title: DL_248_Sox17_24h_rep1

value: 24 hour post doxycycline


title: JT_334_Gata4_ixen_24hr_rep2

status: Public on Jul 29 2021

type: SRA

city: Bethesda

first: Pedro

middle: P

last: Rocha

state: Maryland

address: 6 Center Drive Building 6B 2B220

department: NICHD

country: USA

institute: National Institutes of Health

library_source: genomic

data_processing:
Library strategy: CUT&RUN
Mapping to genome using bowtie2 with the following options (-N 1 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 -x). Reads that mapped to ENCODE mm10 blacklist regions were removed using Samtools (Li et al., 2009). Piccard (broadinstitute.github.io/picard/) was then used to identify non-duplicated reads. Duplicate reads were removed for libraries generated from blastocysts but kept for all others.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files

molecule: genomic DNA

organism: Mus musculus

source_name: Embryonic stem cell line

growth_protocol: Cells were maintained at a density of 1 million cells per 10cm gelatinized plates at 37ºC x% O2, x% CO2 in 2i media (50% DMEM/F12, 50% Neurobasal, Penicillin-Streptomycin, GlutaMAX, 2-Mercaptoethanol, N2, B27, 0.3nM PD0325901, 0.1nM CHIR9902, and 2x105units/mL LIF).

extract_protocol:
Cells were harvested using accutase and 100,000 cells per replicate, per time point, were subjected to CUT&TAG and CUT&RUN. Blastocysts were fixed in 0.1% PFA and subjected to CUT&RUN by physically transferring the embryos into different CUT&RUN buffers under a dissection microscope.
DNA was issolated using phenol-chloroform extraction. For each sample, double stranded DNA (10µl), Template Preparation D Buffer (2µl), and Template Preparation D Enzyme (1µl) were combined and End Repair and A-tailing was performed in a Thermocycler with a heated lid (22ºC, 25 min; 55ºC, 20 min). Library Synthesis D Buffer (1µl) and Library Synthesis D Enzyme (1µl) were subsequently added, and library synthesis was performed (22ºC, 40min). Immediately after, Library Amplification D Buffer (25µl), Library Amplification D Enzyme (1µl), Nuclease-free water (4µl), and a unique Illumina-compatible indexed primer (5µl) were added. Library amplification was performed using the following cycling conditions: 72ºC for 3 min; 85ºC for 2 min; 98ºC for 2 min (denaturation); 4 cycles of 98ºC for 20 s, 67ºC for 20 s, 72ºC for 10 s (addition of indexes); 14 cycles of 98ºC for 20 s, 72ºC for 10 s (library amplification). Post-PCR clean-up was performed on amplified libraries with a SPRIselect bead 0.6X left/1x right double size selection then washed twice gently in 80% ethanol and eluted in 10-12µl 10 mM Tris pH 8.0. For CUT&TAG, DNA (20µl) was mixed with 5X Q5 reaction buffer (10µl), Q5 polymerase (0.5µl), dNTPs (1µl), nuclease free water (16µl), and an equimolar mixture of an universal i5 and a uniquely barcoded i7 primer (2.5µl) , using different barcodes for each sample. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and hold at 8 °C.

treatment_protocol: Differentiation into primitive endoderm was induced in serum containing ESS media (Knockout DMEM, 15% FBS,1% GlutaMAX, 1% Penicillin-Streptomycin, 1% 2-Mercaptoethanol, 1% Sodium Pyruvate, 1% MEM NEAA, 2x105units/mL LIF) containing doxycycline (1ug/mL) for 2 to 12 hours. For time points greater than 12 hours, mES cells were induced in serum media containing doxycycline for 12 hours and switched to serum media in the absence of doxycycline for the remaining time. Blastocysts were collected from 4-5 weeks old C57BL/6N females six days after PMSG/HCG injections. Blastocysts were used right away to profile E3.5 embryos, after removing the zona pellucida using acid tyrode’s solution. E4.5 embryos were isolated seven days after PMSG/HCG injections, and only blastocysts without any zona pellucida were used. Embryos were manipulated in 1% agar-coated 4-well dishes (ThermoFisher scientific, Nunc 4-Well Dishes for IVF) throughout the protocol.

tag: cell line

tag: cell type

value: Embryonic stem cells

tag: time point

tag: strain

tag: transgene

value: Stem cells have TRE:GATA6-DSREd2

tag: antibody

tag: assay

value: CUT&RUN


title: Gata6_48h_ixen_CR_JT_137_rep1_merged

value: 48 hour post doxycycline


title: JT_333_Gata4_ixen_24hr_rep1


title: Gata6_48h_ixen_CR_JT_138_rep2_merged


title: Gata6_8h_ixen_CR_DL_77_rep1

value: 8 hour post doxycycline


title: Gata6_8h_ixen_CR_DL_78_rep2


title: Gata6_4h_ixen_CR_DL_76_rep2

value: 4 hour post doxycycline


title: Gata6_0h_ixen_CR_DL_12_rep1

value: 0 hour no doxycycline


title: Gata6_2h_ixen_CR_DL_73_rep1

value: 2 hour post doxycycline


title: ATAC_8hr_rep2

data_processing:
The ENCODE ATAC-seq pipeline (github.com/ENCODE-DCC/atac-seq-pipeline) was used to process ATAC-seq and to obtain bigwig files for visualization in IGV and to produce heatmaps or signal profiles using Deeptools.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files

growth_protocol: Cells were maintained at a density of 1 million cells per 10cm gelatinized plates at 37ºC x% O2, x% CO2 in 2i media (50% DMEM/F12, 50% Neurobasal, Penicillin-Streptomycin, GlutaMAX, 2-Mercaptoethanol, N2, B27, 0.3nM PD0325901, 0.1nM CHIR9902, and 2x10^5units/mL LIF).

extract_protocol:
Cells were harvested using accutase and 50,000 cells per replicate, per time point, we subjected to ATAC using the manufacturer's protocol.
Following tagmentation, DNA was purified using the Zymo DNA Clean and Concentrator kit (Zymo, D4033). Libraries were prepared using Q5 polymerase and unique indices were added to each sample. First, gap filling was performed at 720C for 5mins followed by five cycles of 980C, 20secs, 630C, 30secs, and 720C 1min. After initial amplification, tubes were held on ice, while quantitative PCR was run on 1 µl of the pre-amplified library to determine additional number of cycles needed. Libraries were sequenced on HiSeq2500 using PE50.

treatment_protocol: Differentiation into primitive endoderm was induced in serum containing ESS media (Knockout DMEM, 15% FBS,1% GlutaMAX, 1% Penicillin-Streptomycin, 1% 2-Mercaptoethanol, 1% Sodium Pyruvate, 1% MEM NEAA, 2x10^5units/mL LIF) containing doxycycline (1ug/mL) for 2 to 12 hours. For time points greater than 12 hours, mES cells were induced in serum media containing doxycycline for 12 hours and switched to serum media in the absence of doxycycline for the remaining time.


title: Gata6_4h_ixen_CR_DL_75_rep1


title: Gata6_0h_ixen_CR_JT_247_rep2


title: Gata6_2h_ixen_CR_DL_74_rep2


title: ATAC_8hr_rep1


title: ATAC_4hr_rep2


title: ATAC_48hr_rep1


title: ATAC_4hr_rep1


title: ATAC_48hr_rep2


title: DL_249_Sox17_24h_rep2


title: ATAC_2hr_rep2


title: ATAC_2hr_rep1


title: ATAC_24hr_rep2


title: ATAC_24hr_rep1


title: ATAC_16hr_rep2

value: 16 hour post doxycycline


title: ATAC_16hr_rep1


title: ATAC_0hr_rep2


title: ATAC_0hr_rep1


title: Huh751_D10_1

status: Public on Jul 19 2021

city: Minneapolis

first: Shijia

last: Zhu

state: Minnesota

address: 1200 Washington Avenue S Suite #175

department: Department of Laboratory Medicine and Pathology

institute: University of Minnesota Medical School

library_source: transcriptomic

data_processing:
The Illumina TruSeq RNA kit was used for 75nt/single end reads, 4 samples were run per lane using the standard Truseq indices.  Raw cDNA reads are aligned to the hg19 reference with the spliced gap aligner STAR, with count-based quantitation carried out via the Subread package featureCounts at the geneic levels for annotation builds.
Genome_build: hg19
Supplementary_files_format_and_content: txt format; the read count for each gene

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Total RNA from each sample was collected using TRIzol (Invitrogen) and quantified by nanodrop (Thermo Fisher). Only RNA samples with RNA integrity number (RIN) > 9 by Agilent 2100 bioanalyzer (Cat# G2939BA, Agilent Technologies) were used.
RNA-Seq libraries were prepared by using TruSeq kit (Cat# RS-122-2001, Illumina)
NextSeq genome sequencer (Cat# SY-415-1002, Illumina), 75nt, Single-End Read, 4 samples per lane

tag: objective response

value: Huh751 DMSO differentiation Day 10 Replicate 1


title: Huh751_D7_3

value: Huh751 DMSO differentiation Day 7 Replicate 3


title: Huh751_D10_2

value: Huh751 DMSO differentiation Day 10 Replicate 2


title: Huh751_D10_3

value: Huh751 DMSO differentiation Day 10 Replicate 3


title: Huh751_D7_1

value: Huh751 DMSO differentiation Day 7 Replicate 1


title: Huh751_D3_3

value: Huh751 DMSO differentiation Day 3 Replicate 3


title: Huh751_D0_3

value: Huh751 DMSO differentiation Day 0 Replicate 3


title: Huh751_D3_2

value: Huh751 DMSO differentiation Day 3 Replicate 2


title: Huh751_D3_1

value: Huh751 DMSO differentiation Day 3 Replicate 1


title: Huh751_D0_1

value: Huh751 DMSO differentiation Day 0 Replicate 1


title: HC-FTAZ:PCBM-4

status: Public on Jul 17 2021

city: Raleigh

first: Heike

last: Sederoff

state: NC

address: 851 Main Campus Dr

department: Plant & Microbial Biology

institute: North Carolina State University

data_processing:
QC metrics were obtained using FastQC and high-quality (Q>30) read pairs were mapped to Lsat_Salinas_v7 genome assembly using HISAT2 with default parameter settings
Aligned reads were assigned genomic features according to Lsat_Salinas_v7 annotations using featureCounts and read abundances quantified at the gene-level with default parameter settings
Raw counts were filtered for zero and low counts (<2) and library normalization was performed using DESeq2 size factor estimates
Genome_build: GCA_002870075.2_Lsat_Salinas_v7
Supplementary_files_format_and_content: Text files with counts for each of the 32 samples by gene

molecule: polyA RNA

organism: Lactuca sativa

source_name: leaf

growth_protocol: 16 plants were grown per box, 2 plants per pot until "transplant" harvest at 3 weeks, 8 plants were grown to final harvest at 5 weeks, water and fertilizer were provided with automated irrigation system, pots were rotated every 2 days to prevent positional effects; leaf tissue was collected from 4 plants per treatment

extract_protocol:
TRIzol + PureLink RNA Mini kit, on-column DNAse and DNAse I treatment
Library was prepared by BGI Genomics Co., Ltd., poly A selection with oligo dT library, all 32 samples were pooled and loaded into all 3 lanes

treatment_protocol: Ceramic metal halide and incandescent lighting filtered through either 1 OPV filter or clear glass control, adjusted for light intensity (PAR controlled) or not adjusted for light intensity (Height Controlled)

tag: intensity experiment

value: Height Controlled

tag: opv filter

tag: tissue

value: leaf


title: HC-FTAZ:IT-M-3


title: HC-FTAZ:IT-M-2


title: HC-FTAZ:PCBM-3


title: HC-FTAZ:PCBM-1


title: HC-FTAZ:PCBM-2


title: HC-FTAZ:IT-M-4


title: HC-FTAZ:IT-M-1


title: HC-Control-3

value: Control


title: HC-Control-4


title: HC-Control-2


title: Huh751_D7_2

value: Huh751 DMSO differentiation Day 7 Replicate 2


title: HC-PTB7-Th:IEICO-4F-2


title: PC-FTAZ:PCBM-3

value: PAR Controlled


title: HC-Control-1


title: PC-FTAZ:PCBM-2


title: HC-PTB7-Th:IEICO-4F-3


title: PC-FTAZ:PCBM-4


title: HC-PTB7-Th:IEICO-4F-4


title: PC-FTAZ:PCBM-1


title: PC-Control-4


title: PC-PTB7-Th:IEIECO-4F-3


title: PC-Control-2


title: PC-PTB7-Th:IEIECO-4F-2


title: HC-PTB7-Th:IEICO-4F-1


title: PC-PTB7-Th:IEIECO-4F-4


title: PC-Control-3


title: PC-PTB7-Th:IEIECO-4F-1


title: Huh751_D0_2

value: Huh751 DMSO differentiation Day 0 Replicate 2


title: PC-Control-1


title: Cells cultured for 18 hours RS12

status: Public on Jul 11 2021

city: La Jolla

first: Robert

last: Signer

state: California

address: 3855 Health Sciences Drive

department: Division of Regenerative Medicine

institute: UCSD

description:
Cells cultured for 18 hours
Cultured for 18h

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the GRCm38 reference genome using tophat (default options)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using htseq-count with default options
Genome_build: mm10
Supplementary_files_format_and_content: read count matrix with rows as genes and columns as cells

source_name: Hematopoietic stem cells

growth_protocol: Prime-XV Mouse Hematopoietic Cell Medium (Prototype; Irvine Scientific) with SCF (50ng/ml; PeproTech), TPO (50ng/ml; PeproTech), 2-Mercaptoethanol (50µM; Sigma) and bovine serum albumin (BSA; 0.1%; Sigma).

extract_protocol:
Rneasy Plus Micro Kit (Qiagen)
SMARTseq2

treatment_protocol: 5nM 17-AAG or 0.02% DMSO (as specified above)

tag: source

value: Young adult mouse bone marrow

value: Hematopoietic stem cell


title: Cells cultured for 18 hours RS11


title: Cells cultured for 4 hours with 17-AAG RS9

description:
Cells cultured for 4 hours with 17-AAG
Cultured for 4h with 5nM 17-AAG

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the GRCm38 reference genome using STAR v2.6.1 (default options)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using featureCounts v 1.6.5 with default options
Genome_build: GRCm38
Supplementary_files_format_and_content: read count matrix with rows as genes and columns as cells


title: Cells cultured for 4 hours with 17-AAG RS7


title: Cells cultured for 4 hours with 17-AAG RS8


title: Freshly isolated cells RS8

description:
Freshly isolated cells
Uncultured


title: Freshly isolated cells RS7

description:
Freshly isolated cells
Uncultured


title: Hsf1-/- cells cultured for 4 hours with vehicle (DMSO) control RS4

description:
Hsf1-/- cells cultured for 4 hours with vehicle (DMSO) control
Cultured for 4h with 0.02% DMSO


title: Hsf1-/- cells cultured for 4 hours with 17-AAG RS12

description:
Hsf1-/- cells cultured for 4 hours with 17-AAG
Cultured for 4h with 5nM 17-AAG


title: Hsf1-/- cells cultured for 4 hours with vehicle (DMSO) control RS5


title: Hsf1-/- cells cultured for 4 hours with 17-AAG RS10


title: Hsf1-/- cells cultured for 4 hours with 17-AAG RS11


title: Cells cultured for 4 hours with vehicle (DMSO) control RS2

description:
Cells cultured for 4 hours with vehicle (DMSO) control
Cultured for 4h with 0.02% DMSO


title: Suboptimal Thickness CC5

status: Public on Jun 15 2021

city: RTP

first: Franco

last: Demayo

address: 111 TW Alexander Drive

institute: NIEHS

data_processing:
Raw reads of 75 nucleotides, paired-end filtered for quality score > 20.
Reads were mapped to the human genome (UCSC hg19) using Tophat version 2.0.4 and assembled using Cufflinks version 2.0.2.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM was calculated for each gene in each sample by using Cufflinks version 2.0.2.

source_name: Suboptimal Thickness

growth_protocol: Not applicable

extract_protocol:
RNA was extracted using TRIzol and Qiagen RNeasy Mini kit according to manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Women diagnosed with unexplained infertility undergoing planned treatment with clomiphene citrate 100mg from menstrual cycle days 3- 7 were grouped by their sonographically measured endometrial thickness in the late proliferative phase. Women who developed a clearly suboptimal endometrial thickness following clomiphene (<6mm) were categorized as suboptimal and those with an optimal lining (≥8,m) were categorized as optimal. Endometrial biopsies were performed at the time of planned ultrasound in the late proliferative phase (cycle days 12-15) and in the presence of a dominant ovarian follicle (≥19mm). Estradiol sufficiency and lack of luteinization were confirmed by serum sex hormone concentration assessment performed within 1 hour of endometrial biopsy.

tag: endometrial thickness

value: Suboptimal Thickness


title: Optimal Thickness CC9 [ChIP]

description: ERα bound DNA

data_processing:
The 75-nt single-end sequence reads generated by Illumina sequencing are mapped to the human genome (UCSC hg19) using the BWA algorithm with default settings.
Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis.
Duplicate reads (“PCR duplicates”) are removed.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files were generated from normalized bedgraph files using bedGraphToBigWig; Scores represent normalized mapped read coverage

source_name: Optimal Thickness

growth_protocol: Not Applicable

extract_protocol:
Chromatin samples were prepared by Active Motif Services - Factor Path assays. The Estrogen Receptor α (ERα) bound DNA were isolated with ERα antibody (Millipore Sigma catalog #06-935).
Libraries were prepared by Active Motif Services - FactorPath assays

value: Optimal Thickness

value: Eralpha


title: Suboptimal Thickness CC10


title: Suboptimal Thickness CC4 [ChIP]

description: ERα bound DNA


title: Optimal Thickness CC8 [ChIP]

description: ERα bound DNA


title: Control, input DNA

source_name: Control, input DNA

value: Pooled endometrium


title: Suboptimal Thickness CC2


title: Optimal Thickness CC12


title: Suboptimal Thickness CC2 [ChIP]

description: ERα bound DNA


title: Cells cultured for 18 hours RS10


title: Freshly isolated cells RS9

description:
Freshly isolated cells
Uncultured


title: Suboptimal Thickness CC4


title: Optimal Thickness CC9


title: Hsf1-/- cells cultured for 4 hours with vehicle (DMSO) control RS6


title: Optimal Thickness CC7


title: Optimal Thickness CC1


title: Cells cultured for 4 hours with vehicle (DMSO) control RS1


title: Cells cultured for 4 hours with vehicle (DMSO) control RS3


title: Sorted SKK-1 cells on high fatty acid uptake 2

status: Public on Jun 13 2021

city: Badalona

first: Roberto

last: Malinverni

state: Barcelona

address: Josep Carreras Building, Ctra de Can Ruti,

country: Spain

institute: Josep Carreras Leukaemia Research Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
For “quasi”aligmen and raw reads counts : salmon software 0.13.1 (Patro et al., Nature Methods. 2017) -salmon quant -l A
Satatistical analysis preformed using DESq2
Genome_build: hg19
Supplementary_files_format_and_content: Comma separated table with raw counts  for all samples (one sample for each column)
Supplementary_files_format_and_content: Comma separated table with normalized counts  for all samples (one sample for each column)

growth_protocol: Cell lines were cultured in RPMI 1640 (ThermoFisher Scientific, USA) supplemented with 10% fetal bovine serum 1% Pen/Strep, and 1% L-glutamine at 37ºC in 5% CO2.

extract_protocol:
Total RNA was extracted from cell pellets using the Maxwell RSC simplyRNA Cells Kit (Promega, USA).  Briefly, pellets were prepared with homogenisation buffer and then lysed with lysis buffer from the kit.  The remaining steps of the extraction protocol were carried out on the Maxwell RSC Instrument.  RNA was eluted in RNase-free water.  RNA concentration and quality were checked on NanoDrop.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SKK-1 cell line were FACS sorted into two populations based on the lowest and highest 10% long chain fatty acid uptake capacity of the parental population

value: MDS/sAML patient-derived cell line

tag: treatment

value: FACS sorted on long chain fatty acid uptake


title: Sorted SKK-1 cells on high fatty acid uptake 3


title: Suboptimal Thickness CC13


title: Sorted SKK-1 cells on low fatty acid uptake 3


title: Sorted SKK-1 cells on low fatty acid uptake 1


title: Sorted SKK-1 cells on low fatty acid uptake 2


title: Optimal Thickness CC8


title: Optimal Thickness CC3


title: Sorted SKK-1 cells on high fatty acid uptake 1


title: EW22_EETS_low_rep3

status: Public on Jun 09 2021

type: RNA

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

country: Germany

institute: German Cancer Research Center (DKFZ)

description: Ewing sarcoma cell line EW-22; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3

hyb_protocol: Affymetrix Clariom D Array one-color based hybridization protocol, cDNA samples were hybridized at 45°C for 16 h on separate Affymetrix Human Clariom D™ Arrays.

scan_protocol: Affymetrix GeneChip 3000 Scanner

data_processing:
Data were processed with Transcriptome Analysis Console (version 4.0) using the SST-RMA analysis algorithm.
Clariom_D_Human.r1.pgf
Clariom_D_Human.r1.mps

label: biotin

source_name: Ewing sarcoma cell line stably transduced with inducible shRNA expressing construct targeting the respective EWSR1-ETS fusion oncogene

label_protocol: Affymetrix GeneChip WT PLUS Reagent Kit, according to the manufacturer's protocol

growth_protocol: Cell lines were cultured in RPMI 1640 medium with stable glutamine (Biochrom, Berlin, Germany), supplemented with 10% FCS tested to be dox-free (Sigma-Aldrich, Taufkirchen, Germany) and penicillin and streptomycin (final concentrations 100 units/ml and 100µg/ml, respectively; Merck, Darmstadt, Germany) in tissue culture flasks and plates (TPP, Trasadingen, Switzerland) in a fully humidified 5% CO2 atmosphere at 37°C.

extract_protocol: Cells were washed with PBS, lysed in lysis buffer from the Macherey-Nagel (Düren, Germany) NucleoSpin RNA kit. Total RNA was isolated following manufacturer's protocol. RNA was stored at -80°C.

treatment_protocol: Addition of 1 µg/ml doxycycline for 96 h, medium renewal at 48 h.

value: Ewing sarcoma cell line

tag: genotype

value: Doxycycline induced EWSR1-ETS knockdown


title: EW24_EETS_high_rep1

description: Ewing sarcoma cell line EW-24; Control sample; replicate 1


title: EW22_EETS_low_rep2

description: Ewing sarcoma cell line EW-22; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2


title: EW22_EETS_low_rep1

description: Ewing sarcoma cell line EW-22; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1


title: EW1_EETS_low_rep3

description: Ewing sarcoma cell line EW-1; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3


title: CHLA25_EETS_low_rep1

description: Ewing sarcoma cell line CHLA-25; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1


title: CHLA25_EETS_low_rep3

description: Ewing sarcoma cell line CHLA-25; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3


title: EW22_EETS_high_rep1

description: Ewing sarcoma cell line EW-22; Control sample; replicate 1


title: EW1_EETS_high_rep3

description: Ewing sarcoma cell line EW-1; Control sample; replicate 3


title: CHLA25_EETS_high_rep2

description: Ewing sarcoma cell line CHLA-25; Control sample; replicate 2


title: CHLA10_EETS_low_rep1

description: Ewing sarcoma cell line CHLA-10; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1


title: CHLA25_EETS_high_rep3

description: Ewing sarcoma cell line CHLA-25; Control sample; replicate 3


title: EW1_EETS_low_rep2

description: Ewing sarcoma cell line EW-1; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2


title: CHLA25_EETS_low_rep2

description: Ewing sarcoma cell line CHLA-25; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2


title: EW1_EETS_low_rep1

description: Ewing sarcoma cell line EW-1; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1


title: EW1_EETS_high_rep1

description: Ewing sarcoma cell line EW-1; Control sample; replicate 1


title: CHLA10_EETS_low_rep2

description: Ewing sarcoma cell line CHLA-10; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2


title: CHLA10_EETS_high_rep2

description: Ewing sarcoma cell line CHLA-10; Control sample; replicate 2


title: CHLA10_EETS_low_rep3

description: Ewing sarcoma cell line CHLA-10; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3


title: EW22_EETS_high_rep2

description: Ewing sarcoma cell line EW-22; Control sample; replicate 2


title: A673_EETS_low_rep3

description: Ewing sarcoma cell line A-673; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3


title: A673_EETS_low_rep1

description: Ewing sarcoma cell line A-673; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1


title: EW22_EETS_high_rep3

description: Ewing sarcoma cell line EW-22; Control sample; replicate 3


title: A673_EETS_high_rep3

description: Ewing sarcoma cell line A-673; Control sample; replicate 3


title: RDES_EETS_low_rep2

description: Ewing sarcoma cell line RD-ES; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2

value: RD-ES


title: CHLA25_EETS_high_rep1

description: Ewing sarcoma cell line CHLA-25; Control sample; replicate 1


title: RDES_EETS_high_rep3

description: Ewing sarcoma cell line RD-ES; Control sample; replicate 3


title: RDES_EETS_low_rep1

description: Ewing sarcoma cell line RD-ES; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1


title: A673_EETS_low_rep2

description: Ewing sarcoma cell line A-673; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2


title: EW1_EETS_high_rep2

description: Ewing sarcoma cell line EW-1; Control sample; replicate 2


title: RDES_EETS_high_rep2

description: Ewing sarcoma cell line RD-ES; Control sample; replicate 2


title: RDES_EETS_high_rep1

description: Ewing sarcoma cell line RD-ES; Control sample; replicate 1


title: RDES_EETS_low_rep3

description: Ewing sarcoma cell line RD-ES; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3


title: EW7_EETS_low_rep1

description: Ewing sarcoma cell line EW-7; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1


title: EW7_EETS_low_rep3

description: Ewing sarcoma cell line EW-7; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3


title: EW7_EETS_high_rep2

description: Ewing sarcoma cell line EW-7; Control sample; replicate 2


title: EW7_EETS_low_rep2

description: Ewing sarcoma cell line EW-7; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2


title: A673_EETS_high_rep2

description: Ewing sarcoma cell line A-673; Control sample; replicate 2


title: CHLA10_EETS_high_rep3

description: Ewing sarcoma cell line CHLA-10; Control sample; replicate 3


title: CHLA10_EETS_high_rep1

description: Ewing sarcoma cell line CHLA-10; Control sample; replicate 1


title: TC71_EETS_low_rep3

description: Ewing sarcoma cell line TC-71; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3


title: A673_EETS_high_rep1

description: Ewing sarcoma cell line A-673; Control sample; replicate 1


title: EW7_EETS_high_rep1

description: Ewing sarcoma cell line EW-7; Control sample; replicate 1


title: TC71_EETS_low_rep2

description: Ewing sarcoma cell line TC-71; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2


title: TC32_EETS_low_rep3

description: Ewing sarcoma cell line TC-32; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3


title: TC71_EETS_low_rep1

description: Ewing sarcoma cell line TC-71; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1


title: TC32_EETS_high_rep3

description: Ewing sarcoma cell line TC-32; Control sample; replicate 3


title: EW7_EETS_high_rep3

description: Ewing sarcoma cell line EW-7; Control sample; replicate 3


title: TC71_EETS_high_rep3

description: Ewing sarcoma cell line TC-71; Control sample; replicate 3


title: TC71_EETS_high_rep2

description: Ewing sarcoma cell line TC-71; Control sample; replicate 2


title: TC32_EETS_low_rep2

description: Ewing sarcoma cell line TC-32; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2


title: TC106_EETS_low_rep1

description: Ewing sarcoma cell line TC-106; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1


title: TC106_EETS_high_rep3

description: Ewing sarcoma cell line TC-106; Control sample; replicate 3


title: TC106_EETS_high_rep2

description: Ewing sarcoma cell line TC-106; Control sample; replicate 2


title: SKNMC_EETS_low_rep3

description: Ewing sarcoma cell line SK-N-MC; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3

value: SK-N-MC


title: TC32_EETS_high_rep1

description: Ewing sarcoma cell line TC-32; Control sample; replicate 1


title: SKNMC_EETS_low_rep1

description: Ewing sarcoma cell line SK-N-MC; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1


title: SKNMC_EETS_low_rep2

description: Ewing sarcoma cell line SK-N-MC; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2


title: SKNMC_EETS_high_rep2

description: Ewing sarcoma cell line SK-N-MC; Control sample; replicate 2


title: SKES1_EETS_low_rep3

description: Ewing sarcoma cell line SK-ES-1; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3


title: SKES1_EETS_low_rep1

description: Ewing sarcoma cell line SK-ES-1; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1


title: SKNMC_EETS_high_rep1

description: Ewing sarcoma cell line SK-N-MC; Control sample; replicate 1


title: RH1_EETS_high_rep2

description: Ewing sarcoma cell line Rh1; Control sample; replicate 2


title: TC32_EETS_low_rep1

description: Ewing sarcoma cell line TC-32; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1


title: TC106_EETS_high_rep1

description: Ewing sarcoma cell line TC-106; Control sample; replicate 1


title: POE_EETS_low_rep3

description: Ewing sarcoma cell line POE; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3

value: POE


title: TC106_EETS_low_rep2

description: Ewing sarcoma cell line TC-106; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2


title: SKNMC_EETS_high_rep3

description: Ewing sarcoma cell line SK-N-MC; Control sample; replicate 3

value: Control


title: SKES1_EETS_high_rep1

description: Ewing sarcoma cell line SK-ES-1; Control sample; replicate 1


title: SKES1_EETS_low_rep2

description: Ewing sarcoma cell line SK-ES-1; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2


title: RH1_EETS_high_rep1

description: Ewing sarcoma cell line Rh1; Control sample; replicate 1


title: RH1_EETS_low_rep2

description: Ewing sarcoma cell line Rh1; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2


title: SKES1_EETS_high_rep3

description: Ewing sarcoma cell line SK-ES-1; Control sample; replicate 3


title: TC106_EETS_low_rep3

description: Ewing sarcoma cell line TC-106; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3


title: RH1_EETS_high_rep3

description: Ewing sarcoma cell line Rh1; Control sample; replicate 3


title: RH1_EETS_low_rep3

description: Ewing sarcoma cell line Rh1; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3


title: TC71_EETS_high_rep1

description: Ewing sarcoma cell line TC-71; Control sample; replicate 1


title: POE_EETS_low_rep1

description: Ewing sarcoma cell line POE; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1


title: POE_EETS_low_rep2

description: Ewing sarcoma cell line POE; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2


title: SKES1_EETS_high_rep2

description: Ewing sarcoma cell line SK-ES-1; Control sample; replicate 2


title: RH1_EETS_low_rep1

description: Ewing sarcoma cell line Rh1; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1


title: TC32_EETS_high_rep2

description: Ewing sarcoma cell line TC-32; Control sample; replicate 2


title: POE_EETS_high_rep3

description: Ewing sarcoma cell line POE; Control sample; replicate 3


title: MIC_EETS_low_rep2

description: Ewing sarcoma cell line MIC; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2

value: MIC


title: MIC_EETS_low_rep3

description: Ewing sarcoma cell line MIC; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3


title: POE_EETS_high_rep2

description: Ewing sarcoma cell line POE; Control sample; replicate 2


title: MIC_EETS_high_rep3

description: Ewing sarcoma cell line MIC; Control sample; replicate 3


title: MHHES1_EETS_low_rep3

description: Ewing sarcoma cell line MHH-ES-1; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3


title: ASC_48h_RNA-seq

status: Public on May 25 2021

city: Hong Kong

first: Yingzhe

last: Ding

state: Shatin NT.

address: Rm503,Li Ka Shing Medical Science Build.,Prince of Wales Hosp.,30-32 Ngan SHing St.

department: Chemical Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using trimmomatic v0.36 with parameter SLIDINGWINDOW:4:15 MINLEN:50, and low-quality or duplication sequence are removed by a in-house scripts, then mapped to mm9 whole genome using tophat2 with parameters -a 8 -m 0 -I 500000 -p 20 -g 20 --library-type fr-firststrand --segment-mismatches 2 --no-coverage-search -r 50 --mate-std-dev 60
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks v2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Skeletal muscle

growth_protocol: Freshly-isolated satellite cells were cultured in Hams F10 medium (Sigma) with 20% FBS, penicillin/streptomycin (1×) and 2.5 ng ml-1 basic fibroblast growth factor (bFGF, 13256, Life Technologies) and harvested at 24h,48h and 72h.

extract_protocol:
RNA from quiescent,freshly isolated or culture muscle stem cells was harvested using Trizol reagent.
RNA libraries were generated and sequenced with DNBseq platform by BGI, Hong Kong. In brief, rRNAs were first depleted from total RNAs and the remaining RNAs were fragmented and then reverse transcribed. The resulting DNA fragments were end-repaired, A-nucleotide added and adaptors ligated. The resulting libraries were heated to seperate into ssDNA and further cyclized to make DNA nanoballs (DNBs). DNBs were sequenced by DNBSEQ-G400 sequencer in BGI-Hong Kong.

value: Skeletal muscle

value: activated siolated muscle stem cell

tag: age

value: 6-8 weeks


title: MHHES1_EETS_high_rep3

description: Ewing sarcoma cell line MHH-ES-1; Control sample; replicate 3


title: MIC_EETS_low_rep1

description: Ewing sarcoma cell line MIC; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1


title: LPS_2_Visium

status: Public on Jun 03 2021

city: New York

first: Philip

last: Hasel

address: 435 E 30th St

institute: NYU Langone Medical Centre

data_processing:
NovaSeq 6000 followed by RTA v3.4.4 for basecalling
SpaceRanger was used to align reads to mm10 and generate the barcode.tsv.gz,features.tsv.gz, filtered_feature_bc_matrix.h5 and matrix.mtx.gz files
Tissue_hires_image.png images of brain sections were acquired on a Keyence BZ-X710 microscope
Supplementary_files_format_and_content: barcode.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_feature_bc_matrix.h5, tissue_hires_image.png

extract_protocol:
Tissue was enzymatically permeabelized accroding to the Visium protocol
Visium library kit

treatment_protocol: Female Aldh1l1egfp mice were either injected with 5 mg/kg LPS or saline for 24h and brains sectioned to 10 um

tag: stimulation

value: Coronal brain section


title: ASC_72h_RNA-seq

value: differentiated siolated muscle stem cell


title: MHHES1_EETS_low_rep2

description: Ewing sarcoma cell line MHH-ES-1; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2

tag: cell line


title: EW3_EETS_low_rep1

description: Ewing sarcoma cell line EW-3; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1

tag: cell type


title: MHHES1_EETS_high_rep2

description: Ewing sarcoma cell line MHH-ES-1; Control sample; replicate 2


title: MIC_EETS_high_rep1

description: Ewing sarcoma cell line MIC; Control sample; replicate 1


title: EW3_EETS_high_rep1

description: Ewing sarcoma cell line EW-3; Control sample; replicate 1


title: ASC_24h_RNA-seq


title: MHHES1_EETS_high_rep1

description: Ewing sarcoma cell line MHH-ES-1; Control sample; replicate 1


title: FISC_RNA-seq

value: freshly siolated muscle stem cell


title: MHHES1_EETS_low_rep1

description: Ewing sarcoma cell line MHH-ES-1; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1


title: MIC_EETS_high_rep2

description: Ewing sarcoma cell line MIC; Control sample; replicate 2


title: QSC_RNA-seq

value: quiescent muscle stem cell


title: EW24_EETS_low_rep3

description: Ewing sarcoma cell line EW-24; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3


title: POE_EETS_high_rep1

description: Ewing sarcoma cell line POE; Control sample; replicate 1


title: EW3_EETS_high_rep3

description: Ewing sarcoma cell line EW-3; Control sample; replicate 3


title: EW24_EETS_low_rep2

description: Ewing sarcoma cell line EW-24; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2


title: SPIM_89

status: Public on May 19 2021

city: Solna

first: Paulo

last: Czarnewski

address: Tomtebodavägen 23b

country: Sweden

institute: KTH

description:
Raw_counts.csv
Counts_batch_removed.csv
Normcounts_batch_removed.csv
phenoData.csv

data_processing:
Basecalling was performed using Illumina Casava v.1.7 software.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequences.
Pair-ended reads were evaluated for sequencing quality using FASTQC, were trimmed for adaptor sequences and aligned using TopHat2 with HGC38 human genome.
Genome_build: HGC38
Supplementary_files_format_and_content: We provided individual comma-separated text files (.csv version2) containing counts for each Sample. We also included a matrix contating counts from all samples (Raw_counts.csv) as well as batch-corrected counts (Counts_batch_removed.csv) and a log2-normalized batch-corrected counts summarized at the gene level (NormCounts_batch_removed.csv).

source_name: intermediate monocyte

extract_protocol:
Blood and BAL was processed within one hour after retrieval for further applications. Peripheral blood mononuclear cells (PBMCs) were isolated from blood using Ficoll density gradient centrifugation. BAL samples were kept on ice, filtered through a 100 μm nylon filter (Syntab) and centrifuged at 400 X g for 15 min before downstream application. Cell suspensions were incubated with LIVE/DEADTM Fixable Aqua/Blue Dead Cell Stain Kit (Life Technologies) and Fc receptors blocked using FcR block (Miltenyi) followed by staining with antibodies against surface molecules. For cell sorting, a FACS Aria Fusion or AriaIII (both BD) were used. Sorted cells were subsequently resuspended in Qiazol Lysis reagent (Qiagen) and stored at -80°C until further use. RNA was isolated using the miRNeasy micro kit (Qiagen) according to the manufacturer’s protocol. Briefly, chloroform was added to cell homogenates and centrifuged. The aqueous phase was mixed with 1.5 volumes of 100% ethanol. The samples were transferred to a RNeasy MinElute spin column and centrifuged. After, the column was washed with RPE buffer and spun down followed by addition of 80% ethanol and centrifugation. RNA was eluted in a collection tube using RNAse-free water. RNA quantity and quality were assessed using a bioanalyzer and samples with an RNA integrity number > 6 used for further application.
Library preparation was performed by Novogene, using TruSeq Stranded mRNA Library Prep Kit (poly-A selection) when the total RNA amount was more than 100ng, if the sample total RNA amount was lower than 100ng, the library preparation was done with SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech). Sequencing was performed using a HiSeq-4000 platform (Illumina) with a 2x150-bp pair-end sequencing setup and the sequencing depth was 20 M reads/sample.

treatment_protocol: 108 sarcoidosis patients and 30 healthy volunteers were included in the study and gave written informed consent. All patients were newly diagnosed with pulmonary sarcoidosis as defined by WASOG guidelines based on clinical signs, chest radiography findings, an elevated CD4/CD8 T cell ratio in BAL, or non-caseating granulomas in tissue biopsies. Blood and BAL was processed within one hour after retrieval for further applications. Peripheral blood mononuclear cells (PBMCs) were isolated from blood using Ficoll density gradient centrifugation.

value: SP

value: Blood

value: IM

value: regular

tag: gender

value: Male


title: SPIM_73

value: Female


title: SPIM_63

value: single cell


title: EW3_EETS_high_rep2

description: Ewing sarcoma cell line EW-3; Control sample; replicate 2

value: Ewing sarcoma cell line


title: SPIM_39


title: EW3_EETS_low_rep2

description: Ewing sarcoma cell line EW-3; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2

value: Doxycycline induced EWSR1-ETS knockdown


title: EW24_EETS_high_rep2

description: Ewing sarcoma cell line EW-24; Control sample; replicate 2

value: Control


title: EW24_EETS_low_rep1

description: Ewing sarcoma cell line EW-24; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1


title: SPCM_89

source_name: classical monocyte

value: CM


title: SPIM_30


title: SPCM_53


title: SPCM_63


title: EW3_EETS_low_rep3

description: Ewing sarcoma cell line EW-3; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3


title: SPIM_53


title: SPCM_51


title: SPIM_36


title: SPIM_37


title: SPCM_36


title: SP1C_73

source_name: CD1C+ dendritic cell


title: SPIM_35


title: SP1C_53


title: SPCM_73


title: SP1C_36


title: EW24_EETS_high_rep3

description: Ewing sarcoma cell line EW-24; Control sample; replicate 3


title: SP1C_35


title: SP1C_37


title: SP141_89

source_name: CD141+ dendritic cell


title: SPCM_39


title: SP141_73


title: SP141_37


title: SBIM_73

value: BAL


title: SP141_35


title: SPCM_37


title: SPCM_30


title: SPCM_35


title: SP1C_89


title: SBIM_39


title: SP1C_30


title: SP1C_39


title: SP1C_63


title: SP1C_51


title: SBCM_89


title: SBCM_63


title: SP141_30


title: SBCM_37


title: SBIM_89


title: SBAM_89

source_name: alveolar macrophage

value: AM


title: SBIM_63


title: SBIM_53


title: SBAM_53


title: SBCM_73


title: SP141_63


title: SBAM_63


title: SBCM_36


title: SBAM_51


title: SBAM_39


title: SBIM_51


title: SB1C_37


title: SB1C_36


title: SB1C_89


title: HPIM_29

value: HC


title: SBAM_73


title: HPIM_27


title: SB1C_73


title: SB1C_63


title: HPIM_25


title: HPIM_24


title: SB1C_53


title: HPIM_02


title: SB141_89


title: HPIM_28


title: HPCM_29


title: SB141_63


title: HPIM_26


title: HPIM_16


title: HPCM_25


title: HPCM_55


title: HPCM_16


title: HP1C_55


title: SBAM_37


title: HPCM_28


title: HPCM_24


title: HP1C_28


title: HP1C_27


title: HP1C_24


title: HP1C_26


title: HP1C_25


title: HP141_29


title: HP1C_02


title: HP141_28


title: HP141_27


title: HPCM_26


title: HPCM_27


title: HP1C_29


title: HPCM_02


title: HP141_24


title: HP141_16


title: HP141_26


title: HP141_25


title: HBIM_27


title: HBIM_29


title: HBIM_28


title: HBIM_26


title: HP141_02


title: HBIM_55


title: HBCM_29


title: HBIM_25


title: HBIM_24


title: HP1C_16


title: HBCM_28


title: HBIM_02


title: HBCM_26


title: HBCM_27


title: HBCM_24


title: HBAM_29


title: HBCM_25


title: HBCM_16


title: HBCM_02


title: HBAM_55


title: HBAM_28


title: HBAM_26


title: HBAM_27


title: HBAM_24


title: HBAM_25


title: HBAM_16


title: HB1C_55


title: HB1C_29


title: HBAM_02


title: HB1C_28


title: HB1C_27


title: HB1C_25


title: HB1C_24


title: HB141_29


title: HB1C_26


title: HB1C_16


title: HB1C_02


title: HB141_24


title: HB141_28


title: HB141_27


title: HB141_02


title: HB141_25


title: Krt14-cre+ Sting-flox S. epi Mice 2

status: Public on May 12 2021

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

institute: NIH

description:
processed data file: Krt14_Lab.txt
RNAseq_KRT14_Cre_pos_Sepi_DJL_210121_rep2_S17

data_processing:
NOT PROVIDED; REQUESTED
Genome_build: NOT PROVIDED; REQUESTED
Supplementary_files_format_and_content: NOT PROVIDED; REQUESTED

source_name: CD49f+ Sca-1+ Keratinocytes

extract_protocol: NOT PROVIDED; REQUESTED

tag: strain

tag: Sex

value: Skin

value: CD49f+ Sca-1+ Keratinocytes

value: S. epidermidis Associated + Control Diet


title: HBIM_16


title: Krt14-cre+ Sting-flox Unassociated Mice 5

description:
processed data file: Krt14_Lab.txt
RNAseq_KRT14_Cre_pos_naive_DJL_210121_rep5_S15

value: Unassociated + Control Diet


title: Krt14-cre+ Sting-flox S. epi Mice 1

description:
processed data file: Krt14_Lab.txt
RNAseq_KRT14_Cre_pos_Sepi_DJL_210121_rep1_S16


title: Krt14-cre+ Sting-flox Unassociated Mice 4

description:
processed data file: Krt14_Lab.txt
RNAseq_KRT14_Cre_pos_naive_DJL_210121_rep4_S14


title: Sting-flox S. epi Mice 4

description:
processed data file: Krt14_Lab.txt
RNAseq_KRT14_Cre_neg_Sepi_DJL_210121_rep5_S10


title: Krt14-cre+ Sting-flox Unassociated Mice 2

description:
processed data file: Krt14_Lab.txt
RNAseq_KRT14_Cre_pos_naive_DJL_210121_rep2_S12


title: Krt14-cre+ Sting-flox Unassociated Mice 3

description:
processed data file: Krt14_Lab.txt
RNAseq_KRT14_Cre_pos_naive_DJL_210121_rep3_S13


title: Krt14-cre+ Sting-flox Unassociated Mice 1

description:
processed data file: Krt14_Lab.txt
RNAseq_KRT14_Cre_pos_naive_DJL_210121_rep1_S11


title: Sting-flox S. epi Mice 2

description:
processed data file: Krt14_Lab.txt
RNAseq_KRT14_Cre_neg_Sepi_DJL_210121_rep2_S7


title: Sting-flox S. epi Mice 1

description:
processed data file: Krt14_Lab.txt
RNAseq_KRT14_Cre_neg_Sepi_DJL_210121_rep1_S6


title: HB141_16

description:
Raw_counts.csv
Counts_batch_removed.csv
Normcounts_batch_removed.csv
phenoData.csv


title: Sting-flox Unassociated Mice 2

description:
processed data file: Krt14_Lab.txt
RNAseq_KRT14_Cre_neg_naive_DJL_210121_rep2_S2


title: Sting-flox Unassociated Mice 4

description:
processed data file: Krt14_Lab.txt
RNAseq_KRT14_Cre_neg_naive_DJL_210121_rep4_S4


title: Krt14-cre+ Sting-flox S. epi Mice 4

description:
processed data file: Krt14_Lab.txt
RNAseq_KRT14_Cre_pos_Sepi_DJL_210121_rep4_S19


title: Sting-flox Unassociated Mice 1

description:
processed data file: Krt14_Lab.txt
RNAseq_KRT14_Cre_neg_naive_DJL_210121_rep1_S1


title: Sting-flox S. epi Mice 3

description:
processed data file: Krt14_Lab.txt
RNAseq_KRT14_Cre_neg_Sepi_DJL_210121_rep4_S9


title: Sting-flox Unassociated Mice 3

description:
processed data file: Krt14_Lab.txt
RNAseq_KRT14_Cre_neg_naive_DJL_210121_rep3_S3


title: Sting-flox Unassociated Mice 5

description:
processed data file: Krt14_Lab.txt
RNAseq_KRT14_Cre_neg_naive_DJL_210121_rep5_S5


title: Mouse Keratinocyte Staphylococcus epidermidis NIHLM087 colonized High Fat Diet Replicate 5 Experiment 2

description:
processed data file: getDiff.Genes.HFD_Unassoc_Sepi.txt
RNAseq_keratinocytes_HFD_diet_Sepi_rep5_S20

value: S. epidermidis Associated + High Fat Diet


title: Krt14-cre+ Sting-flox S. epi Mice 3

description:
processed data file: Krt14_Lab.txt
RNAseq_KRT14_Cre_pos_Sepi_DJL_210121_rep3_S18


title: Mouse Keratinocyte Staphylococcus epidermidis NIHLM087 colonized High Fat Diet Replicate 4 Experiment 2

description:
processed data file: getDiff.Genes.HFD_Unassoc_Sepi.txt
RNAseq_keratinocytes_HFD_diet_Sepi_rep4_S19


title: Mouse Keratinocyte Staphylococcus epidermidis NIHLM087 colonized High Fat Diet Replicate 2 Experiment 2

description:
processed data file: getDiff.Genes.HFD_Unassoc_Sepi.txt
RNAseq_keratinocytes_HFD_diet_Sepi_rep2_S17


title: Mouse Keratinocyte Unassociated on High Fat diet Replicate 5 Experiment 2

description:
processed data file: getDiff.Genes.HFD_Unassoc_Sepi.txt
RNAseq_keratinocytes_HFD_diet_naive_rep5_S15

value: Unassociated + High Fat Diet


title: Mouse Keratinocyte Unassociated on High Fat diet Replicate 2 Experiment 2

description:
processed data file: getDiff.Genes.HFD_Unassoc_Sepi.txt
RNAseq_keratinocytes_HFD_diet_naive_rep2_S12


title: Mouse Keratinocyte Staphylococcus epidermidis NIHLM087 colonized High Fat Diet Replicate 1 Experiment 2

description:
processed data file: getDiff.Genes.HFD_Unassoc_Sepi.txt
RNAseq_keratinocytes_HFD_diet_Sepi_rep1_S16


title: SPIM_51

value: SP

value: Blood

value: IM


title: Mouse Keratinocyte Unassociated on High Fat diet Replicate 4 Experiment 2

description:
processed data file: getDiff.Genes.HFD_Unassoc_Sepi.txt
RNAseq_keratinocytes_HFD_diet_naive_rep4_S14

value: Female


title: Mouse Keratinocyte Unassociated on High Fat diet Replicate 3 Experiment 2

description:
processed data file: getDiff.Genes.HFD_Unassoc_Sepi.txt
RNAseq_keratinocytes_HFD_diet_naive_rep3_S13


title: Mouse Keratinocyte Unassociated on High Fat diet Replicate 1 Experiment 2

description:
processed data file: getDiff.Genes.HFD_Unassoc_Sepi.txt
RNAseq_keratinocytes_HFD_diet_naive_rep1_S11


title: Mouse Keratinocyte Staphylococcus epidermidis NIHLM087 colonized Control Diet Replicate 4 Experiment 2

description:
processed data file: getDiff.Genes.Ctrl_Unassoc_Sepi.txt
RNAseq_keratinocytes_ctrl_diet_Sepi_rep4_S9


title: Mouse Keratinocyte Staphylococcus epidermidis NIHLM087 colonized Control Diet Replicate 3 Experiment 2

description:
processed data file: getDiff.Genes.Ctrl_Unassoc_Sepi.txt
RNAseq_keratinocytes_ctrl_diet_Sepi_rep3_S8


title: Mouse Keratinocyte Staphylococcus epidermidis NIHLM087 colonized Control Diet Replicate 5 Experiment 2

description:
processed data file: getDiff.Genes.Ctrl_Unassoc_Sepi.txt
RNAseq_keratinocytes_ctrl_diet_Sepi_rep5_S10


title: Mouse Keratinocyte Staphylococcus epidermidis NIHLM087 colonized Control Diet Replicate 2 Experiment 2

description:
processed data file: getDiff.Genes.Ctrl_Unassoc_Sepi.txt
RNAseq_keratinocytes_ctrl_diet_Sepi_rep2_S7


title: Mouse Keratinocyte Unassociated on Control diet Replicate 5 Experiment 2

description:
processed data file: getDiff.Genes.Ctrl_Unassoc_Sepi.txt
RNAseq_keratinocytes_ctrl_diet_naive_rep5_S5


title: Mouse Keratinocyte Staphylococcus epidermidis NIHLM087 colonized Control Diet Replicate 1 Experiment 2

description:
processed data file: getDiff.Genes.Ctrl_Unassoc_Sepi.txt
RNAseq_keratinocytes_ctrl_diet_Sepi_rep1_S6


title: Mouse Keratinocyte Unassociated on Control diet Replicate 4 Experiment 2

description:
processed data file: getDiff.Genes.Ctrl_Unassoc_Sepi.txt
RNAseq_keratinocytes_ctrl_diet_naive_rep4_S4


title: Mouse Keratinocyte Staphylococcus epidermidis NIHLM087 colonized High Fat Diet Replicate 3 Experiment 2

description:
processed data file: getDiff.Genes.HFD_Unassoc_Sepi.txt
RNAseq_keratinocytes_HFD_diet_Sepi_rep3_S18


title: Mouse Keratinocyte Unassociated on Control diet Replicate 3 Experiment 2

description:
processed data file: getDiff.Genes.Ctrl_Unassoc_Sepi.txt
RNAseq_keratinocytes_ctrl_diet_naive_rep3_S3


title: Mouse Keratinocyte Unassociated on Control diet Replicate 1 Experiment 2

description:
processed data file: getDiff.Genes.Ctrl_Unassoc_Sepi.txt
RNAseq_keratinocytes_ctrl_diet_naive_rep1_S1


title: Mouse Keratinocyte Unassociated on Control diet Replicate 2 Experiment 2

description:
processed data file: getDiff.Genes.Ctrl_Unassoc_Sepi.txt
RNAseq_keratinocytes_ctrl_diet_naive_rep2_S2


title: Mouse Keratinocyte Staphylococcus epidermidis NIHLM087 colonized High Fat Diet Replicate 3 Experiment 1

data_processing:
Sequencing reads were mapped to the C57BL/6 mouse genome (GRCm38: mm10) with STAR using default parameters (Dobin et al., 2013). Gene expression was assessed using HOMER 4.11 (Heinz et al., 2010), specifically the analyzeRepeats function with parameters mm10, -count exons -condenseGenes -noadj, and differential expression was calculated with DESeq2 using the getDiffExpresion.pl
Sequencing reads were mapped to the C57BL/6 mouse genome (GRCm38: mm10) with STAR using stringent mapping parameters such that reads aligned to multiple regions of the genome were considered unmapped (--outFilterMultimapNmax 2). Retroelement expression was assessed using HOMER 4.11 by defining retroelements using the annotation provided by the Genome-based Endogenous Viral Element Database (gEVE) for GRCm38 (Nakagawa and Takahashi, 2016).  Reads were analyzed using the analyzeRepeats function with parameters mm10, -count genes -noadj, and differential expression was calculated with DESeq2 using the getDiffExpresion.pl
Genome_build: mm10

extract_protocol:
RNEasy Micro Kit (Qiagen)
Illumina TruSeq Stranded Total RNA Library Prep

treatment_protocol: Four week old mice were placed on a high fat or control diet for 6 weeks prior to association with S. epidermidis. Cells were sorted on DAPI– CD45– CD31– CD34– CD49f+ Sca-1+ cells.

value: Staphylococcus epidermidis NIHLM087 + High Fat Diet


title: Mouse Keratinocyte Staphylococcus epidermidis NIHLM087 colonized High Fat Diet Replicate 1 Experiment 1


title: Mouse Keratinocyte Unassociated on High Fat diet Replicate 5 Experiment 1


title: Mouse Keratinocyte Staphylococcus epidermidis NIHLM087 colonized High Fat Diet Replicate 4 Experiment 1


title: Mouse Keratinocyte Unassociated on High Fat diet Replicate 4 Experiment 1


title: Mouse Keratinocyte Unassociated on High Fat diet Replicate 1 Experiment 1


title: Mouse Keratinocyte Unassociated on High Fat diet Replicate 2 Experiment 1


title: Mouse Keratinocyte Staphylococcus epidermidis NIHLM087 colonized Control Diet Replicate 4 Experiment 1

value: Staphylococcus epidermidis NIHLM087 + Control Diet


title: Mouse Keratinocyte Unassociated on Control diet Replicate 4 Experiment 1


title: Mouse Keratinocyte Staphylococcus epidermidis NIHLM087 colonized Control Diet Replicate 3 Experiment 1


title: Mouse Keratinocyte Unassociated on Control diet Replicate 2 Experiment 1


title: Mouse Keratinocyte Unassociated on Control diet Replicate 5 Experiment 1


title: Mouse Keratinocyte Unassociated on Control diet Replicate 3 Experiment 1


title: lane4_keratinocytes_HTO

status: Public on May 05 2021

data_processing:
Cellranger 4.0.0 (10X Genomics) was used to map the raw sequencing data to the mm10 reference genome and HTO and mRNA libraries were processed together with cellranger count. Only singlet cells with less than 10% mitochondrial contamination were used for downstream analysis, leaving 26,646 cells. Downstream analysis was performed using Seurat version 3.1.4. Data was normalized, scaled, principal components analysis was performed, and neighbors were found using 11 dimensions. Uniform manifold approximation and projection (UMAP) reduction was performed on this dataset with 25 dimensions.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: scRNA_seq_keratinocytes_filtered.rds: Processed Seurat object

source_name: keratinocyte single cell HTO hash tags from lane 4 of 10X data set

extract_protocol:
Interfollicular epidermis keratinocytes were purified by cell sorting from the ear epidermis of unassociated and S. epidermidis-associated mice treated or not with antiretroviral drugs. Cell suspensions obtained from ear epidermis were incubated with the following antibodies: anti-CD16/32 (93), anti-CD31 (MEC13.3), anti-CD34 (RAM34), anti-CD45 (30-F11), anti-CD49f (eBioGoH3), anti-Sca-1 (D7) in the presence of DAPI. Interfollicular epidermis keratinocytes were sorted by flow cytometry on a FACSAria (BD Biosciences) as DAPInegCD45–CD31–CD34–CD49f+Sca-1+cells.
Due to the hash tagging, the Chromium Single Cell Controller (10X Genomics) was overloaded with 45,000 cells (3,000 cells per sample) per lane and the library was prepared following the 10X Genomics guidelines.

treatment_protocol: WT mice (n = 5 per group) were unassociated or S. epidermidis-associated and treated with vehicle or antiretroviral drugs by oral gavage, beginning at 1 week before S. epidermidis association for a total of 3 weeks.

value: WT

value: skin keratinocytes


title: Mouse Keratinocyte Staphylococcus epidermidis NIHLM087 colonized Control Diet Replicate 1 Experiment 1


title: Mouse Keratinocyte Staphylococcus epidermidis NIHLM087 colonized Control Diet Replicate 2 Experiment 1


title: Mouse Keratinocyte Unassociated on Control diet Replicate 1 Experiment 1


title: lane3_keratinocytes_HTO

source_name: keratinocyte single cell HTO hash tags from lane 3 of 10X data set


title: lane3_keratinocytes_mRNA

description:
treatment: control, S. epi and S. epi + anti-RT
scRNA_seq_keratinocytes_filtered.rds

source_name: keratinocyte single cell mRNA from lane 3 of 10X data set

value: mixed sample (non-demultiplexed)


title: lane1_keratinocytes_HTO

source_name: keratinocyte single cell HTO hash tags from lane 1 of 10X data set


title: lane2_keratinocytes_mRNA

source_name: keratinocyte single cell mRNA from lane 2 of 10X data set


title: lane4_keratinocytes_mRNA

source_name: keratinocyte single cell mRNA from lane 4 of 10X data set


title: lane1_keratinocytes_mRNA

source_name: keratinocyte single cell mRNA from lane 1 of 10X data set


title: Mouse Keratinocyte Unassociated on High Fat diet Replicate 3 Experiment 1


title: Mouse Keratinocyte Staphylococcus epidermidis NIHLM087 colonized High Fat Diet Replicate 2 Experiment 1


title: CHO1R

status: Public on Apr 07 2021

first: Judy

last: Cho

state: NY

address: 1470 Madison Avenue, 8th Fl., Box 1498;

department: Pathology, Molecular and Cell-Based Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing:
FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grch38 human
Cell barcodes and unique molecular identifiers (UMIs) were extracted and “Raw” UMI matrix generated for each sample
extracted cell-barcodes associated with at least 500 UMIs from the “Raw” output UMI matrices of CellRanger
Downstream analysis was performed using Seurat v3.1
Genome_build: Hg38

source_name: Biopsy

extract_protocol:
Colon tissues were collected in ice cold RPMI 1640 (Corning Inc.) and processed within one hour after termination of the surgery
Epithelial cells were dissociated by incubating the biopsies in an EDTA-enriched dissociation medium
After digestion, the cell suspension was filtered through a 70mm cell strainer, washed in DBPS / 2% FCS / 1mM EDTA and spun down at 400 g for 10 min. After red blood cell lysis (BioLegend), dead cells were depleted using the dead cell depletion kit (Miltenyi Biotec, Germany), following manufacturer’s recommendations
Single cells were processed through the 10X Chromium Single Cell Platform using the Chromium Single Cell 3′ Library and Gel Bead Kit v2 (10X Genomics, PN-120237) and the Chromium Single Cell A Chip Kit (10X Genomics, PN-120236) as per the manufacturer’s protocol
Libraries were sequenced on an Illumina NextSeq 500

tag: patient id

value: Biopsy

value: Rectum

tag: inflammation status

value: INFLAMED

tag: patient age range at the time of sample collection

value: adulthood

value: Epithelial cells +Lamina propria cells


title: lane2_keratinocytes_HTO

source_name: keratinocyte single cell HTO hash tags from lane 2 of 10X data set


title: UC91INF


title: CHO4R


title: 726UN

value: Sigmoid

value: UNINFLAMED


title: 726INF


title: UC92MAR


title: WT/B6 mouse 1 DMXAA injected

status: Public on Mar 26 2021

city: Worcester

first: Katherine

middle: A

last: Fitzgerald

state: Massachusetts

address: 364 Plantation Street

department: Medicine

institute: Umass Chan Medical

hyb_protocol: standard NanoString protocol

scan_protocol: standard NanoString protocol

data_processing:
Raw data was log 2 normalized
Normalized data was plotted as heat map

label: NanoString

source_name: Spleen

label_protocol: Next, 50 ng of RNA was hybridized and quantified with a custom  probe set using t he NanoString nCounter analysis system  (NanoString Technologies

extract_protocol: Total RNA was i solated ( Qiazol; Qiagen) and quantitated via a  Nanodrop ND-1000 spectrophotometer ( Thermo Scientific).


title: cGAS KO /B6 mouse 1


title: cGAS/Mrl mouse 1


title: cGAS/Mrl mouse 4


title: WT/B6 mouse 1


title: XV rep2

status: Public on Mar 23 2021

first: Jun

last: Kim

address: 100 Washington Square East 1009 Silver Center

department: Biology

institute: NYU

description: ExpXV_DJ52_2_ypT47genome_10000_score.bedgraph

data_processing:
Basecalls were performed using CASAVA version 1.8.
Paired end Illumina sequence reads were mapped using default parameters of the juicer pipeline (version=1.5.7) as described in (Durand et al., 2016). For insertions and fusion strains, the reference genome was modified to match the genetic changes. For downstream analysis, inter_30.hic outputs from juicer pipeline were converted to h5 file to be used in HiCExplorer (version=3.5.1)(Ramirez et al., 2018; Wolff et al., 2018). Matrices of replicates were combined using hicSumMatrices. Each replicate or each summed matrix were normalized to match the depth of the smallest matrix in comparison using hicNormalize with the option --smallest. The replicate and summed matrices were ICE normalized using hicCorrectMatrix with the following parameters: --correction_method ICE, -t 1.7 5, --skipDiagonal, --chromosomes I II III IV V X or I II III IV XV for X-V fusion.
The insulation scores were computed using the 10kb-binned normalized matrix function hicFindTADs with the following parameters: --correctForMultipleTesting fdr, --minDepth 80000, --maxDepth 200000, --step 40000. For 2kb-binned normalized matrix, the following parameters were used: --correctForMultipleTesting fdr, --minDepth 16000, --maxDepth 40000, --step 8000. Output score.bedgraph was compared between experimental conditions. The bedgraph file was converted to bigwig using BedgraphToBigwig utility provided from UCSC website (Kent, Zweig, Barber, Hinrichs, & Karolchik, 2010).
In silico 4C plots were generated using the chicViewpoint function of hicexplorer with the following parameters: --averageContactBin 3 --range 20000000 20000000. The plotted values indicate relative contact scores out of 1000. The background model for chicViewpoint was generated using the summed wildtype matrix using the chicViewpointBackgroundModel function.
Genome_build: WS220
Supplementary_files_format_and_content: hic matrix files
Supplementary_files_format_and_content: bedgraphs containing insulation scores
Supplementary_files_format_and_content: bedgraphs containing in silico 4C

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Embryos were isolated by bleaching gravid adults grown on plates at 20C.

extract_protocol:
Frozen embryos were then resuspended in and crosslinked with 2% formaldehyde in M9 for another 30 mins. The embryos were spun down at 6000g for 30 sec and washed once with 100mM Tris Cl pH 7.5 and twice with M9. The embryo pellet was resuspended in 1 ml embryo buffer (110 mM NaCl, 40 mM KCl, 2 mM CaCl2, 2 mM MgCl2, 25 mM HEPES-KOH pH 7.5) containing 1 unit chitinase (Sigma), digested approximately 15 minutes, blastomeres were washed with embryo buffer twice by spinning at 1000g 5 min. The pellet was resuspended in Nuclei Buffer A (15 mM Tris   HCl pH 7.5, 2 mM MgCl2,0.34 M Sucrose,0.15 mM Spermine, 0.5 mM Spermidine, 1 mM DTT,0.5 mM PMSF (1X Calbiochem Protease Inhibitor cocktail I), 0.25% NP-40, 0.1% Triton X-100), centrifuged at 1000g for 5 minutes at 4C then resuspended in 1.5 mL Nuclei Buffer A. The embryos were then dounced 10X with a loose pestle and 10X with a tight pestle. The nuclei were separated from the cellular debris through spinning down the dounced material at 200G, then collecting the supernatant containing the nuclei into a separate tube. The pellet was resuspended in 1.5mL and the douncing process was repeated four times. Each individual supernatant containing nuclei was checked for quality by DAPI staining and those without debris were pooled and spun down at 1000G for 10 mins at 4C. Approximately 20 ul nuclei pellet were used to proceed to Arima Hi-C per the manufacturer's instructions.
Library preparation was performed using the KAPA Hyper Prep Kit using the protocol provided by Arima.

treatment_protocol: Embryos were treated with 2% formaldehyde for 30 minutes, washed with M9, and collected by centifugation and freezing at -80C until extract preparation.

tag: developmental stage

value: mixed embryo

value: X;V fusion


title: WT/Mrl mouse 1


title: WT/Mrl mouse 3


title: UC93HEALTHY


title: BR01 rep3

description: ExpFLIP_insulation_BR01_DJ60_2_DJ68_DJ69_10000_score.bedgraph


title: WT/Mrl mouse 2


title: XV rep1-1Xlinked


title: CHO4S


title: BR01 rep2


title: CHO1S


title: LS01 rep3

description:
ExpTRIPLE_insulation_LS01_DJ53_2_DJ64_DJ64_1_2000_score.bedgraph
ExpTRIPLE_4C_DJ53_2_DJ64_DJ64_1_2000_sw3_center.bedgraph
ExpTRIPLE_4C_DJ53_2_DJ64_DJ64_1_2000_sw3_left.bedgraph
ExpTRIPLE_4C_DJ53_2_DJ64_DJ64_1_2000_sw3_right.bedgraph


title: BR01 rep1


title: LS05 rep1

description: ExpFLIP_insulation_LS05_DJ65_DJ66_10000_score.bedgraph


title: WT/B6 mouse 2 DMXAA injected


title: cGAS/Mrl mouse 3


title: Block rep1

value: pySi[Pfib-1:NLS:scFv:sfGFP/unc-119(+) ] I; pySi[Pfib-1:NLS:dCas9:24xGCN4/unc-119(+) ] II; unc-119(ed3)?III; pyIs(pU6:sgRNA-X227/Punc-122:mcherry).


title: LS05 rep2


title: cGAS/Mrl mouse 2


title: input_GFP_JZ2005_emb_rep1

data_processing:
Basecalls were performed using CASAVA version 1.8.
We aligned 50-75bp single-end ChIP-seq reads to C. elegans genome version WS220 using bowtie2 2.3.2 with default parameters (Langmead & Salzberg, 2012). Bam files were then sorted and indexed using samtools version 2.1.1 (Ramirez-Gonzalez, Bonnal, Caccamo, & Maclean, 2012). ChIP enrichment was normalized by either subtracting or dividing it by the input using DeepTools bamCompare using the following parameters: CPM, bin-size of 10bp, ignore duplicates, extend reads to 200bp, exclude chrM and remove blacklisted regions (Ho et al., 2014).For analyzing ChIP-seq data across the X chromosomal repeat block, --very sensitive option was used in bowtie2 and --minMappingQuality was removed for bamCompare.
MACS2 version 2.1.1 was used for fragment size prediction and for peak calling. For single replicate peak calling a minimum false discovery rate of .05 was used and for merged replicates a minimum false discovery rate of .01 was used to call significant peaks. Bedtools intersect was used to determine overlapping peaks between replicates and only those present in the majority of the replicates were chosen as final peaks.
Genome_build: WS220
Supplementary_files_format_and_content: ChIP to input CPM normalized ratio bigwig files for each replicate
Supplementary_files_format_and_content: ChIP to input CPM normalized ratio bigwig files averages
Supplementary_files_format_and_content: Bed files containing ChIP-seq peaks called by MACS2

extract_protocol:
Embryos were washed and dounced in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). 0.1 sarkosyl was added before sonicating to obtain chromatin fragments of majority between 200-800 bp. 1-2 mg of embryo extract and 3-5 ug of antibody was used per ChIP. Half of the ChIP DNA were ligated to Illumina or home-made multiplexed adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

tag: chip antibody


title: LS01 rep2


title: LS01 rep1


title: WT rep2

description:
ExpFLIP_insulation_N2_DJ73_DJ74_10000_score.bedgraph
ExpTRIPLE_insulation_N2_DJ73_DJ74_2000_score.bedgraph
ExpTRIPLE_4C_DJ73_DJ74_2000_sw3_center.bedgraph
ExpTRIPLE_4C_DJ73_DJ74_2000_sw3_left.bedgraph
ExpTRIPLE_4C_DJ73_DJ74_2000_sw3_right.bedgraph

value: Wild-type


title: input_GFP_JZ2005_emb_rep2


title: WT rep1

description:
ExpFLIP_insulation_N2_DJ73_DJ74_10000_score.bedgraph
ExpBLOCK_DJ73_10000_score.bedgraph
ExpTRIPLE_insulation_N2_DJ73_DJ74_2000_score.bedgraph
ExpTRIPLE_4C_DJ73_DJ74_2000_sw3_center.bedgraph
ExpTRIPLE_4C_DJ73_DJ74_2000_sw3_left.bedgraph
ExpTRIPLE_4C_DJ73_DJ74_2000_sw3_right.bedgraph


title: GFP-JZ2005_emb_ChIP_rep2

tag: antibody target

value: GFP

value: Abcam AB290

tag: antibody antigen

value: Recombinant full length protein corresponding to GFP. Green fluorescent protein (GFP) from Aequorea victoria.

tag: matching input


title: GFP-JZ2005_emb_ChIP_rep1


title: input_DPY27_JZ2005_emb_rep2


title: input_DPY27_JZ2005_emb_rep1


title: DPY27-JZ1973_emb_ChIP_rep1

value: pySi[Pfib-1:NLS:scFv:sfGFP/unc-119(+) ] I; pySi[Pfib-1:NLS:dCas9:24xGCN4/unc-119(+) ] II; unc-119(ed3) III

value: DPY-27 JL


title: DPY27-BR01A_emb_ChIP_rep3

description: DPY27_BR01A_emb_avg_JK12_JK23_JK24_ratio.bw


title: DPY27-BR01A_emb_ChIP_rep2


title: input_BR01A_emb_rep2


title: DPY27-BR01A_emb_ChIP_rep1


title: input_BR01A_emb_rep1


title: input_LS05_emb_rep1


title: DPY27-LS05_emb_ChIP_rep1


title: LS01_emb_RNA_rep3

data_processing:
Basecalls were performed using CASAVA version 1.8.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using cufflinks version 2.2.0 using default parameters supplying gene annotations. FPKMs values were converted to TPMs.
Raw counts for each gene were generated using htseq-count version 0.6.1p1 using default parameters.
Genome_build: WS220
Supplementary_files_format_and_content: TPM text file contains the TPM values for each gene for each replicate
Supplementary_files_format_and_content: Tab-delimited text files include DESEQ2 outputs
Supplementary_files_format_and_content: RNAseq counts text file contains the raw counts for each gene for each of the replicates

growth_protocol: For mixed embryo collections, asynchronus parents were heat shocked at 35C for 30 minutes and were then allowed to recover at RT for 2 hours. Adult worms were then bleached and embryos were collected.

extract_protocol:
RNA was extracted by freeze cracking by freezing in liquid nitrogen and thawing at 37C water bath five times. RNA was isolated according to the manufacturer's (Invitrogen) Trizol extraction protocol. Purified total RNA was cleaned up through Qiagen RNeasy column. mRNA was purified from .5-10 ug of total RNA using Sera-Mag Oligo(dT) beads (ThermoScientific). cDNA preparation was done in the presence of dUTP to prepare stranded RNA-seq libraries as in PMID:19620212
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Packed embryos were resuspended in 10V of Trizol and frozen at -80C.


title: input_COP325_emb_rep2


title: LS01_emb_RNA_rep2


title: DPY27-COP325_emb_ChIP_rep2

description:
DPY-27_COP325_emb_avg_LW24_LW35_ratio.bw
DPY-27_COP325_emb_avg_LW24_LW35_chip_peaks.bed


title: input_COP325_emb_rep1


title: COP325_emb_RNA_rep3

value: knuIs6[pSE-02 undisclosed, unc-119(+))] I; unc-119(ed3) III


title: COP325_emb_RNA_rep2


title: input_LS01_emb_rep1_rep2


title: input_JZ1973_emb_rep1


title: DPY27-JZ2005_emb_ChIP_rep2


title: DPY27-COP325_emb_ChIP_rep1


title: COP325_emb_RNA_rep1


title: DPY27-SEA14_emb_ChIP_rep2

description:
DPY-27_SEA14_emb_avg_LAS04_LAS05_ratio.bw
DPY-27_SEA14_emb_avg_LAS05_LAS04_chip_peaks.bed


title: DPY27-LS01_emb_ChIP_rep2

description:
DPY-27_LS01_emb_avg_LAS06_LAS07_ratio.bw
DPY-27_LS01_emb_avg_LAS06_LAS07_chip_peaks.bed


title: input_SEA14_emb_rep1_rep2


title: DPY27-SEA14_emb_ChIP_rep1


title: DPY27-LS01_emb_ChIP_rep1


title: input_COP284_emb_rep3

value: knuSi254[SNP400bprex-1, unc-119(+)] II; unc-119(ed3) III


title: LS01_emb_RNA_rep1


title: input_COP284_emb_rep2


title: DPY27-COP284_emb_ChIP_rep4

description:
DPY-27_COP284_emb_avg_SE278_LW13_LW14_LW23_ratio.bw
DPY-27_COP284_emb_avg_LW14_LW23_SE278_LW13_chip_peaks.bed


title: input_COP284_emb_rep1


title: input_BR01A_emb_rep3


title: DPY27-JZ2005_emb_ChIP_rep1


title: input_LS05_emb_rep2


title: DPY27-COP284_emb_ChIP_rep3


title: DPY27-COP284_emb_ChIP_rep2


title: s5a_HSCactivated_miRcontrol

status: Public on Mar 11 2021

description: HSCmiR_05a_activated_hsc_mir_control_hs_rz_truseqv2_rnaseq_S9

data_processing:
The Illumina TruSeq RNA kit was used for 80nt/single end reads, 4 samples were run per lane using the standard Truseq indices.  Raw cDNA reads are aligned to the mm10 reference with the spliced gap aligner STAR, with count-based quantitation carried out via the Subread package featureCounts at the geneic levels for annotation builds.
Genome_build: mm10
Supplementary_files_format_and_content: gct format; the read count for each gene

growth_protocol: C57BL/6J (Stock# 000664) and SCID mice (Stock# 001913) were purchased from The Jackson Laboratory and maintained in the specific-pathogen-free (SPF) rooms of Center for Comparative Medicine (CCM) at Massachusetts General Hospital (MGH) with 12-hour light-dark cycles.

extract_protocol:
Total RNA from each sample was collected using TRIzol (Invitrogen) and quantified by nanodrop (Thermo Fisher). Only RNA samples with RNA integrity number (RIN) > 9 by Agilent 2100 bioanalyzer (Cat# G2939BA, Agilent Technologies) were used.
RNA-Seq libraries were prepared by using TruSeq kit (Cat# RS-122-2001, Illumina)
NextSeq genome sequencer (Cat# SY-415-1002, Illumina), 80nt, Single-End Read, 4 samples per lane

value: hepatic stellate cells (HSCs)

tag: cell status


title: DPY27-COP284_emb_ChIP_rep1

tag: genotype


title: DPY27-LS05_emb_ChIP_rep2


title: s3b_HSCactivated_miR15a

description: HSCmiR_03b_activated_hsc_mir_15a_hs_rz_truseqv2_rnaseq_S6


title: WT rep 1-1Xlinked


title: s1a_HSCquiescent

description: HSCmiR_01a_qhsc_hs_rz_truseqv2_rnaseq_S1

source_name: HSCquiescent

value: quiescent


title: s3a_HSCactivated_miR15a

description: HSCmiR_03a_activated_hsc_mir_15a_hs_rz_truseqv2_rnaseq_S5


title: s2a_HSCactivated

description: HSCmiR_02a_activated_hsc_hs_rz_truseqv2_rnaseq_S3

source_name: HSCactivated

value: activated


title: s1b_HSCquiescent

description: HSCmiR_01b_qhsc_hs_rz_truseqv2_rnaseq_S2


title: s2b_HSCactivated

description: HSCmiR_02b_activated_hsc_hs_rz_truseqv2_rnaseq_S4


title: PGR-B:OE replicate 4

status: Public on Feb 24 2021

description:
PGRmBOE_swRNA72
mRNA
processed data file: combined_gene_featureCounts_table1.txt

data_processing:
RTAVersion2.4.11 software was used for NextSeq basecalling.
Sequenced reads with low-quality or adaptor sequence were filtered out, and rRNA reads were removed by mapping to mouse rRNA sequences using bowtie2 (v2.2.5).
Preprocessed reads were normalized and mapped to mm10 whole genome using STAR v2.7.0f.
Fragment counts per gene were calculated with featureCounts command provided by Subread program (v1.6.4).
Differential expressed genes were identified using R package DESeq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: combined_gene_featureCounts_table1.txt: Tab-delimited text file includes gene length and feature count values for each sample.

source_name: Uterine tissue

extract_protocol:
Tissues were homogenized by the bead Mill 24 homogenizer (15-340-163, Fisher Scientific, Waltham, MA) in Bead Mill Tubes (15-340-154 Fisher Scientific, Waltham, MA) with 1 mL Trizol (15596026, Thermo Fisher Scientific, Waltham, MA). Tissue debris was pelleted and removed by centrifugation at 12000 xg for 10 minutes at 4°C. After adding 200 uL 1-Bromo-3-chloropropane, samples were manually shaken for 20 seconds followed by incubation at room temperature for 3 minutes. Phase separation was conducted by centrifugation at 12000 xg for 18 minutes at 4°C. The RNA containing aqueous layer was retained and subsequently mixed with 500 uL 200 proof ethanol. The mixture was then passed through the RNA binding column of RNeasy Mini Kit (74104, Qiagen, Germantown, MD), followed by washing and elution steps described in the manufacturer’s handbook.
RNA libraries were prepared for sequencing using the Illumina TruSeq RNA Library Prep Kit.
Paired end, 75bp.

tag: tissue

value: Uterine tissue

tag: genotype/variation

value: Myh11Cre; LSLPGRB/+


title: PGR-B:OE replicate 2

description:
PGRmBOE_swRNA70
mRNA
processed data file: combined_gene_featureCounts_table1.txt


title: PGR-A:OE replicate 3

description:
PGRmAOE_swRNA67
mRNA
processed data file: combined_gene_featureCounts_table1.txt

value: Myh11Cre; LSLPGRA/+


title: PGR-B:OE replicate 3

description:
PGRmBOE_swRNA71
mRNA
processed data file: combined_gene_featureCounts_table1.txt


title: PGR-A:OE replicate 4

description:
PGRmAOE_swRNA68
mRNA
processed data file: combined_gene_featureCounts_table1.txt


title: PGR-A:OE replicate 1

description:
PGRmAOE_swRNA65
mRNA
processed data file: combined_gene_featureCounts_table1.txt


title: PGR-B:OE replicate 1

description:
PGRmBOE_swRNA69
mRNA
processed data file: combined_gene_featureCounts_table1.txt


title: Myh11Cre replicate 1

description:
Myh11Cre_swRNA61
mRNA
processed data file: combined_gene_featureCounts_table1.txt


title: Myh11Cre replicate 3

description:
Myh11Cre_swRNA63
mRNA
processed data file: combined_gene_featureCounts_table1.txt


title: Myh11Cre replicate 2

description:
Myh11Cre_swRNA62
mRNA
processed data file: combined_gene_featureCounts_table1.txt


title: s5b_HSCactivated_miRcontrol

description: HSCmiR_05b_activated_hsc_mir_control_hs_rz_truseqv2_rnaseq_S10


title: Myh11Cre replicate 4

description:
Myh11Cre_swRNA64
mRNA
processed data file: combined_gene_featureCounts_table1.txt


title: 202_smp_83

status: Public on Jan 27 2021

type: genomic

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software v3.2
Processed data matrix includes Average Beta values.

label: Cy5 and Cy3

source_name: bone marrow aspirate

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted  using the QIAamp DNA Blood Mini Kit (Qiagen, Werfen).

value: bone marrow aspirate

tag: diagnosis

value: high-risk Myelodysplastic Syndromes and secondary Acute Myeloid Leukemia

tag: time afer diagnosis

tag: treatment

value: other

tag: response


title: 198_smp_81


title: 197_smp_81


title: 196_smp_81

value: DX

value: YES


title: 195_smp_80

value: > or equal to 12M

value: AZA


title: 194_smp_80


title: 192_smp_79

value: NO


title: 193_smp_80


title: 190_smp_78


title: 189_smp_78


title: PGR-A:OE replicate 2

description:
PGRmAOE_swRNA66
mRNA
processed data file: combined_gene_featureCounts_table1.txt


title: 188_smp_78


title: 173_smp_74


title: 172_smp_74


title: 166_smp_71


title: 165_smp_71


title: 186_smp_77


title: 200_smp_82


title: 171_smp_74


title: 168_smp_73


title: 153_smp_64


title: 160_smp_69


title: 167_smp_72


title: 155_smp_65


title: 158_smp_67


title: 152_smp_64


title: 151_smp_64


title: 159_smp_68


title: 150_smp_64


title: 191_smp_CTR

value: CTR


title: 147_smp_63


title: 146_smp_62


title: 140_smp_60


title: 139_smp_60


title: 138_smp_60


title: 169_smp_73


title: 137_smp_59


title: 135_smp_58


title: 161_smp_69


title: 134_smp_58


title: 133_smp_57


title: 132_smp_57


title: 131_smp_57


title: 129_smp_CTR


title: 125_smp_CTR


title: 124_smp_54


title: 120_smp_53


title: 121_smp_CTR


title: 118_smp_52


title: 119_smp_52


title: 122_smp_54


title: 115_smp_51


title: 117_smp_52


title: 114_smp_51


title: 111_smp_50


title: 113_smp_51


title: 109_smp_49


title: 105_smp_47


title: 103_smp_CTR


title: 99_smp_44


title: 107_smp_48


title: 102_smp_45


title: 128_smp_56


title: 101_smp_45


title: 95_smp_44


title: 98_smp_44


title: 127_smp_56


title: 96_smp_44


title: 97_smp_44


title: 92_smp_41


title: 91_smp_41


title: 89_smp_40


title: 87_smp_39


title: 85_smp_39


title: 86_smp_39


title: 123_smp_54


title: 84_smp_38


title: 80_smp_38


title: 83_smp_38


title: 78_smp_37


title: 75_smp_34


title: 76_smp_35


title: 94_smp_43


title: 74_smp_34


title: 70_smp_32


title: 71_smp_32


title: 52_smp_22


title: 68_smp_31

value: POST TPH


title: 67_smp_31


title: 60_smp_25


title: 62_smp_27


title: 51_smp_21


title: 53_smp_22


title: 57_smp_CTR


title: 65_smp_30


title: 82_smp_38


title: 47_smp_19


title: 81_smp_38


title: 50_smp_21


title: 45_smp_18


title: 46_smp_18


title: 41_smp_CTR


title: 38_smp_16


title: 39_smp_16


title: 40_smp_16


title: 37_smp_15


title: 36_smp_15


title: 31_smp_CTR


title: 23_smp_11


title: 59_smp_25


title: input_COP284_emb_rep4

tag: strain

value: mixed embryo

value: knuSi254[SNP400bprex-1, unc-119(+)] II; unc-119(ed3) III


title: 30_smp_14


title: 17_smp_7


title: 22_smp_10


title: 16_smp_6


title: 18_smp_7


title: 13_smp_CTR


title: 28_smp_13


title: 20_smp_9


title: 15_smp_6


title: 9_smp_5


title: 7_smp_3


title: 44_smp_18


title: 14_smp_6


title: 6_smp_CTR


title: 35_smp_15


title: 5_smp_2


title: 26_smp_12


title: 4_smp_2


title: 19_smp_8


title: Mouse uterus PPD4.5-cKO5

status: Public on Dec 08 2020

data_processing:
Raw reads of 75 nucleotides, paired-end filtered for quality score > 20.
Reads were mapped to the mouse genome (Genome Reference Consortium Mouse Build 38 from December 2011) using Tophat version 2.0.4 and assembled using Cufflinks version 2.0.2.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM was calculated for each gene in each sample by using Cufflinks version 2.0.2.

source_name: Uterine RNA from WNK1 knock-out mice

extract_protocol:
RNA was extracted using TRIzol according to manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole uterus


title: Mouse uterus PPD4.5-cKO1


title: Mouse uterus PPD4.5-cKO4


title: Mouse uterus PPD4.5-control1

source_name: Uterine RNA from control mouse


title: Mouse uterus PPD4.5-cKO3


title: Pgrcre/+Foxl2LsL/+uterus  Rep2

status: Public on Nov 06 2020

data_processing:
Raw reads of 75 nucleotides, paired-end filtered for quality score > 20 using "filterPE.pl"
Agilgn reads to mm10 genome using STAR aligner (V2.5.2b)
Count reads mapped to each gene using featureCounts ( v1.5.0-p1) function in Subread program
Differential gene expression using R package "DESeq2" (DESeq2_1.12.4).
Genome_build: mm10
Supplementary_files_format_and_content: FPKM was calculated for each gene in each sample by using featureCounts ( v1.5.0-p1) function in Subread program

source_name: Uterus

tag: age

value: 12 weeks old

tag: estrous stage

value: diestrus

value: Uterus


title: Pgrcre/+Foxl2LsL/+uterus  Rep3


title: Mouse uterus PPD4.5-control4


title: Mouse uterus PPD4.5-cKO2


title: Pgrcre/+ uterus Rep2

value: Pgrcre/+


title: Pgrcre/+Foxl2LsL/+uterus  Rep1


title: AG9_CD8AB

status: Public on Oct 07 2020

data_processing:
Following sample de-multiplexing, reads were quality-checked with command-line versions of FastQC and Cut-adapt, and aligned to genomic coordinates of the capture region in the AGM genome (chr11:6815343-6835391, ver ChlSab 1.1) with Bismark bisulfite read mapper (42). Coverage files containing CpG methylation frequency of the capture regions were further processed with the R package Bsseq (43).
Genome_build: NC_023652.1
Supplementary_files_format_and_content: .cov files are output from the R package 'Bsseq' correspond to CpG methylation frequency by coordinate within the capture region

organism: Chlorocebus pygerythrus

source_name: Spleen CD8AB+ T cell

extract_protocol:
To assess CpG methylation across the 20kb region encompassing CD4 regulatory regions, genomic DNA from CD4+, CD4-CD8aa+, and CD4-CD8ab+ T cells of cryopreserved AGM splenic cell suspensions was isolated using the Qiagen allprep DNA/RNA isolation kit (Qiagen).
At least 3ug of genomic DNA was sheared with a Covaris sonicator (Woburn, MA) to 100-175nt fragment sizes. Library preparation was then followed in exact accordance to the Agilent methylseq library prep protocol.  In brief, DNA libraries were prepared first by repairing and dA-tailing the 3’ end of the DNA fragments.  Methylated adapters were subsequently ligated onto the DNA fragments.  Genomic DNA libraries were then hybridized with proprietary hybridization probes designed by Agilent (Santa Clara, CA) to be complimentary to the 20kb capture region of the CD4 locus and incubated overnight at 65 C.  Hybridized fragments were then captured with streptavidin beads, washed, and subsequently deaminated with the EZ DNA methylation lightning kit (Zymo Research).  Bisulfite-converted libraries were indexed, amplified with 12 PCR cycles and subsequently pooled for sequencing on an HTseq 4000 (Illumina).

value: Spleen

tag: cell type

value: Spleen CD8AB+ T cell


title: Mouse uterus PPD4.5-control3


title: AG37_CD8AB


title: Mouse uterus PPD4.5-control2


title: AG37_CD8AA

source_name: Spleen CD8AA+ T cell

value: Spleen CD8AA+ T cell


title: Pgrcre/+Foxl2LsL/+uterus  Rep4


title: Pgrcre/+ uterus Rep4


title: Pgrcre/+ uterus Rep1


title: AG35_CD8AB


title: AG16_CD8AB


title: AG9_CD8AA


title: 8_smp_4

value: bone marrow aspirate

value: high-risk Myelodysplastic Syndromes and secondary Acute Myeloid Leukemia

value: DX

value: other


title: AG16_CD8AA


title: AG37_CD4

source_name: Spleen CD4+ T cell

value: Spleen CD4+ T cell


title: CL7P: CFSE low

data_processing:
Files containing sequence reads and corresponding quality scores from all nonhuman primate samples were aligned to the Mmul_8.0.1 rhesus macaque genome assembly and annotation with STAR (ver2.7.3a) at default parameters (Dobin, Bioinformatics ’10). Bam files were sorted by genomic coordinate with SamTools (Li, Bioinformatics ’09) and subsequently counted with HTseq (Anders, Bioinformatics ’15).  Parwise comparisons of gene counts were performed with DEseq2 (Love, Genome Biol ’14) and all genes with a logCPM < 30 were omitted from any downstream analysis. A p value of <0.01 when corrected for multiple comparison testing (Benjamini-Hochsberg) was used to define genes as significantly differentially expressed.
Genome_build: Mmul_8.0.1
Supplementary_files_format_and_content: tab delimited text files correspond to transcript read counts calculated by Htseq-count

organism: Macaca mulatta

source_name: Peripheral blood CD4+ T cells

extract_protocol:
Total RNA was isolated following the Qiagen RNeasy Micro Kit protocol. Samples were purified through Qiagen columns with on-column DNase treatment for 15 minutes
. Libraries were made from purified total RNA using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit protocol. rRNA was removed from samples by denaturing and then purified on rRNA removal beads. RNA was then fragmented and primed with random hexamers for first-strand synthesis in a single step on a thermocycler for 8 minutes at 94°C. First-strand synthesis immediately followed using Superscript II polymerase (Invitrogen) on a thermocycler with the following parameters: 25°C for 10mins, 42°C for 15 mins and 70°C 15 mins. In order to determine which strand the transcript was transcribed from, dUTP's were used instead of dTTP's during the second strand synthesis. Single adenines were added to the blunted ds cDNA. Illumina adapters containing unique dual-indices were ligated to each library. This allows the samples to be multiplexed on the sequencer. Libraries containing Illumina adapters were enriched using 15-18 cycles of PCR.  Libraries were sequenced on an Illumina HiSeq 2500 (Illumina. San Diego, CA).

treatment_protocol: For in vitro stimulation, peripheral blood mononuclear cell suspensions were labeled with CellTrace CFSE (ThermoFisher.  Waltham, MA) and sorted for CD4+ T cells on a BD FacAria II.  Cells were subsequently cultured in RPMI supplemented with 10% fetal bovine serum, 100 IU/ml Penicillin, 100 ug/ml Streptomycin, and 2.5mM glutamine (all from Gibco. Waltham, MA) in the presence of 1ug/ml Staphylococcal entrotoxin B (SEB) and autologous HLA-DR+CD11b+ antigen presenting cells.  After 5 days of culture, responding cells were re-sorted on the basis of CD4 expression, CFSE dye dilution, and CD69 expression, lysed in 350ul RLT buffer supplemented with 1% b-2-mercaptoethanol (Qiagen. Germantown, MD) and preserved at -80C until further processing.

value: SEB stimulation

value: Blood

value: Peripheral blood CD4+ T cells

tag: dividing cells

value: CFSE low


title: A364: CFSE low


title: CL86: CFSE low


title: AG35_CD4


title: AG35_CD8AA


title: R302: CFSE low CD4 medium

organism: Erythrocebus patas

tag: cd69/cd4 expression

value: CD4 medium


title: EMJ: CFSE low


title: EMJ: CFSE high CD69 pos

value: CFSE high

value: CD69 pos


title: A364: CFSE high CD69 pos


title: R302: CFSE high CD69neg


title: CL7P: CFSE high CD69 pos


title: CL86: CFSE high CD69neg


title: R304: CFSE low CD4 low

value: CD4 low


title: AG9_CD4


title: CL86: CFSE high CD69 pos


title: R302: CFSE low CD4 low


title: EMJ: CFSE high CD69neg


title: AG23: CFSE low CD4 low


title: R304: CFSE low CD4 high

value: CD4 high


title: R304: CFSE low CD4 medium


title: AG23: CFSE low CD4 medium


title: R304: CFSE high CD69neg


title: AG36: CFSE low CD4 low


title: AG23: CFSE low CD4 high


title: R302: CFSE low CD4 high


title: R304: CFSE high CD69 pos


title: AG16_CD4

value: Spleen


title: A364: CFSE high CD69neg


title: AG36: CFSE low CD4 medium


title: R303: CFSE low CD4 low


title: R303: CFSE low CD4 high


title: AG36: CFSE high CD69neg


title: R303: CFSE high CD69neg


title: AG28: CFSE low CD4 low


title: AG36: CFSE high CD69 pos


title: R294: CFSE low CD4 low


title: AG28: CFSE low CD4 medium


title: R294: CFSE low CD4 medium


title: AG28: CFSE low CD4 high


title: R294: CFSE high CD69neg


title: R294: CFSE low CD4 high


title: R294: CFSE high CD69 pos


title: AG28: CFSE high CD69 pos


title: AG28: CFSE high CD69neg


title: AG32: CFSE low CD4 low


title: AG32: CFSE low CD4 high


title: AG32: CFSE low CD4 medium


title: AG32: CFSE high CD69neg


title: AG32: CFSE high CD69 pos


title: R303: CFSE high CD69 pos


title: PFC-WT70-2-2

status: Public on Oct 01 2020

city: Nijmegen

first: Jo Huiqing

last: Zhou

address: Geert Grooteplein 26/28

country: Netherlands

institute: Radboud University

description:
rat_WT_PFC_FPKM_table.txt
Identical (raw data, processed data) to GSM2107395

data_processing:
42bp reads were mapped to the rat genome build rn4 using bwa version 0.6.1
BedGraph tracks were generated from BAM files using 'bedtools genomecov', normalized using the '-scale' option
Genome_build: rn4
Supplementary_files_format_and_content: Gzip-compressed bedgraph files that can be uploaded to the UCSC genome browser as custom tracks.
Supplementary_files_format_and_content: Tab-separated file with normalized Ensembl gene expression values in Fragments per Kilobase per Million mapped reads (FPKM) for all samples, as calculated by the cufflinks program.

organism: Rattus norvegicus

source_name: PFC, WT70

extract_protocol:
RNA extraction was carried out using RNeasy lipid tissue kit (QIAGEN, Venlo, The Netherlands)
2.5 μg RNA was used for rRNA depletion using the Ribo‐Zero rRNA Removal Kit (Human/Mouse/Rat, Epicentre, Madison, Wisconsin, USA) according to the manufacturer's recommendations. RNA fragmentation reactions were performed using fragmentation buffer (5x; 200 mM Tris‐Ac, 500 mM potassium‐Ac, 150 mM magnesium‐Ac, pH 8.2) in a final concentration of 1x per reaction. Fragmentation reactions were incubated at 95°C for 4 min on a thermal cycler and placed on ice for 10 min. Fragmented rRNA-depleted RNA was purified using ethanol precipitation, First and second strand synthesis was performed as described by Kouwenhoven and colleagues (2015). samples were prepared for sequencing by end repair of 5 ng total DNA as measured by Qubit dsDNA HS (Invitrogen). NEXTflex adaptors (Bioo scientific, Austin, Texas, USA) were ligated to the DNA fragments, followed by post-ligation cleanup using Agencourt AMPure XP beads (Beckman Coulter, Woerden, The Netherlands), library amplification by PCR (10 cycles) and size selection (∼300 bp) using Agencourt AMPure XP beads (Beckman Coulter). Quality control of DNA libraries prepared for sequencing was performed by qPCR and by running the products on a Bioanalyzer (Bio-Rad, Veenendaal, The Netherlands). Cluster generation and sequencing (50 bp, single end reads) was performed with the Illumina HiSeq 2000 sequencer according to standard Illumina protocols. Samples were sequenced to a depth of approximately 29 million reads per sample. Reads were aligned to the rn4 rat genome assembly using the gsnap program

value: Wistar

value: WT

tag: developmental stage

value: Post-natal day 70

value: prefrontal cortex


title: PFC-WT70-3-1

description:
rat_WT_PFC_FPKM_table.txt
Identical (raw data, processed data) to GSM2107397


title: PFC-WT70-2-3

description:
rat_WT_PFC_FPKM_table.txt
Identical (raw data, processed data) to GSM2107396


title: PFC-WT70-3-3

description:
rat_WT_PFC_FPKM_table.txt
Identical (raw data, processed data) to GSM2107398


title: PFC-WT21-16-2

description:
rat_WT_PFC_FPKM_table.txt
Identical (raw data, processed data) to GSM2107389

source_name: PFC, WT21

value: Post-natal day 21


title: PFC-WT35-10-2

description:
rat_WT_PFC_FPKM_table.txt
Identical (raw data, processed data) to GSM2107390

source_name: PFC, WT35

value: Post-natal day 35


title: PFC-WT35-10-4

description:
rat_WT_PFC_FPKM_table.txt
Identical (raw data, processed data) to GSM2107391


title: PFC-WT21-15-2

description:
rat_WT_PFC_FPKM_table.txt
Identical (raw data, processed data) to GSM2107387


title: CL7P: CFSE high CD69neg


title: PFC-WT70-4-1

description:
rat_WT_PFC_FPKM_table.txt
Identical (raw data, processed data) to GSM2107399


title: PFC-WT35-8-4

description:
rat_WT_PFC_FPKM_table.txt
Identical (raw data, processed data) to GSM2107394


title: AG36: CFSE low CD4 high


title: PFC-WT14-20-2

description:
rat_WT_PFC_FPKM_table.txt
Identical (raw data, processed data) to GSM2107381

source_name: PFC, WT14

value: Post-natal day 14


title: PFC-WT8-27-4

description:
rat_WT_PFC_FPKM_table.txt
Identical (raw data, processed data) to GSM2107379

source_name: PFC, WT8

value: Post-natal day 8


title: PFC-WT14-20-4

description:
rat_WT_PFC_FPKM_table.txt
Identical (raw data, processed data) to GSM2107382


title: Stage 5 rRNA, COX2, COX3 deplete, 65ºC

status: Public on Oct 02 2020

city: Pittsburgh

first: Miler

middle: T

last: Lee

state: PA

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

description:
xl_tpm.tsv
st5_rrna_cox_65

data_processing:
Reads were mapped to the X. laevis v9.2 or GRCz11 (zebrafish) genomes using HISAT2 v2.0.5 (--no-mixed --no-discordant)
Mapped reads were assigned to genes (Xenbase v9.2 models for X. laevis and Ensembl r99 for zebrafish) using featureCounts v1.5.1 in reversely-stranded paired-end mode with default parameters.
Transcripts per million per gene were calculated in R using gene lengths output by featureCounts
Genome_build: X. laevis v9.2
Genome_build: GRCz11
Supplementary_files_format_and_content: Tab-delimited transcripts per million (TPM) per gene

organism: Xenopus laevis

source_name: Whole embryos

extract_protocol:
For X. laevis, 2 embryos were pooled for RNA extraction; for D. rerio, 20 embryos or 10 fin clips were pooled. Samples were snap frozen in a 1.5ul tube and homogenized with a pestle in 500ul of TRIzol Reagent (Invitrogen #15596026) followed by 100ul of chloroform. Tubes were spun at 18,000 x g at 4C for 15 minutes, the aqueous phase was transferred to a fresh tube with 340 ul of isopropanol and 1 ul of GlycoBlue (Invitrogen #AM9515), then precipitated at -80C for 1 hour. Precipitated RNA was washed with cold 75% ethanol and resuspended in 50ul of nuclease-free water. Concentration was determined by NanoDrop. RNA was stored at -80C until use.
For rRNA depletion, 1ul of antisense nuclear rRNA oligos (final concentration 0.4 uM per oligo) and 1ul of antisense mitochondrial rRNA (plus any other targeted gene) oligos (final concentration 0.1 uM per oligo) were combined with 1ug of total RNA in a 10ul buffered reaction volume (100mM Tris-HCl  pH 7.4, 200mM NaCl, 10mM DTT), heated at 95C for 2 minutes and cooled to 22C at a rate of 0.1C/s in a thermocycler. Next, 10U of thermostable RNaseH (NEB #M0523S) and 2uL of provided 10X RNaseH buffer were added and volume brought to 20uL with nuclease-free water. The reaction was incubated at 65C for 5 minutes (standard) or 45C for 30 minutes, then 5U of TURBO DNase (Invitrogen #AM2238) and 5uL of provided 10x buffer was added, volume brought to 50uL with nuclease-free water and incubated at 37C for 30 minutes. The reaction was purified and size selected to >200 nts using Zymo Clean and Concentrator-5 (Zymo #D4013) according to manufacturer’s protocol, eluting in 10uL of nuclease-free water. For poly(A) selection, the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490L) was used according to the manufacturer’s protocol: 1 ug of total RNA was denatured at 65C for 5 minutes then hybridized to buffered dT magnetic beads at room temperature for 2 minutes. Selected RNA was eluted in 50uL of Tris buffer at 80C for 2 minutes and rehybridized to the same beads for a second round of selection at room temperature for 2 minutes. Re-selected RNA was eluted in a final volume of 17 uL of Tris buffer. Strand-specific RNA-seq libraries were constructed using NEB Ultra II RNA-seq library kit (NEB #E7765) according to manufacturer’s protocol with fragmentation in first-strand buffer at 94C for 15 minutes. Following first and second strand synthesis, DNA was purified with 1.8X AmpureXP beads (Beckman #A63880), end repaired, then ligated to sequencing adaptors diluted 1:5. Ligated DNA was purified with 0.9X AmpureXP beads and PCR amplified for 8 cycles, then purified again with 0.9X AmpureXP beads. Libraries were verified by Qubit dsDNA high sensitivity (Invitrogen #Q32851) and Fragment Analyzer prior to multiplexed sequencing (paired end 38/37bp) on an Illumina NextSeq 500 at the Health Sciences Sequencing Core at Children's Hospital of Pittsburgh.

tag: processing

value: rRNA depleted, COX2 and COX3 depleted


title: PFC-WT8-27-2

description:
rat_WT_PFC_FPKM_table.txt
Identical (raw data, processed data) to GSM2107378


title: PFC-WT8-25-3

description:
rat_WT_PFC_FPKM_table.txt
Identical (raw data, processed data) to GSM2107376


title: PFC-WT21-15-3

description:
rat_WT_PFC_FPKM_table.txt
Identical (raw data, processed data) to GSM2107388


title: PFC-WT8-26-1

description:
rat_WT_PFC_FPKM_table.txt
Identical (raw data, processed data) to GSM2107377


title: PFC-SERT-KO70-6-1

source_name: PFC, SERT KO70

value: SERT knock-out


title: PFC-WT35-11-4

description:
rat_WT_PFC_FPKM_table.txt
Identical (raw data, processed data) to GSM2107393


title: PFC-SERT-KO70-6-2


title: PFC-WT35-11-1

description:
rat_WT_PFC_FPKM_table.txt
Identical (raw data, processed data) to GSM2107392