title: Bend3_WGBS_KO3

status: Public on Aug 26 2023

city: Paris

first: Pierre-Antoine

last: Defossez

address: 35 rue Hélène Brion

institute: Epigenetics and Cell Fate Unit

description: bisulphite converted genomic DNA

data_processing:
RNA-seq data: Trimmomatic (Bolger et al., 2014) (v0.39) and parameters: ILLUMINACLIP:adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36.
Read pairs that survived trimming were aligned to the mouse reference genome (build mm10) using STAR (Dobin et al., 2013) (v2.7.5c) and default single-pass parameters.
PCR duplicate read alignments were flagged using Picard-tools (2019) MarkDuplicates (v2.23.4).
Uniquely aligned, non-PCR-duplicate reads were kept for downstream analysis using Samtools (Li et al., 2009) view (v1.10) and parameters: -q 255 -F 1540.
Bigwig files were generated using deeptools (Ramírez et al., 2016) bamCoverage (v3.3.0) and visualized in IGV (Thorvaldsdottir et al., 2013) (v2.8.9).
ChIP-seq data : FASTQ reads were trimmed using Trimmomatic (v0.39) and parameters:ILLUMINACLIP:illumina_adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36. Trimmed reads were aligned using Bowtie2 (v2.4.1) in --local mode. Following alignment, Picard (v2.23.4) CleanSam, SamFormatConverter, SortSam and Markduplicates were used to generate a duplicate-marked bam file. The resulting bam files were converted to bigwig using deeptools (v3.3.0) Bamcoverage and options –ignoreDuplicates –normalizeUsing CPM –minMappingQuality 10 –ignoreForNormalization chrX chrY chrM.
WGBS data : As described in Miura et al 2019 NAR, the sequenced reads were mapped with BMap and summarized with an in-house pipeline, with custom scripts archived using GitHub (https://github.com/FumihitoMiura/Project-2).
Assembly: mm10
Supplementary files format and content: All processed files are in bigWig format. RNA-seq: genomic coverage counts, WGBS: percent methylation over CpGs covered by at least 5 reads, ChIP-seq: signal coverage.

extract_protocol:
Genomic DNA was extracted from the cells with QIAmp DNA Mini kit (Qiagen), according to the manufacturer’s instructions.
The library preparation for WGBS was performed with the tPBAT protocol described previously (Miura 2012, Miura 2019; NAR). One hundred nanograms of genomic DNA spiked with 1% (w/w) of unmethylated lambda DNA (Promega, Madison, WI) was served for the library preparation. The sequencing was performed by Macrogen Japan Inc. (Tokyo, Japan) using the HiSeq X Ten system.

value: mouse embryonic stem cells

value: Bend3 KO

tag: chip antibody


title: Bend3_WGBS_KO2

type: SRA

country: France

description: bisulphite converted genomic DNA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell line

tag: cell type

tag: genotype


title: Bend3_WGBS_KO1

description: bisulphite converted genomic DNA


title: macrophages co-cultured with fat fibroblasts repetition4

status: Public on Aug 27 2023

city: Rehovot

first: Shimrit

last: Mayer

state: Central

address: Herzl St 234

department: Bimolecular sciences

country: Israel

institute: Weizmann Institute

library_source: transcriptomic

data_processing:
Illumina bcl2fastq software used for base calling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
aligment: STAR v2.4.2a parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No
We used the 3’ end (1000bp) of the transcripts for counting the number of reads per gene. Counting (UMI counts) was done after marking duplicates (in-house script) using HTSeq-count (DOI: 10.1093/bioinformatics/btu638) in union mode.
Further analysis was done for genes having minimum 5 reads in at least one sample
Assembly: mm10
Supplementary files format and content: tab delimited text files include mRNA molecule count values for each sample

molecule: total RNA

source_name: bone marrow drive macrophages

growth_protocol: 8  weeks-old mice housed at the Weizmann Institute animal facility under specific pathogen-free conditions.

extract_protocol:
Bone marrow-derived monocytes from BALB/c female mice were differentiated into macrophages by growth in DMEM with 10% FBS, 5% P/S and 20% L929 CM on the petri dish. The medium was replenished on day 3 and the macrophages were reseeded for the experiment on day 7.
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science
3' RNA-seq for digital gene expression quantitation

treatment_protocol: The macrophages were harvested with non-enzymatic cell dissociation solution (Biological Industries,03-071-1B) and washed with PBS without calcium and magnesium. The  fibroblasts  were isolated and expanded for 7 days, afterwhich the fibroblasts were trypsinized and resuspended in an ice-cold MACS buffer (PBS with 0.5% BSA). The samples were pelleted by centrifugation at 350g for 5 min at 4 °C, incubated with anti-EpCAM (Miltenyi, 130-105-958) and anti-CD45 (Miltenyi, 130-052-301) magnetic beads, transferred to LS columns (Miltenyi, 130-042-401) and the fibroblast-enriched, CD45/EpCAM-depleted flow-through was collected. Both cells seeded together 6-well plates precoated with collagen I. The co-cultures with fibroblasts were grown in DMEM with 10% FBS and 5% P/S . Every 3 days 1ml of medium (6well) were replaced with fresh medium.

tag: strain

value: BALB/c

tag: tissue

value: bone marrow

value: bone marrow drive macrophages

tag: selection marker

tag: treatment

value: Invitro co-cultured with fat fibroblasts

tag: mouse age

value: 8 weeks


title: 41217Brain-a4

city: Davis

first: Chase

middle: Elliott

last: Hawes

state: CA

address: 2005, CIID, County Rd 98 & Hutchinson Drive

department: Center for Immunology and Infectious Diseases

country: USA

institute: University of California, Davis

library_source: transcriptomic single cell

data_processing:
Sample demultiplexing, alignment, gene counting, and aggregation were performed using the Cellranger pipeline version 7.0.1.
Assembly: mmul_10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Macaca mulatta

source_name: Brain (Right Hemishpere)

growth_protocol: Colony bred rhesus macaques were housed and maintained in the California National Primate Research Center.

extract_protocol:
Mononuclear cells were freshly collected from rhesus splenic and brain tissue following euthanasia. Briefly, tissues were mechanically dissociated and digested in DMEM with 0.25% trypsin and 5 units per mL of DNase I for 45 minutes at 37oC. Digested brain tissues were homogenized using a pipette controller and 10mL serological pipette. Subsequently, the homogenized brain tissue was passed through a metallic strainer followed by a 180μm nylon strainer and 100µm SMART strainer. Cells were washed in media and spun down at 1200rpm for 10 minutes. Subsequently, mononuclear cells were collected using a 21% and 75% Percoll gradient. Post gradient enrichment, cells were washed, counted, and stored in heat-inactivated FBS (HI-FBS) with 10% DMSO and stored in liquid nitrogen until subsequent processing. Digested spleen tissues were washed with media and red blood cells subsequently lysed with ACK lysis solution. Similar to brain cells, spleen cells were counted and stored in HI-FBS with 10% DMSO for cryopreservation. Prior to cell sorting and cDNA generation, mononuclear cells were thawed at room temperature, placed in fresh complete media (For splenic cells: RPMI supplemented with 10% HI-FBS, 1% L-glutamine, 1% Penicillin-streptomycin; For brain tissue derived cells: DMEM supplemented with 10% HI-FBS, 1% L-glutamine, 1% Penicillin-streptomycin) and treated with 2 units per mL of DNase I for 15 minutes at 37oC. Cells were washed and CD45+ cells were isolated using CD45 magnetic bead separation for non-human primates (Miltenyi Biotec CD45 Microbeads non-human primate Cat# 130-091-899) in accordance with the manufacturer's protocol. Enriched CD45+ cells were stained with CD45 and a live dead marker for flow cytometric sorting of live CD45+ cells. Live CD45+ cells were characterized and quantified on a BD FACSymphony cell analyzer and sorted utilizing a FACS Aria and resuspended in DMEM.
Sample barcoding, assembly of gel-beads in emulsion (GEM), GEM reverse transcription, cDNA amplification and cleanup, and library construction were performed according to the Chromium Next GEM single cell 3’ v3.1 protocol from 10X Genomics.

treatment_protocol: Rhesus Macaques were infected intravenously with (104 TCID50) SIVmac251 and treated with either an anti-a4 integrin blocking monoclonal antibody or an anti-desipramine (IgG control) antibody. Antibody treatments were administered at 1 week prior to SIV infection and every subsequent 10-day interval at doses of 25mg/kg intravenously (neat) over the course of the study. Animals were euthanized at 3 weeks post-SIV infection with the spleen and right brain hemisphere collected at necropsy. Additionally, the same tissues were also collected from a cohort of uninfected, untreated animals (Control).

value: Brain (Right Hemishpere)

value: Live CD45+

value: Intravenous SIV Infection + anti-a4 integrin blocking monoclonal antibody


title: 40234Brain-a4


title: 40234Spleen-a4

source_name: Spleen

value: Spleen


title: 36798Spleen-a4


title: 34051Brain-a4


title: 41812Brain-IgG

value: Intravenous SIV Infection + anti-desipramine monoclonal antibody (IgG Control)


title: 36798Brain-a4


title: 40742Spleen-IgG


title: 40742Brain-IgG


title: 41812Spleen-IgG


title: 37164Spleen-IgG


title: 37164Brain-IgG


title: 33171Spleen-Control

value: Uninfected + No Treatment


title: 33994Spleen-Control


title: 35488Brain-IgG


title: 33100Spleen-Control


title: 34194Brain-Control


title: 33171Brain-Control


title: T lymphocytes of MS patient 2, scRNAseq, targeting IL7RA

city: Leuven

first: Lies

last: Van Horebeek

address: Herestraat 49

department: Neurosciences

country: Belgium

institute: KU Leuven

description:
IL7R mRNA
Chromium Single Cell V(D)J Reagent Kits v.1.1 (10x Genomics)

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1.
Tagging sequences were extracted from the BAM files outputted by Cell Ranger using samtools and awk commands, and merged while tracking associated transcript and dataset.
Genotypes were called in individual transcripts using VarTrix v1.1.3 in debugging mode.
Assembly: hg38
Supplementary files format and content: Tab separated text files, tsv files and matrix counts

organism: Homo sapiens

source_name: peripheral blood

extract_protocol:
PBMCs were isolated from peripheral blood in EDTA containing tubes using lymphoprep. T cells were enriched using EasySep Human T cell Isolation Kit (STEMCELL Technologies).
Libraries were constructed according to the manufacturer's instructions (10x Genomics, Chromium Single Cell V(D)J Reagent Kits v.1.1) or with our in-house developed targeted sequencing method.

value: peripheral blood

value: T lymphocytes


title: MS-1_CD8_T2_Targeted

description:
CD8+ T lymphocytes of MS patient at T2, scRNAseq, targeting TREX1
TREX1 mRNA
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics)

data_processing:
Downsampled datasets were obtained through random downsampling of fastq filesl with seqtk-1.3.
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1.
Tagging sequences were extracted from the BAM files outputted by Cell Ranger using samtools and awk commands, and merged while tracking associated transcript and dataset.
Genotypes were called in individual transcripts using VarTrix v1.1.3 in debugging mode.
Assembly: hg19
Supplementary files format and content: Tab separated text files, tsv files and matrix counts

extract_protocol:
PBMCs were isolated from peripheral blood in EDTA containing tubes using lymphoprep. B cells or CD8+ T cells were enriched using EasySep Human B Cell or CD8+ T cell Isolation Kits (STEMCELL Technologies).
Libraries were constructed according to the manufacturer's instructions (10x Genomics, Chromium Next GEM Single Cell 3' Reagents Kit) or with our in-house developed targeted sequencing method.

value: CD8+ T lymphocytes


title: T lymphocytes of MS patient 1, scRNAseq, targeting IL7RA


title: MS-1_CD8_T1_Targeted

description:
CD8+ T lymphocytes of MS patient at T1, scRNAseq, targeting TREX1
TREX1 mRNA
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics)


title: 41217Spleen-a4


title: H3K27me3_KO1

data_processing:
FASTQ reads were trimmed using Trimmomatic (v0.39) and parameters: ILLUMINACLIP:illumina_adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36. Trimmed reads were aligned using Bowtie2 (v2.4.1) with parameters: "--local --very-sensitive --no-mixed --dovetail --no-discordant --phred33 -I 10 -X 700". Subsequent steps were conducted as for the ChIP-seq analysis method described in the other samples.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&RUN-seq

extract_protocol:
Genomic DNA was extracted after CUT&RUN with QIAmp DNA Mini kit (Qiagen), according to the manufacturer’s instructions.
Libraries were prepared with KAPA HyperPrep kit (Roche), following the manufacturer’s instructions.


title: H3K27me3_KO3


title: H3K27me3_KO2


title: H3K27me3_WT_rep1

value: WT


title: H3K27me3_WT_rep2

value: mouse embryonic stem cells


title: T lymphocytes of MS patient 2, scRNAseq

description:
mRNA
Chromium Single Cell V(D)J Reagent Kits v.1.1 (10x Genomics)


title: Dip2b_KO-KSR-Day9

city: Taiyuan city

first: yuanqing

last: Pan

address: No. 92 Wucheng road, Xiaodian district, Taiyuan city, Shanxi Province, China

country: China

institute: Shanxi university

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp.
Bowtie index was created based on the GRCm38.p6/mm10 and RefSeq transcriptome.
TPM values for each Sample were performed using Kallisto.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: 46C mESCs

extract_protocol:
RNA was extracted from the 12 cell samples using EZBioscience Tissue RNA Purification Kit PLUS kit and extracted according to the manufacturer's instructions.The 12 cell samples were sequenced using illumina novaseq 6000 platform at PE150 length.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: 46C mESCs

value: embryonic stem cells

value: KO

value: differentiation

tag: time

tag: media

value: KSR


title: WT-KSR-Day9


title: siPDHA1 TNFa input H3K27ac ChIP-seq biol rep 3

city: New Haven

first: Nabil

last: Boutagy

state: CT

address: 10 Amistad St

department: Pharmacology

institute: Yale University

description:
non-immunoprecipitated input chromatin
annotatedpeaks_WOA_h3k27ac_chip_huvec_normalized.xlsx
annotatedsuperEnhancers_WOA_h3k27ac_chip_huvec_normalized.xlsx
annotatedtypicalenhancers_WOA_h3k27ac_chip_huvec.xlsx

data_processing:
demultiplexed ChIP-seq fastq data were aligned to hg38 using Bowtie2 with default parameters
Aligned sam files were made into tagDirectories in HOMER.
ChIP-seq peaks were identified using the findPeaks function with the parameters '-style histone -tbp2 -o auto -i
ChIP-seq peaks for typical and super enhancers were identified using the findPeaks function with the parameters '-style superhistone -tbp 2 -o auto -typical -i'.
The peaks, typical, and super enhancers for all pools were merged together using mergePeaks separate from each other.
Merged peak files for both typical and super enhancers were annotated using annotatePeaks.pl. The annotations were normalized using the parameters 'hg38 -tbp 1 -fpkm -size given' and unnormalized using 'hg38 -raw'.
The raw annotated peaks files were used for differential analysis using edgeR. The results were then merged with the normalized annotated peaks files.
UCSC browser tracks were created for pool D's typical and super enhancers by converting the mergedPeaks file for each to a bed file.
Assembly: hg38
Supplementary files format and content: annotatedsuperEnhancers_WOA_h3k27ac_chip_huvec_normalized.xlsx. This is an Excel-formatted file converted from the annotated peaks .txt file created by HOMER for the super enhancer ChIP-seq peaks. It contains peak annotations and FPKM normalized counts for each ChIP-seq sample.
Supplementary files format and content: annotatedtypicalenhancers_WOA_h3k27ac_chip_huvec.xlsx. This is an Excel-formatted file converted from the annotated peaks .txt file created by HOMER for the typical enhancer ChIP-seq peaks. It contains peak annotations and FPKM normalized counts for each ChIP-seq sample.
Supplementary files format and content: groupD_superenhancers.bed. This is a bed file of the merged super enhancers from pool D created with HOMER.
Supplementary files format and content: poolD_typicalenhancers.bed. This is a bed file of the merged typical enhancers from pool D created with HOMER.
Supplementary files format and content: annotatedpeaks_WOA_h3k27ac_chip_huvec_normalized.xlsx. This is an Excel-formatted file converted from the annotated peaks .txt file created by HOMER for the ChIP-seq peaks. It contains peak annotations and FPKM normalized counts for each ChIP-seq sample.

source_name: primary cells

growth_protocol: HUVEC used in this study were primary isolates of ECs collected from donor umbilical cords through Yale School of Medicine's Vascular Biology and Therapeutic core. They were used at early passage (p4) and cultured in EGM-2 media (Lonza) with 10% fetal bovine serum, penicilllin/streptomycin and glutamine (2.8mM) in a 37C incubator with 5% CO2 supply

extract_protocol:
Cells were fixed at room temperature with with 1% formaldehyde for 15min and quenched with glycin. Between 5 and 15 million cells were used for each ChIP-seq. Cell lysates were sonicated using a BioRuptor Standord or BioRuptor Pico and then immunoprecipitated using antibodies bound to a 2:1 mixture of Protein A Dynabeads and Protein G Dynabeads.
For ChIP-seq, HUVECs were fixed with 1% formaldehyde for 15 minutes and quenched with glycine. Lysates were sonicated, a small fraction of chromatin was removed and prepared as inputs, whereas the remaining complexes were immunoprecipitated with antibody.
For ChIP-seq, double-stranded End Repair was performed and inserts were ligated to barcoded  BioO Nextflex adapters and amplified prior to sequencing.

treatment_protocol: Cells were treated with or without 10ng/mL of TNFa for 10 hour

value: primary cells

value: Human Umbilical Vein Endohtelial Cell (HUVEC)

tag: sirna

value: TNFa treatment

tag: antibody


title: WT-KSR-Day4


title: siPDHA1 NT input H3K27ac ChIP-seq biol rep 3

value: control treatment


title: saline [L03]

city: Shijiazhuang

first: Hongyu

last: Yang

address: Tiyu

institute: Hebei Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC-content of the clean data were calculated. All the downstream analyses were based on clean data with high quality
Supplementary files format and content: FPKM

source_name: nucleus accumben

extract_protocol:
nucleus accumbens were removed, flash frozen on dry ice, and RNA was harvest using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: nucleus accumben

value: Saline injection


title: saline [L02]


title: siCTL TNFa input H3K27ac ChIP-seq biol rep 3

value: siCTL


title: T lymphocytes of MS patient 1, scRNAseq

value: peripheral blood


title: Dip2b_KO-KSR-Day0

value: proliferating


title: nos-Gal4 driven BonusKD RNA-seq biological replicate 3

city: Pasadena

first: Baira

last: Godneeva

address: 1200 E California Blvd

department: Division of Biology and Biological Engineering

institute: California Institute of Technology

data_processing:
RNA-seq libraries were pseudoaligned to the D. melanogaster transcriptome (RefSeq, dm6) and transposon consensuses (from RepBase) using kallisto
Differential expression analysis was done with sleuth using the gene analysis option
The average TPM between three biological replicas in knockdown versus control were calculated for fold changes in gene expression
For RNA-seq coverage tracks reads first were aligned to the D. melanogaster genome (dm6) using bowtie1 (v.1.2.2) allowing 2 mismatches and single mapping position.
Tracks were generated using deepTools (v.3.5.1) bamCoverage function with 10 bp bin sizes.
Assembly: dm6
Supplementary files format and content: a plaintext file of the abundance estimates using kallisto
Supplementary files format and content: genome browser tracks (bigWig format)

organism: Drosophila melanogaster

source_name: fly ovaries

growth_protocol: Fly stocks were maintained at 24C on standard diet

extract_protocol:
Total RNA was extracted from fly ovaries using TRIzol reagent, PolyA+ selection was performed using an NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490)
RNA-seq libraries were made using the NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEB, #E7760) according to the manufacturer’s instructions.

treatment_protocol: young 0-1 day flies were dissected without feeding with yeast

value: fly ovaries

value: nos-Gal4 driven BonusKD


title: nos-Gal4 driven BonusKD RNA-seq biological replicate 2


title: Dip2b_KO-N2B27-Day8


title: Morphine CPP [L06]

value: Morphine injection


title: Morphine CPP [L05]


title: nos-Gal4 driven BonusKD RNA-seq biological replicate 1


title: WT-N2B27-Day8

value: 46C mESCs

value: WT


title: siPDHA1 TNFa input H3K27ac ChIP-seq biol rep 2


title: saline [L01]


title: Dip2b_KO-N2B27-Day4

value: embryonic stem cells

value: KO


title: WT-KSR-Day0

value: KSR


title: siPDHA1 NT input H3K27ac ChIP-seq biol rep 2

value: primary cells


title: siCTL TNFa input H3K27ac ChIP-seq biol rep 2

value: Human Umbilical Vein Endohtelial Cell (HUVEC)


title: nos-Gal4 driven control RNA-seq biological replicate 3

value: nos-Gal4 driven control


title: nos-Gal4 driven control RNA-seq biological replicate 2


title: Dip2b_KO-KSR-Day4

value: differentiation


title: Morphine CPP [L04]

value: nucleus accumben


title: WT-N2B27-Day4


title: siCTL NT input H3K27ac ChIP-seq biol rep 2

value: control treatment


title: siCTL NT input H3K27ac ChIP-seq biol rep 3

value: siCTL


title: nos-Gal4 driven control RNA-seq biological replicate 1


title: Dip2b_KO-N2B27-Day0


title: MT-Gal4 driven whiteKD RNA-seq biological replicate 3

data_processing:
RNA-seq libraries were pseudoaligned to the D. melanogaster transcriptome (RefSeq, dm6) and transposon consensuses (from RepBase) using kallisto
Differential expression analysis was done with sleuth using the gene analysis option
The average TPM between three biological replicas in knockdown versus control were calculated for fold changes in gene expression
Assembly: dm6
Supplementary files format and content: a plaintext file of the abundance estimates using kallisto

source_name: adult fly ovaries

extract_protocol:
Total RNA was extracted from fly ovaries using TRIzol reagent, and ribosomal RNA was depleted with the Zymo-Seq RiboFree Total RNA Library Kit (Zymo Research, #R3000).
RNA-seq libraries were made using the NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEB, #E7760) according to the manufacturer’s instructions.

treatment_protocol: Flies were fed with yeast for 1-2 days prior to dissection

value: adult fly ovaries

value: MT-Gal4 driven whiteKD


title: MT-Gal4 driven whiteKD RNA-seq biological replicate 2


title: D9

description:
Sixth sample of B lymphocytes of MS patient, targeted scRNAseq, 20 µl input cDNA, 15 PCR cycles
CCL5, CD38, ICOSLG, S100A11, TREX1 mRNA
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics)

value: peripheral blood

value: B lymphocytes


title: WT_IP_BEND3_rep2

extract_protocol:
Reverse cross-linked DNA was purified by ChIP DNA Clean&Concentrator kit (Zymo Research).
Libraries were prepared with KAPA HyperPrep kit (Roche), following the manufacturer’s instructions.

value: mouse embryonic stem cells

value: BEND3 (Abcam ab220896)


title: MT-Gal4 driven whiteKD RNA-seq biological replicate 1


title: MT-Gal4 driven BonusKD RNA-seq biological replicate 3

value: MT-Gal4 driven BonusKD


title: WT_input_rep2

value: WT


title: WT_IP_BEND3_rep1


title: D8

description:
Sixth sample of B lymphocytes of MS patient, targeted scRNAseq, 10 µl input cDNA, 15 PCR cycles
CCL5, CD38, ICOSLG, S100A11, TREX1 mRNA
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics)


title: D7

description:
Sixth sample of B lymphocytes of MS patient, targeted scRNAseq, 5 µl input cDNA, 15 PCR cycles
CCL5, CD38, ICOSLG, S100A11, TREX1 mRNA
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics)


title: MT-Gal4 driven BonusKD RNA-seq biological replicate 2


title: WT_input_rep1


title: MT-Gal4 driven BonusKD RNA-seq biological replicate 1


title: V5-BEND3_Bend3KO_IP_V5_rep2

value: Bend3 KO + V5-BEND3

value: V5 (Invitrogen #R960-25)


title: WT-N2B27-Day0

value: 46C mESCs

value: embryonic stem cells

value: proliferating


title: D6

description:
Fifth sample of B lymphocytes of MS patient, targeted scRNAseq, 20 µl input cDNA, 15 PCR cycles
CCL5, CD38, ICOSLG, S100A11, TREX1 mRNA
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics)


title: siPDHA1 NT input H3K27ac ChIP-seq biol rep 1

value: primary cells

value: Human Umbilical Vein Endohtelial Cell (HUVEC)


title: siPDHA1 TNFa input H3K27ac ChIP-seq biol rep 1

value: TNFa treatment


title: D1_sequencingrepliates

description:
Fourth sample of B lymphocytes of MS patient, targeted scRNAseq, 5 µl input cDNA, 15 PCR cycles, downsampled for sequencing replicates
CCL5, CD38, ICOSLG, S100A11, TREX1 mRNA
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics)


title: siPDHA1 NT H3K27ac ChIP-seq biol rep 3

description:
ChIP-seq for human H3K27ac
annotatedpeaks_WOA_h3k27ac_chip_huvec_normalized.xlsx
annotatedsuperEnhancers_WOA_h3k27ac_chip_huvec_normalized.xlsx
annotatedtypicalenhancers_WOA_h3k27ac_chip_huvec.xlsx
poolD_typicalenhancers.bed
groupD_superenhancers.bed

value: control treatment

value: H3K27ac (Active Motif)


title: siCTL NT input H3K27ac ChIP-seq biol rep 1

value: siCTL


title: siCTL TNFa H3K27ac ChIP-seq biol rep 3


title: nos-Gal4 driven Bonus KD H3K9me3-ChIP biological replicate 2

data_processing:
reads were trimmed by removal of the adaptor sequences and to a length of 18-50 bases
reads were aligned to the D. melanogaster genome (dm6) using bowtie1 (v.1.2.2) allowing 2 mismatches and single mapping position.
Genome coverage tracks were generated using deepTools (v.3.5.1) bamCoverage function with 10 bp bin sizes.
Assembly: dm6
Supplementary files format and content: genome browser tracks (bigWig format)

extract_protocol:
Ovaries were crosslinked with 1% formaldehyde in PBS for 10 min, then quenched with Glycine (final concentration 25 mM). Frozen ovaries were dounced in RIPA buffer and then sonicated (Bioruptor sonicator) to a desired fragment sizes of 200–800 bp. The supernatants were first precleared for 2 h at 4°C using Protein G Dynabeads (Invitrogen). Precleared samples were immunoprecipitated with anti-H3K9me3 (abcam, ab8898) antibodies for 3-5 h at 4°C, then 50 μl Protein G Dynabeads were added, and samples were further incubated overnight at 4°C. Beads were washed 3x 10 minutes in LiCL buffer, followed by proteinase K treatment for 2 h at 55°C and then overnight at 65°C. DNA was extracted by standard phenol-chloroform extraction.
ChIP-seq libraries were prepared using NEBNext Ultra DNA Library Prep Kit Illumina (NEB), PE50

value: fly ovaries

value: nos-Gal4 driven BonusKD

value: anti-H3K9me3 antibody(abcam, ab8898)


title: siCTL TNFa input H3K27ac ChIP-seq biol rep 1


title: siPDHA1 TNFa H3K27ac ChIP-seq biol rep 3


title: D5

description:
Fifth sample of B lymphocytes of MS patient, targeted scRNAseq, 10 µl input cDNA, 15 PCR cycles
CCL5, CD38, ICOSLG, S100A11, TREX1 mRNA
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics)

value: peripheral blood

value: B lymphocytes


title: V5-BEND3_Bend3KO_input_rep2

value: mouse embryonic stem cells


title: siCTL NT H3K27ac ChIP-seq biol rep 3


title: nos-Gal4 driven Bonus KD H3K9me3-ChIP biological replicate 1


title: D4

description:
Fifth sample of B lymphocytes of MS patient, targeted scRNAseq, 5 µl input cDNA, 15 PCR cycles
CCL5, CD38, ICOSLG, S100A11, TREX1 mRNA
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics)


title: siPDHA1 TNFa H3K27ac ChIP-seq biol rep 2

description:
ChIP-seq for human H3K27ac
annotatedpeaks_WOA_h3k27ac_chip_huvec_normalized.xlsx
annotatedsuperEnhancers_WOA_h3k27ac_chip_huvec_normalized.xlsx
annotatedtypicalenhancers_WOA_h3k27ac_chip_huvec.xlsx


title: V5-BEND3_Bend3KO_IP_V5_rep1

value: Bend3 KO + V5-BEND3


title: nos-Gal4 driven control KD H3K9me3-ChIP

value: nos-Gal4 driven control KD


title: V5-BEND3_Bend3KO_input_rep1


title: D3

description:
Fourth sample of B lymphocytes of MS patient, targeted scRNAseq, 20 µl input cDNA, 15 PCR cycles
CCL5, CD38, ICOSLG, S100A11, TREX1 mRNA
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics)


title: siPDHA1 NT H3K27ac ChIP-seq biol rep 2


title: nos-Gal4 driven BonusKD input biological replicate 2


title: Bend3_RNA_KO3

extract_protocol:
Total RNA was extracted from the cells with RNEasy Plus Mini kit (Qiagen), according to the manufacturer’s instructions.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNALibrary Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: Bend3 KO


title: D2

description:
Fourth sample of B lymphocytes of MS patient, targeted scRNAseq, 10 µl input cDNA, 15 PCR cycles
CCL5, CD38, ICOSLG, S100A11, TREX1 mRNA
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics)


title: D1

description:
Fourth sample of B lymphocytes of MS patient, targeted scRNAseq, 5 µl input cDNA, 15 PCR cycles
CCL5, CD38, ICOSLG, S100A11, TREX1 mRNA
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics)


title: nos-Gal4 driven control KD input


title: Bend3_RNA_KO2


title: nos-Gal4 driven BonusKD input biological replicate 1


title: C6

description:
Second sample of B lymphocytes of MS patient, targeted scRNAseq, 10 µl input cDNA, 20 PCR cycles
CCL5, CD38, ICOSLG, S100A11, TREX1 mRNA
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics)


title: Bend3_RNA_KO1


title: C5

description:
Second sample of B lymphocytes of MS patient, targeted scRNAseq, 10 µl input cDNA, 15 PCR cycles
CCL5, CD38, ICOSLG, S100A11, TREX1 mRNA
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics)


title: C4

description:
Second sample of B lymphocytes of MS patient, targeted scRNAseq, 10 µl input cDNA, 10 PCR cycles
CCL5, CD38, ICOSLG, S100A11, TREX1 mRNA
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics)


title: Spleen_mGluR-_Replicate_1

city: Riverside

first: Edward

last: Vizcarra

state: California

address: 900 University Ave

institute: UC Riverside

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: refdata-gex-mm10-2020-A [acquired from 10X genomics]
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Purified from murine brain

extract_protocol:
Brain Mononuclear Cell were purified from Toxoplasma (ME49 strain) infected mice. Needle passaged brain tissue was treated with 3mg DNAse and 100μg collagenase/dispase for 1h at 37°C/ 5%CO2. A 30% Percoll density gradient diluted in cRPMI was used to separate cells from myelin layer. Spleens were homogenized through a 40μm strainer using the blunt end of a 5mL syringe.  The homogenate was washed with cRPMI, and 5ml of cold ACK buffer (Lonza) was added for 5min to lyse red blood cells. A cells were prepared for flow cytometry and cell-sorted on CD3+CD8+mGluR1+mGluR5+ and CD3+CD8+mGluR1-mGluR5- T cells. Single Cell RNA sequencing was performed on sorted populations.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, sorted CD8 T cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Purified from murine brain

value: Murine CD8 T cells


title: Spleen_mGluR+__Replicate_1

description: 10x Genomics


title: BAL neu AM-2

city: ROCHESTER

first: Xiaochen

last: Gao

state: MN

address: 200 first street SW

department: Immunology

institute: Mayo Clinic

data_processing:
Paired-end libraries were sequenced on an DNBSEQ resequencing and PE150. Base-calling was performed using DNBSEQ software. Paired-end RNA-seq reads were aligned to the mouse reference genome (GRCm38/mm10) using RNA-seq spliced read mapper Tophat2 (v2.1.1).
Paired-end RNA-seq reads were aligned to the mouse reference genome (GRCm38/mm10) using Bowtie (v2.3.4). Pre- and post-alignment quality controls, gene level raw read count and normalized read count (i.e. FPKM) were performed using RSeQC package (v2.3.6) with NCBI mouse RefSeq gene model.
Differential expression for each gene between various groups was identified by Cuffdiff. For functional analysis, GSEA was used to identify enriched gene sets, from the hallmark,C5 and C2 databases of MSigDB, having up-regulated and down-regulated genes, using a weighted enrichment statistic and a log2 ratio metric for ranking genes.
Assembly: mm10
Supplementary files format and content: raw read count and normalized read count

source_name: cells

extract_protocol:
Total RNA from in vitro cultured AMs was extracted using Trizol assay, and RNA quality was determined (RIN>7) via Agilent Bioanalyzer
Libraries were prepared according to DNBSEQ resequencing and PE150.

tag: age

value: 8-12 weeks

value: co-cultured AMs with BAL

value: Alveolar macrophages


title: PR8 neu AM-1

value: co-cultured AMs with PR8 neutrophils


title: PR8 neu AM-2


title: siPDHA1 TNFa H3K27ac ChIP-seq biol rep 1

value: primary cells

value: Human Umbilical Vein Endohtelial Cell (HUVEC)

value: TNFa treatment

value: H3K27ac (Active Motif)


title: siCTL NT H3K27ac ChIP-seq biol rep 2

value: siCTL

value: control treatment


title: Brain_mGluR+__Replicate_3

description: 10x Genomics


title: siCTL TNFa H3K27ac ChIP-seq biol rep 2


title: C2

description:
First sample of B lymphocytes of MS patient, targeted scRNAseq, 10 µl input cDNA, 15 PCR cycles
CCL5, CD38, ICOSLG, S100A11, TREX1 mRNA
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics)

value: peripheral blood

value: B lymphocytes


title: BAL neu AM-1


title: Brain_mGluR+__Replicate_2

description: 10x Genomics


title: MS-1_CD8_T2_Standard

description:
CD8+ T lymphocytes of MS patient at T2, scRNAseq
mRNA
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics)

value: CD8+ T lymphocytes


title: AM-2

value: mono-cultured AMs


title: C1

description:
First sample of B lymphocytes of MS patient, targeted scRNAseq, 10 µl input cDNA, 10 PCR cycles
CCL5, CD38, ICOSLG, S100A11, TREX1 mRNA
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics)


title: Brain_mGluR+__Replicate_1

description: 10x Genomics


title: MS-1_CD8_T1_Standard

description:
CD8+ T lymphocytes of MS patient at T1, scRNAseq
mRNA
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics)


title: siCTL NT H3K27ac ChIP-seq biol rep 1


title: siPDHA1 NT H3K27ac ChIP-seq biol rep 1


title: Brain_mGluR-_Replicate_1

description: 10x Genomics


title: siCTL TNFa H3K27ac ChIP-seq biol rep 1


title: SH-SY5Y_6hr_ 500μM_rep2

type: RNA

city: Beijing

first: Piye

last: Niu

state: Beijing

address: You An Men Wai Xi Tou Tiao 10#

department: Department of Occupational and Environmental Health,School of Public Health

institute: Capital Medical University

description: Gene expression after 6hr in 500μM MnCl2 dopaminergic SH-SY5Y cells

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity  >10.0 pmol Cy3/μg cRNA) was fragmented at  60°C for 30 minutes in a reaction volume of 22.5μl containing 1xAgilent fragmentation buffer  and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2xAgilent hybridization buffer was added to the  fragmentation mixture and hybridized to Agilent Human lncRNA（4*180K，Design ID：062918）for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using  default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.1(Agilent). The probes that at least 1 condition out of 2 conditions have flags in “P” were chosen for further data analysis.

source_name: SH-SY5Y, 6hr, 500μM Mncl2, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: SH-SY5Y cell line, purchased from Peking union medical college hospital (Beijing, China), was cultivated in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% (w/v) penicillin/streptomycin.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: Cells were exposed to 500μM MnCl2 for 6h and designated as the Mn-exposed group. The remaining cells cultured for 6h without Mn exposure were regarded as the control group (C). Each group contained three samples as biological replicate.

value: 500μM MnCl2


title: AM-1


title: SH-SY5Y_6hr_ 500μM_rep3

source_name: SH-SY5Y, 6hr, 500μM Mncl2, replicate 3


title: CB15 infected with φCbK - 30' post-infection (replicate #2)

status: Public on Aug 25 2023

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

description:
SCR_411
Infection_RNAseq_CB15genes.csv
Infection_RNAseq_CbKgenes.csv

data_processing:
Paired reads were mapped to CP001340.1 and/or JX100813.1 genome with CLC Genomics Workbench 20.
Read count extraction and normalization were performed using CLC Genomic Workbench
Assembly: CP001340.1 (Caulobacter crescentus); JX100813.1 (φCbK)
Supplementary files format and content: csv

organism: Caulobacter vibrioides CB15

source_name: bacterial cell

growth_protocol: Strains grown at 30°C in PYE

extract_protocol:
Cell pellets were resuspended in 1ml TRIzol, then stored at -80°C. Samples were heated at 65°C for 10 min. 0.2 ml chloroform was mixed into samples and incubated for 5 min. Samples pelleted at 17,000xg for 15 min at 4°C. Aqueous layer transferred to fresh tube. 450 µl isopropanol was added and stored at -80°C overnight. Thawed samples were pelleted at 4°C for 30 min, then supernatant was removed. Pellets were washed in 1 ml 70% ethanol, dried, and resuspended in 100 µl RNase-free H2O. Samples were cleaned up with RNeasy Mini Kit (QIAGEN).
Samples were DNAse treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices. Sequencing was done on a NextSeq2000 giving 2x51bp reads. Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v3.9.3)

treatment_protocol: For infection time course, CB15 at 0.1 OD660 was infected with φCbK at 10 MOI. Infected cells were incubated at 30°C for 90 minutes. For CbK_rgrL overexpression, cultures were induced with 50 µM cumate and harvested at 0.18-0.26 OD660

value: bacterial cell

value: CB15 infected with φCbK at 10 MOI, 30' post-infection


title: CB15 infected with φCbK - 60' post-infection (replicate #2)

description:
SCR_412
Infection_RNAseq_CB15genes.csv
Infection_RNAseq_CbKgenes.csv

value: CB15 infected with φCbK at 10 MOI, 60' post-infection


title: CB15 infected with φCbK - 75' post-infection (replicate #2)

description:
SCR_402
Infection_RNAseq_CB15genes.csv
Infection_RNAseq_CbKgenes.csv

value: CB15 infected with φCbK at 10 MOI, 75' post-infection


title: CB15 infected with φCbK - 45' post-infection (replicate #2)

description:
SCR_401
Infection_RNAseq_CB15genes.csv
Infection_RNAseq_CbKgenes.csv

value: CB15 infected with φCbK at 10 MOI, 45' post-infection


title: CB15 infected with φCbK - 45' post-infection (replicate #3)

description:
SCR_404
Infection_RNAseq_CB15genes.csv
Infection_RNAseq_CbKgenes.csv


title: CB15 infected with φCbK - 90' post-infection (replicate #3)

description:
SCR_417
Infection_RNAseq_CB15genes.csv
Infection_RNAseq_CbKgenes.csv

value: CB15 infected with φCbK at 10 MOI, 90' post-infection


title: CB15 ΔrtrA ΔrtrB ΔcdxA ΔcdxB CbK_tgrL overexpression (replicate #2)

description:
SCR_437
CbK_tgrL_RNAseq.csv

value: {delta}rtrA {delta}rtrB {delta}cdxA {delta}cdxB xylX::pMM020 (pPTM057-CbK_tgrL)

value: Expression induced with 50 µM cumate


title: CB15 infected with φCbK - 60' post-infection (replicate #1)

description:
SCR_408
Infection_RNAseq_CB15genes.csv
Infection_RNAseq_CbKgenes.csv


title: CB15 ΔrtrA ΔrtrB ΔcdxA ΔcdxB empty vector (replicate #2)

description:
SCR_434
CbK_tgrL_RNAseq.csv

value: {delta}rtrA {delta}rtrB {delta}cdxA {delta}cdxB xylX::pPTM057 (EV)


title: CB15 infected with φCbK - 15' post-infection (replicate #3)

description:
SCR_403
Infection_RNAseq_CB15genes.csv
Infection_RNAseq_CbKgenes.csv

value: CB15 infected with φCbK at 10 MOI, 15' post-infection


title: CB15 infected with φCbK - 90' post-infection (replicate #1)

description:
SCR_409
Infection_RNAseq_CB15genes.csv
Infection_RNAseq_CbKgenes.csv


title: CB15 infected with φCbK - 30' post-infection (replicate #1)

description:
SCR_407
Infection_RNAseq_CB15genes.csv
Infection_RNAseq_CbKgenes.csv


title: CB15 infected with φCbK - 15' post-infection (replicate #1)

description:
SCR_397
Infection_RNAseq_CB15genes.csv
Infection_RNAseq_CbKgenes.csv


title: CB15 infected with φCbK - 90' post-infection (replicate #2)

description:
SCR_413
Infection_RNAseq_CB15genes.csv
Infection_RNAseq_CbKgenes.csv


title: CB15 ΔrtrA ΔrtrB ΔcdxA ΔcdxB CbK_tgrL overexpression (replicate #1)

description:
SCR_436
CbK_tgrL_RNAseq.csv


title: CB15 ΔrtrA ΔrtrB ΔcdxA ΔcdxB empty vector (replicate #1)

description:
SCR_433
CbK_tgrL_RNAseq.csv


title: CB15 infected with φCbK - pre-infection (replicate #3)

description:
SCR_414
Infection_RNAseq_CB15genes.csv

value: Pre-infected CB15


title: CB15 infected with φCbK - 45' post-infection (replicate #1)

description:
SCR_398
Infection_RNAseq_CB15genes.csv
Infection_RNAseq_CbKgenes.csv


title: CB15 ΔrtrA ΔrtrB ΔcdxA ΔcdxB CbK_tgrL overexpression (replicate #3)

description:
SCR_438
CbK_tgrL_RNAseq.csv


title: CB15 infected with φCbK - 15' post-infection (replicate #2)

description:
SCR_400
Infection_RNAseq_CB15genes.csv
Infection_RNAseq_CbKgenes.csv


title: CB15 infected with φCbK - 75' post-infection (replicate #1)

description:
SCR_399
Infection_RNAseq_CB15genes.csv
Infection_RNAseq_CbKgenes.csv


title: CB15 infected with φCbK - 60' post-infection (replicate #3)

description:
SCR_416
Infection_RNAseq_CB15genes.csv
Infection_RNAseq_CbKgenes.csv


title: CB15 infected with φCbK - 30' post-infection (replicate #3)

description:
SCR_415
Infection_RNAseq_CB15genes.csv
Infection_RNAseq_CbKgenes.csv


title: CB15 infected with φCbK - 75' post-infection (replicate #3)

description:
SCR_405
Infection_RNAseq_CB15genes.csv
Infection_RNAseq_CbKgenes.csv


title: CB15 ΔrtrA ΔrtrB ΔcdxA ΔcdxB empty vector (replicate #3)

description:
SCR_435
CbK_tgrL_RNAseq.csv


title: SH-SY5Y_6hr_ 500μM_rep1

description: Gene expression after 6hr in 500μM MnCl2 dopaminergic SH-SY5Y cells

source_name: SH-SY5Y, 6hr, 500μM Mncl2, replicate 1


title: SH-SY5Y_6hr_0μM_rep1

description: Gene expression after 6hr in 0 MnCl2 dopaminergic SH-SY5Y cells

source_name: SH-SY5Y, 6hr, 0μM Mncl2, replicate 1

value: control


title: SH-SY5Y_6hr_0μM_rep3

source_name: SH-SY5Y, 6hr, 0μM Mncl2, replicate 3


title: SH-SY5Y_6hr_0μM_rep2

source_name: SH-SY5Y, 6hr, 0μM Mncl2, replicate 2


title: CB15 infected with φCbK - pre-infection (replicate #2)

description:
SCR_410
Infection_RNAseq_CB15genes.csv


title: CbK_TgrL-3xFLAG ChIP-seq output replicate #3

data_processing:
Paired reads were mapped to CP001340.1 genome with CLC Genomics Workbench 20. Non-specific matches were ignored.
PCR duplicates were removed, unpaired reads were removed, and peaks were called with Genrich with significance q<0.05
Assembly: CP001340.1
Supplementary files format and content: encodepeak

growth_protocol: Strains grown at 30°C in PYE supplemented with 2 µg/ml oxytetracycline where appropriate.

extract_protocol:
Crosslinking was induced with 1% formaldehyde and quenched with 0.125 mM glycine. Cells were lysed and DNA was sheared by sonication. Samples were pre-cleared on SureBeads Protein A magnetic beads. 5% of total volume sample was removed as input. Samples were incubated on α-FLAG magnetic beads, then eluted with 100 ng/µl 3xFLAG peptide. Samples were subject to RNase & proteinase K treatment, then purified with the Zymo ChIP DNA clean & concentrator kit.
Sample libraries were prepared using the Illumina DNA Prep kit and IDT 10bp UDI indices, and sequenced on an Illumina NextSeq 2000, producing 2x151bp reads. Demultiplexing, quality control and adapter trimming was performed with bcl-convert (v3.9.3)

value: Induce CbK_tgrL-3xFLAG expression with 50 µM cumate for 6h


title: CB15 infected with φCbK - pre-infection (replicate #1)

description:
SCR_406
Infection_RNAseq_CB15genes.csv


title: CdxB-3xFLAG ChIP-seq output replicate #3

value: Induce cdxB-3xFLAG expression with 50 µM cumate for 6h


title: CdxA-3xFLAG ChIP-seq input replicate #3

value: Induce cdxA-3xFLAG expression with 50 µM cumate for 6h


title: CbK_TgrL-3xFLAG ChIP-seq input replicate #1


title: CdxA-3xFLAG ChIP-seq output replicate #3


title: RtrB-3xFLAG ChIP-seq output replicate #2

value: CB15/pPTM022 (pQF-rtrB-3xFLAG)

value: Induce rtrB-3xFLAG expression with 50 µM cumate for 6h


title: CbK_TgrL-3xFLAG ChIP-seq output replicate #2

value: bacterial cell


title: RtrB-3xFLAG ChIP-seq output replicate #1


title: CdxA-3xFLAG ChIP-seq input replicate #2


title: CdxB-3xFLAG ChIP-seq output replicate #2


title: RtrB-3xFLAG ChIP-seq input replicate #3


title: CdxB-3xFLAG ChIP-seq input replicate #1


title: CdxA-3xFLAG ChIP-seq output replicate #1


title: CdxB-3xFLAG ChIP-seq input replicate #2


title: CbK_TgrL-3xFLAG ChIP-seq input replicate #2


title: CbK_TgrL-3xFLAG ChIP-seq output replicate #1


title: CbK_TgrL-3xFLAG ChIP-seq input replicate #3


title: CdxA-3xFLAG ChIP-seq input replicate #1


title: CdxB-3xFLAG ChIP-seq output replicate #1


title: CdxA-3xFLAG ChIP-seq output replicate #2


title: RtrB-3xFLAG ChIP-seq input replicate #1


title: RtrB-3xFLAG ChIP-seq input replicate #2


title: CdxB-3xFLAG ChIP-seq input replicate #3


title: RtrB-3xFLAG ChIP-seq output replicate #3


title: RtrA-3xFLAG ChIP-seq output replicate #3

value: CB15/pPTM021 (pQF-rtrA-3xFLAG)

value: Induce rtrA-3xFLAG expression with 50 µM cumate for 6h


title: RtrA-3xFLAG ChIP-seq output replicate #2


title: RtrA-3xFLAG ChIP-seq input replicate #3


title: RtrA-3xFLAG ChIP-seq output replicate #1


title: SG32 PDX dBET6 vehicle treated 2

city: London

first: Amanda

last: Swain

state: London

address: 237 Fulham Road, 3n17

country: United Kingdom

institute: The Institute of Cancer Research

data_processing:
Read mapping was performed using the STAR alignment software (v.2.7.6a) to Ensembl Human and Mouse reference genomes (Ensembl Human reference genome version GRCh38.92 and Ensembl Mouse reference genome version GRCm38.83)
Once the reads were mapped, XenofilteR R package was used to remove mouse reads from human alignments.
After the filtering, HTSeq-count (HTSeq v2.0.2) was used to count the number of reads mapping unambiguously to genomic features in each sample.
Assembly: Ensembl Human reference genome version GRCh38.92
Supplementary files format and content: tab deliminated text files; normalised counts from DESeq in excel format

source_name: Adenoid cystic carcinoma PDX

growth_protocol: ACC sample SG32 single cells were injected subcutaneously into the flank of NSG mice.

extract_protocol:
Snap frozen tissue was homogenised in Trizol using the Precellys cyrolysis system. The aqueous phase was isolated and transferred to a Qiagen Mini kit column following which kit protocol was followed. At least 500ng of RNA was used for library prep.
RNA libraries for RNA-seq were prepared usingUltra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer's protocols.

treatment_protocol: Once tumours reached 100-200mm3, animals were allocated to receive either 5 mg/kg of dBET6 or vehicle, twice daily by IP injection for at least 4 days.

value: Adenoid cystic carcinoma PDX

value: vehicle


title: SG32 PDX dBET6 treated 3

value: 5 mg/kg dBET6


title: SG32 PDX dBET6 treated 2


title: SG32 PDX dBET6 vehicle treated 1


title: SG32 PDX dBET6 vehicle treated 3


title: SG32 PDX dBET6 treated 1


title: RtrA-3xFLAG ChIP-seq input replicate #1


title: RtrA-3xFLAG ChIP-seq input replicate #2


title: BXD99_HFD

city: Lausanne

first: Xiaoxu

last: Li

address: Station 15 - CH

country: Switzerland

institute: EPFL

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD99 mice fed on high fat diet

hyb_protocol: Labeled cDNA was hybridized on an Affymetrix Clariom S Assay microarray platform (GPL23038) in ~16 hours of incubation, then washed and stained using an Affymetrix 450 Fluidics Station according to Affymetrix protocols.

scan_protocol: Arrays were scanned on Affymetrix GSC3000 7G Scanner.

data_processing: Intensities were processed using the apt-probeset-summarize script from the Array Power Tool suite (version 2.11.3, https://downloads.thermofisher.com/APT/APT_2.11.3/apt_2.11.3_linux_64_bit_x86_binaries.zip) with the gc-sst-rma-sketch standard method. Data processing code deposited at https://doi.org/10.5281/zenodo.4899683.

label: biotin

source_name: proximal colon, chow diet

label_protocol: 100ng of total RNA was amplified using the Ambion® WT Expression Kit from life technologies (part number 4411974) and 5,500ng of cDNA was fragmented and labeled using the Affymetrix WT terminal labeling kit (part number 900671) all following manufacturers protocols

growth_protocol: In groups of 3-5 animals from same strain and under same diet, in isolator cages with individual air filtration (500 cm2, GM500, Tecniplast) and provided water ad libitum

extract_protocol: A ~1 cm portion of the proximal half part of the colon was excised following euthanasia and immediately stored in liquid nitrogen. Total RNA was extracted using trizol. RNA concentration was assessed using a Nanodrop and RNA integrity was assessed using a Bioanalyzer. RNA extracts from approximately 5 animals of the same strain fed the same diet, were pooled at equal mass concentration and cleaned up using the Qiagen RNEasy kit.

treatment_protocol: Mice were fed CD ad libitum until 8 weeks of age. From 8 weeks to 29 weeks, half of the cohort was fed ad libitum HFD and the rest continued to be fed a CD (Fig.1 A). CD composition: 6% kCal fat, 20% kCal protein and 74% kCal of carbohydrates (Harlan, 2018, Indianapolis, IN, USA). HFD composition: 60% kCal fat, 20% kCal protein and 20% kCal of carbohydrates (Harlan, 06414, Indianapolis, IN, USA).

value: 29 weeks

tag: gender

value: Male

value: Proximal colon

value: HFD

value: high fat diet

value: Mice were fed a chow diet (CD) ad libitum until 8 weeks of age. From 8 weeks until heuthanasia, mice were then fed a high-fat diet (HFD) ad libitum.

value: fat:60% kCal, protein:20% kCal

value: Harlan, 06414, Indianapolis, IN, USA


title: BXD65a_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD65a mice fed on high fat diet


title: BXD89_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD89 mice fed on high fat diet


title: BXD83_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD83 mice fed on high fat diet


title: BXD79_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD79 mice fed on high fat diet


title: BXD75_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD75 mice fed on high fat diet


title: BXD73a_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD73a mice fed on high fat diet


title: BXD98_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD98 mice fed on high fat diet


title: BXD81_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD81 mice fed on high fat diet


title: BXD73b_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD73b mice fed on high fat diet


title: BXD87_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD87 mice fed on high fat diet


title: BXD85_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD85 mice fed on high fat diet


title: BXD48a_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD48a mice fed on high fat diet


title: BXD84_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD84 mice fed on high fat diet


title: BXD70_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD70 mice fed on high fat diet


title: BXD69_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD69 mice fed on high fat diet


title: BXD73_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD73 mice fed on high fat diet


title: BXD90_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD90 mice fed on high fat diet


title: BXD101_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD101 mice fed on high fat diet


title: BXD95_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD95 mice fed on high fat diet


title: BXD64_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD64 mice fed on high fat diet


title: BXD65_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD65 mice fed on high fat diet


title: BXD63_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD63 mice fed on high fat diet


title: BXD62_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD62 mice fed on high fat diet


title: BXD66_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD66 mice fed on high fat diet


title: BXD61_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD61 mice fed on high fat diet


title: BXD71_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD71 mice fed on high fat diet


title: BXD67_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD67 mice fed on high fat diet


title: BXD50_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD50 mice fed on high fat diet


title: BXD68_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD68 mice fed on high fat diet


title: BXD49_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD49 mice fed on high fat diet


title: BXD55_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD55 mice fed on high fat diet


title: BXD56_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD56 mice fed on high fat diet


title: BXD60_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD60 mice fed on high fat diet


title: BXD45_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD45 mice fed on high fat diet


title: BXD32_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD32 mice fed on high fat diet


title: BXD34_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD34 mice fed on high fat diet


title: BXD44_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD44 mice fed on high fat diet


title: BXD16_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD16 mice fed on high fat diet


title: BXD51_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD51 mice fed on high fat diet


title: BXD40_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD40 mice fed on high fat diet


title: BXD43_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD43 mice fed on high fat diet


title: BXD12_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD12 mice fed on high fat diet


title: BXD27_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD27 mice fed on high fat diet


title: BXD1_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD1 mice fed on high fat diet


title: C57BL.6J_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male C57BL/6J mice fed on high fat diet


title: BXD99_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD99 mice fed on chow diet

value: CD

value: chow diet

value: Mice were fed a chow diet (CD) ad libitum through their entire life.

value: fat:6% kCal, protein:20% kCal, carbohydrates:74% kCal

value: Harlan, 2018, Indianapolis, IN, USA


title: DBA.2J_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male DBA/2J mice fed on high fat diet


title: BXD65a_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD65a mice fed on chow diet


title: BXD6_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD6 mice fed on high fat diet


title: BXD101_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD101 mice fed on chow diet


title: BXD8_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD8 mice fed on high fat diet


title: BXD98_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD98 mice fed on chow diet


title: BXD95_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD95 mice fed on chow diet


title: BXD90_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD90 mice fed on chow diet


title: BXD65b_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD65b mice fed on chow diet


title: BXD83_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD83 mice fed on chow diet


title: BXD89_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD89 mice fed on chow diet


title: BXD73_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD73 mice fed on chow diet


title: BXD73b_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD73b mice fed on chow diet


title: BXD73a_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD73a mice fed on chow diet


title: BXD81_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD81 mice fed on chow diet


title: BXD87_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD87 mice fed on chow diet


title: BXD65_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD65 mice fed on chow diet


title: BXD71_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD71 mice fed on chow diet


title: BXD63_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD63 mice fed on chow diet


title: BXD84_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD84 mice fed on chow diet


title: BXD69_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD69 mice fed on chow diet


title: BXD85_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD85 mice fed on chow diet


title: BXD64_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD64 mice fed on chow diet


title: BXD79_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD79 mice fed on chow diet


title: BXD67_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD67 mice fed on chow diet


title: BXD66_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD66 mice fed on chow diet


title: BXD61_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD61 mice fed on chow diet


title: BXD62_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD62 mice fed on chow diet


title: BXD55_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD55 mice fed on chow diet


title: BXD49_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD49 mice fed on chow diet


title: BXD68_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD68 mice fed on chow diet


title: BXD56_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD56 mice fed on chow diet


title: BXD60_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD60 mice fed on chow diet


title: BXD44_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD44 mice fed on chow diet


title: BXD45_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD45 mice fed on chow diet


title: BXD43_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD43 mice fed on chow diet


title: BXD32_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD32 mice fed on chow diet


title: BXD75_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD75 mice fed on chow diet


title: BXD34_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD34 mice fed on chow diet


title: BXD27_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD27 mice fed on chow diet


title: ID_2_biol rep 2

city: Boston

first: Bidisha

last: Mitra

state: MA

address: 181 Longwood Avenue, 8th floor

department: Medicine

institute: Brigham and Women's Hospital

description: ID_2_biol rep 2

data_processing:
Adaptor-trimmed Illumina reads for each individual library were mapped back to the human GRCh37.83 transcriptome assembly using STAR v2.5.2b
featureCounts v1.5.1 was used to estimate the number of reads mapped to each contig. Only transcripts with at least 5 cumulative mapping counts were used in this analysis.
DESeq2 v1.14.1 was used to evaluate gene differential expression (DE)
Each DE analysis was composed of a pairwise comparison between experimental (induced) group and the control (uninduced) group. Differentially expressed genes were identified after a correction for false discovery rate (FDR 0.05).
Assembly: GRCh37.83
Supplementary files format and content: Raw files in fastq.gz format
Supplementary files format and content: Tab-delimited text files with normalized counts of genes also provided.

growth_protocol: Cells cultured in GIBCO RPMI 1640 medium (Life Technologies) with 10% fetal bovine serum (FBS) and penicillin-streptomycin in a humidified chamber at 37 degrees Celcius with 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (#74106, Qiagen) as per manufacturer's protocol. An in-column DNA digestion step was included to remove any residual genomic DNA contamination.
To construct RNA-seq libraries, 1ug total RNA was used for polyA mRNA-selection using NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs, Inc.  Ipswich, MA), followed by library construction via NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (#E7765, New England Biolabs, Inc., Ipswich, MA).

treatment_protocol: GM12878 LCL were transduced with lentiviruses expressing doxycycline-inducible vector bearing respective LMP1 (wildtype, TES1mutant and TES2mutant) transgenes. Transduced cells were subjected to 100ug/ml hygromycin(400052, Millipore) selection for 15 days post transduction before confirming dox-induced LMP1 expression in respective stable cell lines (maintained with 25ug/ml hygromycine). Stable cell lines were then transduced with lentiviruses expressing control or LMP1 sgRNA. Transduced cells were subjected to 3ug/ml puromycin(#A1113803, Thermo Fisher) selection for 3 days post transduction. Prior to puromycin selection, the stable cell lines are concomitantly treated with 400ng/ml of  Doxycycline (Sigma #D9891) to express LMP1 from the transgeneto rescue from LMP1 depletion. Cells are collected for RNA extraction day 3 post puromycin selection.

value: Lymphoblastoid

value: TES2mutant LMP1

value: Doxycycline


title: BXD40_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD40 mice fed on chow diet


title: ID_1_biol rep 1

description: ID_1_biol rep 1


title: WT_2_biol rep 2

description: WT_2_biol rep 2

value: Wildtype LMP1


title: BXD8_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD8 mice fed on chow diet

value: 29 weeks


title: BXD2_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD2 mice fed on chow diet

value: Male


title: WT_1_biol rep 1

description: WT_1_biol rep 1


title: PQ_1_biol rep 1

description: PQ_1_biol rep 1

value: TES1mutant LMP1


title: BXD11_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD11 mice fed on chow diet

value: Proximal colon


title: Sorted Full 50 Dextramer Pool Stained, CD3+CD8+ Dextramer+ Pool (n = 50 dextramers), rep2, scTCR-seq

city: Tarrytown

first: Lili

last: Blumenberg

state: NY

address: 777 Old Saw Mill River Road

department: VI Next

institute: Regeneron Pharmaceuticals

description:
dataset6.1263590_2.TCR
scTCRseq
10x Chromium Controller + Illumina Nextseq
dataset6.cd3-cd8.metadata.csv
dataset6.cd3-cd8-dex.metadata.csv

data_processing:
Run through cellranger 2.0
Genomic privacy protection via bamboozle 0.5.0 to mask non-reference sequences
Further processing was done with Seurat 4.0.4 and scanpy 1.9.1 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis, marker gene identification, TCR clonal expansion analysis).
Assembly: GRCh38.84
Supplementary files format and content: csv files are normalized counts of features vs cell for each data type and each experiment
Supplementary files format and content: fasta and annotations files describe TCRs sequenced from individual cells in each experiment
Library strategy: scTCR-seq

source_name: PBMC

extract_protocol:
10x Genomics Chromium Single Cell 5’ V(D)J v1.0
10x Genomics Chromium Single Cell 5’ Gene Expression with V(D)J v1.0

value: T cells

value: FACS enriched pooled dextramer+ CD8+ T cells from CD8+ T cells pre-expanded with experimental peptides for 7 days

tag: fraction

value: TCR RNA


title: BXD12_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD12 mice fed on chow diet


title: BXD51_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD51 mice fed on chow diet


title: BXD1_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD1 mice fed on chow diet


title: Sorted Full 50 Dextramer Pool Stained, CD3+CD8+ Dextramer+ Pool (n = 50 dextramers), rep1, scTCR-seq

description:
dataset6.1263590_1.TCR
scTCRseq
10x Chromium Controller + Illumina Nextseq
dataset6.cd3-cd8.metadata.csv
dataset6.cd3-cd8-dex.metadata.csv


title: Full 50 Dextramer Pool Stained, CD3+CD8+ T Cells, TCR Repertoire Control, scTCR-seq

description:
dataset6.1263589_1.TCR
scTCRseq
10x Chromium Controller + Illumina Nextseq
dataset6.cd3-cd8.metadata.csv
dataset6.cd3-cd8-dex.metadata.csv

value: FACS enriched CD8+ T cells from CD8+ T cells pre-expanded with experimental peptides for 7 days


title: BXD6_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD6 mice fed on chow diet

value: CD


title: BXD16_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD16 mice fed on chow diet

value: chow diet


title: Sorted CD3+CD8+41BB+, scTCR-seq

description:
dataset5.1213856_1.TCR
scTCRseq
10x Chromium Controller + Illumina Nextseq
dataset5.cd8.metadata.csv
dataset5.cd8.41bb.metadata.csv

value: FACS enriched CD137/4-1BB+ CD8+ T cells restimulated with peptide for 24 hrs


title: Sorted CD3+CD8+, scTCR-seq

description:
dataset5.1213855_1.TCR
scTCRseq
10x Chromium Controller + Illumina Nextseq
dataset5.cd8.metadata.csv
dataset5.cd8.41bb.metadata.csv

value: FACS enriched CD8+ T cells from peptide pre-expanded PBMC


title: Pre-Expanded MART1 Cells, overnight re-stimulated CD8+ 41BB+ sorted (pooled n = 12, 2 HTOs each), scTCR-seq

description:
dataset4.1294856_1.TCR
scTCRseq
10x Chromium Controller + Illumina Nextseq
dataset4.metadata.csv

value: FACS enriched CD137/4-1BB+ CD8+ T cells from MART1 pre-expanded PBMC that were restimulated with HLA-A02:01 MART1 peptides for 24 hrs


title: Pre-Expanded CMVpp65 Cells, overnight re-stimulated CD8+ 41BB+ sorted (pooled n = 13, 2 HTOs each), scTCR-seq

description:
dataset4.1294855_1.TCR
scTCRseq
10x Chromium Controller + Illumina Nextseq
dataset4.metadata.csv

value: FACS enriched CD137/4-1BB+ CD8+ T cells from CMV pp65 pre-expanded PBMC that were restimulated with HLA-A02:01 CMV pp65 peptides for 24 hrs


title: Pre-Expanded MART1 Cells, CD8+ MART1+ Dextramer sorted (TCR repertoire control), rep2, scTCR-seq

description:
dataset4.1294854_2.TCR
scTCRseq
10x Chromium Controller + Illumina Nextseq
dataset4.metadata.csv

value: FACS enriched MART1-HLA-A02:01dextramer+ CD8+ T cells from MART1 peptide pre-expanded PBMC


title: PQ_2_biol rep 2

description: PQ_2_biol rep 2

value: Lymphoblastoid

value: Doxycycline


title: DBA.2J_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male DBA/2J mice fed on chow diet

value: 29 weeks

value: Mice were fed a chow diet (CD) ad libitum through their entire life.

value: fat:6% kCal, protein:20% kCal, carbohydrates:74% kCal

value: Harlan, 2018, Indianapolis, IN, USA


title: Pre-Expanded CMVpp65 Cells, CD8+ CMVpp65+ Dextramer sorted (TCR repertoire control), rep2, scTCR-seq

description:
dataset4.1294853_2.TCR
scTCRseq
10x Chromium Controller + Illumina Nextseq
dataset4.metadata.csv

value: T cells

value: FACS enriched CMV pp65-HLA-A02:01dextramer+ CD8+ T cells from CMV pp65 peptide pre-expanded PBMC


title: Pre-Expanded CMVpp65 Cells, CD8+ CMVpp65+ Dextramer sorted (TCR repertoire control), rep1, scTCR-seq

description:
dataset4.1294853_1.TCR
scTCRseq
10x Chromium Controller + Illumina Nextseq
dataset4.metadata.csv

value: TCR RNA


title: Pre-Expanded MART1 Cells, CD8+ MART1+ Dextramer sorted (TCR repertoire control), rep1, scTCR-seq

description:
dataset4.1294854_1.TCR
scTCRseq
10x Chromium Controller + Illumina Nextseq
dataset4.metadata.csv


title: C57BL.6J_CD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male C57BL/6J mice fed on chow diet

value: Male

value: Proximal colon


title: Pre-expanded CEF pool, hashed, 4-1BB sorted, scTCR-seq

description:
dataset3.1158608_1.TCR
scTCRseq
10x Chromium Controller + Illumina Nextseq
dataset3.metadata.csv

value: FACS enriched CD137/4-1BB+ CD8+ T cells from CEF pre-expanded PBMC that were restimulated with HLA-A02:01 CEF peptides for 24 hrs


title: Total Pre-expanded CD3+ T cells , scTCR-seq

description:
dataset3.1158606_1.TCR
scTCRseq
10x Chromium Controller + Illumina Nextseq
dataset3.metadata.csv

value: FACS enriched CD3+ T cells from peptide pre-expanded PBMC


title: Day 7 Pre-expanded sort CD3+ CD8+ Dextramer pool+, scTCR-seq

description:
dataset2.1236399_1.TCR
scTCRseq
10x Chromium Controller + Illumina Nextseq
dataset2.metadata.csv

value: FACS enriched pooled dextramer+ CD8+ T cells from CD8+ T cells pre-expanded with experimental peptides for 7 days


title: Day 1 sort CD3+, CD8+, scTCR-seq

description:
dataset2.1232516_1.TCR
scTCRseq
10x Chromium Controller + Illumina Nextseq
dataset2.metadata.csv

value: FACS enriched CD8+ T cells from PBMC


title: Pre-expandedMART1 restim CD8+ PD1+ Selection, scTCR-seq

description:
dataset1.1229712_1.TCR
scTCRseq
10x Chromium Controller + Illumina Nextseq
dataset1.metadata.csv

value: FACS enriched CD137/4-1BB+ CD8+ T cells restimulated with HLA-A02:01 MART1 peptide for 24 hrs


title: Day 8 Pre-expanded sort CD3+, CD8+, scTCR-seq

description:
dataset2.1236394_1.TCR
scTCRseq
10x Chromium Controller + Illumina Nextseq
dataset2.metadata.csv

value: FACS enriched CD8+ T cells from CD8+ T cells pre-expanded with experimental peptides and then restimulated with experimental peptides  for 24 hrs


title: Day 1 sort CD3+, CD8+ 41BB+, scTCR-seq

description:
dataset2.1232517_1.TCR
scTCRseq
10x Chromium Controller + Illumina Nextseq
dataset2.metadata.csv

value: FACS enriched CD8+ T cells from PBMC restimulated with  experimental peptides for 24 hrs


title: Pre-expandedCMVpp65 restim CD8+ 41BB+ Selection, scTCR-seq

description:
dataset1.1229708_1.TCR
scTCRseq
10x Chromium Controller + Illumina Nextseq
dataset1.metadata.csv

value: FACS enriched CD137/4-1BB+ CD8+ T cells restimulated with HLA-A02:01 CMV pp65 peptide for 24 hrs


title: Pre-expandedMART1 restim CD8+ 41BB+ Selection, scTCR-seq

description:
dataset1.1229711_1.TCR
scTCRseq
10x Chromium Controller + Illumina Nextseq
dataset1.metadata.csv

value: FACS enriched PD-1+ CD8+ T cells  restimulated with HLA-A02:01 MART1 peptide for 24 hrs


title: Sorted Full 50 Dextramer Pool Stained, CD3+CD8+ Dextramer+ Pool (n = 50 dextramers), rep2, scRNA-seq

description:
dataset6.1263590_2
scRNAseq + barcoding
10x Chromium Controller + Illumina Nextseq
dataset6.cd3-cd8.metadata.csv
dataset6.cd3-cd8-dex.metadata.csv
dataset6.cd3-cd8.TPM.csv
dataset6.cd3-cd8-dex.TPM.csv
dataset6.cd3-cd8.ADT.csv
dataset6.cd3-cd8-dex.ADT.csv

data_processing:
Run through cellranger 2.0
Genomic privacy protection via bamboozle 0.5.0 to mask non-reference sequences
Further processing was done with Seurat 4.0.4 and scanpy 1.9.1 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis, marker gene identification, TCR clonal expansion analysis).
Assembly: GRCh38.84
Supplementary files format and content: csv files are normalized counts of features vs cell for each data type and each experiment
Supplementary files format and content: fasta and annotations files describe TCRs sequenced from individual cells in each experiment

extract_protocol:
10x Genomics Chromium Single Cell 5’ Gene Expression v1.0 with Feature Barcoding
10x Genomics Chromium Single Cell 5’ Gene Expression with V(D)J v1.0

value: RNA


title: Day 7 Pre-expanded sort CD3+ CD8+ , scTCR-seq

description:
dataset2.1236398_1.TCR
scTCRseq
10x Chromium Controller + Illumina Nextseq
dataset2.metadata.csv

value: FACS enriched CD8+ T cells from CD8+ T cells pre-expanded with experimental peptides for 7 days


title: Pre-expanded CD8+ CMVpp65+ Multimer Selection, scTCR-seq

description:
dataset1.1229707_1.TCR
scTCRseq
10x Chromium Controller + Illumina Nextseq
dataset1.metadata.csv

value: FACS enriched CMV pp65-HLA-A02:01 dextramer+ CD8+ T cells from CMV pp65 peptide pre-expanded PBMC


title: Pre-expandedCD8+ MART1+ Multimer Selection, scTCR-seq

description:
dataset1.1229710_1.TCR
scTCRseq
10x Chromium Controller + Illumina Nextseq
dataset1.metadata.csv

value: T cells

value: FACS enriched MART1 HLA-A02:01dextramer+ CD8+ T cells from MART1 peptide pre-expanded PBMC


title: Sorted Full 50 Dextramer Pool Stained, CD3+CD8+ Dextramer+ Pool (n = 50 dextramers), rep1, scRNA-seq

description:
dataset6.1263590_1
scRNAseq + barcoding
10x Chromium Controller + Illumina Nextseq
dataset6.cd3-cd8.metadata.csv
dataset6.cd3-cd8-dex.metadata.csv
dataset6.cd3-cd8.TPM.csv
dataset6.cd3-cd8-dex.TPM.csv
dataset6.cd3-cd8.ADT.csv
dataset6.cd3-cd8-dex.ADT.csv


title: Sorted CD3+CD8+41BB+, scRNA-seq

description:
dataset5.1213856_1
scRNAseq + barcoding
10x Chromium Controller + Illumina Nextseq
dataset5.cd8.metadata.csv
dataset5.cd8.41bb.metadata.csv
dataset5.cd8.TPM.csv
dataset5.cd8.41bb.TPM.csv
dataset5.cd8.HTO_norm.csv
dataset5.cd8.41bb.HTO_norm.csv

value: FACS enriched CD137/4-1BB+ CD8+ T cells restimulated with peptide for 24 hrs


title: Pre-expandedCD8+ Tc Total, scTCR-seq

description:
dataset1.1229706_1.TCR
scTCRseq
10x Chromium Controller + Illumina Nextseq
dataset1.metadata.csv

value: FACS enriched CD8+ T cells from peptide pre-expanded PBMC

value: TCR RNA


title: Pre-expandedCMVpp65 restim CD8+ PD1+ Selection, scTCR-seq

description:
dataset1.1229709_1.TCR
scTCRseq
10x Chromium Controller + Illumina Nextseq
dataset1.metadata.csv

value: FACS enriched PD-1+ CD8+ T cells restimulated with HLA-A02:01 CMV pp65 peptide for 24 hrs


title: Full 50 Dextramer Pool Stained, CD3+CD8+ T Cells, TCR Repertoire Control, scRNA-seq

description:
dataset6.1263589_1
scRNAseq + barcoding
10x Chromium Controller + Illumina Nextseq
dataset6.cd3-cd8.metadata.csv
dataset6.cd3-cd8-dex.metadata.csv
dataset6.cd3-cd8.TPM.csv
dataset6.cd3-cd8-dex.TPM.csv
dataset6.cd3-cd8.ADT.csv
dataset6.cd3-cd8-dex.ADT.csv


title: Pre-Expanded CMVpp65 Cells, overnight re-stimulated CD8+ 41BB+ sorted (pooled n = 13, 2 HTOs each), scRNA-seq

description:
dataset4.1294855_1
scRNAseq + barcoding
10x Chromium Controller + Illumina Nextseq
dataset4.metadata.csv
dataset4.TPM.csv
dataset4.HTO_norm.csv

value: FACS enriched CD137/4-1BB+ CD8+ T cells from CMV pp65 pre-expanded PBMC that were restimulated with HLA-A02:01 CMV pp65 peptides for 24 hrs


title: Pre-Expanded MART1 Cells, overnight re-stimulated CD8+ 41BB+ sorted (pooled n = 12, 2 HTOs each), scRNA-seq

description:
dataset4.1294856_1
scRNAseq + barcoding
10x Chromium Controller + Illumina Nextseq
dataset4.metadata.csv
dataset4.TPM.csv
dataset4.HTO_norm.csv

value: FACS enriched CD137/4-1BB+ CD8+ T cells from MART1 pre-expanded PBMC that were restimulated with HLA-A02:01 MART1 peptides for 24 hrs


title: Pre-Expanded MART1 Cells, CD8+ MART1+ Dextramer sorted (TCR repertoire control), rep2, scRNA-seq

description:
dataset4.1294854_2
scRNAseq + barcoding
10x Chromium Controller + Illumina Nextseq
dataset4.metadata.csv
dataset4.TPM.csv
dataset4.HTO_norm.csv

value: FACS enriched MART1-HLA-A02:01dextramer+ CD8+ T cells from MART1 peptide pre-expanded PBMC


title: Sorted CD3+CD8+, scRNA-seq

description:
dataset5.1213855_1
scRNAseq + barcoding
10x Chromium Controller + Illumina Nextseq
dataset5.cd8.metadata.csv
dataset5.cd8.41bb.metadata.csv
dataset5.cd8.TPM.csv
dataset5.cd8.41bb.TPM.csv
dataset5.cd8.HTO_norm.csv
dataset5.cd8.41bb.HTO_norm.csv


title: Pre-Expanded MART1 Cells, CD8+ MART1+ Dextramer sorted (TCR repertoire control), rep1, scRNA-seq

description:
dataset4.1294854_1
scRNAseq + barcoding
10x Chromium Controller + Illumina Nextseq
dataset4.metadata.csv
dataset4.TPM.csv
dataset4.HTO_norm.csv


title: Pre-expanded CEF pool, hashed, 4-1BB sorted, scRNA-seq

description:
dataset3.1158608_1
scRNAseq + barcoding
10x Chromium Controller + Illumina Nextseq
dataset3.metadata.csv
dataset3.TPM.csv

value: FACS enriched CD137/4-1BB+ CD8+ T cells from CEF pre-expanded PBMC that were restimulated with HLA-A02:01 CEF peptides for 24 hrs


title: Day8  Pre-expandedsort CD3+, CD8+ 41BB+, scTCR-seq

description:
dataset2.1236395_1.TCR
scTCRseq
10x Chromium Controller + Illumina Nextseq
dataset2.metadata.csv

value: FACS enriched CD137/4-1BB+ CD8+ T cells restimulated with experimental peptides  for 24 hrs


title: Total Pre-expanded CD3+ T cells , scRNA-seq

description:
dataset3.1158606_1
scRNAseq + barcoding
10x Chromium Controller + Illumina Nextseq
dataset3.metadata.csv
dataset3.TPM.csv

value: FACS enriched CD3+ T cells from peptide pre-expanded PBMC


title: Pre-Expanded CMVpp65 Cells, CD8+ CMVpp65+ Dextramer sorted (TCR repertoire control), rep1, scRNA-seq

description:
dataset4.1294853_1
scRNAseq + barcoding
10x Chromium Controller + Illumina Nextseq
dataset4.metadata.csv
dataset4.TPM.csv
dataset4.HTO_norm.csv

value: FACS enriched CMV pp65-HLA-A02:01dextramer+ CD8+ T cells from CMV pp65 peptide pre-expanded PBMC


title: Day 7 Pre-expanded sort CD3+ CD8+ Dextramer pool+, scRNA-seq

description:
dataset2.1236399_1
scRNAseq + barcoding
10x Chromium Controller + Illumina Nextseq
dataset2.metadata.csv
dataset2.TPM.csv
dataset2.HTO_norm.csv
dataset2.ADT.csv

value: FACS enriched pooled dextramer+ CD8+ T cells from CD8+ T cells pre-expanded with experimental peptides for 7 days


title: Day 7 Pre-expanded sort CD3+ CD8+ , scRNA-seq

description:
dataset2.1236398_1
scRNAseq + barcoding
10x Chromium Controller + Illumina Nextseq
dataset2.metadata.csv
dataset2.TPM.csv
dataset2.HTO_norm.csv
dataset2.ADT.csv

value: RNA


title: Day8  Pre-expandedsort CD3+, CD8+ 41BB+, scRNA-seq

description:
dataset2.1236395_1
scRNAseq + barcoding
10x Chromium Controller + Illumina Nextseq
dataset2.metadata.csv
dataset2.TPM.csv
dataset2.HTO_norm.csv
dataset2.ADT.csv


title: Pre-expandedMART1 restim CD8+ PD1+ Selection, scRNA-seq

description:
dataset1.1229712_1
scRNAseq + barcoding
10x Chromium Controller + Illumina Nextseq
dataset1.metadata.csv
dataset1.TPM.csv

value: FACS enriched CD137/4-1BB+ CD8+ T cells restimulated with HLA-A02:01 MART1 peptide for 24 hrs


title: Pre-expandedCD8+ MART1+ Multimer Selection, scRNA-seq

description:
dataset1.1229710_1
scRNAseq + barcoding
10x Chromium Controller + Illumina Nextseq
dataset1.metadata.csv
dataset1.TPM.csv


title: Day 1 sort CD3+, CD8+, scRNA-seq

description:
dataset2.1232516_1
scRNAseq + barcoding
10x Chromium Controller + Illumina Nextseq
dataset2.metadata.csv
dataset2.TPM.csv
dataset2.HTO_norm.csv
dataset2.ADT.csv

value: FACS enriched CD8+ T cells from PBMC


title: Day 1 sort CD3+, CD8+ 41BB+, scRNA-seq

description:
dataset2.1232517_1
scRNAseq + barcoding
10x Chromium Controller + Illumina Nextseq
dataset2.metadata.csv
dataset2.TPM.csv
dataset2.HTO_norm.csv
dataset2.ADT.csv

value: T cells

value: FACS enriched CD8+ T cells from PBMC restimulated with  experimental peptides for 24 hrs


title: Pre-expandedCMVpp65 restim CD8+ 41BB+ Selection, scRNA-seq

description:
dataset1.1229708_1
scRNAseq + barcoding
10x Chromium Controller + Illumina Nextseq
dataset1.metadata.csv
dataset1.TPM.csv

value: FACS enriched CD137/4-1BB+ CD8+ T cells restimulated with HLA-A02:01 CMV pp65 peptide for 24 hrs


title: Pre-expandedCD8+ Tc Total, scRNA-seq

description:
dataset1.1229706_1
scRNAseq + barcoding
10x Chromium Controller + Illumina Nextseq
dataset1.metadata.csv
dataset1.TPM.csv

value: FACS enriched CD8+ T cells from peptide pre-expanded PBMC


title: Pre-expanded CD8+ CMVpp65+ Multimer Selection, scRNA-seq

description:
dataset1.1229707_1
scRNAseq + barcoding
10x Chromium Controller + Illumina Nextseq
dataset1.metadata.csv
dataset1.TPM.csv

value: FACS enriched CMV pp65-HLA-A02:01 dextramer+ CD8+ T cells from CMV pp65 peptide pre-expanded PBMC


title: RUNX1 KO, NYCB73, replicate 1

city: San Francisco

first: Amy

last: Fan

address: 769 25th Ave

department: Pathology

institute: UCSF

data_processing:
read trimming and quality control was performed using trim_galore
Reads were aligned to the GRCh38 reference genome using bowtie2 and the --very-sensitive option
Aligned reads were converted to bam format and sorted using SAMtools, and deduplicated using Picard MarkDuplicates
Reads were subsequently indexed and mitochondrial reads were removed using SAMTools
TagAlign bed files from technical replicate libraries were generated using bedtools, shifted to find ATAC-seq cut sites, and pooled
Peaks were called using MACS2 using p-value cut-off of 0.01 and peaks falling within black list regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were removed
Count matrices were generated using the consensus peak set, and the number of reads in each peak were calculated using the CountOverlaps function from the Iranges package in R.
Assembly: hg38
Supplementary files format and content: Count matrix of consensus peaks

source_name: Cord blood

growth_protocol: StemSpan II + 20 ng/mL SCF, TPO, FLT3L, IL-6, 35nM UM-171

extract_protocol:
10,000 cells were washed in FACS buffer at 4°C and spun down. Cell pellets were then resuspended in 50 µL of ATAC-seq resuspension buffer (RSB: 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water) with 0.1% NP40, 0.01% digitonin, and 0.1% Tween-20 and incubated on ice for three minutes. After lysis, 1 mL of ATAC-seq RSB with 0.1% Tween-20 was added and tubes were inverted six times to mix. Isolated nuclei were then spun down.
Supernatant was removed and nuclei were resuspended in 50 µL transposition mix (25µL 2xTD buffer, 2.5 µL Tn5 transposase (100 nM final), 16.5 µL PBS, 0.5 µL 1% digitonin, 0.5 µL 10% Tween-20, and 5 µL nuclease-free water). Transposition reactions were incubated at 37°C for 30 minutes in a thermomixer with shaking at 1000 rpm. Reactions were cleaned up using Qiagen MinElute Reaction Cleanup kits and processed as previously described (Corces, M. R. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat. Methods 14, 959–962 (2017)). All libraries were amplified with a target concentration of 20 μl at 4 nM, which is equivalent to 80 femtomoles of product

value: Cord blood

value: CD34+ hematopoietic stem and progenitor cells

value: RUNX1 KO


title: Pre-Expanded CMVpp65 Cells, CD8+ CMVpp65+ Dextramer sorted (TCR repertoire control), rep2, scRNA-seq

description:
dataset4.1294853_2
scRNAseq + barcoding
10x Chromium Controller + Illumina Nextseq
dataset4.metadata.csv
dataset4.TPM.csv
dataset4.HTO_norm.csv


title: AAVS1 control, NYCB73, replicate 2


title: RUNX1 KO, NYCB38, replicate 1


title: RUNX1 KO, NYCB84, replicate 2


title: RUNX1 KO, NYCB84, replicate 1


title: AAVS1 control, NYCB38, replicate 1


title: AAVS1 control, NYCB73, replicate 1


title: RUNX1 KO, NYCB38, replicate 2


title: Day 8 Pre-expanded sort CD3+, CD8+, scRNA-seq

description:
dataset2.1236394_1
scRNAseq + barcoding
10x Chromium Controller + Illumina Nextseq
dataset2.metadata.csv
dataset2.TPM.csv
dataset2.HTO_norm.csv
dataset2.ADT.csv

value: FACS enriched CD8+ T cells from CD8+ T cells pre-expanded with experimental peptides and then restimulated with experimental peptides  for 24 hrs


title: BXD11_HFD

description: Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD11 mice fed on high fat diet

value: 29 weeks

value: Male

value: Proximal colon

value: HFD

value: high fat diet

value: Mice were fed a chow diet (CD) ad libitum until 8 weeks of age. From 8 weeks until heuthanasia, mice were then fed a high-fat diet (HFD) ad libitum.

value: fat:60% kCal, protein:20% kCal

value: Harlan, 06414, Indianapolis, IN, USA


title: AAVS1 control, NYCB38, replicate 2


title: Pre-expandedMART1 restim CD8+ 41BB+ Selection, scRNA-seq

description:
dataset1.1229711_1
scRNAseq + barcoding
10x Chromium Controller + Illumina Nextseq
dataset1.metadata.csv
dataset1.TPM.csv

value: T cells

value: FACS enriched PD-1+ CD8+ T cells  restimulated with HLA-A02:01 MART1 peptide for 24 hrs

value: RNA


title: Pre-expandedCMVpp65 restim CD8+ PD1+ Selection, scRNA-seq

description:
dataset1.1229709_1
scRNAseq + barcoding
10x Chromium Controller + Illumina Nextseq
dataset1.metadata.csv
dataset1.TPM.csv

value: FACS enriched PD-1+ CD8+ T cells restimulated with HLA-A02:01 CMV pp65 peptide for 24 hrs


title: AAVS1 control, NYCB84, replicate 1


title: RUNX1 KO, NYCB73, replicate 2


title: E18.5_ctrl5_cell184

city: Stockholm

first: Kasra

last: Nikouei

address: Solnav. 9

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description:
SmartSeq2
Munguba_Nikouei_E18.5_counts.txt
Munguba_Nikouei_E18.5_cell_annotation.txt

data_processing:
Fastq files demultiplexed by deindexer (https://github.com/ws6/deindexer) using the Nextera index adapters and the 384-well layout. Individual fastq files were then mapped to the genome assembly using the STAR aligner (Dobin et al. 2013; DOI:10.1093/bioinformatics/bts635) using 2-pass alignment to have improved performance of de novo splice junction reads, filtered for only uniquely mapping reads. The expression values were computed per gene as described in (Ramsköld et al. 2009; DOI: 10.1371/journal.pcbi.1000598 ), using uniquely aligned reads and correcting for the uniquely alignable positions using MULTo (Storvall et al. 2013; DOI: 10.1371/journal.pone.0053822). The count matrix shows the individual counts aligning to each gene per cell.
genome build: mm10
Tab-delimited text format, in which cells make up the columns and genes the rows, with corresponding cell annotation file.

source_name: Neocortex

extract_protocol:
Embryonic day 18.5 (E18.5) pups were extracted after sacrificing SstCre/+::R26R CAG-boosted eGFP (RCE)/+::Sox6fl/± females with plugged pregnancies. The neocortices of the pups were dissected in ice-cold HBSS. Genotyping of the pups were done in parallel by using QuickExtract DNA Solution (Lucigen). The tissue was dissociated into a single cell suspension, as previously described (Muñoz-Manchado et al. 2018; DOI: 10.1016/j.celrep.2018.07.053). Briefly, the tissue was dissociated using the Papain dissociation system (Worthington) following the manufacturer’s instructions. Cell suspension obtained was filtered with 20 μm filter and kept in cold oxygenated Hank's balanced salt solution (HBSS) with 0.2% Bovine Serum Albumin (BSA). EGFP positive but DRAQ7 negative (dead cell marker, Invitrogen) cells were FACS sorted into 384-well plates containing lysis buffer and processed in large accordance with the Smartseq2 protocol (Picelli et al. 2014; DOI: 10.1038/nprot.2014.006).
The libraries were generated according to the Smartseq2 protocol (Picelli et al., 2014; DOI: 10.1038/nprot.2014.006). The single-cell transcriptome data was generated at the Eukaryotic Single-cell Genomics facility at Science for Life Laboratory in Stockholm, Sweden.

value: Neocortex

value: Somatostatin interneuron

value: SstCre::RCE::Sox6 +/+


title: E18.5_ctrl5_cell187


title: E18.5_ctrl5_cell181


title: E18.5_ctrl5_cell188


title: E18.5_ctrl5_cell183


title: E18.5_ctrl5_cell179


title: E18.5_ctrl5_cell190

extract_protocol:
Embryonic day 18.5 (E18.5) pups were extracted after sacrificing SstCre/+::R26R CAG-boosted eGFP (RCE)/+::Sox6fl/± females with plugged pregnancies. The neocortices of the pups were dissected in ice-cold HBSS. Genotyping of the pups were done in parallel by using QuickExtract DNA Solution (Lucigen). The tissue was dissociated into a single cell suspension, as previously described (Muñoz-Manchado et al. 2018; DOI: 10.1016/j.celrep.2018.07.053). Briefly, the tissue was dissociated using the Papain dissociation system (Worthington) following the manufacturer’s instructions. Cell suspension obtained was filtered with 20 μm filter and kept in cold oxygenated Hank's balanced salt solution (HBSS) with 0.2% bovine serum albumin (BSA). EGFP positive but DRAQ7 negative (dead cell marker, Invitrogen) cells were FACS sorted into 384-well plates containing lysis buffer and processed in large accordance with the Smartseq2 protocol (Picelli et al. 2014; DOI: 10.1038/nprot.2014.006).
The libraries were generated according to the Smartseq2 protocol (Picelli et al., 2014; DOI: 10.1038/nprot.2014.006). The single-cell transcriptome data was generated at the Eukaryotic Single-cell Genomics facility at Science for Life Laboratory in Stockholm, Sweden.


title: E18.5_ctrl5_cell189


title: E18.5_ctrl5_cell185


title: E18.5_ctrl5_cell178


title: E18.5_ctrl5_cell182


title: E18.5_ctrl5_cell186


title: E18.5_ctrl5_cell180


title: E18.5_ctrl5_cell177


title: E18.5_ctrl5_cell176


title: E18.5_ctrl5_cell175


title: E18.5_ctrl5_cell172


title: E18.5_ctrl5_cell173


title: E18.5_ctrl5_cell174


title: E18.5_ctrl5_cell171


title: E18.5_ctrl5_cell170


title: E18.5_ctrl5_cell169


title: E18.5_ctrl5_cell168


title: E18.5_ctrl5_cell167


title: E18.5_ctrl5_cell166


title: E18.5_ctrl5_cell165


title: E18.5_ctrl5_cell164


title: E18.5_ctrl5_cell163


title: E18.5_ctrl5_cell162


title: E18.5_ctrl5_cell160


title: E18.5_ctrl5_cell156


title: E18.5_ctrl5_cell148


title: E18.5_ctrl5_cell149


title: E18.5_ctrl5_cell159


title: E18.5_ctrl5_cell157


title: E18.5_ctrl5_cell151


title: E18.5_ctrl5_cell154


title: E18.5_ctrl5_cell146


title: E18.5_ctrl5_cell147


title: E18.5_ctrl5_cell155


title: E18.5_ctrl5_cell161


title: E18.5_ctrl5_cell143