigra

library_source: genomic

data_processing:
The count normalized peak matrix was derived using featureCount.
Assembly: hg38
Supplementary files format and content: csv

molecule: genomic DNA

organism: Homo sapiens

source_name: brain

extract_protocol:
Nuclei were isolated from frozen tissue in accordance with protocol dx.doi.org/10.17504/protocols.io.6t8herw. After isolation, nuclei were cryopreserved in BAM Banker (Wako Chemicals) and stored at -80°C for use in other assays such as scATAC-seq and HiChIP.
Transposed fragments were purified and amplified as described previously (Buenrostro et al., Nature Methods 2015) with slight modification. Briefly, transposed fragments were pre-amplified for 3 cycles. Concentration of pre-amplified fragments was determined by qPCR and this concentration was used to estimate the total number of cycles required to obtain 160 femtomoles of fragments. A second PCR was performed to amplify the pre-amplified fragments for the desired number of cycles. Final libraries were again purified. Prior to sequencing, libraries were pooled and run on a 6% PAGE gel and excess primers and primer dimers below 125 bp were removed.

tag: tissue

value: brain

tag: cell type

value: bulk


title: 12132022_w62102681-V1-2_S450_R2C2_21F_S260

city: Toronto

first: Jeff

last: Wrana

state: Ontario

address: 600 University Avenue

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

description:
positive sample
run31_R1BC_count_table.txt
run31_R2BC_count_table.txt
run31_count_table.txt
run31_BC_pair_analysis_filenames.txt

library_source: transcriptomic

data_processing:
Samples sequenced using Illumina NextSeq and demultiplexed using bcl2fastq.
Reads were aligned with Bowtie to standard amplicons from original screens, as well as two rounds of trimming and mapping to forward and reverse 5 bp barcode references.
Counts were quantified with HTSeq-count (v0.13.5 with settings -f sam -t CDS).
Custom python scripts (python v3.9, available at https://github.com/wrana-lab) were used to aggregate the forward and reverse barcodes.
Final analysis of data was done in R v4.1.1.
Assembly: Custom genome consists of amplicons targeting GRCh38 and Sars-CoV-2 (Wuhan-Hu-1) as well as customized sequences for our forward and reverse 5 bp barcode sequences
Supplementary files format and content: run27_R1BC_count_table.txt; run31_R1BC_count_table.txt; run38_R1BC_count_table.txt; run46_R1BC_count_table.txt; run139_R1BC_count_table.txt; run141p3_R1BC_count_table.txt; run141p6_R1BC_count_table.txt
Supplementary files format and content: run27_R2BC_count_table.txt; run31_R2BC_count_table.txt; run38_R2BC_count_table.txt; run46_R2BC_count_table.txt; run139_R2BC_count_table.txt; run141p3_R2BC_count_table.txt; run141p6_R2BC_count_table.txt
Supplementary files format and content: run27_count_table.txt; run31_count_table.txt; run38_count_table.txt; run46_count_table.txt; run139_count_table.txt; run141p3_count_table.txt; run141p6_count_table.txt
Supplementary files format and content: run27_BC_pair_analysis_filenames.txt; run31_BC_pair_analysis_filenames.txt; run38_BC_pair_analysis_filenames.txt; run46_BC_pair_analysis_filenames.txt; run139_BC_pair_analysis_filenames.txt; run141p3_BC_pair_analysis_filenames.txt; run141p6_BC_pair_analysis_filenames.txt

molecule: total RNA

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: human nasopharyngeal swab

extract_protocol:
RNA from positive samples was extracted with MGIEasy Nucleic Acid Extraction Kit.
Libraries were pooled by Biomex Fx. Each sample was pooled (7uL/sample) and library PCR products were purified twice with SPRIselect beads ratio 1:1 (beads/library) (A66514, Beckman Coulter)
Other: RNAseq with limited amplicons.

value: human nasopharyngeal swab

tag: bc run_id

tag: pipeline version

value: BC


title: GEX-2021-04-29-2-4

molecule: polyA RNA

tag: treatment


title: TCR-2021-04-29-2-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-29-2-4_airr_rearrangement.tsv
2021-04-29-2-4_clonotypes.csv
2021-04-29-2-4_filtered_contig.fasta
2021-04-29-2-4_filtered_contig_annotations.csv


title: TCR-2021-04-29-2-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-29-2-3_airr_rearrangement.tsv
2021-04-29-2-3_clonotypes.csv
2021-04-29-2-3_filtered_contig.fasta
2021-04-29-2-3_filtered_contig_annotations.csv


title: CTRL_SUNI_PD_01x31xx_X014_S10_L020_B1_T2_P027.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra


title: GEX-2021-04-29-2-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-29-2-3_barcodes.tsv.gz
2021-04-29-2-3_features.tsv.gz
2021-04-29-2-3_matrix.mtx.gz


title: 12132022_w62102677-V1-2_S1042_R2C2_21N_S431


title: 12132022_w62102709-V1-2_S884_R2C2_17L_S386


title: CTRL_SUNI_PD_01x31xx_X014_S10_L019_B1_T1_P028.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra


title: 12132022_w62102674-V1-2_S276_R2C2_13D_S208


title: YT-Indy transduced with CD3, CD8, a3a TCR; antigen-exposed

city: Vancouver

first: Govinda

last: Sharma

address: 7th floor, 675 W 10th Ave

department: Michael Smith Genome Sciences Centre

institute: British Columbia Cancer Research Institute

data_processing:
Trimmomatic v0.36 run in paired end mode. Seed mismatches set to 2. Palindrome clipping threshold set to 30 matches. Simple clip threshold to 10 matches. Minimum adapter length to 1bp with the “keepBothPairs” option enabled. Leading and Trailing qualities set to 3. Sliding window size set to 4bp (required quality of 15). Minimum read length was thresholded at 30bp.
Trimmed reads mapped to reference genome using STAR aligner v2.5.2b run with default parameters
Alignment output sorted and indexed with Samtools. Unique gene hit counts calculated with featureCounts from Subread package v1.5.2. Largest overlap option turned on.
Differential analysis was performed using DESeq2 v1.30.0 with default parameters
Assembly: GRCh38
Supplementary files format and content: Pairwise DESeq2 normalized read counts for samples to be compared, in csv format

source_name: YT-Indy

growth_protocol:
All cells maintained in RPMI-1640 supplemented with 2 mM GlutaMAX, 1 mM sodium pyruvate, 50 μM β-mercaptoethanol, 10 mM HEPES, 100 U/mL penicillin, 100 U/mL streptomycin, 1X MycoZap™ Prophylactic (Lonza) and 10% heat-inactivated fetal bovine serum
Primary T cells were directly isolated from healthy donor PBMC samples by FACS, stimulated on anti-CD3/28 mAb coated plates for 24h, and allowed to expand for 12 days prior to analysis

extract_protocol:
Flash-frozen pellets were shipped on dry-ice to Azenta/Genewiz. RNA extraction and QC was conducted according to supplier SOPs (July 2022)
polyA selection and RNA-seq library construction were conducted according to supplier SOPs (Azenta/Genewiz, August 2022)

treatment_protocol: Cells were either co-cultured with K562-based APC expressing HLA-A*01:01 transgene and MAGEA3 antigen for 12h or left non-co-cultured. All conditions were FACS re-purified and immediately flash frozen

tag: cell line

value: YT-Indy

value: 12 hour co-culture with target APC expressing known cognate epitope from MAGEA3


title: TCR-2021-04-29-2-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-29-2-2_airr_rearrangement.tsv
2021-04-29-2-2_clonotypes.csv
2021-04-29-2-2_filtered_contig.fasta
2021-04-29-2-2_filtered_contig_annotations.csv


title: CTRL_SUNI_PD_00x38xx_X015_S10_L044_B1_T2_P027.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra


title: GEX-2021-04-29-2-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-29-2-2_barcodes.tsv.gz
2021-04-29-2-2_features.tsv.gz
2021-04-29-2-2_matrix.mtx.gz


title: Feature-2021-04-29-2-2


title: CTRL_SUNI_PD_00x38xx_X015_S10_L043_B1_T1_P029.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra


title: 12132022_w62102672-V1-2_S1145_R2C2_4P_S459


title: TCR-2021-04-29-2-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-29-2-1_airr_rearrangement.tsv
2021-04-29-2-1_clonotypes.csv
2021-04-29-2-1_filtered_contig.fasta
2021-04-29-2-1_filtered_contig_annotations.csv

value: 12-211 Follow Up 3 (hash10), 12-267 Follow Up 2 (hash8), 13-471 Follow Up 2 (hash9), 14-1319 Follow Up 1 (hash4), 17-2865 Follow Up 2 (hash2)


title: CTRL_MDFG_PD_16x32xx_X016_S11_L070_B1_T2_P022.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle frontal Gyri


title: Feature-2021-04-29-2-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-29-2-1_barcodes.tsv.gz
2021-04-29-2-1_features.tsv.gz
2021-04-29-2-1_matrix.mtx.gz


title: GEX-2021-04-29-2-1


title: CTRL_MDFG_PD_16x32xx_X016_S11_L069_B1_T1_P026.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle frontal Gyri


title: TCR-2021-04-29-1-8

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-29-1-8_airr_rearrangement.tsv
2021-04-29-1-8_clonotypes.csv
2021-04-29-1-8_filtered_contig.fasta
2021-04-29-1-8_filtered_contig_annotations.csv


title: GEX-2021-04-29-1-8

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-29-1-8_barcodes.tsv.gz
2021-04-29-1-8_features.tsv.gz
2021-04-29-1-8_matrix.mtx.gz


title: Feature-2021-04-29-1-8


title: 12132022_w62102649-V1-2_S895_R2C2_21L_S389


title: TCR-2021-04-29-1-7

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-29-1-7_airr_rearrangement.tsv
2021-04-29-1-7_clonotypes.csv
2021-04-29-1-7_filtered_contig.fasta
2021-04-29-1-7_filtered_contig_annotations.csv


title: 12132022_W62102638-V1-2_S745_R2C2_20J_S346


title: GEX-2021-04-29-1-7

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-29-1-7_barcodes.tsv.gz
2021-04-29-1-7_features.tsv.gz
2021-04-29-1-7_matrix.mtx.gz


title: Feature-2021-04-29-1-7


title: 12132022_w62102657-V1-2_S255_R2C2_6D_S201


title: TCR-2021-04-29-1-6

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-29-1-6_airr_rearrangement.tsv
2021-04-29-1-6_clonotypes.csv
2021-04-29-1-6_filtered_contig.fasta
2021-04-29-1-6_filtered_contig_annotations.csv

value: 12-211 Follow Up 1 (hash9), 12-267 Baseline (hash4), 13-508 Follow Up 3 (hash8), 14-1138 Baseline (hash10), 17-2865 Baseline (hash2)


title: CTRL_MDFG_PD_16x10xx_X025_S09_L015_B1_T1_P051.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle frontal Gyri


title: 12132022_w62102579-V1-2_S148_R2C2_21B_S172


title: Feature-2021-04-29-2-3


title: Feature-2021-04-29-1-6

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-29-1-6_barcodes.tsv.gz
2021-04-29-1-6_features.tsv.gz
2021-04-29-1-6_matrix.mtx.gz


title: TCR-2021-04-29-1-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-29-1-5_airr_rearrangement.tsv
2021-04-29-1-5_clonotypes.csv
2021-04-29-1-5_filtered_contig.fasta
2021-04-29-1-5_filtered_contig_annotations.csv


title: 12132022_W62102523-V1-2_S264_R2C2_9D_S204


title: GEX-2021-04-29-1-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-29-1-5_barcodes.tsv.gz
2021-04-29-1-5_features.tsv.gz
2021-04-29-1-5_matrix.mtx.gz


title: CTRL_MDFG_PD_15x78xx_X006_S10_L044_B1_T2_P011.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle frontal Gyri


title: 12132022_W62102669-V1-2_S106_R2C2_7B_S158


title: GEX-2021-04-29-1-6


title: Feature-2021-04-29-1-5


title: CTRL_MDFG_PD_09x50xx_X021_S03_L005_B1_T1_PMRG.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle frontal Gyri


title: GEX-2021-04-29-1-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-29-1-4_barcodes.tsv.gz
2021-04-29-1-4_features.tsv.gz
2021-04-29-1-4_matrix.mtx.gz


title: 12132022_W62102534-V1-2_S124_R2C2_13B_S164

description:
positive sample
run31_R1BC_count_table.txt
run31_R2BC_count_table.txt
run31_count_table.txt
run31_BC_pair_analysis_filenames.txt


title: TCR-2021-04-29-1-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-29-1-4_airr_rearrangement.tsv
2021-04-29-1-4_clonotypes.csv
2021-04-29-1-4_filtered_contig.fasta
2021-04-29-1-4_filtered_contig_annotations.csv


title: CTRL_MDFG_PD_09x50xx_X021_S03_L006_B1_T2_P043.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle frontal Gyri


title: Feature-2021-04-29-1-4


title: CTRL_MDFG_PD_16x10xx_X025_S09_L016_B1_T2_P050.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle frontal Gyri


title: CTRL_MDFG_PD_09x35xx_X016_S12_L072_B1_T2_P029.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle frontal Gyri


title: TCR-2021-04-29-1-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-29-1-3_airr_rearrangement.tsv
2021-04-29-1-3_clonotypes.csv
2021-04-29-1-3_filtered_contig.fasta
2021-04-29-1-3_filtered_contig_annotations.csv

value: 12-211 Follow Up 2 (hash9), 12-267 Follow Up 1 (hash4), 13-508 Follow Up 2 (hash8), 14-1138 Follow Up 3 (hash10), 14-1319 Baseline (hash2)


title: GEX-2021-04-29-1-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-29-1-3_barcodes.tsv.gz
2021-04-29-1-3_features.tsv.gz
2021-04-29-1-3_matrix.mtx.gz


title: CTRL_MDFG_PD_09x35xx_X016_S12_L071_B1_T1_P023.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle frontal Gyri


title: 12132022_W62102452-V1-2_S570_R2C2_11H_S294


title: Feature-2021-04-29-1-3


title: GEX-2021-04-29-1-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-29-1-2_barcodes.tsv.gz
2021-04-29-1-2_features.tsv.gz
2021-04-29-1-2_matrix.mtx.gz


title: Feature-2021-04-29-1-2


title: CTRL_MDFG_PD_15x78xx_X006_S10_L043_B1_T1_P012.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle frontal Gyri


title: CTRL_MDFG_PD_05x16xx_X008_S09_L090_B1_T2_PMRG.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle frontal Gyri


title: TCR-2021-04-29-1-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-29-1-2_airr_rearrangement.tsv
2021-04-29-1-2_clonotypes.csv
2021-04-29-1-2_filtered_contig.fasta
2021-04-29-1-2_filtered_contig_annotations.csv


title: 12132022_W62102439-V1-2_S133_R2C2_16B_S167


title: 12132022_w62102440-V1-2_S1178_R2C2_15P_S470


title: CTRL_MDFG_PD_05x16xx_X008_S09_L089_B1_T1_P012.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle frontal Gyri


title: TCR-2021-04-29-1-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-29-1-1_airr_rearrangement.tsv
2021-04-29-1-1_clonotypes.csv
2021-04-29-1-1_filtered_contig.fasta
2021-04-29-1-1_filtered_contig_annotations.csv


title: GEX-2021-04-29-1-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-29-1-1_barcodes.tsv.gz
2021-04-29-1-1_features.tsv.gz
2021-04-29-1-1_matrix.mtx.gz


title: 12132022_W62102499-V1-2_S848_R2C2_5L_S374


title: 12132022_w62102438-V1-2_S998_R2C2_6N_S417


title: CTRL_MDFG_PD_04x38xx_X005_S04_L008_B1_T2_P010.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle frontal Gyri


title: TCR-2021-04-28-2-7

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-2-7_airr_rearrangement.tsv
2021-04-28-2-7_clonotypes.csv
2021-04-28-2-7_filtered_contig.fasta
2021-04-28-2-7_filtered_contig_annotations.csv

value: 12-211 Baseline (hash9), 13-471 Baseline (hash8), 13-508 Baseline (hash4), 14-1138 Follow Up 1 (hash10), 17-2865 Follow Up 1 (hash2)


title: 12132022_W62102490-V1-2_S718_R2C2_11J_S337


title: 12132022_w62102427-V1-2_S730_R2C2_15J_S341


title: Feature-2021-04-28-2-7

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-2-7_barcodes.tsv.gz
2021-04-28-2-7_features.tsv.gz
2021-04-28-2-7_matrix.mtx.gz


title: GEX-2021-04-28-2-7


title: CTRL_MDFG_PD_04x38xx_X005_S04_L007_B1_T1_PMRG.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle frontal Gyri


title: CTRL_MDFG_PD_03x66xx_X018_S11_L022_B1_T2_P034.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle frontal Gyri


title: 12132022_w62102418-V1-2_S405_R2C2_6F_S245


title: TCR-2021-04-28-2-6

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-2-6_airr_rearrangement.tsv
2021-04-28-2-6_clonotypes.csv
2021-04-28-2-6_filtered_contig.fasta
2021-04-28-2-6_filtered_contig_annotations.csv


title: Feature-2021-04-28-2-6

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-2-6_barcodes.tsv.gz
2021-04-28-2-6_features.tsv.gz
2021-04-28-2-6_matrix.mtx.gz


title: 12132022_w62102413-V1-2_S1151_R2C2_6P_S461


title: TCR-2021-04-28-2-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-2-5_airr_rearrangement.tsv
2021-04-28-2-5_clonotypes.csv
2021-04-28-2-5_filtered_contig.fasta
2021-04-28-2-5_filtered_contig_annotations.csv


title: CTRL_MDFG_PD_03x66xx_X018_S11_L021_B1_T1_P030.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle frontal Gyri


title: GEX-2021-04-28-2-6


title: CTRL_MDFG_PD_03x41xx_X026_S02_L026_B1_T2_P049.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle frontal Gyri


title: GEX-2021-04-28-2-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-2-5_barcodes.tsv.gz
2021-04-28-2-5_features.tsv.gz
2021-04-28-2-5_matrix.mtx.gz


title: 12132022_W62102402-V1-2_S420_R2C2_11F_S250


title: Feature-2021-04-28-2-5


title: GEX-2021-04-28-2-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-2-4_barcodes.tsv.gz
2021-04-28-2-4_features.tsv.gz
2021-04-28-2-4_matrix.mtx.gz

value: 13-344 Follow Up 3 (hash9), 13-348 Baseline (hash10), 14-745 Follow Up 3 (hash8), 17-3041 Follow Up 1 (hash2), 18-3313 Follow Up 2 (hash4)


title: CTRL_MDFG_PD_03x41xx_X026_S02_L025_B1_T1_P050.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle frontal Gyri


title: Feature-2021-04-29-1-1


title: CTRL_MDFG_PD_03x39xx_X005_S05_L010_B1_T2_P011.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle frontal Gyri


title: Feature-2021-04-28-2-4


title: 12132022_w62102387-V1-2_S878_R2C2_15L_S384


title: TCR-2021-04-28-2-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-2-3_airr_rearrangement.tsv
2021-04-28-2-3_clonotypes.csv
2021-04-28-2-3_filtered_contig.fasta
2021-04-28-2-3_filtered_contig_annotations.csv


title: Feature-2021-04-28-2-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-2-3_barcodes.tsv.gz
2021-04-28-2-3_features.tsv.gz
2021-04-28-2-3_matrix.mtx.gz


title: CTRL_MDFG_PD_03x39xx_X005_S05_L009_B1_T1_P014.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle frontal Gyri


title: 12132022_w62102384-V1-2_S691_R2C2_2J_S328

description:
positive sample
run31_R1BC_count_table.txt
run31_R2BC_count_table.txt
run31_count_table.txt
run31_BC_pair_analysis_filenames.txt


title: TCR-2021-04-28-2-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-2-2_airr_rearrangement.tsv
2021-04-28-2-2_clonotypes.csv
2021-04-28-2-2_filtered_contig.fasta
2021-04-28-2-2_filtered_contig_annotations.csv


title: 12132022_w62102416-V1-2_S561_R2C2_8H_S291


title: Feature-2021-04-28-2-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-2-2_barcodes.tsv.gz
2021-04-28-2-2_features.tsv.gz
2021-04-28-2-2_matrix.mtx.gz


title: 12132022_W62102379-V1-2_S1160_R2C2_9P_S464


title: CTRL_MDFG_PD_00x38xx_X007_S04_L056_B1_T2_P013.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle frontal Gyri


title: CTRL_MDFG_PD_01x37xx_X023_S04_L056_B1_T2_P041.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle frontal Gyri


title: GEX-2021-04-28-2-2


title: CTRL_MDFG_PD_00x38xx_X007_S04_L055_B1_T1_P014.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle frontal Gyri


title: Feature-2021-04-28-2-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-2-1_barcodes.tsv.gz
2021-04-28-2-1_features.tsv.gz
2021-04-28-2-1_matrix.mtx.gz

value: 13-344 Baseline (hash9), 13-348 Follow Up 2 (hash10), 14-745 Follow Up 2 (hash8), 17-3041 Baseline (hash2), 18-3313 Follow Up 3 (hash4)


title: TCR-2021-04-28-2-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-2-1_airr_rearrangement.tsv
2021-04-28-2-1_clonotypes.csv
2021-04-28-2-1_filtered_contig.fasta
2021-04-28-2-1_filtered_contig_annotations.csv

value: peripheral blood


title: TCR-2021-04-28-2-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-2-4_airr_rearrangement.tsv
2021-04-28-2-4_clonotypes.csv
2021-04-28-2-4_filtered_contig.fasta
2021-04-28-2-4_filtered_contig_annotations.csv

value: CD3+ T cells


title: TCR-2021-04-28-1-8

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-1-8_airr_rearrangement.tsv
2021-04-28-1-8_clonotypes.csv
2021-04-28-1-8_filtered_contig.fasta
2021-04-28-1-8_filtered_contig_annotations.csv

value: melanoma


title: GEX-2021-04-28-1-8

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-1-8_barcodes.tsv.gz
2021-04-28-1-8_features.tsv.gz
2021-04-28-1-8_matrix.mtx.gz

value: immune checkpoint blockade


title: 12132022_W62102371-V1-2_S860_R2C2_9L_S378


title: GEX-2021-04-28-2-1


title: 12132022_W62102372-V1-2_S1007_R2C2_9N_S420


title: CTRL_PTMN_PD_16x32xx_X019_S08_L040_B1_T2_P030.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Putamen


title: 12132022_W62102396-V1-2_S1001_R2C2_7N_S418


title: TCR-2021-04-28-1-7

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-1-7_airr_rearrangement.tsv
2021-04-28-1-7_clonotypes.csv
2021-04-28-1-7_filtered_contig.fasta
2021-04-28-1-7_filtered_contig_annotations.csv


title: 12132022_w62102370-V1-2_S1025_R2C2_15N_S426


title: GEX-2021-04-28-2-3


title: GEX-2021-04-28-1-7

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-1-7_barcodes.tsv.gz
2021-04-28-1-7_features.tsv.gz
2021-04-28-1-7_matrix.mtx.gz


title: Feature-2021-04-28-1-7


title: 12132022_W62102365-V1-2_S270_R2C2_11D_S206


title: CTRL_PTMN_PD_16x32xx_X019_S08_L039_B1_T1_P033.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Putamen


title: Feature-2021-04-28-1-8


title: 12132022_W62102363-V1-2_S118_R2C2_11B_S162


title: TCR-2021-04-28-1-6

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-1-6_airr_rearrangement.tsv
2021-04-28-1-6_clonotypes.csv
2021-04-28-1-6_filtered_contig.fasta
2021-04-28-1-6_filtered_contig_annotations.csv

value: 13-344 Follow Up 1 (hash9), 13-348 Follow Up 3 (hash10), 14-745 Baseline (hash8), 17-3041 Follow Up 3 (hash2), 18-3313 Follow Up 1 (hash4)


title: CTRL_PTMN_PD_15x78xx_X001_S02_L004_B1_T2_P007.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Putamen

value: brain


title: CTRL_PTMN_PD_15x78xx_X001_S02_L003_B1_T1_P001.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Putamen

value: bulk


title: CTRL_PTMN_PD_09x50xx_X016_S07_L061_B1_T1_P029.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Putamen


title: 12132022_W62102360-V1-2_S712_R2C2_9J_S335

value: human nasopharyngeal swab


title: 12132022_W62102359-V1-2_S546_R2C2_3H_S286

value: BC


title: Feature-2021-04-28-1-6

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-1-6_barcodes.tsv.gz
2021-04-28-1-6_features.tsv.gz
2021-04-28-1-6_matrix.mtx.gz


title: TCR-2021-04-28-1-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-1-5_airr_rearrangement.tsv
2021-04-28-1-5_clonotypes.csv
2021-04-28-1-5_filtered_contig.fasta
2021-04-28-1-5_filtered_contig_annotations.csv


title: GEX-2021-04-28-1-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-1-5_barcodes.tsv.gz
2021-04-28-1-5_features.tsv.gz
2021-04-28-1-5_matrix.mtx.gz


title: CTRL_PTMN_PD_09x35xx_X011_S10_L068_B1_T2_P018.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Putamen


title: 12132022_w62102348-V1-2_S709_R2C2_8J_S334


title: 12132022_W62102356-V1-2_S112_R2C2_9B_S160


title: Feature-2021-04-28-1-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-1-4_barcodes.tsv.gz
2021-04-28-1-4_features.tsv.gz
2021-04-28-1-4_matrix.mtx.gz


title: Feature-2021-04-28-1-5


title: CTRL_PTMN_PD_07x28xx_X010_S09_L042_B1_T2_P017.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Putamen


title: TCR-2021-04-28-1-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-1-4_airr_rearrangement.tsv
2021-04-28-1-4_clonotypes.csv
2021-04-28-1-4_filtered_contig.fasta
2021-04-28-1-4_filtered_contig_annotations.csv


title: GEX-2021-04-28-1-4


title: CTRL_PTMN_PD_05x16xx_X027_S11_L068_B1_T2_P048.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Putamen


title: 12132022_w62102344-V1-2_S594_R2C2_19H_S302


title: GEX-2021-04-28-1-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-1-3_barcodes.tsv.gz
2021-04-28-1-3_features.tsv.gz
2021-04-28-1-3_matrix.mtx.gz

value: 13-344 Follow Up 2 (hash9), 13-348 Follow Up 1 (hash10), 14-745 Follow Up 1 (hash8), 17-3041 Follow Up 2 (hash2), 18-3313 Baseline (hash4)


title: 12132022_w62102343-V1-2_S294_R2C2_19D_S214

description:
positive sample
run31_R1BC_count_table.txt
run31_R2BC_count_table.txt
run31_count_table.txt
run31_BC_pair_analysis_filenames.txt


title: TCR-2021-04-28-1-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-1-3_airr_rearrangement.tsv
2021-04-28-1-3_clonotypes.csv
2021-04-28-1-3_filtered_contig.fasta
2021-04-28-1-3_filtered_contig_annotations.csv


title: Feature-2021-04-28-1-3


title: CTRL_PTMN_PD_04x38xx_X002_S05_L034_B1_T2_P004.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Putamen


title: GEX-2021-04-28-1-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-1-2_barcodes.tsv.gz
2021-04-28-1-2_features.tsv.gz
2021-04-28-1-2_matrix.mtx.gz


title: TCR-2021-04-28-1-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-1-2_airr_rearrangement.tsv
2021-04-28-1-2_clonotypes.csv
2021-04-28-1-2_filtered_contig.fasta
2021-04-28-1-2_filtered_contig_annotations.csv


title: GEX-2021-04-28-1-6


title: TCR-2021-04-28-1-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-1-1_airr_rearrangement.tsv
2021-04-28-1-1_clonotypes.csv
2021-04-28-1-1_filtered_contig.fasta
2021-04-28-1-1_filtered_contig_annotations.csv


title: 12132022_w62102338-V1-2_S1031_R2C2_17N_S428


title: 12132022_w62102339-V1-2_S1184_R2C2_17P_S472


title: Feature-2021-04-28-1-2


title: CTRL_PTMN_PD_03x66xx_X005_S02_L004_B1_T2_P009.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Putamen


title: Feature-2021-04-28-1-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-28-1-1_barcodes.tsv.gz
2021-04-28-1-1_features.tsv.gz
2021-04-28-1-1_matrix.mtx.gz


title: CTRL_PTMN_PD_04x38xx_X002_S05_L033_B1_T1_P003.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Putamen


title: TCR-2021-04-27-2-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-27-2-4_airr_rearrangement.tsv
2021-04-27-2-4_clonotypes.csv
2021-04-27-2-4_filtered_contig.fasta
2021-04-27-2-4_filtered_contig_annotations.csv

value: 13-349 Follow Up 3 (hash8), 13-660 Follow Up 3 (hash10), 14-970 Follow Up 1 (hash9), 17-2631 Baseline (hash2), 17-2865 Follow Up 3 (hash4)


title: CTRL_PTMN_PD_09x35xx_X011_S10_L067_B1_T1_P016.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Putamen


title: 12132022_W62102325-V1-2_S854_R2C2_7L_S376


title: GEX-2021-04-27-2-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-27-2-4_barcodes.tsv.gz
2021-04-27-2-4_features.tsv.gz
2021-04-27-2-4_matrix.mtx.gz


title: Feature-2021-04-27-2-4


title: CTRL_PTMN_PD_05x16xx_X027_S11_L067_B1_T1_P046.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Putamen


title: CTRL_PTMN_PD_03x41xx_X017_S06_L012_B1_T2_P035.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Putamen


title: TCR-2021-04-27-2-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-27-2-3_airr_rearrangement.tsv
2021-04-27-2-3_clonotypes.csv
2021-04-27-2-3_filtered_contig.fasta
2021-04-27-2-3_filtered_contig_annotations.csv


title: 12132022_W62102321-V1-2_S414_R2C2_9F_S248


title: TCR-2021-04-27-2-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-27-2-2_airr_rearrangement.tsv
2021-04-27-2-2_clonotypes.csv
2021-04-27-2-2_filtered_contig.fasta
2021-04-27-2-2_filtered_contig_annotations.csv


title: 12132022_w62102317-V1-2_S588_R2C2_17H_S300


title: GEX-2021-04-27-2-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-27-2-3_barcodes.tsv.gz
2021-04-27-2-3_features.tsv.gz
2021-04-27-2-3_matrix.mtx.gz


title: 12132022_w62102311-V1-2_S438_R2C2_17F_S256


title: CTRL_PTMN_PD_03x41xx_X017_S06_L011_B1_T1_P034.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Putamen


title: GEX-2021-04-27-2-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-27-2-2_barcodes.tsv.gz
2021-04-27-2-2_features.tsv.gz
2021-04-27-2-2_matrix.mtx.gz


title: Feature-2021-04-27-2-2


title: GEX-2021-04-28-1-1


title: CTRL_PTMN_PD_03x66xx_X005_S02_L003_B1_T1_P012.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Putamen


title: TCR-2021-04-27-2-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-27-2-1_airr_rearrangement.tsv
2021-04-27-2-1_clonotypes.csv
2021-04-27-2-1_filtered_contig.fasta
2021-04-27-2-1_filtered_contig_annotations.csv

value: 13-349 Follow Up 2 (hash8), 13-447 Follow Up 2 (hash4), 13-660 Follow Up 2 (hash10), 14-970 Follow Up 2 (hash9), 17-2631 Follow Up 1 (hash2)


title: GEX-2021-04-27-2-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-27-2-1_barcodes.tsv.gz
2021-04-27-2-1_features.tsv.gz
2021-04-27-2-1_matrix.mtx.gz


title: CTRL_PTMN_PD_03x39xx_X008_S03_L077_B1_T1_P010.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Putamen


title: 12132022_w62102298-V1-2_S399_R2C2_4F_S243


title: Feature-2021-04-27-2-1


title: CTRL_PTMN_PD_03x39xx_X008_S03_L078_B1_T2_P014.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Putamen


title: 12132022_w62102300-V1-2_S703_R2C2_6J_S332


title: CTRL_PTMN_PD_00x38xx_X020_S07_L062_B1_T2_P033.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Putamen


title: Feature-2021-04-27-1-8

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-27-1-8_barcodes.tsv.gz
2021-04-27-1-8_features.tsv.gz
2021-04-27-1-8_matrix.mtx.gz


title: 12132022_W62102294-V1-2_S139_R2C2_18B_S169


title: GEX-2021-04-27-1-8


title: TCR-2021-04-27-1-8

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-27-1-8_airr_rearrangement.tsv
2021-04-27-1-8_clonotypes.csv
2021-04-27-1-8_filtered_contig.fasta
2021-04-27-1-8_filtered_contig_annotations.csv


title: CTRL_PTMN_PD_00x38xx_X020_S07_L061_B1_T1_P036.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Putamen


title: Feature-2021-04-27-2-3


title: 12132022_w62102284-V1-2_S411_R2C2_8F_S247


title: GEX-2021-04-27-1-7

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-27-1-7_barcodes.tsv.gz
2021-04-27-1-7_features.tsv.gz
2021-04-27-1-7_matrix.mtx.gz


title: TCR-2021-04-27-1-7

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-27-1-7_airr_rearrangement.tsv
2021-04-27-1-7_clonotypes.csv
2021-04-27-1-7_filtered_contig.fasta
2021-04-27-1-7_filtered_contig_annotations.csv


title: CTRL_SMTG_PD_16x32xx_X003_S04_L008_B1_T2_P003.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle Temporal Gyri


title: Feature-2021-04-27-1-7


title: 12132022_w62102276-V1-2_S875_R2C2_14L_S383

description:
positive sample
run31_R1BC_count_table.txt
run31_R2BC_count_table.txt
run31_count_table.txt
run31_BC_pair_analysis_filenames.txt


title: TCR-2021-04-27-1-6

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-27-1-6_airr_rearrangement.tsv
2021-04-27-1-6_clonotypes.csv
2021-04-27-1-6_filtered_contig.fasta
2021-04-27-1-6_filtered_contig_annotations.csv

value: 13-349 Baseline (hash8), 13-447 Follow Up 1 (hash4), 13-660 Baseline (hash10), 14-970 Baseline (hash9), 17-2631 Follow Up 2 (hash2)


title: GEX-2021-04-27-1-6

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-27-1-6_barcodes.tsv.gz
2021-04-27-1-6_features.tsv.gz
2021-04-27-1-6_matrix.mtx.gz


title: CTRL_SMTG_PD_16x32xx_X003_S04_L007_B1_T1_P005.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle Temporal Gyri


title: 12132022_w62102319-V1-2_S288_R2C2_17D_S212


title: Feature-2021-04-27-1-6


title: 12132022_w62102268-V1-2_S851_R2C2_6L_S375


title: 12132022_w62102271-V1-2_S715_R2C2_10J_S336


title: CTRL_SMTG_PD_16x10xx_X020_S11_L069_B1_T1_P034.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle Temporal Gyri


title: 12132022_W62102250-V1-2_S881_R2C2_16L_S385


title: Feature-2021-04-27-1-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-27-1-5_barcodes.tsv.gz
2021-04-27-1-5_features.tsv.gz
2021-04-27-1-5_matrix.mtx.gz


title: TCR-2021-04-27-1-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-27-1-4_airr_rearrangement.tsv
2021-04-27-1-4_clonotypes.csv
2021-04-27-1-4_filtered_contig.fasta
2021-04-27-1-4_filtered_contig_annotations.csv


title: TCR-2021-04-27-1-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-27-1-5_airr_rearrangement.tsv
2021-04-27-1-5_clonotypes.csv
2021-04-27-1-5_filtered_contig.fasta
2021-04-27-1-5_filtered_contig_annotations.csv


title: GEX-2021-04-27-1-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-27-1-4_barcodes.tsv.gz
2021-04-27-1-4_features.tsv.gz
2021-04-27-1-4_matrix.mtx.gz


title: CTRL_SMTG_PD_15x78xx_X003_S05_L010_B1_T2_P001.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle Temporal Gyri


title: GEX-2021-04-27-1-5


title: 12132022_W62102237-V1-2_S468_R2C2_4G_S264


title: 12132022_W62102238-V1-2_S821_R2C2_19K_S366


title: CTRL_SMTG_PD_15x78xx_X003_S05_L009_B1_T1_P002.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle Temporal Gyri


title: Feature-2021-04-27-1-4


title: GEX-2021-04-27-1-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-27-1-3_barcodes.tsv.gz
2021-04-27-1-3_features.tsv.gz
2021-04-27-1-3_matrix.mtx.gz

value: 13-349 Follow Up 1 (hash8), 13-447 Baseline (hash4), 13-660 Follow Up 1 (hash10), 14-970 Follow Up 3 (hash9), 17-2631 Follow Up 3 (hash2)


title: CTRL_SMTG_PD_09x50xx_X023_S10_L068_B1_T2_P039.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle Temporal Gyri


title: Feature-2021-04-27-1-3


title: 12132022_w62102234-V1-2_S243_R2C2_2D_S197


title: TCR-2021-04-27-1-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-27-1-2_airr_rearrangement.tsv
2021-04-27-1-2_clonotypes.csv
2021-04-27-1-2_filtered_contig.fasta
2021-04-27-1-2_filtered_contig_annotations.csv


title: CTRL_SMTG_PD_09x50xx_X023_S10_L067_B1_T1_P040.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle Temporal Gyri


title: GEX-2021-04-27-1-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-27-1-2_barcodes.tsv.gz
2021-04-27-1-2_features.tsv.gz
2021-04-27-1-2_matrix.mtx.gz


title: CTRL_SMTG_PD_16x10xx_X020_S11_L070_B1_T2_P031.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle Temporal Gyri


title: 12132022_W62102222-V1-2_S190_R2C2_10C_S182


title: Feature-2021-04-27-1-2


title: GEX-2021-04-27-1-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-27-1-1_barcodes.tsv.gz
2021-04-27-1-1_features.tsv.gz
2021-04-27-1-1_matrix.mtx.gz


title: TCR-2021-04-27-1-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-27-1-1_airr_rearrangement.tsv
2021-04-27-1-1_clonotypes.csv
2021-04-27-1-1_filtered_contig.fasta
2021-04-27-1-1_filtered_contig_annotations.csv


title: CTRL_SMTG_PD_09x35xx_X001_S04_L008_B1_T2_P006.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle Temporal Gyri


title: 12132022_W62102221-V1-2_S30_R2C2_8A_S136


title: CTRL_SMTG_PD_05x16xx_X017_S09_L018_B1_T2_P034.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle Temporal Gyri


title: Feature-2021-04-27-1-1


title: 12132022_W62102220-V1-2_S211_R2C2_16C_S188


title: TCR-2021-04-27-1-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2021-04-27-1-3_airr_rearrangement.tsv
2021-04-27-1-3_clonotypes.csv
2021-04-27-1-3_filtered_contig.fasta
2021-04-27-1-3_filtered_contig_annotations.csv


title: GEX-2020-11-02-3-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-3-3_barcodes.tsv.gz
2020-11-02-3-3_features.tsv.gz
2020-11-02-3-3_matrix.mtx.gz

value: non-naive T cells

value: 14-1063 Baseline (hash6), 14-1063 Follow Up 1 (hash7), 14-1063 Follow Up 2 (hash8), 14-1063 Follow Up 3 (hash9)


title: CTRL_SMTG_PD_09x35xx_X001_S04_L007_B1_T1_P007.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle Temporal Gyri


title: TCR-2020-11-02-3-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-3-2_airr_rearrangement.tsv
2020-11-02-3-2_clonotypes.csv
2020-11-02-3-2_filtered_contig.fasta
2020-11-02-3-2_filtered_contig_annotations.csv


title: Feature-2020-11-02-3-3


title: CTRL_SMTG_PD_04x38xx_X017_S04_L008_B1_T2_P036.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle Temporal Gyri


title: 12132022_W62102215-V1-2_S158_R2C2_2C_S174


title: 12132022_W62102201-V1-2_S201_R2C2_13C_S185


title: TCR-2020-11-02-3-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-3-3_airr_rearrangement.tsv
2020-11-02-3-3_clonotypes.csv
2020-11-02-3-3_filtered_contig.fasta
2020-11-02-3-3_filtered_contig_annotations.csv


title: TCR-2020-11-02-3-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-3-1_airr_rearrangement.tsv
2020-11-02-3-1_clonotypes.csv
2020-11-02-3-1_filtered_contig.fasta
2020-11-02-3-1_filtered_contig_annotations.csv


title: Feature-2020-11-02-3-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-3-2_barcodes.tsv.gz
2020-11-02-3-2_features.tsv.gz
2020-11-02-3-2_matrix.mtx.gz


title: GEX-2020-11-02-3-2


title: CTRL_SMTG_PD_04x38xx_X017_S04_L007_B1_T1_P035.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle Temporal Gyri


title: GEX-2020-11-02-3-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-3-1_barcodes.tsv.gz
2020-11-02-3-1_features.tsv.gz
2020-11-02-3-1_matrix.mtx.gz


title: CTRL_SMTG_PD_05x16xx_X017_S09_L017_B1_T1_P035.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle Temporal Gyri


title: 12132022_W62102195-V1-2_S961_R2C2_17M_S406

description:
positive sample
run31_R1BC_count_table.txt
run31_R2BC_count_table.txt
run31_count_table.txt
run31_BC_pair_analysis_filenames.txt


title: 12132022_W62102223-V1-2_S519_R2C2_18G_S278


title: Feature-2020-11-02-3-1


title: 12132022_W62102193-V1-2_S975_R2C2_21M_S410


title: CTRL_SMTG_PD_03x66xx_X018_S03_L006_B1_T2_P030.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle Temporal Gyri


title: TCR-2020-11-02-2-8

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-2-8_airr_rearrangement.tsv
2020-11-02-2-8_clonotypes.csv
2020-11-02-2-8_filtered_contig.fasta
2020-11-02-2-8_filtered_contig_annotations.csv

value: 13-588 Follow Up 2 (hash6), 13-687 Follow Up 2 (hash7), 13-588 Follow Up 4 (hash8), 13-588 Follow Up 5 (hash9), 13-588 Follow Up 6 (hash10)


title: GEX-2020-11-02-2-8

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-2-8_barcodes.tsv.gz
2020-11-02-2-8_features.tsv.gz
2020-11-02-2-8_matrix.mtx.gz

value: peripheral blood


title: CTRL_SMTG_PD_03x66xx_X018_S03_L005_B1_T1_P031.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle Temporal Gyri


title: Feature-2020-11-02-2-8


title: 12132022_W62102191-V1-2_S921_R2C2_6M_S395


title: TCR-2020-11-02-2-7

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-2-7_airr_rearrangement.tsv
2020-11-02-2-7_clonotypes.csv
2020-11-02-2-7_filtered_contig.fasta
2020-11-02-2-7_filtered_contig_annotations.csv


title: CTRL_SMTG_PD_03x41xx_X030_S02_L052_B1_T2_P054.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle Temporal Gyri


title: Feature-2020-11-02-2-7

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-2-7_barcodes.tsv.gz
2020-11-02-2-7_features.tsv.gz
2020-11-02-2-7_matrix.mtx.gz


title: 12132022_W62102187-V1-2_S940_R2C2_11M_S400


title: CTRL_SMTG_PD_03x41xx_X030_S02_L051_B1_T1_P053.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle Temporal Gyri


title: GEX-2020-11-02-2-7


title: 12132022_W62102183-V1-2_S334_R2C2_8E_S224


title: GEX-2020-11-02-2-6

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-2-6_barcodes.tsv.gz
2020-11-02-2-6_features.tsv.gz
2020-11-02-2-6_matrix.mtx.gz


title: TCR-2020-11-02-2-6

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-2-6_airr_rearrangement.tsv
2020-11-02-2-6_clonotypes.csv
2020-11-02-2-6_filtered_contig.fasta
2020-11-02-2-6_filtered_contig_annotations.csv


title: CTRL_SMTG_PD_03x39xx_X004_S03_L030_B1_T2_P009.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle Temporal Gyri


title: 12132022_w62102173-V1-2_S872_R2C2_13L_S382


title: Feature-2020-11-02-2-6


title: CTRL_SMTG_PD_03x39xx_X004_S03_L029_B1_T1_P006.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle Temporal Gyri


title: 12132022_W62102171-V1-2_S641_R2C2_10I_S314


title: CTRL_SMTG_PD_03x15xx_X029_S07_L038_B1_T2_P056.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle Temporal Gyri


title: TCR-2020-11-02-2-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-2-5_airr_rearrangement.tsv
2020-11-02-2-5_clonotypes.csv
2020-11-02-2-5_filtered_contig.fasta
2020-11-02-2-5_filtered_contig_annotations.csv


title: 12132022_w62102170-V1-2_S136_R2C2_17B_S168


title: Feature-2020-11-02-2-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-2-5_barcodes.tsv.gz
2020-11-02-2-5_features.tsv.gz
2020-11-02-2-5_matrix.mtx.gz


title: GEX-2020-11-02-2-5


title: GEX-2020-11-02-2-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-2-4_barcodes.tsv.gz
2020-11-02-2-4_features.tsv.gz
2020-11-02-2-4_matrix.mtx.gz

value: 13-588 Baseline (hash9), 13-588 Follow Up 1 (hash10), 17-2864 Baseline (hash6), 17-2864 Follow Up 1 (hash7), 17-2864 Follow Up 2 (hash8)


title: CTRL_SMTG_PD_03x15xx_X029_S07_L037_B1_T1_P051.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle Temporal Gyri


title: Feature-2020-11-02-2-4

value: melanoma


title: TCR-2020-11-02-2-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-2-4_airr_rearrangement.tsv
2020-11-02-2-4_clonotypes.csv
2020-11-02-2-4_filtered_contig.fasta
2020-11-02-2-4_filtered_contig_annotations.csv

value: immune checkpoint blockade


title: 12132022_W62102168-V1-2_S1115_R2C2_19O_S450


title: CTRL_SMTG_PD_00x38xx_X020_S05_L058_B1_T2_P036.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle Temporal Gyri


title: GEX-2020-11-02-2-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-2-3_barcodes.tsv.gz
2020-11-02-2-3_features.tsv.gz
2020-11-02-2-3_matrix.mtx.gz


title: 12132022_W62102162-V1-2_S380_R2C2_21E_S237


title: CTRL_SMTG_PD_00x38xx_X020_S05_L057_B1_T1_P037.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Middle Temporal Gyri


title: Feature-2020-11-02-2-3


title: TCR-2020-11-02-2-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-2-2_airr_rearrangement.tsv
2020-11-02-2-2_clonotypes.csv
2020-11-02-2-2_filtered_contig.fasta
2020-11-02-2-2_filtered_contig_annotations.csv


title: 12132022_W62102147-V1-2_S222_R2C2_19C_S191


title: CTRL_CAUD_PD_16x32xx_X009_S04_L008_B1_T2_P016.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Caudate


title: GEX-2020-11-02-2-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-2-2_barcodes.tsv.gz
2020-11-02-2-2_features.tsv.gz
2020-11-02-2-2_matrix.mtx.gz


title: Feature-2020-11-02-2-2


title: 12132022_W62102146-V1-2_S523_R2C2_19G_S279


title: 12132022_W62102143-V1-2_S352_R2C2_13E_S229


title: Feature-2020-11-02-2-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-2-1_barcodes.tsv.gz
2020-11-02-2-1_features.tsv.gz
2020-11-02-2-1_matrix.mtx.gz


title: GEX-2020-11-02-2-1


title: CTRL_CAUD_PD_16x10xx_X019_S12_L048_B1_T2_P035.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Caudate


title: CTRL_CAUD_PD_16x32xx_X009_S04_L007_B1_T1_P017.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Caudate


title: CTRL_CAUD_PD_16x10xx_X019_S12_L047_B1_T1_P032.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Caudate


title: 12132022_W62102140-V1-2_S505_R2C2_14G_S274


title: 12132022_W62102142-V1-2_S530_R2C2_21G_S281


title: TCR-2020-11-02-2-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-2-3_airr_rearrangement.tsv
2020-11-02-2-3_clonotypes.csv
2020-11-02-2-3_filtered_contig.fasta
2020-11-02-2-3_filtered_contig_annotations.csv


title: Feature-2020-11-02-1-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-1-5_barcodes.tsv.gz
2020-11-02-1-5_features.tsv.gz
2020-11-02-1-5_matrix.mtx.gz

value: PBMC


title: 12132022_W62102138-V1-2_S1087_R2C2_11O_S442

description:
positive sample
run31_R1BC_count_table.txt
run31_R2BC_count_table.txt
run31_count_table.txt
run31_BC_pair_analysis_filenames.txt


title: GEX-2020-11-02-1-5


title: TCR-2020-11-02-1-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-1-4_airr_rearrangement.tsv
2020-11-02-1-4_clonotypes.csv
2020-11-02-1-4_filtered_contig.fasta
2020-11-02-1-4_filtered_contig_annotations.csv


title: CTRL_CAUD_PD_15x78xx_X027_S02_L049_B1_T1_P048.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Caudate

value: brain


title: CTRL_CAUD_PD_09x35xx_X029_S09_L042_B1_T2_P054.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Caudate

value: bulk


title: GEX-2020-11-02-1-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-1-4_barcodes.tsv.gz
2020-11-02-1-4_features.tsv.gz
2020-11-02-1-4_matrix.mtx.gz


title: Feature-2020-11-02-1-4


title: 12132022_W62102126-V1-2_S49_R2C2_13A_S141

value: human nasopharyngeal swab


title: TCR-2020-11-02-1-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-1-3_airr_rearrangement.tsv
2020-11-02-1-3_clonotypes.csv
2020-11-02-1-3_filtered_contig.fasta
2020-11-02-1-3_filtered_contig_annotations.csv


title: TCR-2020-11-02-2-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-2-1_airr_rearrangement.tsv
2020-11-02-2-1_clonotypes.csv
2020-11-02-2-1_filtered_contig.fasta
2020-11-02-2-1_filtered_contig_annotations.csv


title: 12132022_W62102133-V1-2_S318_R2C2_4E_S220

value: BC


title: Feature-2020-11-02-1-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-1-3_barcodes.tsv.gz
2020-11-02-1-3_features.tsv.gz
2020-11-02-1-3_matrix.mtx.gz


title: TCR-2020-11-02-1-6

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-1-6_airr_rearrangement.tsv
2020-11-02-1-6_clonotypes.csv
2020-11-02-1-6_filtered_contig.fasta
2020-11-02-1-6_filtered_contig_annotations.csv


title: CTRL_CAUD_PD_08x90xx_X013_S12_L048_B1_T2_P029.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Caudate


title: GEX-2020-11-02-1-6

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-1-6_barcodes.tsv.gz
2020-11-02-1-6_features.tsv.gz
2020-11-02-1-6_matrix.mtx.gz


title: Feature-2020-11-02-1-6


title: CTRL_CAUD_PD_15x78xx_X027_S02_L050_B1_T2_P047.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Caudate


title: CTRL_CAUD_PD_05x16xx_X003_S03_L006_B1_T2_P008.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Caudate


title: GEX-2020-11-02-1-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-1-2_barcodes.tsv.gz
2020-11-02-1-2_features.tsv.gz
2020-11-02-1-2_matrix.mtx.gz


title: CTRL_CAUD_PD_09x35xx_X029_S09_L041_B1_T1_P056.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Caudate


title: 12132022_W62102123-V1-2_S1108_R2C2_17O_S448


title: 12132022_W62102114-V1-2_S218_R2C2_18C_S190


title: 12132022_W62102112-V1-2_S476_R2C2_6G_S266


title: CTRL_CAUD_PD_05x16xx_X003_S03_L005_B1_T1_P005.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Caudate


title: TCR-2020-11-02-1-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-1-1_airr_rearrangement.tsv
2020-11-02-1-1_clonotypes.csv
2020-11-02-1-1_filtered_contig.fasta
2020-11-02-1-1_filtered_contig_annotations.csv


title: 12132022_W62102108-V1-2_S166_R2C2_4C_S176


title: Feature-2020-11-02-1-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-1-1_barcodes.tsv.gz
2020-11-02-1-1_features.tsv.gz
2020-11-02-1-1_matrix.mtx.gz


title: GEX-2020-11-02-1-1


title: CTRL_CAUD_PD_04x38xx_X011_S01_L050_B1_T2_P015.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Caudate


title: TCR-2020-11-02-1-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-1-5_airr_rearrangement.tsv
2020-11-02-1-5_clonotypes.csv
2020-11-02-1-5_filtered_contig.fasta
2020-11-02-1-5_filtered_contig_annotations.csv


title: TCR-2020-10-29-3-8

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-3-8_airr_rearrangement.tsv
2020-10-29-3-8_clonotypes.csv
2020-10-29-3-8_filtered_contig.fasta
2020-10-29-3-8_filtered_contig_annotations.csv

value: 14-1189_aPD1 Baseline (hash6), 14-1189_aPD1 Follow Up 1 (hash7), 14-1189_aPD1 Follow Up 2 (hash8), 14-1189_aPD1 Follow Up 3 (hash9), 14-1189_aPD1 Follow Up 4 (hash10)


title: GEX-2020-11-02-1-3


title: 12132022_W62102103-V1-2_S1125_R2C2_22O_S453


title: Feature-2020-10-29-3-8

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-3-8_barcodes.tsv.gz
2020-10-29-3-8_features.tsv.gz
2020-10-29-3-8_matrix.mtx.gz


title: 12132022_W62102094-V1-2_S229_R2C2_21C_S193


title: CTRL_CAUD_PD_04x38xx_X011_S01_L049_B1_T1_P020.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Caudate


title: GEX-2020-10-29-3-8


title: TCR-2020-10-29-3-7

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-3-7_airr_rearrangement.tsv
2020-10-29-3-7_clonotypes.csv
2020-10-29-3-7_filtered_contig.fasta
2020-10-29-3-7_filtered_contig_annotations.csv


title: TCR-2020-11-02-1-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-11-02-1-2_airr_rearrangement.tsv
2020-11-02-1-2_clonotypes.csv
2020-11-02-1-2_filtered_contig.fasta
2020-11-02-1-2_filtered_contig_annotations.csv


title: CTRL_CAUD_PD_03x66xx_X005_S12_L024_B1_T2_P011.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Caudate


title: 12132022_W62102093-V1-2_S14_R2C2_4A_S132


title: CTRL_CAUD_PD_03x66xx_X005_S12_L023_B1_T1_P012.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Caudate


title: GEX-2020-10-29-3-7

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-3-7_barcodes.tsv.gz
2020-10-29-3-7_features.tsv.gz
2020-10-29-3-7_matrix.mtx.gz


title: TCR-2020-10-29-3-6

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-3-6_airr_rearrangement.tsv
2020-10-29-3-6_clonotypes.csv
2020-10-29-3-6_filtered_contig.fasta
2020-10-29-3-6_filtered_contig_annotations.csv


title: Feature-2020-11-02-1-2


title: CTRL_CAUD_PD_03x41xx_X031_S04_L080_B1_T2_P055.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Caudate


title: 12132022_W62102086-V1-2_S673_R2C2_19I_S323

description:
positive sample
run31_R1BC_count_table.txt
run31_R2BC_count_table.txt
run31_count_table.txt
run31_BC_pair_analysis_filenames.txt


title: CTRL_CAUD_PD_03x39xx_X013_S07_L038_B1_T2_P020.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Caudate


title: Feature-2020-10-29-3-6

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-3-6_barcodes.tsv.gz
2020-10-29-3-6_features.tsv.gz
2020-10-29-3-6_matrix.mtx.gz


title: 12132022_W62102089-V1-2_S77_R2C2_21A_S149


title: TCR-2020-10-29-3-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-3-5_airr_rearrangement.tsv
2020-10-29-3-5_clonotypes.csv
2020-10-29-3-5_filtered_contig.fasta
2020-10-29-3-5_filtered_contig_annotations.csv


title: 12132022_W62102083-V1-2_S70_R2C2_19A_S147


title: Feature-2020-10-29-3-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-3-5_barcodes.tsv.gz
2020-10-29-3-5_features.tsv.gz
2020-10-29-3-5_matrix.mtx.gz


title: GEX-2020-10-29-3-5


title: CTRL_CAUD_PD_03x39xx_X013_S07_L037_B1_T1_P024.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Caudate


title: TCR-2020-10-29-3-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-3-4_airr_rearrangement.tsv
2020-10-29-3-4_clonotypes.csv
2020-10-29-3-4_filtered_contig.fasta
2020-10-29-3-4_filtered_contig_annotations.csv

value: 13-588 Follow Up 3 (hash6), 13-687 Follow Up 3 (hash7), 13-687 Follow Up 4 (hash8), 13-687 Follow Up 5 (hash9), 13-687 Follow Up 6 (hash10)


title: GEX-2020-10-29-3-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-3-4_barcodes.tsv.gz
2020-10-29-3-4_features.tsv.gz
2020-10-29-3-4_matrix.mtx.gz


title: Feature-2020-10-29-3-4


title: 12132022_W62102081-V1-2_S182_R2C2_8C_S180


title: GEX-2020-10-29-3-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-3-3_barcodes.tsv.gz
2020-10-29-3-3_features.tsv.gz
2020-10-29-3-3_matrix.mtx.gz


title: CTRL_CAUD_PD_03x15xx_X008_S12_L096_B1_T2_PMRG.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Caudate


title: CTRL_CAUD_PD_01x31xx_X020_S04_L055_B1_T1_P036.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Caudate


title: CTRL_CAUD_PD_00x38xx_X014_S01_L002_B1_T2_P028.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Caudate


title: Feature-2020-10-29-3-7


title: TCR-2020-10-29-3-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-3-3_airr_rearrangement.tsv
2020-10-29-3-3_clonotypes.csv
2020-10-29-3-3_filtered_contig.fasta
2020-10-29-3-3_filtered_contig_annotations.csv


title: Feature-2020-10-29-3-3


title: 12132022_W62102074-V1-2_S373_R2C2_19E_S235


title: GEX-2020-10-29-3-6


title: TCR-2020-10-29-3-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-3-2_airr_rearrangement.tsv
2020-10-29-3-2_clonotypes.csv
2020-10-29-3-2_filtered_contig.fasta
2020-10-29-3-2_filtered_contig_annotations.csv


title: Feature-2020-10-29-3-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-3-2_barcodes.tsv.gz
2020-10-29-3-2_features.tsv.gz
2020-10-29-3-2_matrix.mtx.gz


title: CTRL_HIPP_PD_09x35xx_X028_S06_L012_B1_T2_P052.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Hippocampus


title: GEX-2020-10-29-3-2


title: Feature-2020-10-29-3-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-3-1_barcodes.tsv.gz
2020-10-29-3-1_features.tsv.gz
2020-10-29-3-1_matrix.mtx.gz

value: 13-687 Baseline (hash9), 13-687 Follow Up 1 (hash10), 14-998 Baseline (hash6), 14-998 Follow Up 1 (hash7), 14-998 Follow Up 2 (hash8)


title: GEX-2020-10-29-3-1


title: TCR-2020-10-29-3-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-3-1_airr_rearrangement.tsv
2020-10-29-3-1_clonotypes.csv
2020-10-29-3-1_filtered_contig.fasta
2020-10-29-3-1_filtered_contig_annotations.csv


title: 12132022_W62102082-V1-2_S680_R2C2_21I_S325


title: 12132022_W62102069-V1-2_S326_R2C2_6E_S222


title: TCR-2020-10-29-2-8

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-2-8_airr_rearrangement.tsv
2020-10-29-2-8_clonotypes.csv
2020-10-29-2-8_filtered_contig.fasta
2020-10-29-2-8_filtered_contig_annotations.csv


title: 12132022_W62102067-V1-2_S1122_R2C2_21O_S452


title: GEX-2020-10-29-2-8

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-2-8_barcodes.tsv.gz
2020-10-29-2-8_features.tsv.gz
2020-10-29-2-8_matrix.mtx.gz


title: 12132022_W62102066-V1-2_S814_R2C2_17K_S364


title: CTRL_HIPP_PD_05x16xx_X004_S11_L046_B1_T2_P008.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Hippocampus


title: Feature-2020-10-29-2-8


title: TCR-2020-10-29-2-7

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-2-7_airr_rearrangement.tsv
2020-10-29-2-7_clonotypes.csv
2020-10-29-2-7_filtered_contig.fasta
2020-10-29-2-7_filtered_contig_annotations.csv


title: CTRL_HIPP_PD_05x16xx_X004_S11_L045_B1_T1_P006.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Hippocampus


title: Feature-2020-10-29-2-7

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-2-7_barcodes.tsv.gz
2020-10-29-2-7_features.tsv.gz
2020-10-29-2-7_matrix.mtx.gz


title: 12132022_W62102049-V1-2_S968_R2C2_19M_S408


title: 12132022_W62102075-V1-2_S828_R2C2_21K_S368


title: GEX-2020-10-29-2-7


title: CTRL_HIPP_PD_04x38xx_X024_S07_L086_B1_T2_P043.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Hippocampus


title: CTRL_CAUD_PD_00x38xx_X014_S01_L001_B1_T1_P025.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Caudate


title: TCR-2020-10-29-2-6

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-2-6_airr_rearrangement.tsv
2020-10-29-2-6_clonotypes.csv
2020-10-29-2-6_filtered_contig.fasta
2020-10-29-2-6_filtered_contig_annotations.csv


title: CTRL_HIPP_PD_04x38xx_X024_S07_L085_B1_T1_P040.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Hippocampus


title: 12132022_W62102008-V1-2_S733_R2C2_16J_S342

description:
positive sample
run31_R1BC_count_table.txt
run31_R2BC_count_table.txt
run31_count_table.txt
run31_BC_pair_analysis_filenames.txt


title: Feature-2020-10-29-2-6

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-2-6_barcodes.tsv.gz
2020-10-29-2-6_features.tsv.gz
2020-10-29-2-6_matrix.mtx.gz


title: GEX-2020-10-29-2-6


title: CTRL_HIPP_PD_09x35xx_X028_S06_L011_B1_T1_P056.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Hippocampus


title: TCR-2020-10-29-2-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-2-5_airr_rearrangement.tsv
2020-10-29-2-5_clonotypes.csv
2020-10-29-2-5_filtered_contig.fasta
2020-10-29-2-5_filtered_contig_annotations.csv


title: CTRL_HIPP_PD_00x38xx_X002_S11_L045_B1_T1_P002.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Hippocampus


title: CTRL_HIPP_PD_00x38xx_X002_S11_L046_B1_T2_P003.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Hippocampus


title: 12132022_W62101999-V1-2_S52_R2C2_14A_S142


title: GEX-2020-10-29-2-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-2-5_barcodes.tsv.gz
2020-10-29-2-5_features.tsv.gz
2020-10-29-2-5_matrix.mtx.gz


title: 12132022_w62101972-V1-2_S1004_R2C2_8N_S419


title: TCR-2020-10-29-2-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-2-4_airr_rearrangement.tsv
2020-10-29-2-4_clonotypes.csv
2020-10-29-2-4_filtered_contig.fasta
2020-10-29-2-4_filtered_contig_annotations.csv


title: 12132022_w62101928-V1-2_S721_R2C2_12J_S338


title: Feature-2020-10-29-2-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-2-4_barcodes.tsv.gz
2020-10-29-2-4_features.tsv.gz
2020-10-29-2-4_matrix.mtx.gz


title: GEX-2020-10-29-2-4


title: ADPD_SUNI_PD_97x52xx_X015_S08_L040_B1_T2_P025.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Sustantia Nigra


title: TCR-2020-10-29-2-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-2-3_airr_rearrangement.tsv
2020-10-29-2-3_clonotypes.csv
2020-10-29-2-3_filtered_contig.fasta
2020-10-29-2-3_filtered_contig_annotations.csv


title: ADPD_SUNI_PD_97x52xx_X015_S08_L039_B1_T1_P027.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Sustantia Nigra


title: GEX-2020-10-29-2-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-2-3_barcodes.tsv.gz
2020-10-29-2-3_features.tsv.gz
2020-10-29-2-3_matrix.mtx.gz


title: 12132022_w62102072-V1-2_S512_R2C2_16G_S276


title: ADPD_SUNI_PD_94x31xx_X019_S06_L036_B1_T2_P032.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Sustantia Nigra


title: 12132022_W62102048-V1-2_S793_R2C2_11K_S358


title: 12132022_W62101864-V1-2_S573_R2C2_12H_S295


title: TCR-2020-10-29-2-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-2-2_airr_rearrangement.tsv
2020-10-29-2-2_clonotypes.csv
2020-10-29-2-2_filtered_contig.fasta
2020-10-29-2-2_filtered_contig_annotations.csv

value: 13-687 Baseline (hash9), 13-687 Follow Up 1 (hash10), 14-998 Follow Up 1 (hash7), 14-998 Follow Up 2 (hash8)


title: 12132022_w62101841-V1-2_S1022_R2C2_14N_S425


title: ADPD_SUNI_PD_13x22xx_X014_S07_L014_B1_T2_P026.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Sustantia Nigra


title: Feature-2020-10-29-2-5


title: GEX-2020-10-29-2-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-2-2_barcodes.tsv.gz
2020-10-29-2-2_features.tsv.gz
2020-10-29-2-2_matrix.mtx.gz


title: ADPD_SUNI_PD_94x31xx_X019_S06_L035_B1_T1_P031.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Sustantia Nigra


title: GEX-2020-10-29-2-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-2-1_barcodes.tsv.gz
2020-10-29-2-1_features.tsv.gz
2020-10-29-2-1_matrix.mtx.gz


title: TCR-2020-10-29-1-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-1-1_airr_rearrangement.tsv
2020-10-29-1-1_clonotypes.csv
2020-10-29-1-1_filtered_contig.fasta
2020-10-29-1-1_filtered_contig_annotations.csv

value: 14-998 Baseline (NA)


title: 12132022_w62101782-V1-2_S567_R2C2_10H_S293


title: Feature-2020-10-29-2-1


title: Feature-2020-10-29-2-2


title: 12132022_w62101781-V1-2_S863_R2C2_10L_S379


title: ADPD_SUNI_PD_12x65xx_X027_S12_L070_B1_T2_P050.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Sustantia Nigra


title: 12132022_w62101776-V1-2_S261_R2C2_8D_S203


title: TCR-2020-10-28-3-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-28-3-1_airr_rearrangement.tsv
2020-10-28-3-1_clonotypes.csv
2020-10-28-3-1_filtered_contig.fasta
2020-10-28-3-1_filtered_contig_annotations.csv

value: 12-153 Baseline (hash10), 608 Baseline (hash6), 608 Follow Up 2 (hash9), 608 Follow Up 3 (hash8)


title: GEX-2020-10-29-1-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-1-1_barcodes.tsv.gz
2020-10-29-1-1_features.tsv.gz
2020-10-29-1-1_matrix.mtx.gz


title: 12132022_W62101865-V1-2_S1028_R2C2_16N_S427


title: ADPD_SUNI_PD_12x50xx_X013_S03_L030_B1_T2_P022.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Sustantia Nigra


title: GEX-2020-10-28-3-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-28-3-1_barcodes.tsv.gz
2020-10-28-3-1_features.tsv.gz
2020-10-28-3-1_matrix.mtx.gz


title: Feature-2020-10-28-3-1


title: Feature-2020-10-29-2-3


title: 12132022_w62101773-V1-2_S97_R2C2_4B_S155


title: ADPD_SUNI_PD_12x65xx_X027_S12_L069_B1_T1_P047.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Sustantia Nigra


title: TCR-2020-10-28-2-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-28-2-2_airr_rearrangement.tsv
2020-10-28-2-2_clonotypes.csv
2020-10-28-2-2_filtered_contig.fasta
2020-10-28-2-2_filtered_contig_annotations.csv

value: non-naive T cells

value: 12-153 Follow Up 1 (hash6), 12-153 Follow Up 3 (hash8), 12-153 Follow Up 4 (hash9), 12-153 Follow Up 5 (hash10)


title: ADPD_SUNI_PD_12x50xx_X013_S03_L029_B1_T1_P027.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Sustantia Nigra


title: TCR-2020-10-29-2-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-29-2-1_airr_rearrangement.tsv
2020-10-29-2-1_clonotypes.csv
2020-10-29-2-1_filtered_contig.fasta
2020-10-29-2-1_filtered_contig_annotations.csv

value: peripheral blood


title: GEX-2020-10-28-2-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-28-2-2_barcodes.tsv.gz
2020-10-28-2-2_features.tsv.gz
2020-10-28-2-2_matrix.mtx.gz


title: 12132022_w62101769-V1-2_S727_R2C2_14J_S340

description:
positive sample
run31_R1BC_count_table.txt
run31_R2BC_count_table.txt
run31_count_table.txt
run31_BC_pair_analysis_filenames.txt


title: Feature-2020-10-28-2-2


title: ADPD_SUNI_PD_11x90xx_X030_S01_L050_B1_T2_P053.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Sustantia Nigra


title: TCR-2020-10-28-2-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-28-2-1_airr_rearrangement.tsv
2020-10-28-2-1_clonotypes.csv
2020-10-28-2-1_filtered_contig.fasta
2020-10-28-2-1_filtered_contig_annotations.csv


title: GEX-2020-10-28-2-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-28-2-1_barcodes.tsv.gz
2020-10-28-2-1_features.tsv.gz
2020-10-28-2-1_matrix.mtx.gz


title: Feature-2020-10-28-2-1


title: ADPD_SUNI_PD_11x90xx_X030_S01_L049_B1_T1_P052.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Sustantia Nigra


title: 12132022_W62101676-V1-2_S45_R2C2_12A_S140


title: 12132022_W62101689-V1-2_S38_R2C2_10A_S138


title: ADPD_SUNI_PD_10x37xx_X010_S11_L046_B1_T2_P016.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Sustantia Nigra


title: TCR-2020-10-28-1-7

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-28-1-7_airr_rearrangement.tsv
2020-10-28-1-7_clonotypes.csv
2020-10-28-1-7_filtered_contig.fasta
2020-10-28-1-7_filtered_contig_annotations.csv

value: 12-153 Baseline (hash10), 12-153 Follow Up 2 (hash7), 608 Baseline (hash6), 608 Follow Up 2 (hash9), 608 Follow Up 3 (hash8)


title: GEX-2020-10-28-1-7

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-28-1-7_barcodes.tsv.gz
2020-10-28-1-7_features.tsv.gz
2020-10-28-1-7_matrix.mtx.gz

value: melanoma


title: Feature-2020-10-28-1-7

value: immune checkpoint blockade


title: ADPD_SUNI_PD_10x37xx_X010_S11_L045_B1_T1_P016.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Sustantia Nigra


title: ADPD_SUNI_PD_07x41xx_X002_S12_L048_B1_T2_P003.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Sustantia Nigra


title: Feature-2020-10-28-1-6

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-28-1-6_barcodes.tsv.gz
2020-10-28-1-6_features.tsv.gz
2020-10-28-1-6_matrix.mtx.gz


title: GEX-2020-10-28-1-6


title: 12132022_W62101577-V1-2_S866_R2C2_11L_S380


title: 12132022_W62101666-V1-2_S491_R2C2_10G_S270


title: TCR-2020-10-28-1-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-28-1-5_airr_rearrangement.tsv
2020-10-28-1-5_clonotypes.csv
2020-10-28-1-5_filtered_contig.fasta
2020-10-28-1-5_filtered_contig_annotations.csv


title: 12132022_w62101516-V1-2_S393_R2C2_2F_S241


title: ADPD_SUNI_PD_04x37xx_X003_S09_L017_B1_T1_P009.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Sustantia Nigra


title: Feature-2020-10-28-1-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-28-1-5_barcodes.tsv.gz
2020-10-28-1-5_features.tsv.gz
2020-10-28-1-5_matrix.mtx.gz


title: GEX-2020-10-28-1-5


title: 12132022_W62101403-V1-2_S831_R2C2_22K_S369


title: TCR-2020-10-28-1-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-28-1-4_airr_rearrangement.tsv
2020-10-28-1-4_clonotypes.csv
2020-10-28-1-4_filtered_contig.fasta
2020-10-28-1-4_filtered_contig_annotations.csv

value: PBMC

value: 12-153 Follow Up 1 (hash6), 12-153 Follow Up 2 (hash7), 12-153 Follow Up 3 (hash8), 12-153 Follow Up 4 (hash9), 12-153 Follow Up 5 (hash10)


title: GEX-2020-10-28-1-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-28-1-4_barcodes.tsv.gz
2020-10-28-1-4_features.tsv.gz
2020-10-28-1-4_matrix.mtx.gz


title: ADPD_SUNI_PD_04x10xx_X022_S06_L036_B1_T2_P041.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Sustantia Nigra

value: brain

value: bulk


title: 12132022_W62101307-V1-2_S1013_R2C2_11N_S422

value: human nasopharyngeal swab

value: BC


title: Feature-2020-10-28-1-4


title: TCR-2020-10-28-1-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-28-1-3_airr_rearrangement.tsv
2020-10-28-1-3_clonotypes.csv
2020-10-28-1-3_filtered_contig.fasta
2020-10-28-1-3_filtered_contig_annotations.csv


title: Feature-2020-10-28-1-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-28-1-3_barcodes.tsv.gz
2020-10-28-1-3_features.tsv.gz
2020-10-28-1-3_matrix.mtx.gz


title: 12132022_w62101290-V1-2_S1166_R2C2_11P_S466


title: ADPD_SUNI_PD_03x51xx_X031_S08_L088_B1_T2_P052.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Sustantia Nigra


title: GEX-2020-10-28-1-3


title: TCR-2020-10-28-1-6

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-28-1-6_airr_rearrangement.tsv
2020-10-28-1-6_clonotypes.csv
2020-10-28-1-6_filtered_contig.fasta
2020-10-28-1-6_filtered_contig_annotations.csv


title: ADPD_SUNI_PD_04x10xx_X022_S06_L035_B1_T1_P043.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Sustantia Nigra


title: 12132022_W62101241-V1-2_S683_R2C2_22I_S326


title: TCR-2020-10-28-1-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-28-1-1_airr_rearrangement.tsv
2020-10-28-1-1_clonotypes.csv
2020-10-28-1-1_filtered_contig.fasta
2020-10-28-1-1_filtered_contig_annotations.csv

value: 12-153 Baseline (hash10), 608 Baseline (hash6), 608 Follow Up 1 (hash7), 608 Follow Up 2 (hash9), 608 Follow Up 3 (hash8)


title: GEX-2020-10-28-1-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-28-1-1_barcodes.tsv.gz
2020-10-28-1-1_features.tsv.gz
2020-10-28-1-1_matrix.mtx.gz


title: ADPD_SUNI_PD_07x41xx_X002_S12_L047_B1_T1_P002.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Sustantia Nigra


title: ADPD_SUNI_PD_03x51xx_X031_S08_L087_B1_T1_P053.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Sustantia Nigra


title: 12132022_W62101554-V1-2_S803_R2C2_14K_S361


title: 12132022_W62100962-V1-2_S1104_R2C2_16O_S447


title: ADPD_SUNI_PD_03x43xx_X024_S05_L082_B1_T2_P045.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Sustantia Nigra


title: TCR-2020-10-02-1-6

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-02-1-6_airr_rearrangement.tsv
2020-10-02-1-6_clonotypes.csv
2020-10-02-1-6_filtered_contig.fasta
2020-10-02-1-6_filtered_contig_annotations.csv

value: 18-3253 Baseline (hash6), 18-3253 Follow Up 1 (hash7), 18-3253 Follow Up 2 (hash8), 18-3253 Follow Up 3 (hash9), 18-3253 Follow Up 4 (hash10)


title: Feature-2020-10-28-1-1


title: Feature-2020-10-02-1-6

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-02-1-6_barcodes.tsv.gz
2020-10-02-1-6_features.tsv.gz
2020-10-02-1-6_matrix.mtx.gz


title: ADPD_SUNI_PD_03x43xx_X024_S05_L081_B1_T1_P042.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Sustantia Nigra


title: GEX-2020-10-02-1-6


title: 12132022_W62100325-V1-2_S80_R2C2_22A_S150

description:
positive sample
run31_R1BC_count_table.txt
run31_R2BC_count_table.txt
run31_count_table.txt
run31_BC_pair_analysis_filenames.txt


title: GEX-2020-10-02-1-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-02-1-5_barcodes.tsv.gz
2020-10-02-1-5_features.tsv.gz
2020-10-02-1-5_matrix.mtx.gz


title: ADPD_SUNI_PD_00x45xx_X023_S05_L057_B1_T1_P040.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Sustantia Nigra


title: Feature-2020-10-02-1-5


title: 12132022_W62100257-V1-2_S2_R2C2_1A_S129


title: TCR-2020-10-02-1-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-02-1-4_airr_rearrangement.tsv
2020-10-02-1-4_clonotypes.csv
2020-10-02-1-4_filtered_contig.fasta
2020-10-02-1-4_filtered_contig_annotations.csv


title: 12132022_W62100250-V1-2_S472_R2C2_5G_S265


title: GEX-2020-10-02-1-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-02-1-4_barcodes.tsv.gz
2020-10-02-1-4_features.tsv.gz
2020-10-02-1-4_matrix.mtx.gz


title: ADPD_SUNI_PD_00x26xx_X017_S01_L002_B1_T2_P036.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Sustantia Nigra


title: Feature-2020-10-02-1-4


title: TCR-2020-10-02-1-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-02-1-3_airr_rearrangement.tsv
2020-10-02-1-3_clonotypes.csv
2020-10-02-1-3_filtered_contig.fasta
2020-10-02-1-3_filtered_contig_annotations.csv


title: 12132022_W62100237-V1-2_S10_R2C2_3A_S131


title: GEX-2020-10-02-1-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-02-1-3_barcodes.tsv.gz
2020-10-02-1-3_features.tsv.gz
2020-10-02-1-3_matrix.mtx.gz


title: TCR-2020-10-02-1-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-02-1-5_airr_rearrangement.tsv
2020-10-02-1-5_clonotypes.csv
2020-10-02-1-5_filtered_contig.fasta
2020-10-02-1-5_filtered_contig_annotations.csv


title: 12132022_W62100235-V1-2_S533_R2C2_22G_S282


title: 12132022_W62100245-V1-2_S314_R2C2_3E_S219


title: GEX-2020-10-02-1-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-02-1-2_barcodes.tsv.gz
2020-10-02-1-2_features.tsv.gz
2020-10-02-1-2_matrix.mtx.gz


title: ADPD_SUNI_PD_00x26xx_X017_S01_L001_B1_T1_P037.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Sustantia Nigra


title: 12132022_w62005551-V1-2_S1139_R2C2_2P_S457


title: ADPD_MDFG_PD_97x52xx_X002_S03_L030_B1_T2_P001.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: GEX-2020-10-02-1-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-02-1-1_barcodes.tsv.gz
2020-10-02-1-1_features.tsv.gz
2020-10-02-1-1_matrix.mtx.gz


title: Feature-2020-10-02-1-1


title: Feature-2020-10-02-1-3


title: ADPD_MDFG_PD_97x52xx_X002_S03_L029_B1_T1_P004.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: TCR-2020-10-02-1-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-02-1-2_airr_rearrangement.tsv
2020-10-02-1-2_clonotypes.csv
2020-10-02-1-2_filtered_contig.fasta
2020-10-02-1-2_filtered_contig_annotations.csv


title: TCR-2020-10-02-1-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-02-1-1_airr_rearrangement.tsv
2020-10-02-1-1_clonotypes.csv
2020-10-02-1-1_filtered_contig.fasta
2020-10-02-1-1_filtered_contig_annotations.csv


title: ADPD_MDFG_PD_94x31xx_X013_S01_L025_B1_T1_P025.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: Feature-2020-10-02-1-2


title: ADPD_SUNI_PD_00x27xx_X006_S07_L038_B1_T2_PMRG.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Sustantia Nigra


title: TCR-2020-10-01-2-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-01-2-4_airr_rearrangement.tsv
2020-10-01-2-4_clonotypes.csv
2020-10-01-2-4_filtered_contig.fasta
2020-10-01-2-4_filtered_contig_annotations.csv

value: 14-1128 Baseline (hash6), 14-1128 Follow Up 1 (hash7), 14-1128 Follow Up 2 (hash8), 14-1128 Follow Up 3 (hash9), 14-1128 Follow Up 4 (hash10)


title: ADPD_MDFG_PD_93x19xx_X024_S02_L076_B1_T2_P042.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: GEX-2020-10-01-2-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-01-2-4_barcodes.tsv.gz
2020-10-01-2-4_features.tsv.gz
2020-10-01-2-4_matrix.mtx.gz


title: 12132022_W62100264-V1-2_S376_R2C2_20E_S236


title: 12132022_w62005438-V1-2_S857_R2C2_8L_S377


title: 12132022_W62005488-V1-2_S762_R2C2_3K_S350


title: ADPD_MDFG_PD_93x19xx_X024_S02_L075_B1_T1_P041.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: TCR-2020-10-01-2-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-01-2-3_airr_rearrangement.tsv
2020-10-01-2-3_clonotypes.csv
2020-10-01-2-3_filtered_contig.fasta
2020-10-01-2-3_filtered_contig_annotations.csv


title: ADPD_MDFG_PD_13x60xx_X019_S02_L028_B1_T2_P030.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: 12132022_W62005339-V1-2_S817_R2C2_18K_S365


title: GEX-2020-10-01-2-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-01-2-3_barcodes.tsv.gz
2020-10-01-2-3_features.tsv.gz
2020-10-01-2-3_matrix.mtx.gz


title: 12132022_W62005095-V1-2_S73_R2C2_20A_S148


title: TCR-2020-10-01-2-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-01-2-2_airr_rearrangement.tsv
2020-10-01-2-2_clonotypes.csv
2020-10-01-2-2_filtered_contig.fasta
2020-10-01-2-2_filtered_contig_annotations.csv


title: Feature-2020-10-01-2-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-01-2-2_barcodes.tsv.gz
2020-10-01-2-2_features.tsv.gz
2020-10-01-2-2_matrix.mtx.gz


title: ADPD_MDFG_PD_13x22xx_X012_S08_L016_B1_T2_P026.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: ADPD_MDFG_PD_13x22xx_X012_S08_L015_B1_T1_P023.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: GEX-2020-10-01-2-2


title: 12132022_W62005093-V1-2_S362_R2C2_16E_S232

description:
positive sample
run31_R1BC_count_table.txt
run31_R2BC_count_table.txt
run31_count_table.txt
run31_BC_pair_analysis_filenames.txt


title: 12132022_W62005088-V1-2_S1111_R2C2_18O_S449


title: TCR-2020-10-01-2-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-01-2-1_airr_rearrangement.tsv
2020-10-01-2-1_clonotypes.csv
2020-10-01-2-1_filtered_contig.fasta
2020-10-01-2-1_filtered_contig_annotations.csv


title: ADPD_MDFG_PD_12x69xx_X030_S06_L060_B1_T2_P054.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: GEX-2020-10-01-2-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-01-2-1_barcodes.tsv.gz
2020-10-01-2-1_features.tsv.gz
2020-10-01-2-1_matrix.mtx.gz


title: Feature-2020-10-01-2-1


title: 12132022_W62005087-V1-2_S754_R2C2_1K_S348


title: ADPD_MDFG_PD_12x65xx_X010_S05_L033_B1_T1_P018.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: 12132022_W62005085-V1-2_S59_R2C2_16A_S144


title: 12132022_W62005079-V1-2_S1064_R2C2_5O_S436


title: GEX-2020-10-01-1-8

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-01-1-8_barcodes.tsv.gz
2020-10-01-1-8_features.tsv.gz
2020-10-01-1-8_matrix.mtx.gz

value: 14-1189_aCTLA-4 Baseline (hash6), 14-1189_aCTLA-4 Follow Up 1 (hash7), 14-1189_aCTLA-4 Follow Up 2 (hash8), 14-1189_aCTLA-4 Follow Up 3 (hash9), 14-1189_aCTLA-4 Follow Up 4 (hash10)


title: Feature-2020-10-01-2-4


title: TCR-2020-10-01-1-8

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-01-1-8_airr_rearrangement.tsv
2020-10-01-1-8_clonotypes.csv
2020-10-01-1-8_filtered_contig.fasta
2020-10-01-1-8_filtered_contig_annotations.csv


title: Feature-2020-10-01-1-8


title: TCR-2020-10-01-1-7

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-01-1-7_airr_rearrangement.tsv
2020-10-01-1-7_clonotypes.csv
2020-10-01-1-7_filtered_contig.fasta
2020-10-01-1-7_filtered_contig_annotations.csv


title: GEX-2020-10-01-1-7

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-01-1-7_barcodes.tsv.gz
2020-10-01-1-7_features.tsv.gz
2020-10-01-1-7_matrix.mtx.gz


title: Feature-2020-10-01-1-7


title: 12132022_W62005075-V1-2_S162_R2C2_3C_S175


title: ADPD_MDFG_PD_11x90xx_X003_S02_L004_B1_T2_P008.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: Feature-2020-10-01-2-3


title: ADPD_MDFG_PD_11x90xx_X003_S02_L003_B1_T1_P002.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: TCR-2020-10-01-1-6

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-01-1-6_airr_rearrangement.tsv
2020-10-01-1-6_clonotypes.csv
2020-10-01-1-6_filtered_contig.fasta
2020-10-01-1-6_filtered_contig_annotations.csv


title: GEX-2020-10-01-1-6

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-01-1-6_barcodes.tsv.gz
2020-10-01-1-6_features.tsv.gz
2020-10-01-1-6_matrix.mtx.gz


title: 12132022_W62005073-V1-2_S943_R2C2_12M_S401


title: Feature-2020-10-01-1-6


title: ADPD_MDFG_PD_12x65xx_X010_S05_L034_B1_T2_P017.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: ADPD_MDFG_PD_07x41xx_X020_S12_L072_B1_T2_P035.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: GEX-2020-10-01-1-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-01-1-5_barcodes.tsv.gz
2020-10-01-1-5_features.tsv.gz
2020-10-01-1-5_matrix.mtx.gz


title: TCR-2020-10-01-1-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-01-1-5_airr_rearrangement.tsv
2020-10-01-1-5_clonotypes.csv
2020-10-01-1-5_filtered_contig.fasta
2020-10-01-1-5_filtered_contig_annotations.csv


title: 12132022_W62005067-V1-2_S355_R2C2_14E_S230


title: 12132022_W62005065-V1-2_S369_R2C2_18E_S234


title: ADPD_MDFG_PD_07x41xx_X020_S12_L071_B1_T1_P034.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: ADPD_MDFG_PD_04x37xx_X001_S01_L002_B1_T2_P007.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: ADPD_MDFG_PD_04x37xx_X001_S01_L001_B1_T1_P004.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: Feature-2020-10-01-1-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-01-1-4_barcodes.tsv.gz
2020-10-01-1-4_features.tsv.gz
2020-10-01-1-4_matrix.mtx.gz


title: ADPD_MDFG_PD_04x10xx_X004_S08_L040_B1_T2_P008.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: 12132022_W62005064-V1-2_S810_R2C2_16K_S363


title: GEX-2020-10-01-1-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-01-1-3_barcodes.tsv.gz
2020-10-01-1-3_features.tsv.gz
2020-10-01-1-3_matrix.mtx.gz


title: TCR-2020-10-01-1-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-01-1-4_airr_rearrangement.tsv
2020-10-01-1-4_clonotypes.csv
2020-10-01-1-4_filtered_contig.fasta
2020-10-01-1-4_filtered_contig_annotations.csv


title: GEX-2020-10-01-1-4


title: 12132022_W62005032-V1-2_S971_R2C2_20M_S409


title: Feature-2020-10-01-1-5


title: 12132022_W62005059-V1-2_S66_R2C2_18A_S146


title: Feature-2020-10-01-1-3


title: TCR-2020-10-01-1-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-01-1-2_airr_rearrangement.tsv
2020-10-01-1-2_clonotypes.csv
2020-10-01-1-2_filtered_contig.fasta
2020-10-01-1-2_filtered_contig_annotations.csv


title: TCR-2020-10-01-1-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-01-1-3_airr_rearrangement.tsv
2020-10-01-1-3_clonotypes.csv
2020-10-01-1-3_filtered_contig.fasta
2020-10-01-1-3_filtered_contig_annotations.csv


title: ADPD_MDFG_PD_04x10xx_X004_S08_L039_B1_T1_P009.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: ADPD_MDFG_PD_03x51xx_X023_S08_L064_B1_T2_P040.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: GEX-2020-10-01-1-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-01-1-2_barcodes.tsv.gz
2020-10-01-1-2_features.tsv.gz
2020-10-01-1-2_matrix.mtx.gz


title: 12132022_W62005029-V1-2_S648_R2C2_12I_S316

description:
positive sample
run31_R1BC_count_table.txt
run31_R2BC_count_table.txt
run31_count_table.txt
run31_BC_pair_analysis_filenames.txt


title: 12132022_W62005024-V1-2_S170_R2C2_5C_S177


title: Feature-2020-10-01-1-2


title: TCR-2020-10-01-1-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-01-1-1_airr_rearrangement.tsv
2020-10-01-1-1_clonotypes.csv
2020-10-01-1-1_filtered_contig.fasta
2020-10-01-1-1_filtered_contig_annotations.csv


title: GEX-2020-10-01-1-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-10-01-1-1_barcodes.tsv.gz
2020-10-01-1-1_features.tsv.gz
2020-10-01-1-1_matrix.mtx.gz


title: ADPD_MDFG_PD_03x51xx_X023_S08_L063_B1_T1_P038.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: Feature-2020-10-01-1-1


title: 12132022_W62005018-V1-2_S739_R2C2_18J_S344


title: ADPD_MDFG_PD_03x43xx_X031_S02_L076_B1_T2_P053.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: GEX-2020-09-04-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-09-04-5_barcodes.tsv.gz
2020-09-04-5_features.tsv.gz
2020-09-04-5_matrix.mtx.gz

value: 14-839 Baseline (hash6), 14-839 Follow Up 1 (hash7), 14-839 Follow Up 2 (hash8), 14-839 Follow Up 3 (hash9), 14-839 Follow Up 4 (hash10)


title: 12132022_W62005013-V1-2_S917_R2C2_5M_S394


title: TCR-2020-09-04-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-09-04-5_airr_rearrangement.tsv
2020-09-04-5_clonotypes.csv
2020-09-04-5_filtered_contig.fasta
2020-09-04-5_filtered_contig_annotations.csv

value: non-naive T cells


title: ADPD_MDFG_PD_03x43xx_X031_S02_L075_B1_T1_P055.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: Feature-2020-09-04-5


title: 12132022_W62004997-V1-2_S606_R2C2_1I_S305


title: 12132022_W62004986-V1-2_S950_R2C2_14M_S403


title: ADPD_MDFG_PD_00x45xx_X025_S03_L006_B1_T2_P046.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: GEX-2020-09-04-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-09-04-4_barcodes.tsv.gz
2020-09-04-4_features.tsv.gz
2020-09-04-4_matrix.mtx.gz


title: TCR-2020-09-04-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-09-04-4_airr_rearrangement.tsv
2020-09-04-4_clonotypes.csv
2020-09-04-4_filtered_contig.fasta
2020-09-04-4_filtered_contig_annotations.csv


title: ADPD_MDFG_PD_00x45xx_X025_S03_L005_B1_T1_P047.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: Feature-2020-09-04-4


title: ADPD_MDFG_PD_00x27xx_X027_S01_L048_B1_T2_P051.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: 12132022_W62004980-V1-2_S901_R2C2_1M_S390


title: TCR-2020-09-04-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-09-04-2_airr_rearrangement.tsv
2020-09-04-2_clonotypes.csv
2020-09-04-2_filtered_contig.fasta
2020-09-04-2_filtered_contig_annotations.csv


title: Feature-2020-09-04-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-09-04-3_barcodes.tsv.gz
2020-09-04-3_features.tsv.gz
2020-09-04-3_matrix.mtx.gz


title: TCR-2020-09-04-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-09-04-3_airr_rearrangement.tsv
2020-09-04-3_clonotypes.csv
2020-09-04-3_filtered_contig.fasta
2020-09-04-3_filtered_contig_annotations.csv


title: GEX-2020-09-04-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-09-04-2_barcodes.tsv.gz
2020-09-04-2_features.tsv.gz
2020-09-04-2_matrix.mtx.gz


title: 12132022_W62004770-V1-2_S456_R2C2_1G_S261


title: Feature-2020-09-04-2


title: 12132022_W62004768-V1-2_S154_R2C2_1C_S173


title: ADPD_MDFG_PD_00x27xx_X027_S01_L047_B1_T1_P048.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: TCR-2020-09-04-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-09-04-1_airr_rearrangement.tsv
2020-09-04-1_clonotypes.csv
2020-09-04-1_filtered_contig.fasta
2020-09-04-1_filtered_contig_annotations.csv


title: GEX-2020-09-04-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-09-04-1_barcodes.tsv.gz
2020-09-04-1_features.tsv.gz
2020-09-04-1_matrix.mtx.gz


title: 12132022_W62004767-V1-2_S464_R2C2_3G_S263


title: Feature-2020-09-04-1


title: ADPD_PTMN_PD_97x52xx_X022_S09_L042_B1_T2_P044.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: ADPD_PTMN_PD_97x52xx_X022_S09_L041_B1_T1_P039.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: GEX-2020-08-19-1-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-08-19-1-5_barcodes.tsv.gz
2020-08-19-1-5_features.tsv.gz
2020-08-19-1-5_matrix.mtx.gz

value: non-naive CD8 T cells

value: 14-835 Baseline (hash6), 14-835 Follow Up 1 (hash7), 14-835 Follow Up 2 (hash8), 14-835 Follow Up 3 (hash9), 14-835 Follow Up 4 (hash10)


title: TCR-2020-08-19-1-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-08-19-1-5_airr_rearrangement.tsv
2020-08-19-1-5_clonotypes.csv
2020-08-19-1-5_filtered_contig.fasta
2020-08-19-1-5_filtered_contig_annotations.csv

value: peripheral blood


title: 12132022_W62004750-V1-2_S306_R2C2_1E_S217


title: GEX-2020-09-04-3

value: melanoma


title: TCR-2020-08-19-1-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-08-19-1-4_airr_rearrangement.tsv
2020-08-19-1-4_clonotypes.csv
2020-08-19-1-4_filtered_contig.fasta
2020-08-19-1-4_filtered_contig_annotations.csv

value: non-naive CD4 T cells

value: immune checkpoint blockade


title: 12132022_W62004705-V1-2_S1083_R2C2_10O_S441


title: Feature-2020-08-19-1-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-08-19-1-4_barcodes.tsv.gz
2020-08-19-1-4_features.tsv.gz
2020-08-19-1-4_matrix.mtx.gz


title: ADPD_MDFG_PD_00x26xx_X011_S02_L052_B1_T2_P019.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle frontal Gyri


title: TCR-2020-08-19-1-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-08-19-1-3_airr_rearrangement.tsv
2020-08-19-1-3_clonotypes.csv
2020-08-19-1-3_filtered_contig.fasta
2020-08-19-1-3_filtered_contig_annotations.csv


title: GEX-2020-08-19-1-4


title: 12132022_W62004644-V1-2_S676_R2C2_20I_S324

description:
positive sample
run31_R1BC_count_table.txt
run31_R2BC_count_table.txt
run31_count_table.txt
run31_BC_pair_analysis_filenames.txt


title: 12132022_W62004640-V1-2_S964_R2C2_18M_S407


title: ADPD_PTMN_PD_93x19xx_X023_S07_L061_B1_T1_P038.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: ADPD_PTMN_PD_93x19xx_X023_S07_L062_B1_T2_P040.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: 12132022_W62004684-V1-2_S174_R2C2_6C_S178


title: Feature-2020-08-19-1-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-08-19-1-2_barcodes.tsv.gz
2020-08-19-1-2_features.tsv.gz
2020-08-19-1-2_matrix.mtx.gz

value: PBMC


title: TCR-2020-08-19-1-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-08-19-1-2_airr_rearrangement.tsv
2020-08-19-1-2_clonotypes.csv
2020-08-19-1-2_filtered_contig.fasta
2020-08-19-1-2_filtered_contig_annotations.csv


title: ADPD_PTMN_PD_13x60xx_X007_S07_L062_B1_T2_P011.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen

value: brain


title: Feature-2020-08-19-1-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-08-19-1-3_barcodes.tsv.gz
2020-08-19-1-3_features.tsv.gz
2020-08-19-1-3_matrix.mtx.gz


title: 12132022_W62004766-V1-2_S887_R2C2_18L_S387


title: 12132022_w62004638-V1-2_S655_R2C2_14I_S318


title: GEX-2020-08-19-1-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-08-19-1-1_barcodes.tsv.gz
2020-08-19-1-1_features.tsv.gz
2020-08-19-1-1_matrix.mtx.gz


title: TCR-2020-08-19-1-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-08-19-1-1_airr_rearrangement.tsv
2020-08-19-1-1_clonotypes.csv
2020-08-19-1-1_filtered_contig.fasta
2020-08-19-1-1_filtered_contig_annotations.csv


title: ADPD_PTMN_PD_13x60xx_X007_S07_L061_B1_T1_P010.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen

value: bulk


title: Feature-2020-08-19-1-5


title: 12132022_W62004634-V1-2_S591_R2C2_18H_S301

value: human nasopharyngeal swab


title: TCR-2020-08-17-1-6

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-08-17-1-6_airr_rearrangement.tsv
2020-08-17-1-6_clonotypes.csv
2020-08-17-1-6_filtered_contig.fasta
2020-08-17-1-6_filtered_contig_annotations.csv

value: 15-1471 Baseline (hash6), 15-1471 Follow Up 1 (hash7), 15-1471 Follow Up 2 (hash8), 15-1471 Follow Up 3 (hash9), 15-1471 Follow Up 4 (hash10)


title: ADPD_PTMN_PD_94x31xx_X021_S10_L020_B1_T2_P040.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: ADPD_PTMN_PD_13x22xx_X019_S03_L030_B1_T2_P031.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: 12132022_W62004625-V1-2_S622_R2C2_5I_S309

value: BC


title: ADPD_PTMN_PD_94x31xx_X021_S10_L019_B1_T1_P039.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: Feature-2020-08-17-1-6

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-08-17-1-6_barcodes.tsv.gz
2020-08-17-1-6_features.tsv.gz
2020-08-17-1-6_matrix.mtx.gz


title: ADPD_PTMN_PD_13x22xx_X019_S03_L029_B1_T1_P032.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: GEX-2020-08-19-1-3


title: 12132022_W62004624-V1-2_S770_R2C2_5K_S352


title: GEX-2020-08-17-1-6


title: GEX-2020-08-17-1-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-08-17-1-5_barcodes.tsv.gz
2020-08-17-1-5_features.tsv.gz
2020-08-17-1-5_matrix.mtx.gz


title: GEX-2020-08-19-1-2


title: ADPD_PTMN_PD_12x69xx_X013_S02_L028_B1_T2_P023.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: 12132022_W62004611-V1-2_S208_R2C2_15C_S187


title: ADPD_PTMN_PD_12x69xx_X013_S02_L027_B1_T1_P024.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: TCR-2020-08-17-1-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-08-17-1-5_airr_rearrangement.tsv
2020-08-17-1-5_clonotypes.csv
2020-08-17-1-5_filtered_contig.fasta
2020-08-17-1-5_filtered_contig_annotations.csv


title: Feature-2020-08-17-1-5


title: TCR-2020-08-17-1-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-08-17-1-4_airr_rearrangement.tsv
2020-08-17-1-4_clonotypes.csv
2020-08-17-1-4_filtered_contig.fasta
2020-08-17-1-4_filtered_contig_annotations.csv

value: 15-1471 Follow Up 1 (hash7), 15-1471 Follow Up 2 (hash8), 15-1471 Follow Up 4 (hash10)


title: Feature-2020-08-17-1-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-08-17-1-4_barcodes.tsv.gz
2020-08-17-1-4_features.tsv.gz
2020-08-17-1-4_matrix.mtx.gz


title: GEX-2020-08-17-1-4


title: 12132022_W62004616-V1-2_S800_R2C2_13K_S360


title: GEX-2020-08-17-1-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-08-17-1-3_barcodes.tsv.gz
2020-08-17-1-3_features.tsv.gz
2020-08-17-1-3_matrix.mtx.gz


title: 12132022_W62004607-V1-2_S441_R2C2_18F_S257


title: Feature-2020-08-19-1-1


title: ADPD_PTMN_PD_12x65xx_X030_S05_L058_B1_T2_P054.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: TCR-2020-08-17-1-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-08-17-1-3_airr_rearrangement.tsv
2020-08-17-1-3_clonotypes.csv
2020-08-17-1-3_filtered_contig.fasta
2020-08-17-1-3_filtered_contig_annotations.csv


title: ADPD_PTMN_PD_12x65xx_X030_S05_L057_B1_T1_P051.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: 12132022_W62004495-V1-2_S659_R2C2_15I_S319


title: TCR-2020-08-17-1-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-08-17-1-2_airr_rearrangement.tsv
2020-08-17-1-2_clonotypes.csv
2020-08-17-1-2_filtered_contig.fasta
2020-08-17-1-2_filtered_contig_annotations.csv


title: Feature-2020-08-17-1-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-08-17-1-2_barcodes.tsv.gz
2020-08-17-1-2_features.tsv.gz
2020-08-17-1-2_matrix.mtx.gz


title: ADPD_PTMN_PD_11x90xx_X003_S01_L002_B1_T2_P007.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: ADPD_PTMN_PD_11x90xx_X003_S01_L001_B1_T1_P004.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: TCR-2020-08-17-1-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-08-17-1-1_airr_rearrangement.tsv
2020-08-17-1-1_clonotypes.csv
2020-08-17-1-1_filtered_contig.fasta
2020-08-17-1-1_filtered_contig_annotations.csv


title: Feature-2020-08-17-1-1

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-08-17-1-1_barcodes.tsv.gz
2020-08-17-1-1_features.tsv.gz
2020-08-17-1-1_matrix.mtx.gz