title: CD4+_T-cell  HFD-MI

status: Public on Feb 06 2023

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina RTA 1.18.64 software was used for base calling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.1.1 in combination with Bowtie2.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 5000000.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: CD4+ T-cell

extract_protocol:
Total RNA was extracted from cells with an miRNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio, Mountain View, CA) according to the manufacturer’s instructions. An Illumina library was prepared using a Nextera DNA Library Preparation Kit (Illumina, San Diego, CA) according to SMARTer kit instructions.

value: spleen

value: CD4+ T-cell sorted from spleen Day14

value: untreated


title: A2v-6_A4KD_chemo

status: Public on Feb 07 2023

type: SRA

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

library_source: transcriptomic

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: hg19
Supplementary files format and content: *_FPKM.txt: Tab-delimited text files include FPKM values for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: OVSAHO

extract_protocol:
Total RNA was extracted from cells with a miRNeasy Micro kit (Qiagen) following the manufacturer’s instruction.
Each cDNA was generated using a Clontech SMART-Seq HT Kit (Takara Clontech, Mountain View, CA, USA), and each library was prepared using a Nextera XT DNA Library Prep Kit (Illumina, San Diego, USA).

tag: cell line

value: OVSAHO

tag: cell type

value: ovarian cancer cell

tag: genotype

value: SMARCA2 stable, SMARCA4 knockdown

tag: treatment

value: carboplatin, 25uM, 2days


title: Test_rep2

library_source: genomic

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101+101-base paired-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Adaptor sequence CTGTCTCTTATACACATCT was removed by cutadapt 3.2.
Bowtie2 (v 2.3.5.1, options: --no-discordant,--no-mixed,--dovetail,--very-sensitive) was used for alignment with human reference genome hg19.
For shifting reads, alignmentSieve function from deeptools (v 3.5.1) was used.
Picard MarkDuplicates (v 1.128) was used for duplicate removal.
For the narrow peak detection, only the open chromatin paired-reads with distance less than 100bp were kept.
Peaks were identified by callpeaks function of MACS2 (v2.2.7.1, options [For narrow peaks/For broad peaks]: callpeak -f BAMPE -g 2.7e9 -q 0.05 / callpeak -f BAMPE -g 2.7e9 --broad --broad-cutoff 0.05 --keep-dup all).
Differentially accessible analyses were computed through the use of R packages csaw (v 1.26.0) and edgeR (v 3.34.1) with detected peaks and ENCODE hg19 blacklists.
Assembly: hg19
Supplementary files format and content: *_peaks.tsv: Tab-delimited text files for peak information.

molecule: genomic DNA

extract_protocol:
Cells were lysed and purified DNA were tagmented with ATAC-seq kit (Active Motif, Inc., #53150), following the manufacturer’s instructions.
Libraries were prepared using ATAC-seq kit (Active Motif, Inc., #53150), following the manufacturer’s instructions.


title: brain, GD

status: Public on Feb 03 2023

library_source: transcriptomic single cell

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 26+90 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were input into the cellranger count pipeline (Cell Ranger v.6.0.0, 10x Genomics) for alignment to the mm10 genome, UMI collapsing, and UMI counting for each gene-cell (barcode) combination.
Assembly: mm10
Supplementary files format and content: comma-delimited text files include raw counts for all cells detected

organism: Mus musculus

source_name: brain

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller, and cDNAs with UMIs were generated at single-cell level.
Single-cell RNA library construction was processed through the 10x Genomics Chromium Controller following the protocol outlined in the Chromium Single Cell 5' Reagent Kits v2 User Guide.

treatment_protocol: Whole brains were enzymatically dissociated with EBSS containing papain (20 U/mL), L-cyctein (1 mM), DNase I (400 U/mL), and EDTA (0.5 mM). After the treatment, the tissues were washed with papain inhibitor buffer containing BSA (1.0 mg/mL) and ovomucoid (1.0 mg/mL) and then mechanically dissociated by gentle pipetting. The dissociated cells were resuspended 20% (v/v) Percoll in PBS and centrifuged at 400 × g for 25 min at 4 °C to remove the myelin and debris.  Finally, the brain cells were resuspended in PBS supplemented with 0.04% (w/v) BSA.

tag: tissue

value: brain

value: brain cells

value: Gba flox/flox; nestin-Cre


title: P1

status: Public on Feb 14 2023

data_processing:
Sequencing was performed on NextSeq500 System in a 76-base single-end mode.
NextSeq Control Software 2.0 was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat2 v2.0.7.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks 2.1.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Omentum

extract_protocol:
Total RNA was harvested using RNeasy micro kit with DNase treatment (Qiagen) following the manufacturer’s instruction.
RNA libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina.

value: Omentum

value: stromal fraction P1

value: WT

tag: strain


title: Cv-10_NC_chemo


title: CD4+_T-cell  HFD-MI + probucol

value: treated with probucol


title: Heart HFD-MI

source_name: RNA later treated cryopreserved heart tissue

extract_protocol:
Total RNA was extracted from cells with an miRNeasy Mini kit (Qiagen) according to the manufacturer’s protocol.
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit.

value: heart

tag: age

value: day 14


title: P3

value: stromal fraction P3


title: Heart HFD-MI + probucol


title: GD, KO3, microglia

data_processing:
Sequencing was performed on HiSeq 3000 or NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v2.7.7 or v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

extract_protocol:
RNA was harvested using QIAzol Lysis Reagent (Qiagen).
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).

value: microglia

value: Gba flox/flox; nestin-Cre; Mincle-/-


title: GD3, microglia


title: GD2, microglia


title: GD, KO1, microglia


title: GD1, microglia


title: Test_rep1


title: Control_rep2


title: WT3, microglia

value: wild type


title: brain, WT


title: Control_rep1

value: OVSAHO


title: IWS1 KO parasite_2

status: Public on Jan 30 2023

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the Toxoplasma gondii (GCA_000149715.2_TGGT1) reference genome using hisat2 v2.1.0.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1.
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

organism: Toxoplasma gondii

source_name: tachyzoites

extract_protocol:
Total RNA was extracted from cells with a miRNeasy Mini kit (Qiagen) following the manufacturer’s instruction.
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).

value: tachyzoites

value: IWS1 knock out


title: WT1, microglia


title: IWS1 KO parasite_1


title: WT parasite_3


title: WT2, microglia


title: WT parasite_2


title: WT parasite_1


title: IWS1 KO parasite_3


title: GD, KO2, microglia


title: KG1A cells treated with DMSO-replicate 4

status: Public on Jan 11 2023

city: Arcadia

first: WEI

last: CHEN

state: CA

address: 655 e huntington dr

department: Shared Resource

country: USA

institute: City of Hope National Medical Center

data_processing:
Base calling was done using Illumina RTA and bcl2fastq v2.18.0.12
Sequences were aligned to hg19 using Tophat2 with default settings
Gene expression level of Ensembl GRCh37 coding genes were quantified using HTSeq v0.11.2
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text file gene expression counts

source_name: AML cell line

growth_protocol: RPMI 1640 supplemented with 10% dialyzed FBS (Cytiva) and 1% streptomycin/penicillin

extract_protocol:
Total RNA was isolated using Trizol Reagent (Life technologies) and purified by spin column using Direct-zol™ RNA MicroPrep (Zymo Research)
RNA libraries were prepared for sequencing using Kapa mRNA HyperPrep kit (Cat:KK8581) with 200ng of total RNA
stranded polyA RNA-Seq

treatment_protocol: Cells were treated with 10 µM of NEL or vehicle control (DMSO)

value: DMSO


title: OX40

status: Public on Jan 10 2023

city: Leiden

first: Ramon

last: Arens

address: Albinusdreef 2

department: Immunology

country: Netherlands

institute: Leiden University Medical Center

data_processing:
Seurat package version 2
Genome_build: mm10
Supplementary_files_format_and_content: mtx (matrix count)

source_name: Enriched CD3+T cells - blood

extract_protocol:
Debris removal and CD3+ T cells enrichment
Chromium Single Cell 3' Reagent / Illumina platform Novaseq6000
sc-RNA-seq with 50 000 reads per cell

treatment_protocol: MC38 injection subcutaneously in C57BL/6 mice treated by immunotherapy

tag: tissue/cell type

value: Enriched CD3+T cells - blood


title: PDOX

value: PDOX


title: Subject 071 VisitDay 119 Cohort IMRAS_Cohort 1_True Immunized

status: Public on Dec 31 2022

city: Seattle

first: Raphael

last: Gottardo

state: WA

address: 1100 Fairview Ave N

department: VIDD

institute: Fred Hutch

description:
IMRAS071.119
processed data file: GEO_IMRAS_mapped_rawCounts.tsv

data_processing:
a. Reads were aligned to the UCSC hg38 genome using Kallisto alignment tool.
b. Reads were quantified with RSEM.
c. Raw counts from two separate batches were combined into one matrix.
d. Original sample names used during processing were mapped to standardized sample names to include subjectId and visit day.
e. Four samples that could not be mapped to standardized subject-visit day format were excluded.
Genome_build: UCSC hg38 (GRCh38)
Supplementary_files_format_and_content: GEO_IMRAS_mapped_rawCounts.tsv: Tab-delimited file with raw counts for 265 samples.

source_name: Whole Blood

extract_protocol:
Whole blood samples taken from participants via venipuncture and collected into PaxGene tubes. Total RNA was extracted using PAXgene Blood Kit (PreAnalytiX) and globin mRNA removed using GLOBINclear Human Kit (Ambion).
RNA libraries were generated using standard manufacturers’ protocols for the two platforms (BGI’s BGIseq500 and Illumina’s HiSeq2000).

tag: cohort

value: Cohort 1

tag: subject

value: Whole Blood

value: True Immunized

tag: visit day


title: Subject 078 VisitDay 141 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS078.141
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 062 VisitDay 147 Cohort IMRAS_Cohort 1_Mock Immunized

description:
IMRAS062.147
processed data file: GEO_IMRAS_mapped_rawCounts.tsv

value: Mock Immunized


title: Subject 078 VisitDay 119 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS078.119
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Untreated

value: Untreated


title: Subject 071 VisitDay 141 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS071.141
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 078 VisitDay 140 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS078.140
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 071 VisitDay 147 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS071.147
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 071 VisitDay 140 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS071.140
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: PDL1


title: Subject 071 VisitDay 035 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS071.035
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 062 VisitDay 141 Cohort IMRAS_Cohort 1_Mock Immunized

description:
IMRAS062.141
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 062 VisitDay 140 Cohort IMRAS_Cohort 1_Mock Immunized

description:
IMRAS062.140
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 062 VisitDay 119 Cohort IMRAS_Cohort 1_Mock Immunized

description:
IMRAS062.119
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 061 VisitDay 141 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS061.141
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 061 VisitDay 140 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS061.140
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 062 VisitDay 035 Cohort IMRAS_Cohort 1_Mock Immunized

description:
IMRAS062.035
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 061 VisitDay 035 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS061.035
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 061 VisitDay 119 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS061.119
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 078 VisitDay 147 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS078.147
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 060 VisitDay 141 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS060.141
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 060 VisitDay 140 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS060.140
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 060 VisitDay 119 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS060.119
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 060 VisitDay 035 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS060.035
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 057 VisitDay 147 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS057.147
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 057 VisitDay 140 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS057.140
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 057 VisitDay 119 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS057.119
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 061 VisitDay 147 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS061.147
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 057 VisitDay 035 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS057.035
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 057 VisitDay 141 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS057.141
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 045 VisitDay 147 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS045.147
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 054 VisitDay 119 Cohort IMRAS_Cohort 1_Mock Immunized

description:
IMRAS054.119
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 049 VisitDay 141 Cohort IMRAS_Cohort 1_Mock Immunized

description:
IMRAS049.141
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 054 VisitDay 035 Cohort IMRAS_Cohort 1_Mock Immunized

description:
IMRAS054.035
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 049 VisitDay 147 Cohort IMRAS_Cohort 1_Mock Immunized

description:
IMRAS049.147
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 045 VisitDay 141 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS045.141
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 054 VisitDay 147 Cohort IMRAS_Cohort 1_Mock Immunized

description:
IMRAS054.147
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 049 VisitDay 119 Cohort IMRAS_Cohort 1_Mock Immunized

description:
IMRAS049.119
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 049 VisitDay 140 Cohort IMRAS_Cohort 1_Mock Immunized

description:
IMRAS049.140
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 054 VisitDay 140 Cohort IMRAS_Cohort 1_Mock Immunized

description:
IMRAS054.140
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 054 VisitDay 141 Cohort IMRAS_Cohort 1_Mock Immunized

description:
IMRAS054.141
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 049 VisitDay 035 Cohort IMRAS_Cohort 1_Mock Immunized

description:
IMRAS049.035
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 045 VisitDay 035 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS045.035
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 060 VisitDay 147 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS060.147
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 039 VisitDay 147 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS039.147
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 045 VisitDay 119 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS045.119
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 039 VisitDay 140 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS039.140
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 045 VisitDay 140 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS045.140
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 039 VisitDay 141 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS039.141
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 039 VisitDay 119 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS039.119
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 033 VisitDay 147 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS033.147
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 033 VisitDay 141 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS033.141
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 033 VisitDay 119 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS033.119
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 021 VisitDay 147 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS021.147
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 033 VisitDay 140 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS033.140
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 021 VisitDay 141 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS021.141
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 033 VisitDay 035 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS033.035
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 021 VisitDay 140 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS021.140
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 021 VisitDay 119 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS021.119
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 039 VisitDay 035 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS039.035
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 021 VisitDay 035 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS021.035
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 005 VisitDay 141 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS005.141
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 002 VisitDay 141 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS002.141
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 071 VisitDay 126 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS071.126
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 002 VisitDay 035 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS002.035
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 005 VisitDay 140 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS005.140
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 005 VisitDay 119 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS005.119
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 005 VisitDay 147 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS005.147
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 033 VisitDay 126 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS033.126
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 057 VisitDay 126 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS057.126
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 045 VisitDay 126 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS045.126
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 078 VisitDay 126 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS078.126
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 002 VisitDay 147 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS002.147
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 005 VisitDay 035 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS005.035
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 002 VisitDay 119 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS002.119
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 060 VisitDay 126 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS060.126
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 039 VisitDay 126 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS039.126
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 005 VisitDay 126 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS005.126
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 078 VisitDay 122 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS078.122
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 071 VisitDay 122 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS071.122
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 060 VisitDay 122 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS060.122
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 061 VisitDay 122 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS061.122
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 057 VisitDay 122 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS057.122
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 061 VisitDay 126 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS061.126
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 021 VisitDay 126 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS021.126
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 002 VisitDay 126 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS002.126
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 002 VisitDay 140 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS002.140
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 039 VisitDay 122 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS039.122
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 045 VisitDay 122 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS045.122
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 002 VisitDay 122 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS002.122
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 033 VisitDay 122 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS033.122
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 061 VisitDay 120 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS061.120
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 060 VisitDay 120 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS060.120
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 005 VisitDay 120 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS005.120
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 057 VisitDay 120 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS057.120
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 071 VisitDay 120 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS071.120
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 033 VisitDay 120 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS033.120
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 045 VisitDay 120 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS045.120
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 002 VisitDay 120 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS002.120
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 071 VisitDay 091 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS071.091
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 060 VisitDay 091 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS060.091
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 021 VisitDay 120 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS021.120
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 061 VisitDay 091 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS061.091
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 039 VisitDay 120 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS039.120
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 021 VisitDay 091 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS021.091
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 057 VisitDay 091 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS057.091
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 078 VisitDay 087 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS078.087
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 002 VisitDay 091 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS002.091
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 071 VisitDay 087 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS071.087
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 060 VisitDay 087 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS060.087
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 045 VisitDay 091 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS045.091
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 061 VisitDay 087 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS061.087
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 021 VisitDay 122 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS021.122
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 078 VisitDay 120 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS078.120
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 078 VisitDay 084 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS078.084
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 057 VisitDay 087 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS057.087
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 039 VisitDay 087 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS039.087
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 039 VisitDay 091 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS039.091
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 045 VisitDay 087 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS045.087
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 005 VisitDay 091 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS005.091
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 005 VisitDay 087 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS005.087
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 033 VisitDay 091 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS033.091
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 033 VisitDay 087 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS033.087
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 071 VisitDay 084 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS071.084
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 021 VisitDay 087 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS021.087
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 057 VisitDay 084 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS057.084
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 033 VisitDay 084 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS033.084
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 078 VisitDay 070 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS078.070
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 045 VisitDay 070 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS045.070
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 045 VisitDay 084 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS045.084
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 039 VisitDay 084 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS039.084
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 060 VisitDay 084 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS060.084
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 005 VisitDay 084 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS005.084
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 060 VisitDay 070 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS060.070
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 061 VisitDay 070 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS061.070
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 071 VisitDay 070 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS071.070
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 002 VisitDay 084 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS002.084
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 061 VisitDay 084 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS061.084
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 021 VisitDay 084 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS021.084
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 057 VisitDay 070 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS057.070
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 033 VisitDay 070 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS033.070
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 005 VisitDay 070 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS005.070
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 021 VisitDay 070 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS021.070
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 002 VisitDay 070 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS002.070
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 002 VisitDay 087 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS002.087
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 039 VisitDay 070 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS039.070
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 061 VisitDay 063 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS061.063
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 071 VisitDay 063 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS071.063
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 078 VisitDay 063 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS078.063
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 002 VisitDay 063 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS002.063
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 045 VisitDay 063 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS045.063
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 060 VisitDay 063 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS060.063
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 021 VisitDay 063 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS021.063
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 039 VisitDay 056 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS039.056
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 071 VisitDay 042 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS071.042
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 057 VisitDay 063 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS057.063
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 061 VisitDay 042 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS061.042
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 002 VisitDay 056 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS002.056
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 039 VisitDay 063 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS039.063
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 021 VisitDay 056 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS021.056
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 078 VisitDay 042 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS078.042
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 021 VisitDay 042 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS021.042
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 057 VisitDay 042 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS057.042
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 045 VisitDay 056 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS045.056
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 005 VisitDay 056 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS005.056
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 005 VisitDay 042 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS005.042
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 033 VisitDay 063 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS033.063
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 033 VisitDay 056 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS033.056
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 060 VisitDay 042 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS060.042
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 078 VisitDay 059 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS078.059
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 033 VisitDay 042 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS033.042
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 039 VisitDay 042 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS039.042
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 045 VisitDay 042 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS045.042
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 071 VisitDay 059 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS071.059
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 005 VisitDay 063 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS005.063
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 061 VisitDay 059 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS061.059
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 060 VisitDay 059 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS060.059
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 057 VisitDay 059 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS057.059
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 045 VisitDay 059 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS045.059
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 033 VisitDay 059 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS033.059
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 002 VisitDay 059 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS002.059
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 005 VisitDay 059 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS005.059
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 039 VisitDay 059 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS039.059
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 061 VisitDay 056 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS061.056
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 057 VisitDay 056 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS057.056
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 071 VisitDay 031 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS071.031
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 078 VisitDay 056 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS078.056
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 057 VisitDay 031 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS057.031
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 039 VisitDay 031 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS039.031
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 045 VisitDay 031 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS045.031
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 021 VisitDay 031 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS021.031
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 002 VisitDay 042 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS002.042
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 060 VisitDay 031 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS060.031
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: UC133-2

status: Public on Dec 27 2022

data_processing:
Sequencing was performed on HiSeq 3000 or NovaSeq 6000 platform in a 100+100 or 101+101 base paired-end mode.
Illumina RTA 2.7.7 or RTA 3.4.4 software was used for base calling.
Generated reads were input into the BD Targeted Rhapsody Analysis Pipeline Version 1.8 for UMI counting for each cell(index)-gene combination.
Assembly: the fasta file ("1072_Osaka_Univ_MM_20190809_amplicons_5.fasta") based on the customized BD Rhapsody Immune Response Panel Hs
Supplementary files format and content: comma-delimited text files including UMI count for each cell(index)-gene combination

molecule: polyA RNA

source_name: colon

extract_protocol:
Single-cell RNA-seq analysis was conducted using BD Rhapsody Single-Cell Analysis System (BD BioScience) following the manufacture’s protocol.
For library construction, we used a customized BD Rhapsody Immune Response Panel Hs.

value: colon

tag: disease

value: Ulcerative colitis

value: CD3+ T cell

tag: Sex

value: Male


title: CD139

value: Crohn's disease


title: UC141


title: Subject 033 VisitDay 031 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS033.031
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 021 VisitDay 059 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS021.059
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 071 VisitDay 056 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS071.056
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: CK118

value: Control (normal colonic mucosa from patients with colon cancer)

value: Female


title: Subject 002 VisitDay 031 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS002.031
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: CK258


title: Subject 061 VisitDay 031 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS061.031
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: UC309


title: CK119


title: Liver, NASH+7-ketocholesterol diet, 3weeks, rep1

status: Public on Dec 26 2022

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10
Supplementary files format and content: *.FPKM.txt: Tab-delimited text file includes FPKM values for each sample.

source_name: Liver

extract_protocol:
Total RNA was extracted from cells with a miRNeasy kit (Qiagen) following the manufacturer’s instruction.
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).

value: Liver

value: NASH+7-ketocholesterol diet for 3 weeks


title: UC287


title: CD134-2


title: Liver, NASH diet, 3weeks, rep2

value: NASH diet for 3 weeks


title: Dorsal skin, NASH diet, 3weeks, imiquimod cream, 1 day, rep1

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 5000000.
Assembly: mm10
Supplementary files format and content: *.FPKM.txt: Tab-delimited text files include FPKM values for each sample.

source_name: Dorsal skin

value: Dorsal skin

value: NASH diet for 3 weeks, imiquimod cream for 1 day


title: CK254


title: Subject 005 VisitDay 031 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS005.031
processed data file: GEO_IMRAS_mapped_rawCounts.tsv

value: Cohort 1


title: CD303


title: GA35927 hMono_KO_plts_3

status: Public on Dec 20 2022

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.1.1 in combination with Bowtie2.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: human monocytes

growth_protocol: Human monocytes were purified from peripheral blood mononuclear cells.

treatment_protocol: Human monocytes (5 × 10E5 cells) were stimulated with murine platelets from wild-type or Clec1b-/- (1 × 10E7 cells) mice for 8 hours at 37 ℃.

value: human monocytes

value: treated  with murine platelets from Clec1b-/- mice


title: Dorsal skin, NASH+7-ketocholesterol diet, 3weeks, imiquimod cream, 1 day, rep2

value: NASH+7KC diet for 3 weeks, imiquimod cream for 1 day


title: Dorsal skin, NASH diet, 3weeks, imiquimod cream, 1 day, rep2


title: GA35921 hMono_non_stim_3

value: untreated


title: Dorsal skin, NASH+7-ketocholesterol diet, 3weeks, imiquimod cream, 1 day, rep1


title: Subject 060 VisitDay 056 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS060.056
processed data file: GEO_IMRAS_mapped_rawCounts.tsv

value: Whole Blood

value: True Immunized


title: GA35919 hMono_non_stim_1


title: Liver, NASH diet, 3weeks, rep1


title: Liver, NASH+7-ketocholesterol diet, 3weeks, rep2


title: GA35923 hMono_WT_plts_2

value: treated  with murine platelets from wild-type mice


title: GA35924 hMono_WT_plts_3


title: GA35926 hMono_KO_plts_2


title: GA35922 hMono_WT_plts_1


title: GA35920 hMono_non_stim_2


title: C2

status: Public on Dec 15 2022

data_processing:
Sequencing was performed on Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina RTA v1.18.64 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 5000000.
Assembly: mm10
Supplementary files format and content: *.FPKM.txt: Tab-delimited text files include FPKM values for each sample.

source_name: inner ear

extract_protocol:
Total RNA was extracted using TRIzol reagent.
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).

value: inner ear

value: primary culture of cochlear cells


title: C1


title: GA35925 hMono_KO_plts_1


title: CD293

value: colon

value: Crohn's disease

value: CD3+ T cell

value: Male


title: V2

value: primary culture of vestibular cells


title: V1


title: T3

status: Public on Dec 14 2022

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Bone marrow-derived dendritic cells

growth_protocol: For obtaining bone marrow-derived dendritic cells, mouse bone marrow cells were cultured in RPMI1640 medium containing FBS and GM-CSF for 9 days.

extract_protocol:
RNA was harvested using QIAzol Lysis Reagent (Qiagen).
Library preparation was performed using the TruSeq Stranded mRNA sample prep kit (Illumina, San Diego, CA), according to the manufacturer’s instructions.

treatment_protocol: Bone marrow-derived dendritic cells were stimulated with Isopropanol, PEG-TGL, or TDB for 4 hours

value: Bone marrow-derived dendritic cells

value: Wild type


title: T2


title: R3


title: N3


title: Bastle-3-F_GTGAAA_L007

status: Public on Dec 06 2022

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description: TMN tissues were collected every 4 hr at five time points (n=3/time point): ZT0 (the beginning of lights on for mice, which marks the beginning of their inactive phase), ZT4 (4 hr later), ZT8 (4 hr after that), ZT12 (the beginning of lights off, which marks the beginning of their active phase), ZT16 (4 hr later) and ZT20 (4 hr after that).

data_processing:
Raw sequencing reads from mice were mapped to mm10 using HISAT2.
Counts of reads mapping to genes were obtained using featureCounts software of Subread package against Ensembl v90 annotation.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file containing counts

source_name: Brain (TMN)

extract_protocol:
TMN tissue punches were homogenized in Trizol (Thermo Fisher), and RNA was isolated on RNeasy Microcolumns (Qiagen) following manufacturer’s instructions. RNA concentrations were assessed using a Qubit spectrophotometer and quality was confirmed using a bioanalyzer.
RNA-seq libraries were prepared according to manufacturer’s protocols using the Illumina TruSeq RNA Library Preparation Kit v2 (Illumina cat# RS-122-2001).

value: Brain (TMN)

tag: time point


title: Bastle-3-E_CTTGTA_L007


title: N1


title: Bastle-2-D_GCCAAT_L006


title: Bastle-2-E_CTTGTA_L006


title: Bastle-3-B_TGACCA_L007


title: Bastle-3-D_GCCAAT_L007


title: Bastle-3-A_CGATGT_L007


title: Bastle-2-A_CGATGT_L006


title: R2


title: Bastle-2-F_GTGAAA_L006


title: Bastle-2-B_TGACCA_L006


title: Bastle-1-E_CTTGTA_L005


title: Bastle-1-B_TGACCA_L005


title: Bastle-3-C_ACAGTG_L007


title: T1


title: Bastle-2-C_ACAGTG_L006


title: Bastle-1-C_ACAGTG_L005


title: Bastle-1-D_GCCAAT_L005


title: R1


title: Bastle-1-A_CGATGT_L005


title: N2


title: ATAC_PPC027

status: Public on Dec 02 2022

city: La Jolla

first: Kelly

middle: Ann

last: Frazer

address: 9500 Gilman Drive

department: Pediatrics

institute: UC San Diego

data_processing:
Single-cell gene read counts for each sample were generated using CellRanger V3.0.2 with default parameters using Gencode V19 gene annotations. Read1 and read2 are asociated with R1 and R2, respectively.
Single-nuclei peak read counts for each sample were generated using CellRanger V3.0.2 with default parameters using Gencode V19 gene annotations. Read1, barcode, read2, sample index are associated with R1, R2, R3, I1 respectively.
Bulk ATAC-seq FASTQ files were aligned using STAR-2.7.3 and Genecode v34 as the reference. Duplicate reads were marked using bammarkduplicates and filtered for read inserts <= 140 bp in length. Following processing, we called peaks using MACS2 with the following parameters: --nomodel --nolambda --keep-dup all --call-summits -f BAMPE -g hs
Genome_build: hg19
Supplementary_files_format_and_content: Matrix containing raw read counts for each peak per cell in snATAC-seq are stored in matrix exchange format for sparse matrices (matrix.mtx,peaks.bed, barcodes.tsv)
Supplementary_files_format_and_content: Matrix containing raw read counts for each gene per cell in scRNA-seq are stored in matrix exchange format for sparse matrices (features.tsv, matrix.mtx, barcodes.tsv)
Supplementary_files_format_and_content: ATAC-seq narrow peak locations with p-value and q-value are stored in narrowPeak bed files
Supplementary_files_format_and_content: ATAC-seq summit peak locations with p-value and q-value are stored in summits bed files

source_name: iPSC-PPC

extract_protocol:
scRNA-seq: Cells from 1 iPSC line and 10 iPSC-PPCs derived from 9 individuals were used for scRNA-seq generation. 7 iPSC-PPCs from 6 individuals were captured individually as fresh at D15 immediately after differentiation, of which 4 iPSC-PPCs were also captured as cryopreserved cells along with 3 iPSC-PPC samples that were captured only as cryopreserved cells. Cells from 4 cryopreserved iPSC-PPC samples were pooled (MIX_PPC_001), and cells from the other 3 iPSC-PPC samples were pooled (MIX_PPC_002) prior to capture. Single cells were captured using 10x Chromium controller (10x Genomics) according to the manufacturer's specifications and manual. Cells from each scRNA-seq sample were loaded on an individual lane of a Chromium Single Cell Chip B. snATAC-seq: Cells from 7 cryopreserved iPSC-PPC samples derived from 7 individuals were evenly pooled into 2 pools (4 iPSC-PPCs and 3 iPSC-PPCs), and nuclei were isolated according to the manufacturer's recommendations (Manual CG000169, Rev B), transposed and captured as independent two samples according to the manufacturer’s recommendations (Manual CG000168, Rev B). Single nuclei were captured using 10x Chromum Controller according to the manufacturer's specifications, and single cells were loaded onto the individual lane of a Chromium Chip E. Bulk ATAC-seq: ATAC-seq was performed using the protocol from Buenrostro et al., 2013 with small modifications. Frozen nuclear pellets at 5x10^4 iPSC-PPCs at D15 were thawed on ice and tagmented in 25ul of permeabilization buffer containing digitonin and 2.5ul of Tn5 from Nextera DNA Library Preparation Kit (Illumina) for 45min at 37C, 500 RPM.
scRNA-seq: Libraries were generated using Chromium Single Cell 3’ Library Gel Bead Kit v3 (10xGenomics) following manufacturer’s manual with small modifications. Specifically, the purified cDNA was eluted in 24ul of Buffer EB, half of which was used for the subsequent step of the library construction. cDNA was amplified for 10 cycles and libraries were amplified for 8 cycles. Libraries were loaded on individual lanes and sequenced on HiSeq 4000 using a custom program (28-8-98 Pair End). snATAC-seq: Libraries were generated using Chromium Single Cell ATAC Library Gel & Bead Kit following the manufacturer's protocol and sequenced using a custom paired-end program on HiSeq 4000 (50-8-16-50 Pair End). Two libraries from 7 cryopreserved samples were sequenced on individual lanes. Bulk ATAC-seq: Libraries within a pool were indexed with unique i7 and i5 barcodes. Libraries were amplified for 12 cycles using NEBNext High-Fidelity 2X PCR Master Mix (NEB) and custom barcoded primers from Integrated DNA Technologies (IDT), and then sequenced on Illumina HiSeq 4000 using paired-end 100bp reads.

value: iPSC-PPC

tag: developmental stage

value: 15 days


title: ATAC_PPC029


title: Bastle-1-F_GTGAAA_L005


title: scRNA_PPC036

extract_protocol:
Bulk RNA-seq: RNA was isolated from total-cell lysates using the Quick-RNA™ MiniPrep Kit (Zymo Research) from frozen total-cell lysate, including on-column DNAse treatment steps and eluted in 48 μl RNAse-free water. Samples with RNA integrity number values of 10 were processed.
scRNA-seq: 1 iPSC and 7 iPSC-PPCs from 6 individuals were captured individually as fresh at D15 immediately after differentiation, of which 4 iPSC-PPCs were also captured as cryopreserved cells. Single cells were captured using 10x Chromium controller (10x Genomics) according to the manufacturer's specifications and manual. Cells from each scRNA-seq sample were loaded on an individual lane of a Chromium Single Cell Chip B.
Bulk ATAC-seq: ATAC-seq was performed using the protocol from Buenrostro et al., 2013 with small modifications. Frozen nuclear pellets at 5x10^4 iPSC-PPCs at D15 were thawed on ice and tagmented in 25ul of permeabilization buffer containing digitonin and 2.5ul of Tn5 from Nextera DNA Library Preparation Kit (Illumina) for 45min at 37C, 500 RPM.
snATAC-seq: Cells from 7 cryopreserved iPSC-PPC samples derived from 7 individuals were evenly pooled into 2 pools (4 iPSC-PPCs and 3 iPSC-PPCs), and nuclei were isolated according to the manufacturer's recommendations (Manual CG000169, Rev B), transposed and captured as independent two samples according to the manufacturer’s recommendations (Manual CG000168, Rev B). Single nuclei were captured using 10x Chromum Controller according to the manufacturer's specifications, and single cells were loaded onto the individual lane of a Chromium Chip E.
Bulk RNA-seq: Illumina Truseq Stranded mRNA libraries were prepared and sequenced on HiSeq 4000 with paired-end 100bp reads.
scRNA-seq: Libraries were generated using Chromium Single Cell 3’ Library Gel Bead Kit v3 (10xGenomics) following manufacturer’s manual with small modifications. Specifically, the purified cDNA was eluted in 24ul of Buffer EB, half of which was used for the subsequent step of the library construction. cDNA was amplified for 10 cycles and libraries were amplified for 8 cycles. Libraries were loaded on individual lanes and sequenced on HiSeq 4000 using a custom program (28-8-98 Pair End).
Bulk ATAC-seq:  Libraries within a pool were indexed with unique i7 and i5 barcodes. Libraries were amplified for 12 cycles using NEBNext High-Fidelity 2X PCR Master Mix (NEB) and custom barcoded primers from Integrated DNA Technologies (IDT), and then sequenced on Illumina HiSeq 4000 using paired-end 100bp reads.
snATAC-seq: Libraries were generated using Chromium Single Cell ATAC Library Gel & Bead Kit following the manufacturer's protocol and sequenced using a custom paired-end program on HiSeq 4000 (50-8-16-50 Pair End). Two libraries from 7 cryopreserved samples were sequenced on individual lanes.


title: scRNA_PPC028


title: scRNA_PPC027


title: scRNA_PPC030


title: ATAC_PPC023


title: scRNA_PPC029


title: Bulk RNA_PPC036

data_processing:
Single-cell gene read counts for each sample were generated using CellRanger V3.0.2 with default parameters using Gencode V19 gene annotations. Read1 and read2 are asociated with R1 and R2, respectively.
Single-nuclei peak read counts for each sample were generated using CellRanger V3.0.2 with default parameters using Gencode V19 gene annotations. Read1, barcode, read2, sample index are associated with R1, R2, R3, I1 respectively.
Read gene or peak counts for each bulk sample were generated using RSEM or MACS2, respectively, with Gencode v34 annotations.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix containing raw read counts for each peak per cell in snATAC-seq are stored in matrix exchange format for sparse matrices (matrix.mtx,peaks.bed, barcodes.tsv)
Supplementary_files_format_and_content: Matrix containing raw read counts for each gene per cell in scRNA-seq are stored in matrix exchange format for sparse matrices (features.tsv, matrix.mtx, barcodes.tsv)
Supplementary_files_format_and_content: ATAC-seq narrow peak locations with p-value and q-value are stored in narrowPeak  bed files
Supplementary_files_format_and_content: ATAC-seq summit peak locations with p-value and q-value are stored in summits bed files
Supplementary_files_format_and_content: Raw read counts for each gene per RNA-seq sample are stored in .gene.results
Supplementary_files_format_and_content: Raw read counts for each isoform per RNA-seq sample are stored in .isoform.results


title: Bulk RNA_PPC030


title: Bulk RNA_PPC051


title: scRNA_PPC034

value: iPSC


title: Bulk RNA_PPC028


title: Bulk RNA_PPC134


title: Bulk RNA_PPC069


title: scRNA_PPC023


title: Bulk RNA_PPC034


title: Bulk RNA_PPC027


title: Bulk RNA_PPC023


title: scRNA_MIX_PPC_002

tag: differentiations

value: Consists of cells from 3 differentiations - PPC_150, PPC_051, PPC_134


title: Bulk RNA_PP150


title: snATAC_MIX_PPC_002


title: scRNA_MIX_PPC_001

value: Consists of cells from 4 differentiations - PPC_023, PPC_027, PPC_034, PPC_029


title: snATAC_MIX_PPC_001

source_name: iPSC


title: scRNA_iPSC_PPC034


title: HEC-1B_ALDH-high accel v2

status: Public on Nov 30 2022

data_processing:
Sequencing was performed on HiSeq 2500 platform in a 75-base single-end mode.
Illumina RTA v1.18.64 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat-2.0.13.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffnorm 2.2.1.
Assembly: hg19
Supplementary files format and content: *_FPKM.txt: Tab-delimited text files include FPKM values for each sample.

extract_protocol:
Total RNA was extracted from cells with a miRNeasy kit (Qiagen) following the manufacturer’s instruction.
Each cDNA was generated using a Clontech SMART-Seq v4 Kit (Takara Clontech, Mountain View, CA, USA), and each library was prepared using a Nextera DNA Library Prep Kit (Illumina, San Diego, USA).

value: human endometrioid carcinoma


title: Bulk RNA_PPC029


title: HEC-1B_ALDH-high accel v1


title: ATAC_PPC034


title: HEC-1B_ALDH-high to low v2


title: Tumor-macrophage, 3

status: Public on Nov 23 2022

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina RTA 1.18.64 software was used for base calling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.1.1 in combination with Bowtie2.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 100000000.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Lung

extract_protocol:
Total RNA was extracted from cells with an miRNeasy Mini kit (Qiagen) according to the manufacturer’s protocol.
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio, Mountain View, CA) according to the manufacturer’s instructions. An Illumina library was prepared using a Nextera DNA Library Preparation Kit (Illumina, San Diego, CA) according to SMARTer kit instructions.

treatment_protocol: Alveolar macrophages from orthotopic vehicle-control or tumor model mice were isolated using an SH800 cell sorter.

value: lung

value: Tumor-macrophage

value: post natal week 10


title: HEC-1B_ALDH-high to low v1


title: HEC-1B-high ALDH potential_ALDH-high accel v1


title: HEC-1B-high ALDH potential_ALDH-high accel v2


title: Tumor-AM, 3

value: Tumor-alveolar macrophage (AM)


title: Tumor-AM, 2


title: Tumor-AM

data_processing:
Libraries were sequenced on an Illumina Novaseq 6000 in a 28+91 bp paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Converting from base call files into FASTQ files was performed using bcl2fastq v2.20.
Raw FASTQ files were input into the cellranger count pipeline (Cell Ranger v4.0.0, 10x Genomics) for alignment to the mm10 genome, UMI collapsing, and UMI counting for each gene-cell (barcode) combination.
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited text files include raw counts for all cells detected

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller, and cDNAs with UMIs were generated at single-cell level.
Single-cell RNA library construction was processed through the 10x Genomics Chromium Controller following the protocol outlined in the Chromium Single Cell 3' Reagent Kits User Guide.


title: Tumor-macrophage, 1


title: tumour cells from tumour region 2 (gene expression)

status: Public on Nov 15 2022

city: Oxford

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Reads were aligned to GRCh38 and count matrix for features were calculated using cellranger 3.1.0
Seurat 4.0.1 was used for downstream analysis, including removing doublets and negatives, other cell filtering, PCA, tSNE and Umap and clustering
Assembly: GRCh38
Supplementary files format and content: Seurat R object

source_name: primary patient-derived cell cultures (ccRCC tumour)

growth_protocol: Primary renal cell cultures were generated from freshly excised ccRCC tissue and tumor-adjacent normal kidney. All samples were from the same patient, and the tumour samples were taken from different regions of the same tumour. Briefly, tissue blocks were minced, incubated with 193U/ml Collagenase II and 3.33ug/ml DNase I for one hour at 37 °C with agitation every 5 minutes, and sequentially passed through 100um, 70um and 40um filters. Cell pellets were resuspended in growth medium (DMEM/F12 1:1, supplemented with L-glutamax, penicillin-streptomycin, insulin-transferrin-sodium selenite, 4 ng/ml triiodo-L-thyronine, 100 ng/ml epidermal growth factor, 36 ng/ml hydrocortisone and 10% fetal bovine serum*) and plated on gelatinized dishes. Experiments were performed after the 2nd or 3rd passage. *Except the low serum conditions sample, which was cultured in the same medium but with 0.5% fetal bovine serum.

extract_protocol:
Primary cell cultures were detached and made into single cell suspensions using TrypLE Express (Thermo Scientific) with pipetting. Single cell suspensions were incubated with TotalSeq-A ‘hashtag’ antibodies (1ug antibody with approximately 5x10E5 cells) to enable multiplexing. The hashtag antibodies and the barcode sequences were anti-human 1 (GTCAACTCTTTAGCG), anti-human 2 (TGATGGCCTATTGGG), anti-human 3 (TTCCGCCTCTCTTTG), anti-human 4 (AGTAAGTTCAGCGTA) and anti-human 5 (AAGTATCGTTTCGCA). Cell viability and concentration were assessed using Trypan Blue and a TC10 automated cell counter (Bio-Rad). 2500 cells from each sample were pooled, loaded onto a single channel of a 10x genomics 3' GEX chip for GEM generation as per the 10x genomics 3' GEX protocol (GEX-v3.1 chemistry).
Single cell 3’ GEX RNA libraries were prepared according to manufacturer’s instructions (10x genomics, GEX-v3.1 chemistry, single index).

treatment_protocol: Hypoxia incubations were performed at 0.5% O2 for 16 hours in a hypoxia chamber (In Vivo2 400 Hypoxia Work Station, Ruskinn Technology).

value: ccRCC tumour

tag: ambient o2 concentration

tag: sequenced molecule

value: RNA

tag: hashtag number

value: Hashtag 4


title: Ctrl-AM, 3

tag: cell type

value: Ctrl-alveolar macrophage (AM)


title: Ctrl-AM, 1


title: Tumor-macrophage, 2


title: normal cells in normoxia, cultured in low serum conditions (gene expression)

source_name: primary patient-derived cell cultures (tumour-adjacent normal kidney)

value: normal renal (tumour adjacent)

value: Hashtag 5


title: Ctrl-AM, 2


title: Control-AM


title: normal cells in hypoxia (gene expression)

value: Hashtag 2


title: P06K

status: Public on Nov 11 2022

city: Hamburg

first: Yu

last: Zhao

address: Falkenried 94

department: Institute of Medical Systems Biology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description: scRNA-seq

data_processing:
10x Genomics raw sequencing data were processed using CellRanger software (version 5.0.0, 10x Genomics, Pleasanton, CA) and the human genome hg19-1.2.0 release or mouse mm10-3.0.0 as the reference (function cellranger count). The matrices of cells and the unique molecular identifier (UMI) count were obtained and further processed by the R package Seurat (version 4.0.1).
To remove potential doublets, cutoff values for number of expressed genes (nGene) were determined for samples following visual inspection of the distribution of nGene and nUMI for each cell. The cells with higher nGene values were excluded. We further removed low-quality cells with high mitochondrial genes of all detected genes.
Assembly: hg19-1.2.0 and mm10-3.0.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample (matrix.mtx, barcodes.tsv, features.tsv).

source_name: kidney steroid treated

growth_protocol: For single cell suspension kidneys were dissected and incubated for 40 min at 37°C in RPMI medium (including 0.01 M HEPES; 0.5 mL filtered FBS and 0.4µg/ mL DNase and 8 µg/ mL collagenase D). The samples were homogenized using a gentleMACS (Miltenyi Biotec).

extract_protocol:
Cells were loaded on a 10x Chromium single cell instrument.
All steps were performed according to standard protocol of the Chromium single cell 3' v2 or 5' v1.1 kit to generate high-quality cDNA libraries.

value: kidney T cells

value: ANCA-GN

tag: treatment

value: steroid

tag: patient id


title: normal cells in normoxia (gene expression)

value: Hashtag 1


title: tumour cells from tumour region 1 (gene expression)

value: Hashtag 3


title: WT_CD45+Immune_3M

status: Public on Nov 08 2022

first: Zeguo

last: Sun

address: 1468 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

description:
Wild type mouse at 3 months old
Barcodes for this sample are appended with "_1".

data_processing:
The 10X Libraries were sequenced on the Illumina NovaSeq6000 sequencer with pair-end reads (28 bp for read 1 and 91 bp for read 2). The sequencing data were primarily analyzed by the 10X cellranger pipeline (v3.0.2) in two steps. In the first step, cellranger mkfastq demultiplexed samples and generated fastq files; and in the second step, cellranger count aligned fastq files to the 10X pre-built mouse reference (mm10)   and extracted gene expression UMI counts matrix.
We filtered cells with less than 300 or more than 5000 genes detected, and cells with mitochondria gene content greater than 20%, and used the remaining cells  for downstream analysis..
Genome_build: mm10
Supplementary_files_format_and_content: gene-cell expression matrix of raw read counts in xls file format

source_name: Kidney CD45+ cells

growth_protocol: Diabetic OVE26 mice (FVB(Cg)-Tg(Cryaa-Tag, Ins2-CALM1)26Ove/PneJ) in FVB background were obtained from The Jackson Laboratory. Bodyweight and fasting blood glucose levels were monitored biweekly by glucometer readings. DM was conﬁrmed by fasting blood glucose level 300 mg/dl. The age-and sex-matched WT littermates served as non-diabetic controls.

extract_protocol:
CD45+ enriched immune cell fraction:  Briefly, minced kidney were digested in the digestion buffer for 20 minutes at 37°C, passed through a 70-micron cell strainer, and collected by centrifugation. Cells were resuspended in blocking solution (PBS without calcium and magnesium containing 0.04% BSA and Fc blocking solution) and incubated for 30 minutes on ice. Cells were then washed with PBS with 0.04% BSA and incubated for 30 minutes at room temperature with the PE rat anti-mouse CD45 (1:200, catalog no. 12–0451, 30-F11; eBioscience). After washing, the cell suspension was sieved through a 40-micron cell strainer and centrifuged at 4°C. Cells were also stained with viability dye (DAPI). Samples were sorted using a BD FACS Aria II.
Sequencing libraries were constructed according to 10x standard protocol by following the steps cDNA fragmentation, end repair and A-tailing, size selection by SPRIselect beads (Beckman Coulter), adaptor ligation, sample index PCR amplification, and repeat SPRIselect beads size selection. The final constructed single-cell libraries were sequenced by Illumina Novaseq machine with total reads per cell targeted for a minimum of 30,000.

tag: genotype

value: WT

tag: tissue

value: kidney

value: CD45+ Immune cells

value: 3 months


title: Patients COVID-19, HTO-derived cDNA

status: Public on Oct 13 2022

description: Hashtag-derived oligonucleotide (HTO)

library_source: other

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 28+90 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were input into the cellranger pipeline (Cell Ranger v.6.0.0, 10x Genomics) for UMI counting for each gene (or tag sequence)-cell (barcode) combination and T cell receptor repertoire profiling.
Assembly: GRCh38 and refdata-cellranger-vdj-GRCh38-alts-ensembl-4.0.0
Supplementary files format and content: genematrix.csv: comma-delimited text files including raw counts for all cells detected
Supplementary files format and content: airr_rearrangement.tsv: tab-delimited text file including detected clonotypes for each cell (barcode)
Supplementary files format and content: clonotypes.csv: comma-delimited text file including the TCR clonotype information
Supplementary files format and content: surface_protein.csv: comma-delimited text file including barcode sequences associated with each hashtag ID and name
Supplementary files format and content: Hashtag-condition.xlsx: Excel file including condition/treatment information for each hashtag

molecule: protein

source_name: peripheral blood

extract_protocol:
Chromium Next GEM Chip G Single Cell Kit (10x Genomics) was used to extract RNA from single cells.
The single cell libraries were prepared following the protocol outlined in the Chromium Single Cell 5' Reagent Kits v2 User Guide.

treatment_protocol: Frozen human PBMCs were thawed and HLA-A*24:02 M198-206 tetramer positive CD8+ T cells were isolated. Then the cells were subjected to single cell sequencing analysis.

value: peripheral blood

value: CD8+ T cells

value: steady state


title: OVE26_CD45+Immune_3M

description:
OVE26 mouse at 3 months old
Barcodes for this sample are appended with "_2".

tag: age


title: Patients COVID-19, TCR-derived cDNA

description: TCR V(D)J segments


title: Patients COVID-19, mRNA-derived cDNA

description: poly A RNA


title: ND_and_NT_and_T mixed sample (non-demultiplexed)

status: Public on Sep 28 2022

description: CD31-/CD45.2- cells from Normal Diet-fed mouse livers, Non-Tumor region of high fat diet-fed mouse livers and Tumor region of high fat diet-fed mouse livers

data_processing:
Libraries were sequenced on an Illumina Novaseq 6000 with 25-150 bp paired end reads using NovaSeq Control Software v1.6.0 and Real Time Analysis v3.4.4 accoding to NovaSeq 6000 Sequencing system Guide v11.
Converting from base call files into FASTQ files was performed using bcl2fasta2 v2.20 accoding to  bcl2fastq2 Conversion Software v2.20 Software Guide, February 2019.
Reads included FASTQ files were demultiplexed using mappa_demuxer v1.0 and estimated the read counts using mappa_analyzer v1.0. In detecting barcode, Read sequences that were allowed a single base mismatch with the predicted candidate barcodes were classified.
The data processing was performed based on "mappa Analysis Pipeline User Guide" (available at https://www.takarabio.com/documents/User%20Manual/mappa%20Analysis%20Pipeline%20v1.0%20User%20Guide/mappa%20Analysis%20Pipeline%20v1.0%20User%20Guide_120319.pdf) .
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited text files include raw counts for all cells detected
Supplementary_files_format_and_content: tab-delimited text files include cell serial number, cell barcode index and sample name

extract_protocol:
Cells were isolated from mouse livers by perfusion method, and the cells were stained with antibodies against CD31 and CD45.2. The cells in the CD31-/CD45.2- fraction were sorted.
Single-cell dispensing and library preparation were performed according to the ICELL8 cx 3' DE kit standard protocol (information is available at https://www.takarabio.com/documents/User%20Manual/ICELL8%20cx%203%27%20DE%20User%20Manual/ICELL8%20cx%203%27%20DE%20User%20Manual_022720.pdf).

tag: strain

value: Liver

value: 35 weeks

value: wild type


title: hepatic stellate cells isolated at 6 degrees from the non-tumor region of high fat diet-fed mouse livers  [HSC_NT_6]

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.1.1 in combination with Bowtie2.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: hepatic stellate cell

extract_protocol:
Hepatic stellate cells were isolated from mouse livers by perfusion method, and the cells were stained with antibodies against CD31, CD45.2, and CD49a. The cells in the CD31-/CD45.2-/CD49a+ fraction were sorted, and total RNA was extracted using Trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: liver

value: hepatic stellate cell


title: hepatic stellate cells isolated at 37degrees from normal diet-fed mouse livers [HSC_ND_37]


title: hepatic stellate cells isolated at 6 degrees from the tumor region of high fat diet-fed mouse livers [HSC_T_6]


title: hepatic stellate cells isolated at 37degrees from the non-tumor region of high fat diet-fed mouse livers [HSC_NT_37]


title: hepatic stellate cells isolated at 37degrees from the tumor region of high fat diet-fed mouse livers  [HSC_T_37]


title: Tumor-AM, 1

value: lung

value: Tumor-alveolar macrophage (AM)

value: post natal week 10


title: IL-33 6DKO_03

status: Public on Aug 28 2022

description:
rmIL-33 (50ng) i.n. for 3 days
KO_stim_3

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina RTA 1.18.64 software was used for base calling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.1.1 in combination with Bowtie2.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 5000000.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted from cells with a miRNeasy Micro kit (Qiagen) according to the manufacturer’s protocol.
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio, Mountain View, CA) according to the manufacturer’s instructions. An Illumina library was prepared using a Nextera DNA Library Preparation Kit (Illumina, San Diego, CA) according to SMARTer kit instructions.

value: Lung ILC2


title: IL-33 6DKO_01

description:
rmIL-33 (50ng) i.n. for 3 days
KO_stim_1


title: IL-33 WT_01

description:
rmIL-33 (50ng) i.n. for 3 days
WT_stim_1


title: IL-33 6DKO_02

description:
rmIL-33 (50ng) i.n. for 3 days
KO_stim_2


title: PBS 6DKO_03

description:
PBS i.n. for 3 days
KO_ctrl_3

value: PBS


title: IL-33 WT_02

description:
rmIL-33 (50ng) i.n. for 3 days
WT_stim_2

value: WT


title: PBS WT_01

description:
PBS i.n. for 3 days
WT_ctrl_1


title: 63_ARM-070

status: Public on Aug 26 2022

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Alignment was performed using STAR version 2.5.2b
Transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count
Assembly: GRCh38, Emsembl annotation v86
Supplementary files format and content: comma delimited text file containing ensembl ID, gene symbol, gene description and raw read counts for each sample (in columns) for each annotated transcript (in rows).

source_name: rectal biopsy

extract_protocol:
RNA was isolated from two rectal biopsy pinches for each patient using the RNeasy Micro kit (Qiagen) with on-column DNase digestion. RNA quality was assessed using an Agilent Bioanalyzer
Ten nanograms of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the NexteraXT DNA Library Preparation kit (Illumina).

value: rectal biopsy

tag: race group

value: Black

tag: age group

value: Adult

tag: msm

value: Control

tag: p24 logauc


title: 62_ARM-045

value: NonBlack

value: MSM


title: IL-33 WT_03

description:
rmIL-33 (50ng) i.n. for 3 days
WT_stim_3


title: PBS WT_03

description:
PBS i.n. for 3 days
WT_ctrl_3


title: 57_STI-018

value: Youth


title: 56_STI-021


title: 59_ARM-002


title: 60_ARM-035


title: hepatic stellate cells isolated at 6 degrees from normal diet-fed mouse livers [HSC_ND_6]

value: 35 weeks


title: ND, NT, T

description: ND: CD49+ cells isolated from normal diet-fed mouse livers; NT: CD49+ cells isolated from non-tumor region of high fat diet-fed mouse livers; T: CD49a+ cells isolated from tumor region of high fat diet-fed mouse livers

data_processing:
Sequencing was performed on an MGI DNBSEQ-G400RS platform in a 26+108-base paired-end mode.
Demaltiplex, mapping and quantification were performed with using Cogent NGS Analysis Pipeline v1.0.
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited text files include raw counts for all cells detected
Supplementary_files_format_and_content: tab-delimited text files include cell barcode index and sample name

extract_protocol:
Cells were isolated from mouse livers by perfusion method, and the cells were stained with antibodies against CD31, CD45.2, and CD49a. The cells in the CD31-/CD45.2-/CD49a+ fraction were sorted.
Single-cell dispensing and library preparation were performed according to the ICELL8 cx 3′ DE kit standard protocol.

value: Liver

value: wild type


title: 54_ARM-073


title: 51_ARM-031


title: 52_ARM-042


title: 53_ARM-048


title: 49_ARM-064


title: 58_STI-046


title: PBS WT_02

description:
PBS i.n. for 3 days
WT_ctrl_2


title: 48_ARM-063


title: 55_ARM-078


title: PBS 6DKO_01

description:
PBS i.n. for 3 days
KO_ctrl_1


title: 61_ARM-038


title: 47_ARM-062


title: 43_ARM-025


title: 45_ARM-044


title: 46_ARM-061


title: 44_ARM-027


title: 42_ARM-010


title: 41_ARM-008


title: 40_ARM-072


title: 50_ARM-069


title: 39_ARM-068


title: 36_ARM-060


title: 33_ARM-053


title: 31_ARM-046


title: 34_ARM-056


title: 29_ARM-043


title: 37_ARM-065


title: 28_ARM-034


title: PBS 6DKO_02

description:
PBS i.n. for 3 days
KO_ctrl_2


title: 26_ARM-029


title: 25_ARM-026


title: 23_ARM-019


title: 30_ARM-047


title: 20_STI-017


title: 21_ARM-006


title: 19_STI-011


title: 18_STI-012


title: 22_ARM-007


title: 17_STI-007


title: 14_ARM-015


title: 16_STI-006


title: 9_ARM-023


title: 7_ARM-022


title: 24_ARM-024


title: 15_STI-035


title: 6_ARM-021


title: 2_ARM-005


title: 1_ARM-003


title: 10_ARM-052


title: 4_ARM-017


title: 38_ARM-066


title: SIRPA_KD_rep3

status: Public on Aug 18 2022

city: Houston

first: Han

last: Liang

state: Texas

address: 7007 Bertner Avenue

department: Department of Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Fastq files were quality-controlled using multiQC v1.11.
Quality-controlled reads were pseudo-aligned to the GENCODE mm39 genome assembly and then quantified at the transcript level using Salmon v1.4.0.
R package Tximport v1.20.0 was used to aggregate transcript-level quantifications to the gene level. The option "ScaledTPM" for countsFromAbundance in tximport was used to obtain the estimated counts at the gene level.
Differential expression was performed using DESeq2 v1.34.0 which performed built-in library size normalization.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include TPM values and read counts estimated by Salmon

growth_protocol: B16F10 cells were cultured in complete DMEM media (10% FBS and 50U/mL Penicillin-Streptomycin).

extract_protocol:
Total RNA were extracted from B16F10 cells using the Qiagen RNeasy Mini kit according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit following manufacturer's protocols.  Non-directional libraries were barcoded and sequenced on the NovaSeq S4 flowcell by pair-end sequencing of 150bp.

tag: cell line

value: Melanoma cells

value: SIRPA knockdown


title: SIRPA_KD_rep1


title: 3_ARM-012


title: SIRPA_OE_rep3

value: SIRPA overexpression


title: SIRPA_NTC_rep1

value: Non-target control


title: SIRPA_NTC_rep2


title: SIRPA_OE_rep2


title: SHSY-Rep-3-Untreated

status: Public on Jul 28 2022

city: Dubai

first: Fahad

last: Ali

address: Bldg 14, Dubai Healthcare City

country: United Arab Emirates

institute: Mohammed Bin Rashid University of Medicine and Health Sciences

data_processing:
Reads were trimmed using TrimGalore (version 0.6.4) to remove sequencing adaptors and poor-quality base calls, using a minimum Phred score cut-off of 20.
Trimmed reads were aligned to the hg19 genome with Bowtie2 (version 2.4.1). Reads that were unmapped, improperly paired, had > 4 mismatches, or insert size > 2000 bp were removed.
H3K27ac peaks were called for each replicate-input pairing, using Macs2 version 2.2.7.1 in narrow peak mode, using the following options: -f BAMPE -g hs --SPMR --qvalue 0.05 --keep-dup all.
Super-enhancer regions were identified from Macs2 peaks using ROSE (version 0.1) with a stitching distance of 12.5 kb and without removal of TSS regions.
Assembly: hg19
Supplementary files format and content: Bigwig, MACS2 narrowpeak, ROSE enhancer table

source_name: Neuroblastoma cell line

growth_protocol: Cells were cultured in DMEM/F12 media containing 10 % FBS and 1% antibiotics

extract_protocol:
Cells were fixed with 1% formaldehyde. Cultured cells were lysed, and the DNA was sheared to 100- to 300-bp fragments. Histone-bound DNA was precipitated using antibodies against H3K27ac (ab4729, Abcam). Cross-linking was reversed, and DNA was purified using the Qiagen PCR purification kit (Qiagen) and quantified with Qubit HS assay kit (Invitrogen).
The DNA was used to generate sequencing libraries according to the manufacturer’s procedure (NEBNext® Ultra™ II DNA Library Prep Kit for Illumina). The DNA was end polished and dA tailed, and adaptors with barcodes were ligated. The fragments were amplified and quantified with KAPA quantification kit (Roche) and the library size was determined using tape station (Agilent). Libraries were sequenced on NovaSeq (Illumina), using SP-flow cell resulting in 150-bp paired-end reads.

treatment_protocol: To differentiate, cells were treated with 10 µM all-trans-retinoic acid (ATRA) and serum concentration was reduced gradually to a final concentration of 1%. The duration of treatment varied for the different cell lines, which was determined by when a homogenous neuronal cell population was observed. For SK-N-BE (2)C and SH-SY5Y it was 10 days and 14 days, respectively. For SH-EP, we used 7 days of treatment even though neuronal cells were not visible. In all cases, media was refreshed every 48 hours. For SH-SY5Y, we followed the protocol developed by Shipley, M.M. et al. (J. Vis. Exp. (108), e53193 (2016)) with slight modifications. After initial treatment with 10 µM ATRA and reduced serum concentration (6th day), neuronal cells were trypsinized and plated to ATRA containing neurobasal medium supported with ECM, and other growth factors such as BDNF. Following differentiation treatment, ATRA was removed and cells were grown in DMEM/F12 media (10 % FBS and 1% antibiotics) for 4 days. Media was refreshed every 48 hours.

value: SH-SY5Y (CVCL_0019)

tag: chip antibody

tag: replicate


title: SIRPA_NTC_rep3


title: 8_ARM-028


title: SHSY-Rep-3-Input


title: 5_ARM-018


title: SIRPA_KD_rep2


title: SHSY-Rep-2-Treated

value: Withdrawn


title: SIRPA_OE_rep1


title: SHSY-Rep-2-Untreated


title: SHSY-Rep-3-Reverted

value: ATRA treated


title: SHSY-Rep-2-Input


title: SHSY-Rep-2-Reverted


title: SHSY-Rep-1-Treated


title: SHSY-Rep-1-Untreated


title: SHSY-Rep-1-Reverted


title: SHSY-Rep-3-Treated


title: SHEP-Rep-3-Treated

value: SH-EP (CVCL_0524)


title: SHEP-Rep-3-Input


title: SHEP-Rep-3-Reverted


title: SHEP-Rep-2-Untreated


title: SHEP-Rep-1-Reverted


title: SHEP-Rep-2-Treated


title: SHEP-Rep-1-Untreated


title: BE2C-Rep-3-Treated


title: SHEP-Rep-1-Treated


title: BE2C-Rep-3-Untreated


title: BE2C-Rep-2-Reverted


title: BE2C-Rep-2-Untreated


title: BE2C-Rep-2-Treated


title: BE2C-Rep-1-Untreated


title: BE2C-Rep-3-Input


title: BE2C-Rep-2-Input


title: BE2C-Rep-3-Reverted


title: BE2C-Rep-1-Treated


title: SHSY-Rep-1-Input


title: BE2C-Rep-1-Input


title: SHEPRep3Reverted_S36

data_processing:
Reads were trimmed using TrimGalore (version 0.6.4) to remove sequencing adaptors and poor-quality base calls, using a minimum Phred score cut-off of 20.
Trimmed reads were aligned to the hg19 genome with STAR (STAR_2.6.1d) and quantified using the quantMode option.
Assembly: hg19
Supplementary files format and content: raw_counts.tsv: STAR raw counts.

growth_protocol: Cells were cultured in DMEM/F12 media containing 10 % FBS and 1% antibiotics.

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiagen Inc.), according to manufacturer’s protocol.
RNA was quantified using Qubit RNA kit (Invitrogen) and the integrity of RNA was determined in Tape station (Agilent). Strand-specific mRNA sequencing libraries were prepared using Illumina Stranded mRNA Library Prep Kit (Illumina), following the manufacturer’s procedure. The fragments were amplified and quantified with KAPA quantification kit (Roche) and the library size was determined using tape station (Agilent). Experiment was performed in three biological replicates for each cell line.

value: ATRA withdrawn


title: SHEP-Rep-2-Input


title: BE2C-Rep-1-Reverted


title: SHEPRep1Reverted_S30


title: SHEP-Rep-3-Untreated


title: SHEPRep3Treated_S35


title: SHEPRep2Treated_S32


title: SHEPRep1Treated_S29


title: SHEPRep2Untreated_S31


title: SHEP-Rep-1-Input


title: SHEPRep1Untreated_S28


title: SHEP-Rep-2-Reverted


title: SHSYRep3Reverted_S9


title: SHSYRep1Reverted_S3


title: SHSYRep2Treated_S5


title: SHSYRep3Treated_S8


title: SHSYRep1Treated_S2


title: SHEPRep2Reverted_S33


title: BE2CRep3Reverted_S18


title: SHSYRep3Untreated_S7


title: SHSYRep2Untreated_S4


title: BE2CRep2Treated_S14


title: BE2CRep3Untreated_S16


title: BE2CRep1Treated_S11


title: BE2CRep3Treated_S17


title: cell line 1F4 repl1

status: Public on Jul 08 2022

city: Basel

first: Luca

last: Giorgetti

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: Cell line with Teto laco integration without flanking ectopic CTCF sites

data_processing:
cHi-C paired end datasets were processed using HiC-Pro (version 2.11.4). HiC-Pro covers the whole analysis from fastq files to the interaction matrix
Assembly: mm9
Supplementary files format and content: iced and binned matrix (6.4kb). The format of the matrix is the standard from HiC-Pro, namely, 3 columns: start end interactions. It's a sparce matrix annotation, no zero values are reported. The conversion bead to genomic coordinate file is also provided.
Library strategy: Capture C

source_name: cell line 1F4 repl1

growth_protocol: Cells were cultured on gelatin-coated culture plates in Glasgow Minimum Essential Medium (Sigma) supplemented with 15% foetal calf serum (Eurobio Abcys), 1% L-Glutamine (Thermo Fisher Scientific -25030024), 1% Sodium Pyruvate MEM (Thermo Fisher Scientific -11360039), 1% MEM Non-Essential Amino Acids (Thermo Fisher Scientific-11140035) 100 µM β-mercaptoethanol, 20 U/ml leukemia inhibitory factor (Miltenyi Biotec, premium grade), 1 µM MEK inhibitor PDO35901 (Axon, 1408) and 3 µM GSK3 inhibitor CHIR 99021 (Axon, 1386) in 8% CO2 at 37°C.

extract_protocol:
Cross-linking with 1%  formaldehyde. Cells lysed with 1M Tris-HCL pH8.0; 5M NaCl; 10% NP40
SureSelect XT Library Prep kit Agilent

treatment_protocol: for -cohesin sample: 2h with 500nM dTag-13 (Sigma Aldrich, SML2601-1MG)

tag: clone

value: cell line 1F4 repl1

value: Embyonic stem cell (E14)


title: BE2CRep2Reverted_S15


title: BE2CRep2Untreated_S13

value: Control


title: BE2CRep1Reverted_S12


title: SHEPRep3Untreated_S34


title: control brain_2

status: Public on Jul 07 2022

description: control mouse embryos at E17.5

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.1.1 in combination with Bowtie2.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 5000000.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Brain

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen).
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).

value: brain

value: embryonic day 17.5


title: control brain_1

description: control mouse embryos at E17.5


title: control brain_3

description: control mouse embryos at E17.5


title: miR-124a-1/2 DKO brain_3

description: miR-124a-1/2 DKO mouse embryos at E17.5


title: miR-124a-1/2 DKO brain_2

description: miR-124a-1/2 DKO mouse embryos at E17.5


title: 10 passaged HFSCs rep2

status: Public on Jun 30 2022

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: follicle stem cell

extract_protocol:
Total RNA was extracted from cultured cells using TRIzol reagent.
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).

value: follicle stem cell

tag: passages


title: 48 passaged HFSCs rep2


title: BE2CRep1Untreated_S10


title: 10 passaged HFSCs rep1


title: SHSYRep1Untreated_S1


title: Dnmt3a;Tnfr2KO biol_rep4

status: Public on May 25 2022

city: Bar Harbor

first: Jennifer

last: Trowbridge

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: 10X Genomics

data_processing:
Illumina base call files for all libraries were demultiplexed and converted to FASTQs using bcl2fastq v2.20.0.422 (Illumina).
A filtered digital gene expression matrix was generated for each single cell gene expression library against the 10X Genomics mm10 reference build (version 2020-A, GRCm38 assembly with GENCODE M23 annotations) using 10X Genomics CellRanger count version 6.0.0  for all samples.
For all single cell samples, R1 contains a 16bp cell barcode + 12bp UMI barcode.  For all samples, R2 contains a 91bp biological read.
The resultant counts matrices were input into PartekFlow (version 10.0.22.0428) for downstream analysis and visualization.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz (column labels (cell barcodes) of gene expression counts matrix)
Supplementary files format and content: features.tsv.gz (row labels (genes) of gene expression counts matrix)
Supplementary files format and content: matrix.mtx.gz (digital counts matrix for gene expression (matrix market format))

organism: Mus

source_name: Bone Marrow

extract_protocol:
Secondary transplant (of CD45.2+ cells) recipient (CD45.1+) mice were harvested. Single cell suspensions from each mouse were prepared by crushing spines, sternums, humeri, tibias, femurs, and iliac crests, passing through a ficol gradient, stained and sorterd on a FACSAria II sorter for a Lin-Kit+CD45.2+ population.
The cells were immediately processed as follows. Cells were counted on a Countess II automated cell counter (ThermoFisher), and 12,000 cells were loaded into one lane of a 10X Chromium microfluidic chip. Single cell capture, barcoding and library preparation were performed using the 10X Chromium version 3.1 NEXTGEM chemistry, according to the manufacturer’s protocol (#CG000315). cDNA and libraries were checked for quality on Agilent 4200 Tapestation and quantified by KAPA qPCR before sequencing. each gene expression library was sequenced at 18.75% of an Illumina NovaSeq 6000 S4 flow cell lane, targeting 6,000 barcoded cells with an average sequencing depth of 75,000 reads per cell.
3' scRNA-seq

value: Bone Marrow

value: Lin-Kit+CD45.2+ cell


title: Dnmt3a;Tnfr2KO biol_rep2

description: 10X Genomics


title: Dnmt3a;Tnfr2KO biol_rep3

description: 10X Genomics


title: 48 passaged HFSCs rep1


title: Dnmt3a;Tnfr2KO biol_rep1

description: 10X Genomics


title: Dnmt3a;Tnfr1KO biol_rep3

description: 10X Genomics


title: Dnmt3a;Tnfr1KO biol_rep1

description: 10X Genomics


title: Dnmt3a;Tnfr1KO biol_rep2

description: 10X Genomics


title: MxCre biol_rep3

description: 10X Genomics

value: MxCre


title: Dnmt3a biol_rep3

description: 10X Genomics


title: Dnmt3a biol_rep4

description: 10X Genomics


title: non-viral HCC liver 113

status: Public on May 22 2022

data_processing:
Sequencing was performed on an Illumina HiSeq 3000 platform in a 75-base single-end mode.
Illumina RTA 2.7.7 software was used for base calling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.1.1 in combination with Bowtie2.
Read counts were calculated using featureCounts and Transcripts Per Million (TPM) were calculated using Excel.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Liver

extract_protocol:
mRNA was extracted from frozen tissues with the RNeasy Plus Mini kit (Qiagen). Concentrations and quality were assessed using the Agilent Pico 6000 kit on the Bioanalyzer 2100.
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit

value: surgically-resected liver tissue

tag: disease state

value: non-viral hepatocellular carcinoma (HCC)

tag: gender

value: M


title: MxCre biol_rep2

description: 10X Genomics

tag: cell type


title: MxCre biol_rep1

description: 10X Genomics


title: non-viral HCC liver 110

value: F


title: non-viral HCC liver 112


title: non-viral HCC liver 108


title: non-viral HCC liver 109


title: miR-124a-1/2 DKO brain_1

description: miR-124a-1/2 DKO mouse embryos at E17.5


title: SHSYRep2Reverted_S6

value: SH-SY5Y (CVCL_0019)

tag: treatment


title: non-viral HCC liver 106


title: Dnmt3a biol_rep2

description: 10X Genomics

tag: genotype


title: Dnmt3a biol_rep1

description: 10X Genomics

tag: tissue


title: non-viral HCC liver 107

tag: age


title: non-viral HCC liver 104