title: TG HFD sperm H3K4me3 rep 5

source_name: Sperm

extract_protocol:
For sperm isolation, spermatozoa were collected from paired caudal epididymides as previously described (Hisano et al., 2013). ChIP-sequencing was performed using a previously described protocol (Hisano et al., 2013), 10 million spermatozoa used per sample. Samples were thawed on ice and washed with PBS. The chromatin was decondensed with 1M dithiothreitol and the reaction quenched with N-ethylmaleimide. Cells were lysed and aliquoted into 5 tubes and 15 units of MNase enzyme were added in each tube for 5 minutes, and the reaction was stopped with EDTA. Samples were centrifuged and the supernatants of aliquots from each sample were pooled back together. Pre-clearing of the chromatin was done for 1 hour and immunoprecipitation of the chromatin was performed for 8 hours with 5 µg of antibody targeting histone H3 lysine 4 trimethylation (H3K4me3). Samples were subjected to a 3-step wash, and the chromatin eluted and then treated with RNase A followed by Proteinase K. DNA was extracted and purified using the ChIP DNA Clean and Concentrator kit (Zymo Research) using the manufacturer’s protocol. Mononucleosomes were selected size-selected before library preparation.
Libraries were prepared using Qiagen’s Ultra-low Input Library kit following manufacturer’s protocol.

treatment_protocol: Wildtype or KDM1A transgenic male mice were fed either a low- or high-fat diet (10% or 60% kcal fat, respectively) for 10-12 weeks starting at weaning.

value: Sperm

value: KDM1A transgenic

tag: chip antibody

value: H3K4me3, Cell Signaling Technology, cat#9751


title: TG HFD sperm H3K4me3 rep 4

status: Public on Mar 30 2022

type: SRA

city: Sainte-Anne-de-Bellevue

first: Anne-Sophie

last: Pépin

state: QC

address: 21111 Lakeshore road

department: Department of Pharmacology and Therapeutics

country: Canada

institute: McGill University

library_source: genomic

data_processing:
ChIP:Sequencing reads were trimmed using Trimmomatic on single-end mode to remove adapters and filter out low-quality reads (version 0.36, parameters: 2:30:15 LEADING:30 TRAILING:30) (Bolger, Lohse and Usadel, 2014). Trimmed reads were aligned to the Mus Musculus mm10 genome assembly using Bowtie2 (version 2.3.4) (Salzberg, 2013). Unmapped reads were removed using SAMtools (version 1.9) (Li et al., 2009), and those with 3 mismatches or more were filtered out using Perlcode. BAM coverage files (BigWig) were generated using deeptools2 bamCoverage function (version 3.2.1, parameters: -of bigwig -bs 25 -p 20 --normalizeUsing RPKM -e 160 --ignoreForNormalization chrX) (Ramírez et al., 2016).
RNA: Reads were trimmed using Trim Galore (version 0.5.0, parameters for HiSeq: --phred33 --length 36 -q 5 --stringency 1 -e 0.1; parameters for NovaSeq: --paired --retain_unpaired --phred33 --length 36 -q 5 --stringency 1 -e 0.1) (Krueger, 2015). Trimmed reads were aligned to the Ensembl Genome Reference Consortium mouse reference 38 (GRCm38) primary assembly using hisat2 (version 2.1.0, parameters: -p 8 --dta) (Kim, Langmead and Salzberg, 2015). Aligned files with SAM format were converted to binary SAM format (BAM) and sorted by genomic position using SAMtools (version 1.9) (Li et al., 2009). Transcripts were assembled and gene abundances calculated using Stringtie (version 2.1.2, parameters: -p 8 -e -B -A) (Pertea et al., 2015).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, gtf [fpkm, tpm]

molecule: genomic DNA

organism: Mus musculus

tag: strain

tag: tissue

tag: age

value: 22 weeks

tag: genotype

tag: diet

value: high-fat diet

tag: Sex

value: male

tag: generation


title: AC192 EV

city: Seattle

first: Kai

last: Wang

state: WA

address: 401 Terry Ave N

country: USA

institute: Institute for Systems Biology

library_source: transcriptomic

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt), with an adapter sequence of [] and random barcode length [] (on []). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

molecule: total RNA

organism: Homo sapiens

source_name: Plasma

extract_protocol:
RNA Isolation method was . RNA Isolation kit was Homebrew Kit.
Library construction kit was Homebrew Kit. Samples were multiplexed. Type of Starting Material was total RNA.

tag: condition

value: Healthy Subject

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

value: extracellular vesicle

tag: rna isolation kit

value: Homebrew Kit


title: AC532 EV


title: CAM20.0118

type: genomic

city: Toronto

first: Yasin

last: Mamatjan

state: Ontario

address: 610 University Ave.

institute: Princess Margaret Cancer Center

description: Tumor methylation

hyb_protocol: Samples were fragmented, amplified and hybridized to the Illumina Infinium MethylationEPIC BeadChip as per standard Illumina protocols.

scan_protocol: per standard Illumina protocols

data_processing: Normalization and background correction of raw IDAT files was performed using ssNoob in the Bioconductor package minfi (version minfi_1.36.0). Beta values were calculated for each probe across all samples after post-processing.

source_name: fresh-frozen human meningioma

label_protocol: 250-500 ng of converted DNA was used as input, and labelled as per standard Illumina protocols.

extract_protocol: Genomic DNA was extracted from fresh-frozen tumor specimens and 250-500ng of bisulfite-treated DNA (EZ DNA Methylation Kit, Zymo, California, USA) per sample was used to obtain genome-wide DNA methylation profiles

treatment_protocol: During sample processing, genomic DNA from each specimen was processed.

value: meningioma

tag: molecule subtype

value: bisulfite-treated DNA


title: AC/ST217-5/05/2004-33 EV

description: EXR-KWANG1PlasmaEVACfST217h5f05f2004h33-BS


title: CAM20.0114

description: Tumor methylation


title: 133_OR13140_0

type: RNA

city: Chapel Hill

first: Merrie

last: Mosedale

state: North Carolina

address: 301 Pharmacy Lane, Kerr Hall CB#7569

department: Division of Pharmacotherapy and Experimental Therapeutics

institute: UNC Eshelman School of Pharmacy

description: mouse liver RNA

hyb_protocol: Fifteen micrograms of labeled cRNA was fragmented and prepared for hybridization on HT MG430 PM peg arrays.

scan_protocol: The Gene Titan robotic instrumentation (Affymetrix) was used to perform the hybridization, washing and scanning of the peg arrays.

data_processing: Probes containing SNPs in the genome of 45 CC strains were masked using the “kill-list” option in the APT module “apt-probeset-summarize”. Affymetrix CEL files were normalized using the Robust Multi-array Average (RMA) method with log2 transformation implemented in Affymetrix Power Tools (APT, v 1.17.0). A second pre-filtering step was then performed to eliminate lowly expressed probe sets defined as the maximum of log2 transformed expression level across samples less than an empirically chosen cutoff. Principal component analysis (PCA) and hierarchical clustering was used to evaluate the overall performance of the arrays. Seven (7) animals were identified as outliers (strains CC004, CC010, CC023, CC027, CC028, CC042, CC053, one animal each strain) and were removed from subsequent analysis.

label: biotin

source_name: mouse, liver

label_protocol: Double-stranded cDNA was synthesized from 50-150 ng (dependent on RNA yield) of total RNA, then transcribed to biotin-labeled cRNA using the 3’ Express IVT kit (Affymetrix).

growth_protocol: Eight (8) male mice from each of 45 CC lines  were purchased from the University of North Carolina, Chapel Hill.  Animals were acclimated for approximately 7 days prior to dosing. At the initiation of treatment, mice were approximately 8-10 weeks of age.

extract_protocol: Total cellular RNA was isolated using Trizol reagent (Invitrogen) and further purified using the QIAcube automated system (Qiagen). Following purification, the quantity of RNA was determined spectrophotometrically and the integrity of the RNA was evaluated with the Agilent 2100 Bioanalyzer.

treatment_protocol: Within each CC line, 4 animals were treated with a single dose of vehicle (0.5% w/v methylcellulose in purified water) and 4 were treated with TAK-875 (600 mg/kg). Test and control articles were administered by oral gavage in a dosing volume of 10 ml/kg. Animals were assigned to treatment groups using a randomization method based on bodyweight. Vehicle- and TAK-875-treated animals within each line were treated in pairs, and pairs within each line were randomized over the course of the study to minimize batch (treatment group) effects.

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: AC184 EV


title: 127_IL16211_600

description: mouse liver RNA


title: 132_OR13140_0

description: mouse liver RNA


title: 128_IL16211_600

description: mouse liver RNA


title: AC098 EV


title: 126_IL16211_600

description: mouse liver RNA


title: TG HFD sperm H3K4me3 rep 1

tag: strain

tag: chip antibody


title: TG HFD sperm H3K4me3 rep 2

tag: tissue

tag: age


title: 131_OR13140_0

description: mouse liver RNA


title: #2BQ0268 EV


title: CAM20.0112

description: Tumor methylation


title: CAM20.0110

description: Tumor methylation


title: 124_IL16211_0

description: mouse liver RNA


title: AC069 EV


title: 125_IL16211_600

description: mouse liver RNA


title: TG HFD sperm H3K4me3 rep 3

tag: genotype

tag: diet


title: CAM20.0109

description: Tumor methylation


title: CAM20.0108

description: Tumor methylation


title: BQ356 EV


title: CAM20.0113

description: Tumor methylation


title: 122_IL16211_0

description: mouse liver RNA


title: 123_IL16211_0

description: mouse liver RNA


title: AC093-8/26/2002-33 EV


title: TG LFD sperm H3K4me3 rep 2

value: low-fat diet

tag: Sex

tag: generation


title: CAM20.0105

description: Tumor methylation


title: TG LFD sperm H3K4me3 rep 3


title: BQ9114 EV

tag: condition

tag: anatomical location


title: CAM20.0106

description: Tumor methylation


title: TG LFD sperm H3K4me3 rep 1


title: TG LFD sperm H3K4me3 rep 4


title: 121_IL16211_0

description: mouse liver RNA


title: WT HFD sperm H3K4me3 rep 4

value: Wildtype


title: TG LFD sperm H3K4me3 rep 5


title: WT HFD sperm H3K4me3 rep 5


title: BQ/AC0486 EV

tag: rna source

tag: rna isolation kit


title: CAM20.0103

description: Tumor methylation

tag: molecule subtype


title: AC089 EV


title: 2BQ325 EV


title: BQ/AC0397 EV


title: WT HFD sperm H3K4me3 rep 3


title: CAM20.0101

description: Tumor methylation


title: CAM20.0102

description: Tumor methylation


title: CAM20.0100

description: Tumor methylation


title: WT HFD sperm H3K4me3 rep 2


title: AC157 EV


title: 118_OR13421_600

description: mouse liver RNA

tag: unc line name

tag: unc alias


title: 117_OR13421_600

description: mouse liver RNA

tag: dose (mg/kg)

tag: strain pair #


title: CAM20.0104

description: Tumor methylation


title: WT HFD sperm H3K4me3 rep 1

tag: strain


title: 116_OR13421_600

description: mouse liver RNA

tag: study pair #


title: CAM20.0099

description: Tumor methylation

tag: tissue


title: AC-066 EV


title: WT LFD sperm H3K4me3 rep 5

tag: age

tag: chip antibody


title: 112_OR13421_0

description: mouse liver RNA


title: 114_OR13421_0

description: mouse liver RNA


title: WT LFD sperm H3K4me3 rep 4

tag: genotype

tag: diet


title: CAM20.0098

description: Tumor methylation


title: 2BQ0292 EV


title: 113_OR13421_0

description: mouse liver RNA


title: 115_OR13421_600

description: mouse liver RNA


title: WT LFD sperm H3K4me3 rep 3

tag: Sex

tag: generation


title: CAM20.0097

description: Tumor methylation


title: WT LFD sperm H3K4me3 rep 2


title: AC-062 EV

tag: condition

tag: anatomical location


title: CAM20.0096

description: Tumor methylation


title: BQ9123 EV

tag: rna source

tag: rna isolation kit


title: 107_OR15156_600

description: mouse liver RNA

tag: unc line name


title: 108_OR15156_600

description: mouse liver RNA

tag: unc alias


title: WT LFD sperm H3K4me3 rep 1


title: CAM20.0094

description: Tumor methylation

tag: molecule subtype


title: CAM20.0095

description: Tumor methylation


title: BQ/AC0442 EV


title: 111_OR13421_0

description: mouse liver RNA

tag: dose (mg/kg)

tag: strain pair #


title: 105_OR15156_600

description: mouse liver RNA

tag: study pair #


title: Muscle cells, RANKL.3

city: Indianapolis

first: Andrea

last: Bonetto

state: IN

address: 980 W. Walnut Street, R3-C522

institute: Indiana University School of Medicine

data_processing:
The sequencing data were first assessed using FastQC (Babraham Bioinformatics, Cambridge, UK) for quality control
Then all sequenced libraries were mapped to the mouse genome (mm10) using STAR RNA-seq aligner
The reads distribution across the genome was assessed using bamutils
Genes with read count per million (CPM) < 0.5 in more than 4 of the samples were removed.
Differential expression analysis was performed using edgeR
Genome_build: UCSC Mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts, normalized counts for each sample

source_name: Muscle cells, RANKL.3

extract_protocol:
RNA extraction and purification from tissue snap frozen in liquid nitrogen was done via homogenization in Trizol and the Qiagen miRNeasy Mini Kit (C2C12s).
Five microliters of 2 nM pooled libraries per lane will then be denatured, neutralized and applied to the cBot for flow cell deposition and cluster amplification, before loading to HiSeq 4000 for 75b paired-end sequencing (Illumina, Inc.). Approximately 30M reads per library is generated

treatment_protocol: RNA isolation, sequencing for all C2C12 samples were done at one time.

tag: cell line

tag: cell type

value: Muscle cell

tag: treatment

value: Recombinant murine RANKL


title: Muscle cells, RANKL.2

source_name: Muscle cells, RANKL.2


title: Muscle cells, RANKL.1

source_name: Muscle cells, RANKL.1


title: CAM20.0092

description: Tumor methylation

tag: tissue


title: CAM20.0093

description: Tumor methylation


title: AC169 EV


title: 106_OR15156_600

description: mouse liver RNA


title: S9_Control rep4

city: Nice

first: Minoo

last: Rassoulzadegan

address: parc Valrose

department: Institut de Biologie Valrose: iBV

country: France

institute: Nice Sophia Antipolis

data_processing:
FastQC version 0.11.7 was used to do some quality control on the RAW sequencing data. Illumina adapters sequences removed by cutadapt v1.16. Based on the FastQC results, trimming of bad-quality reads was performed using Trimmomatic version 0.36 . Then aligned to the reference assembly (GRCh38) using Hisat2. Quality of alignment assessed using plot-bamstats utilities of samtools.
Bam files converted to BigWig format using deeptools. Visualization of BigWig files was performed using web-based UCSC genome browser.
HOMER version 4.9 was used for peak finding. Genome-wide locations of TERRA repeats were found by aligning sequences with lengths of 24 and 48 nucleotides composed of 4 and 8 copies of TERRA to the reference genome using bowtie2 using “-a” argument to report all alignment.   Statistically significant peaks of expression were identified using HOMER (10000 size of region used for local filtering, 4-fold over local region, Poisson p-value over local region < 0.0001, false discovery rate (FDR) rate threshold < 0.001).
Genome_build: GRCh38
Supplementary_files_format_and_content: Files include BigWig files for each Sample ...

source_name: skin biopsy

extract_protocol:
After extraction with TRIzol-chloroform the nucleic acids of cutaneous cells, are purified into two RNAs fractions, a small but reproducible amount of RNA is retained, along with genomic DNA, at the chloroform-water interface, while -free RNA molecules are found in the upper aqueous phase. The cutaneous cells were treated with proteinase K and then the DNA and RNAs fractions were recovered by column separation. The RNAs retained in DNA-RNA complexes were then recovered by chromatography on a column binding the DNA followed by treatment with DNase. The RNA fraction recovered from DNA is referred to as fraction D or DRNA.
DNA-associated RNA molecules were purified form 7 skin biopsy samples (2 Lesional, 2 Non-lesional, and 3 Control). 10-100 ng of RNA after Dnase digestion were recovered and analyzed by high throughput sequencing on Illumina.

value: skin biopsy

value: Control

tag: individual

value: DNA-associated RNA (dRNA)


title: S9_Control rep3


title: Muscle cells, Control.3

source_name: Muscle cells, Control.3

value: Vehicle


title: CAM20.0091

description: Tumor methylation


title: 102_OR15156_0

description: mouse liver RNA


title: S9_Control rep2


title: 104_OR15156_0

description: mouse liver RNA


title: 103_OR15156_0

description: mouse liver RNA


title: AC088-7/08/2002-33 EV


title: CAM20.0090

description: Tumor methylation


title: S9_Control rep1


title: Muscle cells, Control.1

source_name: Muscle cells, Control.1


title: CAM20.0089

description: Tumor methylation


title: 101_OR15156_0

description: mouse liver RNA


title: S8_Control rep4


title: HUVEC_circRAB3IP_OE_EV_rep2

city: Goettingen

first: Argyris

last: Papantonis

address: Robert-Koch-Str 40

department: Department of Pathology

country: Germany

institute: University Medical Center Goettingen

description:
NJ_4
mRNA-Seq

data_processing:
Alignment with STAR aligner for differential gene expression analysis or pseudoalignment with Salmon for isoform switching analysis.
Count quantification with featureCounts for differential gene expression analysis.
Normalization with RUV-seq for differential gene expression analysis.
Differential gene expression analysis with DESeq2.
Assembly: hg19
Supplementary files format and content: HUVEC_circOE_qval0.01.csv: Comma-separated table of differentially expressed genes.
Supplementary files format and content: merged_counts_featurecounts.txt: Tab-delimited text file of raw read counts for all the samples.
Supplementary files format and content: merged_counts_salmon.txt: Tab-delimited text file of pseudoaligned TPM counts for all the samples.
Supplementary files format and content: topswitchesraboe0.2.csv: Comma-separated table of differential isoform usage.

molecule: polyA RNA

source_name: HUVEC

growth_protocol: Normal HUVEC and circRNA-piggyBAC transfected HEK293 cells were grown in exosome-depleted media (normal FBS (Gibco) in complete media replaced with Exosome-Depleted FBS, Life Technologies).

extract_protocol:
HUVECs were then washed in PBS 2 times and collected in TRIzol. RNA was purified with Direct-zol RNA Microprep kit (Zymo).
TruSeq RNA library kit (Illumina).

treatment_protocol: HEK293 cells were additionally induced with 3 μg/ml of doxycycline (DOX, Sigma) and 400 μg/ml of G418 (Sigma). After 48 h, cells were collected in TRIzol for qPCR analysis of overexpression levels, while the medium was collected on ice and EVs were purified through series of centrifugation steps. Namely, first round of centrifugation at 750 x g for 10 min was performed to remove leftover cells from the medium. Supernatants were then collected and spun at 1500 x g for 10 min, followed by 14000 x g for 35 min and 100000 x g for 2 h to separate microvesicles and exosomes. Pellets containing exosomes were then washed in PBS (Sigma) and subjected to another centrifugation at 100000 x g for 1h. Pellets representing exosome fraction were resuspended in 200 μl of PBS and kept in -80°C until use.

value: Human Umbilical Vein Endothelial Cells

value: circRAB3IP-piggyBAC EVs


title: CAM20.0088

description: Tumor methylation


title: 98_OR13067_600

description: mouse liver RNA


title: S8_Control rep3


title: 96_OR13067_600

description: mouse liver RNA


title: S8_Control rep2


title: HUVEC_circRAB3IP_OE_EV_rep1

description:
NJ_3
mRNA-Seq


title: CAM20.0087

description: Tumor methylation


title: CAM20.0085

description: Tumor methylation


title: 97_OR13067_600

description: mouse liver RNA


title: HUVEC_Control_EV_rep2

description:
NJ_2
mRNA-Seq

value: Empty-vector piggyBAC EVs


title: S7_Control rep4


title: Muscle cells, Control.2

source_name: Muscle cells, Control.2


title: HUVEC_circRAB3IP_KD_rep2

description:
K002000252_90543
mRNA-Seq

data_processing:
Alignment with STAR aligner for differential gene expression analysis or pseudoalignment with Salmon for isoform switching analysis.
Count quantification with featureCounts for differential gene expression analysis.
Normalization with RUV-seq for differential gene expression analysis.
Differential gene expression analysis with DESeq2.
Assembly: hg19
Supplementary files format and content: siRAB3IP_sign_log2fc06.csv: Comma-separated table of differentially expressed genes upon circRAB3IP knock-down.
Supplementary files format and content: siCAMSAP1_sign_log2fc06.csv: Comma-separated table of differentially expressed genes upon circCAMSAP1 knock-down.
Supplementary files format and content: merged_counts_featurecounts.txt: Tab-delimited text file of raw read counts for all the samples.
Supplementary files format and content: merged_counts_salmon.txt: Tab-delimited text file of pseudoaligned TPM counts for all the samples.
Supplementary files format and content: topswitchesrab0.3.csv: Comma-separated table of differential isoform usage upon circRAB3IP knock-down.

growth_protocol: HUVECs from pooled, apparently healthy, donors (passage 4-9; Lonza) were grown and passaged in complete Endopan-3 medium kit (PAN-Biotech) under 5% CO2.

extract_protocol:
48 hours post-transfection, cells were collected in TRIzol (Invitrogen) and RNA extraction was performed with Direct-Zol RNA purification kit (Zymo).
TruSeq RNA library kit (Illumina).

treatment_protocol: Approximately 35 x 10^4 HUVEC cells were seeded per 60 mm plate day before the transfection. Each siRNA (180 pmol) was mixed with Opti-MEM (Gibco) and Lipofectamine RNAiMAX reagents according to manufacturer’s instructions (Thermo Fisher). Cells were washed once in PBS and incubated in 2.5 ml of Opti-MEM and 500 μl of transfection mix for 4 hours, after which the medium was replaced with complete Endopan-3 medium.

tag: genotype/variation

value: circRAB3IP knock-down


title: HUVEC_Control_EV_rep1

description:
NJ_1
mRNA-Seq


title: CAM20.0084

description: Tumor methylation


title: S7_Control rep3


title: CAM20.0083

description: Tumor methylation


title: HUVEC_circRAB3IP_KD_rep1

description:
K002000252_90541
mRNA-Seq


title: CAM20.0082

description: Tumor methylation


title: HUVEC_circCAMSAP1_KD_rep2

description:
K002000252_90539
mRNA-Seq

value: circCAMSAP1 knock-down


title: 95_OR13067_600

description: mouse liver RNA


title: CAM20.0081

description: Tumor methylation


title: 92_OR13067_0

description: mouse liver RNA


title: CAM20.0080

description: Tumor methylation


title: HUVEC_circCAMSAP1_KD_rep1

description:
K002000252_90537
mRNA-Seq


title: S5_Non-lesional rep4

value: Non-lesional


title: 93_OR13067_0

description: mouse liver RNA


title: S8_Control rep1


title: HUVEC_Control_rep2

description:
K002000252_90535
mRNA-Seq

value: No template control (NTC)


title: CAM20.0079

description: Tumor methylation

value: meningioma


title: 91_OR13067_0

description: mouse liver RNA


title: 88_AU8048_600

description: mouse liver RNA


title: 87_AU8048_600

description: mouse liver RNA


title: S5_Non-lesional rep3


title: CAM20.0078

description: Tumor methylation

value: bisulfite-treated DNA


title: CAM20.0077

description: Tumor methylation


title: CAM20.0076

description: Tumor methylation


title: S7_Control rep1


title: S5_Non-lesional rep2


title: S7_Control rep2


title: 86_AU8048_600

description: mouse liver RNA


title: HEK293_circCAMSAP1_KD_rep2

description:
K002000164_76269
mRNA-seq

data_processing:
Alignment with STAR aligner.
Count quantification with featureCounts.
Normalization with RUV-seq for differential gene expression analysis.
Differential gene expression analysis with DESeq2.
Assembly: hg19
Supplementary files format and content: siRAB3IP_HEK293_new_sign_padj.csv: Comma-separated table of differentially expressed genes upon circRAB3IP knock-down.
Supplementary files format and content: siCAMSAP1_HEK293_new_sign_padj.csv: Comma-separated table of differentially expressed genes upon circCAMSAP1 knock-down.
Supplementary files format and content: merged_counts_featurecounts.txt: Tab-delimited text file of raw read counts for all the samples.

growth_protocol: HEK293s were grown and passaged in DMEM (Sigma) under 5% CO2.

treatment_protocol: HEK293 cells were transfected with NTC or circRNA targeting siRNA with Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer's protocol.


title: 85_AU8048_600

description: mouse liver RNA


title: S5_Non-lesional rep1


title: HEK293_circCAMSAP1_KD_rep1

description:
K002000164_76267
mRNA-seq


title: S4_Non-lesional rep4


title: 94_OR13067_0

description: mouse liver RNA


title: HEK293_circRAB3IP_KD_rep1

description:
K002000164_76263
mRNA-seq


title: HEK293_circRAB3IP_KD_rep2

description:
K002000164_76265
mRNA-seq


title: S4_Non-lesional rep2


title: HEK293_Control_rep2

description:
K002000164_76261
mRNA-seq


title: 82_AU8048_0

description: mouse liver RNA


title: CAM20.0075

description: Tumor methylation


title: 84_AU8048_0

description: mouse liver RNA


title: HEK293_Control_rep1

description:
K002000164_76259
mRNA-seq


title: HUVEC_Control_rep1

description:
K002000252_90533
mRNA-Seq


title: S4_Non-lesional rep3


title: 81_AU8048_0

description: mouse liver RNA


title: 78_OR5358_600

description: mouse liver RNA


title: 83_AU8048_0

description: mouse liver RNA


title: CAM20.0071

description: Tumor methylation


title: CAM20.0073

description: Tumor methylation


title: 77_OR5358_600

description: mouse liver RNA


title: S4_Non-lesional rep1


title: S2_Lesional rep4

value: Lesional


title: CAM20.0070

description: Tumor methylation


title: CAM20.0074

description: Tumor methylation


title: S2_Lesional rep2


title: CAM20.0068

description: Tumor methylation


title: 76_OR5358_600

description: mouse liver RNA


title: S2_Lesional rep3


title: LNCaP_sgPRRX2_ENZ_3

city: Chicago

first: Sarki

last: Abdulkadir

state: IL

address: 303 E Superior St

institute: Northwestern University

data_processing:
Alignment: Sequenced reads were aligned to the hg38 reference human genome using Bowtie2.
Read Counting: Reads per gene were counted using htseq.
Assembly: hg38
Supplementary files format and content: htseq read counts

source_name: LNCaP prostate cancer cells

growth_protocol: LNCaP cells were routinely grown in RPMI media with 10% FBS and 1% Pen-strep.

extract_protocol:
Total RNA was extracted using Qiagen Rneasy plus mini kit
A total amount of 50ng RNA used to prepared single-indexed strand-specific cDNA library using TruSeq RNA Access Library Prep Kit (Illumina).

treatment_protocol: Cells were plated, and next day 5 µM of enzalutamide (in DMSO) was added in LNCaP cells for 7 day treatment. Control groups were treated with DMSO.

value: PRRX2 overexpressing LNCaP cells

value: LNCaP

value: ENZ


title: CAM20.0069

description: Tumor methylation


title: CAM20.0067

description: Tumor methylation


title: S1_Lesional rep4

value: skin biopsy


title: LNCaP_sgPRRX2_ENZ_2


title: S2_Lesional rep1


title: LNCaP_sgPRRX2_ENZ_1


title: LNCaP_sgNC_ENZ_3

value: Control LNCaP cells


title: CAM20.0064

description: Tumor methylation


title: 74_OR5358_0

description: mouse liver RNA


title: CAM20.0066

description: Tumor methylation


title: CAM20.0063

description: Tumor methylation


title: LNCaP_sgPRRX2_DMSO_2

value: DMSO


title: S1_Lesional rep3

value: DNA-associated RNA (dRNA)


title: S1_Lesional rep1


title: LNCaP_sgNC_ENZ_2


title: 71_OR5358_0

description: mouse liver RNA


title: 75_OR5358_600

description: mouse liver RNA


title: 72_OR5358_0

description: mouse liver RNA


title: 68_AU8027_600

description: mouse liver RNA


title: 73_OR5358_0

description: mouse liver RNA


title: CAM20.0065

description: Tumor methylation


title: S1_Lesional rep2


title: LNCaP_sgPRRX2_DMSO_1


title: LNCaP_sgPRRX2_DMSO_3


title: 67_AU8027_600

description: mouse liver RNA


title: LNCaP_sgNC_ENZ_1


title: LNCaP_sgNC_DMSO_2


title: 65_AU8027_600

description: mouse liver RNA


title: CAM20.0060

description: Tumor methylation


title: 42D-ENZR-shASCL1-Rep3-RNAseq

city: Vancouver

first: Amina

last: Zoubeidi

state: BC

address: 2660 Oak Street

institute: Vancouver Prostate Centre

data_processing:
Base calling and de-multiplexing were performed using either bcl2fastq2 Conversion Software (v2.20) or bcl-convert (v3.8.4) with default parameters as per Illumina recommendation.
RNA-seq data processing was performed by sequencing facilty using Illumina RNA-Seq Alignment (BaseSpace Workflow) v1.1.0
Briefly, Read sequences were aligned to the hg19 human reference genome using STAR aligner v2.5.0b. Assembly and differential expression was estimated using Cufflinks software (version 2.2.1).
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: 42D Prostate cancer cell line generated from mouse xenograft of LNCaP

growth_protocol: 16D cells were cultured in RPMI-1640 media containing 5% fetal bovine serum, 42D ENZ-resistant (ENZR) cells were cultured in RPMI-1640 media containing 5% fetal bovine serum supplemented with 10mM ENZ, NCI-H660 cells were cultured HITES medium following ATCC recommendation.

extract_protocol:
Total RNA was isolated from cell lines using the RNeasy Mini Kit (Qiagen, Cat No. 74104).
Library constructions were performed using the NEBnext Ultra II Directional RNA Library Prep Kit (Cat E7760L) and NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat E7490L). Sequencing was performed on an Illumina NextSeq 500 (43x43 bp paired-end reads)

treatment_protocol: 16D cells in RPMI-1640 media containing 5% fetal bovine serum were treated with 10mM ENZ for 3 or 10 days. First, ASCL1 was knock down using short-hairpin (sh) RNA strategy in 42D-ENZR to generate 42D-ENZR-shASCL1 cell line before being used for RNA-seq sample preparation. ASCL1 was silenced using siRNA strategy in NCI-H660 to generate NCI-H660-siASCL1 cell line before being used for RNA-seq sample preparation.

value: ENZ-resistant CRPC-NE

value: Enzalutamide

tag: disease state

value: AR positive, Neuro Endocrine like

tag: shRNA


title: CAM20.0062

description: Tumor methylation


title: CAM20.0057

description: Tumor methylation


title: NCI-H660-siASCL1-RNAseq

source_name: Cell line generated from patient (ATCC CRL-5813)

value: Neuro Endocrine Prostate Cancer

value: AR negative, Neuro Endocrine


title: 42D-ENZR-shASCL1-Rep1-RNAseq


title: 42D-ENZR-shASCL1-Rep2-RNAseq


title: CAM20.0061

description: Tumor methylation


title: NCI-H660-Rep2-RNAseq


title: 63_AU8027_0

description: mouse liver RNA


title: 42D-ENZR-Rep2-RNAseq


title: NCI-H660-Rep1-RNAseq


title: 66_AU8027_600

description: mouse liver RNA


title: 62_AU8027_0

description: mouse liver RNA


title: 64_AU8027_0

description: mouse liver RNA


title: CAM20.0059

description: Tumor methylation


title: LNCaP_sgNC_DMSO_1

tag: condition


title: 47_OR3460_600

description: mouse liver RNA


title: 48_OR3460_600

description: mouse liver RNA


title: CAM20.0056

description: Tumor methylation


title: 42D-ENZR-Rep3-RNAseq


title: CAM20.0058

description: Tumor methylation


title: LNCaP_sgNC_DMSO_3


title: CAM20.0055

description: Tumor methylation


title: CAM20.0052

description: Tumor methylation


title: CAM20.0051

description: Tumor methylation


title: HEK293T - PABPC RIP Rep3

city: La Jolla

first: Amy

last: Pasquinelli

state: CA

address: 9500 Gilman Drive

department: Biological Sciences

institute: University of California, San Diego

data_processing:
All reads were aligned to the human genome hg38 primary assembly using STAR.
featureCounts version 2.0.2 was used to annotate reads, using the flag --minOverlap 20 and a custom GTF file derived from gencode v34
Differential expression was calculated using DESeq2. Cut-offs used to determine significant differential expression were baseMean > 50 and padj <=0.01
Genes which had substantial upstream intergenic reads (similar to DoGs) were removed from DE tables. Upstream intergenic regions were extracted using bedtools flank -l 2000 -r 0 -s. Intervening upstream genes that had any overlap with this region were removed with bedtools subtract. Reads that did not align to intronic or exonic regions were extracted from bam files with fgrep. Coverage across the 2000 bp upstream region was determined with bedtools coverage -S -split. A TPM value was determined for this upstream region and compared to the TPM of the adjacent downstream gene. If a ratio of 20% of the signal (determined by TPM) was present in the upstream region, and a breadth of 70% of that region was covered, that gene was determined to have significant enough upstream transcription so as to not be a reliable functional coding product, and was removed from subsequent analysis. Genes that showed this pattern in either the input or IP condition were both removed from that IP analysis.
Genome_build: hg38
Supplementary_files_format_and_content: comma separated files with output of DESeq2; normalized abundance measurements for all genes when comparing RIP condition to total input condition

source_name: HEK293T Total cell lysate

growth_protocol: HEK293T cells were cultured as recommended by the manufacturer, in Dulbecco’s modified Eagle medium (DMEM, Gibco #11965092) supplemented with 10% fetal bovine serum (Gibco #10437-028) and 1% penicillin/streptomycin (Gibco).

extract_protocol:
RNA was isolated using a standard Trizol (Life Technologies) RNA extraction. RNA was DNAse treated before libraries were prepared for sequencing.
cDNA libraries from three independent biological replicates were prepared from 1ug RNA using Illumina ribodepleted RNA stranded kit. Libraries were sequenced on the Illumina HiSeq 4000, single-end reads (75 nucleotides).

treatment_protocol: Formaldehyde crosslinking was performed as follows, before RNA Immunoprecipitation of PABPC or PABPN: Cells were washed twice on the plate with phosphate-buffered saline (PBS) and then collected into conical tubes with PBS and spun down. Cell pellets were resuspended in 0.1% formaldehyde in PBS and incubated at room temperature for 10 minutes. Glycine was added to a final concentration of 0.17 mM to quench the formaldehyde and incubated for 5 min. Cells were then spun down and washed with PBS two times before pellets were snap frozen on liquid nitrogen for storage at -80C. Cells were resuspended in RIPA buffer supplemented with rRNAseIn Plus, DTT, EDTA, and protease inhibitors. Cell pellets were sonicated and RNA Immunprecipitation was performed. After washing, reverse crosslinking was performed.

tag: genotype

value: wildtype

value: formaldehyde crosslinked

tag: immunoprecipitation

value: PABPC


title: HEK293T - PABPC RIP Rep2


title: 16D-CRPC-RNAseq

source_name: 16D Prostate cancer cell line generated from mouse xenograft of LNCaP

value: Castration Resistant Prostate Cancer (CRPC)

value: Castration resistant


title: 42D-ENZR-Rep1-RNAseq


title: 16D-CRPC-H3K27me3-ChIP

data_processing:
Basecalling was performed by Illumina Real Time Analysis (RTA) v2.11.3 with default settings
Demultiplexing was perfoemed by Illumina bcl2fastq v2.20.0.422 using parameters --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --barcode-mismatch 1
Raw reads were aligned to the hg38 (human) reference genome using BWA-MEM software (version 0.7.17) with default parameters. Alignments with mapping quality less than 60 were filtered out (leaving only uniquely mapped reads) and subsequently sam files were converted to bam files using Samtools software (version 1.1.2).
Narrow peaks were called using MACS2 callpeak (version 2.2.7.1) with options -f BAMPE -g 2.9e9 --keep-dup=1 -B -q 0.05. Broad peaks were called using MACS2 callpeak (version 2.2.7.1) with options -f BAM --broad -g 2.9e9 --keep-dup 1 --broad-cutoff 0.05. Bedtools intersect (v2.28.0) program suite was used to generate shared (-wa -u -f 0.5 -F 0.5 -e) and unique (-v -f 0.5 -F 0.5 -e) peak set between samples.
Deeptools (v2.30.0) program suite was used to generate bigWig files.
HOMER (v4.11) program suite was used to annotate peaks and perform motif enrichment analysis.
Genome_build: hg38
Supplementary_files_format_and_content: NARROWPEAK (BED format)
Supplementary_files_format_and_content: bigWig

growth_protocol: 16D cells were cultured in RPMI-1640 media containing 5% fetal bovine serum (Gibco #A3160701), 42D ENZ-resistant (ENZR) cells were cultured in RPMI-1640 media containing 5% fetal bovine serum supplemented with 10mM ENZ, NCI-H660 cells were cultured HITES medium following ATCC recommendation.

extract_protocol:
Cell lines were grown in media supplemented with 5% FBS (Gibco #A3160701) and processed for ChIP using the Magna ChIP Kit (Millipore #17-10085) according to manufacturer’s instructions with the following antibodies: ASCL1 (5 µg, Abcam#556604, EZH2 (5 μg, Active Motif #39933), H3K27Me3 (5 µg; Millipore #07-449). 10 million cells were fixed with 1% formaldehyde for 10 minutes at room temperature. Cells were collected. Chromatin was sonicated to approximately 500bp.
For ChIP-seq, sequencing libraries (100 ng DNA per sample) were constructed using the KAPA library Prep Kit (Roche, Cat KK8510) with Illumina TruSeq indexes. Libraries were assessed for quality using gel electrophoresis and libraries passing quality control (e.g., no primer dimers) were quantified using the KAPA Library Quantification Kit for Illumina (Roche, Cat KK4824). Libraries were sequenced using the Illumina NextSeq 500 (75 bp single-end reads; cell lines).

treatment_protocol: ASCL1 was knock down using short-hairpin (sh) RNA strategy in 42D-ENZR to generate 42D-ENZR-shASCL1 cell line before being used for ChIP seq sample preparation.

tag: antibody


title: CAM20.0054

description: Tumor methylation

value: meningioma

value: bisulfite-treated DNA


title: 16D-CRPC-ASCL1OE-RNAseq


title: 43_OR3460_0

description: mouse liver RNA

tag: unc line name

tag: unc alias


title: 16D-CRPC-10d ENZ-RNAseq

tag: time point


title: CAM20.0053

description: Tumor methylation

tag: molecule subtype


title: 46_OR3460_600

description: mouse liver RNA

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: CAM20.0048

description: Tumor methylation


title: CAM20.0049

description: Tumor methylation


title: CAM20.0050

description: Tumor methylation


title: 41_OR3460_0

description: mouse liver RNA


title: HEK293T - PABPC RIP Rep1

tag: cell line

tag: treatment


title: HEK293T - PABPN RIP Rep2

value: PABPN


title: 61_AU8027_0

description: mouse liver RNA


title: 45_OR3460_600

description: mouse liver RNA


title: 42_OR3460_0

description: mouse liver RNA


title: 42D-ENZR-shASCL1-H3K27me3-ChIP

tag: cell type


title: 16D-CRPC-3d ENZ-RNAseq


title: HEK293T - PABPN RIP Rep3


title: CAM20.0046

description: Tumor methylation

tag: tissue


title: 16D-CRPC-Input


title: 44_OR3460_0

description: mouse liver RNA


title: 42D-ENZR-shASCL1-Input

tag: disease state


title: 42D-ENZR-shASCL1-EZH2-ChIP

tag: shRNA


title: CAM20.0047

description: Tumor methylation


title: CAM20.0045

description: Tumor methylation


title: HEK293T- Input RNA Rep3


title: 38_OR3154_600

description: mouse liver RNA


title: NCI-H660-ASCL1-ChIP


title: HEK293T- Input RNA Rep1


title: CAM20.0043

description: Tumor methylation


title: HEK293T - PABPN RIP Rep1


title: 37_OR3154_600

description: mouse liver RNA


title: HHSteC-NGB-3

city: Osaka

first: Hieu

middle: Ngoc

last: Vu

address: 1-4-3 Asahimachi, Abeno-ku

department: Department of Hepatology

country: Japan

institute: Osaka City University

data_processing:
Analyze the quality control of the sequenced raw reads. Overall reads’ quality, total bases, total reads, GC (%) and basic statistics are calculated using FastQC v0.11.7
In order to reduce biases in analysis, artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed
Trimmed reads are mapped to reference genome with HISAT2 version 2.1.0, splice-aware aligner
Transcript is assembled by StringTie version 2.1.3b with aligned reads
Expression profiles are represented as read count and normalization value which is based on transcript length and depth of coverage. The FPKM value or the RPKM is used as a normalization value.
In groups with different conditions, genes or transcripts that express differentially are filtered out through statistical hypothesis testing
In case of known gene annotation, functional annotation and gene-set enrichment analysis are performed using GO and KEGG database on differentially expressed genes
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Liver

growth_protocol: HHSteCs were cultured in SteCM complete consisted of 2% fetal bovine serum (FBS), 1% stellate cell growth supplement (S) and 1% penicillin-streptomycin (P/S) in a humidified atmosphere containing 95% air and 5% CO2. HHSteCs were passaged when sub-confluent and were used between passages 3 - 10 for the experiments

extract_protocol:
1 μg of total RNA was subjected to library synthesis using TruSeq Stranded mRNA LT Sample Prep Kit. The resulting mRNA was fragmented, reverse transcribed using random primers into cDNA, and ligated adapters onto both ends of the cDNA fragments. After amplifying fragments using PCR, select fragments with insert sizes between 200-400 bp. For paired-end sequencing, both ends of the cDNA is sequenced by the read length
TruSeq Stranded mRNA Sample Preparation Guide.

treatment_protocol: HHSteCs were plated into 12-well plate at 1 × 105 cells/well, in the final volume of 1 ml DMEM supplemented 2% FBS, 1 %S, 1% P/S . After 24 hours, MB and NGB were added and incubated for 48 hours.

value: HHSteCs

value: Human hepatic stellate cells

value: treated with NGB (4 uM) for 48 hours.


title: 42D-ENZR-ASCL1-ChIP

description: ASCL1 is over-expressed


title: HHSteC-NGB-2


title: HEK293T- Input RNA Rep2


title: CAM20.0042

description: Tumor methylation


title: 42D-ENZR-Input


title: NCI-H660-ASCL1-Input


title: HHSteC-NGB-1


title: HHSteC-MB-3

value: treated with MB (4 uM) for 48 hours.


title: CAM20.0041

description: Tumor methylation


title: CAM20.0040

description: Tumor methylation


title: 35_OR3154_600

description: mouse liver RNA


title: 34_OR3154_0

description: mouse liver RNA


title: TregEVs3

city: Gdansk

first: Jakub

last: Mieczkowski

address: Debinki 12

country: Poland

institute: Medical University of Gdansk

data_processing:
Reads were aligned to the human genome (Homo_sapiens.GRCh38) using Hisat2 (version 2.1.0) as a fast and sensitive alignment program
Converting SAM files to BAM diles using Samtools (Version: 1.9)
Obtaining the count matrix using Htseq (version 0.11.2)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: bw

source_name: Regulatoy T cells/PBMC

growth_protocol: Regulatory T cells (Treg) were first sorted from PBMCs, as CD4+ CD25hi CD127lo cells and used for culture. Treg were cultured in AIMV medium, supplemented with 50IU/ml IL-2, on 6-well, U-bottom plates, stimulated with plate bound anti-CD3 (5 μg/ml) and soluble anti-CD28 (1 μg/ml), in 200μl volume/well. Cultured for 5 days. After culture, viable, CD4+ CD25hi CD127lo cells were again sorted for RNA isolation for sequencing.

extract_protocol:
Sorted Treg were first stored in Trizol reagent. RNA was isolated using Total RNA Mini column purification kit (A&A Biotechnology #031-100).
Libraries were constructed using NEB Next Ultra II Directional RNA library Prep kit for Illumina (#E7335S/L), using standard Ilumina protocols.

treatment_protocol: In above described culture, leukemic EVs were added at start of the culture till collection of cells at day 5. EVs from 100x10^6 K562 were added per well (3x10^9 particles/EVs).

value: T lymphocyte/Treg

value: leukemic extracellular vesicles/EVs


title: CAM20.0044

description: Tumor methylation

source_name: fresh-frozen human meningioma


title: TregEVs2


title: 31_OR3154_0

description: mouse liver RNA

source_name: mouse, liver


title: 36_OR3154_600

description: mouse liver RNA


title: TregEVs1


title: 28_OR1566_600

description: mouse liver RNA


title: CAM20.0039

description: Tumor methylation


title: HHSteC-MB-1


title: 33_OR3154_0

description: mouse liver RNA


title: HHSteC-MB-2


title: 32_OR3154_0

description: mouse liver RNA


title: CAM20.0038

description: Tumor methylation


title: TregCTR3

value: untreated/control


title: 27_OR1566_600

description: mouse liver RNA


title: HHSteC-Cont-2

value: untreated


title: HHSteC-Cont-3


title: TregCTR2


title: CAM20.0036

description: Tumor methylation


title: 26_OR1566_600

description: mouse liver RNA


title: CAM20.0035

description: Tumor methylation


title: 25_OR1566_600

description: mouse liver RNA


title: 24_OR1566_0

description: mouse liver RNA


title: HHSteC-Cont-1


title: RNA-Seq non-Tfh patient 0114 [N506N702-208-30-0114-LMC-CD4pos-CXCR5neg-PD1neg_S10]

city: Umbilo

first: Werner

last: Smidt

state: KZN

address: 719 Umbilo Rd

country: South Africa

institute: African Health Research Insititute

description:
N506N702-208-30-0114-LMC-CD4pos-CXCR5neg-PD1neg_S10_val
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv

data_processing:
ATAC-Seq reads were trimmed with trim_galore
ATAC-Seq reads were aligned to the hg19 genome with BWA
Peak calling was performed with MACS2 with an IDR threshold of 0.1
RNA-Seq data were quantified with Kallisto using Ensembl release 75 of the human transcriptome
Genome_build: hg19
Supplementary_files_format_and_content: bed, normalized tpm

source_name: Non-Tfh cells from Lymph Node

extract_protocol:
ATAC-Seq extraction protocol as described by Buenrostro et. al., 2013
ATAC-Seq libraries were constructed as described by Buenrostro et. al. 2013
Total RNA was isolated from lysed cells using Qiagen RANeasy mini columns
RNA-Seq libraries were prepared with the NEBNext ultra RNA library preparation kit

value: Non-Tfh


title: CAM20.0033

description: Tumor methylation


title: BULK REP3 GOE800

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0.422
Using cutadapt version 2.5, sequences were removed if they had more than 70% N’s, had bases with quality <20 in the 3’ end trimmed,  had N bases trimmed at both ends, were trimmed for various adapters (polyA, polyT, Illumina sequencing regular and reverse complement primers, polyG, SINGV6 and SMART) and were finally discarded if the trimmed reads was shorter than 15 bases
Trimmed sequences were aligned to the genome reference hg38 sequence using the STAR aligner 2.7.2b using default parameters
Primary, unstranded aligned sequences were counted for all genes using featureCounts version 1.6.4
Genome_build: hg38 gene version 103
Supplementary_files_format_and_content: Tab-delimited text file with reads count per gene for each sample

source_name: dermal fibroblasts primary cell cultures

growth_protocol: primary cell culture derived from patients

extract_protocol:
Trizol (Thermo Fischer)
non stranded mRNS Seq (Illumina TruSeq)

treatment_protocol: No treatment

value: HGPS phenotype 6

tag: karyotype

value: Fibroblasts cells-bulk rep3 GOE800


title: 23_OR1566_0

description: mouse liver RNA


title: BULK REP3 GOE615

value: HGPS phenotype 5

value: Fibroblasts cells-bulk rep3 GOE615


title: BULK REP3 GOE486

value: HGPS phenotype 4

value: Fibroblasts cells-bulk rep3 GOE486


title: RNA-Seq non-Tfh patient 0069 [N502N702-208-30-0069-LMC-CD4pos-CXCR5neg-PD1neg_S9]

description:
N502N702-208-30-0069-LMC-CD4pos-CXCR5neg-PD1neg_S9_val
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv


title: RNA-Seq non-Tfh patient 0068 [N502N703-208-30-0068-LMC-CD4pos-CXCR5neg-PD1neg_S2]

description:
N502N703-208-30-0068-LMC-CD4pos-CXCR5neg-PD1neg_S2_val
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv


title: CAM20.0034

description: Tumor methylation

value: meningioma

value: bisulfite-treated DNA


title: BULK REP3 GOE247

value: HGPS phenotype 3

value: Fibroblasts cells-bulk rep3 GOE247


title: CAM20.0030

description: Tumor methylation


title: CAM20.0031

description: Tumor methylation


title: RNA-Seq non-Tfh patient 0054 [N502N702-208-30-0054-LMC-CD4posCXCR5negPD1neg_S4]

description:
N502N702-208-30-0054-LMC-CD4posCXCR5negPD1neg_S4_val
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv


title: BULK REP3 GOE1360

value: HGPS phenotype 2

value: Fibroblasts cells-bulk rep3 GOE1360


title: RNA-Seq Naive CD8 patient 0062 [208_30_0062_Naive_CD8-47053]

description:
208_30_0062_Naive_CD8-47053
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv

source_name: Naive CD8 cells from Lymph Node


title: RNA-Seq Naive CD8 patient 0074 [208_30_0074_Naive_CD8-45058]

description:
208_30_0074_Naive_CD8-45058
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv


title: RNA-Seq Naive CD8 patient 0068 [208_30_0068_Naive_CD8-45046]

description:
208_30_0068_Naive_CD8-45046
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv


title: CAM20.0029

description: Tumor methylation


title: RNA-Seq Naive CD8 patient 0054 [208_30_0054_Naive_CD8-45049]

description:
208_30_0054_Naive_CD8-45049
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv


title: BULK REP3 GOE1309

value: HGPS phenotype 1

value: Fibroblasts cells-bulk rep3 GOE1309


title: 21_OR1566_0

description: mouse liver RNA


title: BULK REP3 GOE1303

value: Control

value: Fibroblasts cells-bulk rep3 GOE1303


title: TregCTR1

value: T lymphocyte/Treg

value: untreated/control


title: BULK REP2 GOE800

value: HGPS phenotype 6

value: Fibroblasts cells-bulk rep2 GOE800


title: CAM20.0023

description: Tumor methylation


title: CAM20.0037

description: Tumor methylation


title: CAM20.0027

description: Tumor methylation


title: 15_AU8004_600

description: mouse liver RNA


title: 14_AU8004_0

description: mouse liver RNA


title: 18_AU8004_600

description: mouse liver RNA


title: 17_AU8004_600

description: mouse liver RNA


title: CAM20.0028

description: Tumor methylation


title: 22_OR1566_0

description: mouse liver RNA


title: CAM20.0025

description: Tumor methylation


title: RNA-Seq GCTfh patient 0069 [208_30_0069_GCTfh-47059]

description:
208_30_0069_GCTfh-47059
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv

source_name: GCTfh cells from Lymph Node

value: GCTfh


title: 13_AU8004_0

description: mouse liver RNA


title: 12_AU8004_0

description: mouse liver RNA


title: BULK REP2 GOE615

value: HGPS phenotype 5

value: Fibroblasts cells-bulk rep2 GOE615


title: CAM20.0022

description: Tumor methylation

value: meningioma


title: BULK REP3 GOE1305

value: Fibroblasts cells-bulk rep3 GOE1305


title: 16_AU8004_600

description: mouse liver RNA


title: LN7-1281AL ATAC

city: Palo Alto

first: Nathan

middle: Edward

last: Reticker-Flynn

address: 3373 Hillview Ave

department: Pathology

institute: Stanford University

description: Samples were prepared for ATAC-seq following the Omni-ATAC protocol (Corces et al., 2017). Briefly, cells detached with Accutase, washed in PBS, and resuspended in 50μL of ATAC-Resuspension Buffer (RSB, water with 10mM Tris-HCL, 10mM NaCl, and 3mM MhCl2) supplemented with 0.1% NP40 (Sigma), 0.1% Tween-20 (Sigma), and 0.01% Digitonin (Promega). Cells were incubated on ice for 3 minutes prior to adding 1mL RSB + 0.1% Tween-20. Samples were centrifuged and resuspended in 50μL of transposition mixture (2X TDE buffer + 2.5μL Tn5 Transposase (Illumina Tagment DNA Enzyme) + PBS + Digitonin + Tween-20 + water) incubated for 30min at 37°C on an orbital shaker. Samples were cleaned with the Zymo DNA Clean and Concentrator-5 Kit. Samples were amplified for 5 cycles using the NEBNext 2X Master Mix, after which 5μL of the reaction was subjected to qRT-PCR amplification to determine the optimum number of additional cycles for each sample. The remainder of the initial reactions were then amplified these additional number of cycles (ranging from 5 to 7). Library cleanup was performed using the Zymo DNA Clean and Concentrator-5 Kit, samples were eluted in water, and library quantification was performed using the KAPA Library Quantification Kit according to the manufacturer’s protocol.

data_processing:
Raw sequencing reads were filtered and adapters trimmed using Trimmomatic v0.36. Quality was assessed using FastQC v0.11.3.
Transcript abundance was quantified using Salmon v0.7.2 in quasi-mapping mode and using the sequence, GC, and position bias correction parameters.
Differential expression analysis was performed using DESeq2.
Assembly: GRCm38 GENCODE release M11
Supplementary files format and content: tab-delimeted files contain TPM values for each sample generated by Salmon

source_name: melanoma cell line

growth_protocol: All cell lines are grown in DMEM supplemented with 10% FBS, glutamine, and penicillin/streptomycin

extract_protocol:
Cell lines were trypsinized, washed with complete serum, centrifuged, and washed with PBS. Following washing cell pellets were frozen at -80C. After thawing, cells were resuspended in buffer RLT and lysed using QiaShredders. Extraction was performed using the Qiagen RNEasy Plus mini kit according to the manufacturer's protocol.
Library construction (RNA-seq) was performed by MedGenome using the Illumina TruSeq stranded mRNA kit

tag: strain


title: BULK REP2 GOE486

value: HGPS phenotype 4

value: Fibroblasts cells-bulk rep2 GOE486


title: RNA-Seq GCTfh patient 0074 [208_30_0074_GCTfh-45060]

description:
208_30_0074_GCTfh-45060
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv


title: RNA-Seq GCTfh patient 0062 [208_30_0062_GCTfh-47051]

description:
208_30_0062_GCTfh-47051
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv


title: CAM20.0021

description: Tumor methylation

value: bisulfite-treated DNA


title: LN7-1134BL ATAC


title: RNA-Seq GCTfh patient 0054 [208_30_0054_GCTfh-45051]

description:
208_30_0054_GCTfh-45051
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv


title: LN7-1112AR ATAC


title: BULK REP2 GOE247

value: HGPS phenotype 3

value: Fibroblasts cells-bulk rep2 GOE247


title: LN7-1120BL ATAC


title: CAM20.0020

description: Tumor methylation


title: BULK REP2 GOE1309

value: HGPS phenotype 1

value: Fibroblasts cells-bulk rep2 GOE1309


title: CAM20.0017

description: Tumor methylation


title: RNA-Seq fCD8 patient 0074 [208_30_0074_CXCR5Pos_CD8-45054]

description:
208_30_0074_CXCR5Pos_CD8-45054
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv

source_name: fCD8 cells from Lymph Node


title: RNA-Seq GCTfh patient 0068 [208_30_0068_GCTfh-45048]

description:
208_30_0068_GCTfh-45048
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv


title: BULK REP2 GOE1305

value: Control

value: Fibroblasts cells-bulk rep2 GOE1305


title: CAM20.0016

description: Tumor methylation


title: BULK REP1 GOE800

value: Fibroblasts cells-bulk rep1 GOE800


title: RNA-Seq fCD8 patient 0054 [208_30_0054_CXCR5Pos_CD8-45045]

description:
208_30_0054_CXCR5Pos_CD8-45045
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv


title: LN3-384IR ATAC


title: RNA-Seq fCD8 patient 0069 [208_30_0069_CXCR5_Pos_CD8-47055]

description:
208_30_0069_CXCR5_Pos_CD8-47055
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv


title: CAM20.0015

description: Tumor methylation


title: LN3-386IL ATAC


title: 11_AU8004_0

description: mouse liver RNA


title: BULK REP2 GOE1303

value: Fibroblasts cells-bulk rep2 GOE1303


title: RNA-Seq fCD8 patient 0068 [208_30_0068_CXCR5Pos_CD8-45057]

description:
208_30_0068_CXCR5Pos_CD8-45057
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv


title: BULK REP2 GOE1360

value: HGPS phenotype 2

value: Fibroblasts cells-bulk rep2 GOE1360


title: CAM20.0014

description: Tumor methylation


title: RNA-Seq fCD8 patient 0062 [208_30_0062_CXCR5_Pos_CD8-47047]

description:
208_30_0062_CXCR5_Pos_CD8-47047
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv


title: LN3-392AL ATAC


title: B16-F0 #4 ATAC


title: CAM20.0018

description: Tumor methylation


title: CAM20.0013

description: Tumor methylation


title: B16-F0 #2 ATAC


title: BULK REP1 GOE486

value: Fibroblasts cells-bulk rep1 GOE486


title: BULK REP1 GOE1360

value: Fibroblasts cells-bulk rep1 GOE1360


title: LN3-377IR ATAC


title: RNA-Seq non-fCD8 patient 0074 [208_30_0074_CXCR5Neg_CD8-45056]

description:
208_30_0074_CXCR5Neg_CD8-45056
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv

source_name: Non-fCD8 cells from Lymph Node


title: CAM20.0012

description: Tumor methylation

value: meningioma


title: RNA-Seq non-fCD8 patient 0068 [208_30_0068_CXCR5Neg_CD8-45059]

description:
208_30_0068_CXCR5Neg_CD8-45059
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv


title: B16-F0 #3 ATAC


title: BULK REP1 GOE615

value: HGPS phenotype 5

value: Fibroblasts cells-bulk rep1 GOE615


title: RNA-Seq non-fCD8 patient 0069 [208_30_0069_CXCR5_Neg_CD8-47057]

description:
208_30_0069_CXCR5_Neg_CD8-47057
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv


title: RNA-Seq non-fCD8 patient 0054 [208_30_0054_CXCR5Neg_CD8-45047]

description:
208_30_0054_CXCR5Neg_CD8-45047
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv


title: B16-F0 #1 ATAC


title: CAM20.0007

description: Tumor methylation


title: BULK REP1 GOE247

value: Fibroblasts cells-bulk rep1 GOE247


title: CAM20.0011

description: Tumor methylation

value: bisulfite-treated DNA


title: BULK REP1 GOE1303

value: Fibroblasts cells-bulk rep1 GOE1303


title: ATAC-Seq non-Tfh patient 0069

description:
208-30-0069-LMC-CD4pos-CXCR5neg-PD1neg-N702N517_S1_val
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed

value: Non-Tfh


title: CAM20.0010

description: Tumor methylation


title: LN6-987AL-sgStat1-2


title: RNA-Seq non-fCD8 patient 0062 [208_30_0062_CXCR5_Neg_CD8-47049]

description:
208_30_0062_CXCR5_Neg_CD8-47049
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv: cxcr5_study_ndhlovu_rnaseq_normalized_tpm.csv


title: CAM20.0006

description: Tumor methylation


title: BULK REP1 GOE1309

value: HGPS phenotype 1

value: Fibroblasts cells-bulk rep1 GOE1309


title: BULK REP1 GOE1305

value: Control

value: Fibroblasts cells-bulk rep1 GOE1305


title: NBF0IFNRKOLN1-6480IL


title: CAM20.0008

description: Tumor methylation


title: ATAC-Seq non-Tfh patient 0114

description:
208-30-0114-LMC-CD4pos-CXCR5neg-PD1neg-N706N517_S3_val
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed


title: LN6-987AL-sgLacZ-v4


title: CAM20.0009

description: Tumor methylation


title: NBF0IFNRKOLN1-6476IL


title: LN6-987AL-sgIfngr1-3


title: cellenone

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which were converted to fastq files with bcl2fastq v2.20.0.422
Sequences were demultiplexed using Cogent version 1.0 from TAKARA
Using cutadapt version 2.5, sequences were removed if they had more than 70% N’s, had bases with quality <20 in the 3’ end trimmed,  had N bases trimmed at both ends, were trimmed for various adapters (polyA, polyT, Illumina sequencing regular and reverse complement primers, polyG, SINGV6 and SMART) and were finally discarded if the trimmed reads was shorter than 15 bases
Trimmed sequences were aligned to the genome reference hg38 sequence using the STAR aligner 2.7.2b using default parameters
Primary, unstranded aligned sequences were counted for all genes using featureCounts version 1.6.4
Gene matrices, metadata and gene info files were generated for all cells in all samples by Cogent version 1.0 from Takara
Genome_build: hg38 gene version 103
Supplementary_files_format_and_content: GeneMatrix – CSV file with read count per gene for each cell
Supplementary_files_format_and_content: Metadata – CSV file with sample affiliation for each cell and number of reads at different steps of the analysis
Supplementary_files_format_and_content: gene_info – CSV file with gene information for which reads were counted

extract_protocol:
Cell lysis froozen -80°
Nextera single cell SMART Technology full length approach
ScRNA-seq

value: Fibroblasts single-cells


title: ATAC-Seq non-Tfh patient 0068

description:
N702N517-208-30-0068-LMC-CD4pos-CXCR5neg-PD1neg_S1_val
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed: cd4.ln.cxcr5_neg.pd1_neg.bed


title: CAM20.0005

description: Tumor methylation

data_processing: Normalization and background correction of raw IDAT files was performed using ssNoob in the Bioconductor package minfi (version minfi_1.36.0). Beta values were calculated for each probe across all samples after post-processing.


title: ICELL8_CHIP3

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which were converted to fastq files with bcl2fastq v2.20.0.422
Sequences were demultiplexed using Cogent version 1.0 from TAKARA
Using cutadapt version 2.5, sequences were removed if they had more than 70% N’s, had bases with quality <20 in the 3’ end trimmed,  had N bases trimmed at both ends, were trimmed for various adapters (polyA, polyT, Illumina sequencing regular and reverse complement primers, polyG, SINGV6 and SMART) and were finally discarded if the trimmed reads was shorter than 15 bases
Trimmed sequences were aligned to the genome reference hg38 sequence using the STAR aligner 2.7.2b using default parameters
Primary, unstranded aligned sequences were counted for all genes using featureCounts version 1.6.4
Gene matrices, metadata and gene info files were generated for all cells in all samples by Cogent version 1.0 from Takara
Genome_build: hg38 gene version 103
Supplementary_files_format_and_content: GeneMatrix – CSV files with read count per gene for each cell (3 files, one per chip)
Supplementary_files_format_and_content: Metadata – CSV files with sample affiliation for each cell and number of reads at different steps of the analysis (3 files, one per chip)
Supplementary_files_format_and_content: Gene_info – CSV file with gene information for which reads were counted

extract_protocol:
ICELL8 cx single cell system TAKARA
Nextera single cell SMART Technology full length approach
scRNA-seq

value: Fibroblasts single-cells Chip3


title: LN6-987AL-sgIfnar1-2


title: CAM20.0004

description: Tumor methylation

extract_protocol: Genomic DNA was extracted from fresh-frozen tumor specimens and 250-500ng of bisulfite-treated DNA (EZ DNA Methylation Kit, Zymo, California, USA) per sample was used to obtain genome-wide DNA methylation profiles


title: ATAC-Seq non-Tfh patient 0054

description:
N706N517-208-30-0054-LMC-CD4pos-CXCR5neg-PD1neg_S3_val
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.cxcr5_neg.pd1_neg.bed


title: ATAC-Seq GCTfh patient 0054

description:
GCTfh.LMC.208-30-0054.S9
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed

value: GCTfh


title: ATAC-Seq GCTfh patient 0074

description:
GCTfh.LMC.208-30-0074.S2
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed


title: CAM20.0003

description: Tumor methylation


title: Healthy control scRNA-seq 3 [re-analysis]

city: New Haven

first: William

last: Damsky

state: CT

address: 333 Cedar St

institute: Yale School of Medicine

description:
scHealthy3_HHT_S2
scHeatlhy 3 (re analysis of GSM4815805)

data_processing:
Cellranger software suite (v3.1.0) was used to process the scRNAseq data
The Seurat package for R v3.1.5  was used for downstream analysis
Pathway analysis for the entire data set was performed using IPA (Ingenuity Pathway Analysis)
Genome_build: hg38
Supplementary_files_format_and_content: counts

source_name: Skin

extract_protocol:
4 mm punch biopsies of skin were obtained on separate days from 3 patients with GA and 3 healthy volunteers.. Biopsies were immediately bisected and placed in dispase (10 mg/mL) (Dispase II Sigma Cat# D4693) in RPMI with 2% FBS for 45 minutes at 37°C with shaking at 125 RPM. The tissue was removed from the dispase solution, minced in a sterile plate with a scalpel, and then subsequently incubated with liberase (0.5 mg/mL) (Liberase TH Sigma Cat# 5401135001) in RPMI with 2% FBS for 45 minutes at 37°C with shaking at 125 RPM. The dispase solution was placed on ice. After incubation in the liberase, the dispase solution was combined (to recover any additional cells from the dispase) and the mixture was triturated and filtered through a 100 mM sterile filter. Cells were washed with RPMI + 2% FBS and RBCs were lysed with ACK Lysing Buffer (Lonza Cat# 10-548E) and washed again in RPMI + 2% FBS. Cells were stained with LIVE/DEAD Red viability dye (ThermoFisher Cat# L23102), FC block (Biolegend Cat#422301) and CD45 Alexa Fluor 488 (Biolegend Cat# 304017) in RPMI + 0.1% FBS. Viable cells were isolated using a BD FACS Aria cell sorter and sorted into cold RPMI + 2% FBS. CD45 positivity was recorded but not used as a criterion for sorting. Up to 10,000 cells (depending on yield) were loaded onto a 10X chromium controller for each sample according to the manufacturer’s instructions.
Single cell libraries were created according to the manufacturer’s instructions by the Yale Center for Genome Analysis (YCGA).

tag: subject status

value: Healthy control

value: Skin


title: CAM20.0001

description: Tumor methylation


title: ATAC-Seq GCTfh patient 0068

description:
GCTfh.LMC.208-30-0068.S8
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed


title: ATAC-Seq GCTfh patient 0052

description:
GCTfh.LMC.208-30-0052.S11
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed


title: B16-F0-sgIfngr1-3


title: B16-F0-sgStat1-2


title: ATAC-Seq GCTfh patient 0040

description:
GCTfh.LMC.208-30-0040.S2
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed: cd4.ln.tfh.bed


title: B16-F0-sgIfnar1-1_sgIfngr1-3


title: CAM20.0002

description: Tumor methylation


title: ICELL8_CHIP1

value: Fibroblasts single-cells Chip1


title: Healthy control scRNA-seq 2 [re-analysis]

description:
scHealthy2_HHT_S1
scHealthy 2 (re analysis of GSM4815804)


title: ATAC-Seq GCTfh patient 0037

description:
GCTfh.LMC.208-30-0037.S5
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd4.ln.tfh.bed


title: B16-F0-sgIfnar1-2


title: Healthy control scRNA-seq 1 [re-analysis]

description:
scHealthy1_HHT_S3
scHealthy 1 (re analysis of GSM4815803)


title: Sarcoidosis patient scRNA-seq 5

description:
SAR3_HHT_S1
scSAR 3

source_name: Lesional skin

value: Sarcoidosis patient


title: ICELL8_CHIP2

value: Fibroblasts single-cells Chip2


title: Sarcoidosis patient scRNA-seq 2

description:
SAR2_HHT_S1
scSAR 2


title: ATAC-Seq Naive CD8 patient 0037

description:
Naive_CD8.LMC.208-30-0037.S2
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed


title: Sarcoidosis patient scRNA-seq 1

description:
SAR1-v3_HHT_S3
scSAR 1


title: B16-F0-sgLacZ