title: RBJ-/- colon tumor, AOM/DSS-untreated

city: Shanghai

first: Taoyong

address: 800 Xiangyin Road

institute: Second Military Medical University

description: Gene expression data from RBJ KO colon

hyb_protocol: The hybridization was done at the Shanghai Biotechnology Corporation (Shanghai, China). Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat #900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat #00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat #00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: The scanning was done at the Shanghai Biotechnology Corporation (Shanghai, China). Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US). The genes in each Matrix template are arranged according to affymetrix probe set id.

label: Biotin

source_name: Colon tumor RNA, untreated

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’ IVT Express Kit (Cat #901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA at the Shanghai Biotechnology Corporation (Shanghai, China).

extract_protocol: Total RNA was isolated from the entire colon from each mouse using the TRIZOL method (InVitrogen), followed by digestion with RNase-free DNase (Qiagen) and purification on RNeasy spin columns using RNeasy Minikit (Qiagen).

treatment_protocol: RBJ+/+ and RBJ-/- mice (5/group) were either untreated or treated with AOM (12 mg/kg) on day 0. On day 7, 3 cycles of DSS (2.5%, 3%, 3% in drinking water; 7 days/cycle) were itiated, each separated by 14 days of vehicle control (water). Mice were sacrificed on day 80 day after AOM treatments.Tumor tissues in distal colon of the mice were prepared for total RNA individually. Equal amounts of RNA derived from 3 individual mice per group were mixed together, and assayed for gene expression using Affymetrix mouse 430 2.0 arrays.

tag: strain

value: 17-19 weeks

tag: genotype/variation

value: RBJ-/-

tag: site

value: Distal colon


title: RBJ+/+ colon tumor, AOM/DSS-treated

status: Public on Jul 01 2021

type: RNA

last: Chen

country: China

description: Gene expression data from normal colon tumor

molecule: total RNA

organism: Mus musculus

source_name: Colon tumor RNA, on day 80 after AOM treatment

tag: age

value: RBJ+/+


title: RBJ+/+ colon tumor, AOM/DSS-untreated

description: Gene expression data from normal colon


title: RBJ-/- colon tumor, AOM/DSS-treated

description: Gene expression data from RBJ KO colon tumor

source_name: Colon tumor RNA, on day 81 after AOM treatment


title: hiPSC line_19

type: genomic

city: New York

first: Shuibing

state: NY

address: A 827B, 1300 York Ave

department: Surgery

country: USA

institute: Weill Cornell Medical College

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
Genotyping was performed using the default parameters in the Birdseed v2 algorithm of Genotyping Console (GTC) 4.2 software (Affymetrix). As a quality control for the genotyping, Contrast QC values were calculated as implemented in the GTC 4.2, and samples used passed the recommended values. Genome annotations applied in data analysis referred to the human reference assembly GRCh37/hg19 as provided by the Affymetrix annotation file
primary data description: Genotype-matrix_42_hPSC_lines.txt contains Genotype Call (SNP call, Forward Strand Base Calls): AA, AT, AC, AG, TT, TC, TG, CC, CG, GG, and NoCall; 'Signal' = Summarized signal

label: cy3, cy5

molecule: genomic DNA

organism: Homo sapiens

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: cells were culture in mTESR medium and passaged every 5 days.

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

tag: cell type

value: induced pluripotent stem cell (iPSC) line


title: Developing mouse embryo sections E01G02_S337

type: SRA

city: Seattle

first: Sanjay

middle: R

last: Srivatsan

state: WA

address: 3720 15TH Ave NE Genome Sciences S Foefe Bldg

department: Genome Sciences

institute: University of Washington

description:
Developing mouse embryo sections
sci-Space Slides 1-6
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell

library_source: transcriptomic

data_processing:
Basecalls performed using bcl2fastq version 2.20
Poly-dT adapters were trimmed using Trimmomatic and aligned to mm10 using STAR. Mapped reads were then deduplicated and assigned to a gene (GENCODE vM15 - mouse). UMIs were enumerated for each cell/gene combination and finally a count matrix was made.
Count matrix was loaded into Monocle3 for further analysis
Genome_build: mm10
Supplementary_files_format_and_content: Count Matrix (matrix marker file- .mtx), Cell Metadata (tab separated values- .tsv), Gene Metadata (tab separated values- .tsv)

molecule: polyA RNA

source_name: E14 saggital sections 8-10um thick

extract_protocol:
Nuclei were extracted with a permeabilization buffer, sonicated and fixed. cDNA molecules within nuclei are extracted after tagmentation through the use of denaturants.
3' end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis, tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it, a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.

tag: genotype

tag: tissue

value: E14 Mouse Embryo

tag: sample type

value: Sagigital section


title: Exp1 72h UL79HF Flavo dTAG Pro-seq

city: Iowa City

first: Jeffery

middle: L

last: Meier

state: IA

address: SW34 GH, Department of Internal Medicine, University of Iowa. 200 Hawkins Drive

department: Departments of Internal Medicine and Epidemiology

institute: University of Iowa and Iowa City Veterans Affairs Health Care System

data_processing:
Adapter trimming using trim_galore 0.4.4.
Alignment of trimmed reads to concatenated hg38 (human), FJ616285.1 or KF297339.1 (Towne and TB40, respectively), and, for samples that included moth spike-in cells, JQCY02.1 (spodoptera) genome assemblies.
Deduplication of mapped reads according to unique molecular identifiers using dedup (https://github.com/P-TEFb/dedup).
Reads were parsed out based on the genome to which they aligned.
Bedgraphs were generated using bedTools genomecov 2.26 and Data were normalized by library size and spike-in reads accorind to Ball et. al. (2019, PMID: 30743000).
Bigwigs were generated using kentUtils.
Custom UCSC track hubs were set up for Towne and TB40/E data.
For analysis of host transcription effects upon depletion of UL87LTF or UL79LTF and annotation of gene 5' ends based on PRO-Seq data, we applied a new truQuant algorithm that utilizes our previously published tsrfinder tool. Our application of these tools is described in the manuscript. Source code is avaliable on GitHub at https://github.com/meierjl/truQuant.
Genome_build: hg38 (human), FJ616285.1 (HCMV Towne), KF297339.1 (HCMV TB40/E), JQCY02.1 (Spodoptera).
Supplementary_files_format_and_content: bigwigs contain PRO-Seq pileups, bigwigs for ChIP-Seq samples

source_name: HCMV-infected primary human foreskin fibroblast

growth_protocol: HFF were isolated and cultured as described in the manuscript. Cells were maintained in Minimum Essential Medium and grown to confluence for at least one week before infection. All HFF used for these studies were at passage number ≤ 6.

extract_protocol:
Nuclei isolation was carried out as described in Parida et. al. (2019, PMID: 30755505) and Li et. al. (2020, PMID: 32251483) .
PRO-Seq library preparation to extract and sequence nascent RNAs and ChIP-seq library preparation to extract and sequence is carefully detailed in the manuscript and was carried out as previously described by  Li et. al. (2020, PMID: 32251483), with noted modifications.

treatment_protocol:
Cells were treated with the indicated drugs (dTAG 6h and Flavo 1h) during the final hours of infection before harvest.
HFF were infected with the indicated virus at an MOI of 1-3 for the indicated duration. Cells were treated with the indicated drugs (dTAG, Flavo, and/or PFA) or appropriate vehicle controls for the indicated times during the final hours of infection before harvest.

value: HFF

tag: infection

value: HCMV strain TB40 BAC4

tag: infection duration

value: 72 hours

tag: ltf depletion

tag: treatment

value: dTAG 6h and Flavo 1h

tag: fraction

value: nascent RNA


title: IRIS, 15913

city: Salvador

first: Artur

middle: Trancoso Lopo

last: Queiroz

address: Rua Waldemar Falcão, 121

country: Brazil

institute: Instituto Gonçalo Moniz

data_processing:
bcl2fastq software (Illumina inc.)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with trimmomatic, then mapped to transcriptome GRCh38 version using salmon
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample and Matrix table with raw mRNA counts for every mRNA and every sample

source_name: whole blood

extract_protocol:
RNA was isolated using the miRNeasy Serum/Plasma Advanced Kit (50) (cat# 217204) according to the manufacturers’ recommendation (QIAGEN).
The library preparation was done using the QIAseq RNA Library Kit (QIAGEN). A total of 5ul total RNA was converted into RNA NGS libraries. Adapters containing UMIs were ligated to the RNA. Then RNA was converted to cDNA. The cDNA was amplified using PCR (22 cycles) and during the PCR indices were added. After PCR, the samples were purified. Library preparation QC was performed using either Bioanalyzer 2100 (Agilent) or TapeStation 4200 (Agilent).

tag: disease state

value: IRIS

tag: iris condition

value: Mycobacterial

tag: gender

value: Female

tag: bmi

value: whole blood


title: Exp1 72h UL79HF Flavo Pro-seq

treatment_protocol:
Cells were treated with Flavo 1 h and DMSO 6h during the final hours of infection before harvest.
HFF were infected with the indicated virus at an MOI of 1-3 for the indicated duration. Cells were treated with the indicated drugs (dTAG, Flavo, and/or PFA) or appropriate vehicle controls for the indicated times during the final hours of infection before harvest.

value: Flavo 1h and DMSO 6h


title: Developing mouse embryo sections E01G06_S145


title: Developing mouse embryo sections E01G01_S241


title: Developing mouse embryo sections D12G06_S144


title: not IRIS, 15912

value: not IRIS

value: not Mycobacterial

value: Male


title: WT_IL-1B_rep3_P-4_G03

city: Research Triangle Park

first: Christopher

last: Corton

state: NC

address: 109 TW Alexander Dr.

institute: US-EPA

data_processing:
TempO-Seq data are analyzed using the Tempo-SeqR software package which uses the statistical computing language R. The input data analyzed was taken from the FASTQ files. Each file was aligned to a pseudo-transcriptome input using the Bowtie algorithm. The data analysis output is a table of counts with each column representing a sample and each row representing a gene.
Supplementary_files_format_and_content: a table of counts with each column representing a sample and each row representing a gene.

source_name: HeLa cells

growth_protocol: Wild-type and the NFKB1-null HeLa cells were cultured in DMEM media (GIBCO) supplemented with 10% FBS (Omega Scientific, Australia) and 1x penicillin/streptomycin/glutamine. Cells were plated at 8 x10^5 cells per well in 24-well plates and cultured for 20 hours then exposed to test chemicals for 6 hours.

extract_protocol: Following cell lysis in Trizol, total RNA was extracted from each lysate and prepared for gene expression analysis using the human 1500+ Tempo-Seq platform (BioSpyder, Inc, Carlsbad, CA).

treatment_protocol: Chemicals, purchased from Sigma-Aldrich, were ≥ 95% pure. All chemical stock solutions were made in DMSO. After 20 hours of exposure, media was replaced with dosing media containing  IL1beta (1 ng/mL), TNFalpha (5 ng/mL), chlorhexidine diacetate (50 µM), or carbocyanine (50 µM) in DMSO (0.05%). Cells were treated for 6 hours then media was removed and cells lysed with 0.3 mL Trizol.

tag: agent

tag: concentration

value: 0.1 ng/mL

value: Wild type

tag: cell line

value: HeLa


title: hiPSC line_17

value: induced pluripotent stem cell (iPSC) line


title: Exp1 72h UL79HF dTAG Pro-seq

treatment_protocol:
Cells were treated with dTAG 6h during the final hours of infection before harvest.
HFF were infected with the indicated virus at an MOI of 1-3 for the indicated duration. Cells were treated with the indicated drugs (dTAG, Flavo, and/or PFA) or appropriate vehicle controls for the indicated times during the final hours of infection before harvest.

value: HFF

value: dTAG 6h


title: not IRIS, 15911

tag: age


title: Developing mouse embryo sections D12G05_S48

value: E14 Mouse Embryo

value: Sagigital section


title: Exp1 72h UL79HF Pro-seq

treatment_protocol:
Cells were treated with DMSO 6h during the final hours of infection before harvest.
HFF were infected with the indicated virus at an MOI of 1-3 for the indicated duration. Cells were treated with the indicated drugs (dTAG, Flavo, and/or PFA) or appropriate vehicle controls for the indicated times during the final hours of infection before harvest.

tag: cell type

value: HCMV strain TB40 BAC4

value: 72 hours

value: DMSO 6h

value: nascent RNA


title: hiPSC line_16


title: Developing mouse embryo sections D12G02_S336

tag: genotype


title: IRIS, 15910

value: IRIS

tag: tissue

value: whole blood


title: IRIS, 15909


title: hiPSC line_15


title: Exp3 72h UL87HF PFA Flavo Pro-seq

treatment_protocol:
Cells were treated with the indicated drugs (PFA 72h and Flavo 1h ) during the final hours of infection before harvest.
HFF were infected with the indicated virus at an MOI of 1-3 for the indicated duration. Cells were treated with the indicated drugs (dTAG, Flavo, and/or PFA) or appropriate vehicle controls for the indicated times during the final hours of infection before harvest.

value: HCMV strain Towne BAC

value: PFA 72h and Flavo 1h


title: Developing mouse embryo sections D12G01_S240

tag: sample type


title: hiPSC line_18


title: hiPSC line_13


title: hiPSC line_14


title: not IRIS, 15907

value: not IRIS

value: not Mycobacterial

value: Female


title: hiPSC line_12


title: Developing mouse embryo sections D11G05_S47


title: PC-3_OICR-9429

city: Guangzhou

first: Qianghua

last: Zhou

address: 107th Yanjiangxi Road, Guangzhou

institute: sun yat-sen university

data_processing:
Base-calling: bcl2fastq2 v2.19.1
Data filtering : in house
Read alignment: hisat2 v2.1.0
transcript assemble: htseq-count v0.6.1
Genome_build: hg19
Supplementary_files_format_and_content: excel files include normalize values for each Sample

source_name: prostate cancer cell line PC-3

growth_protocol: DU145 was cultured in DMEM (Gibco) and PC-3 was cultured in RPMI1640 (Gibco) supplemented with 10% FBS (Biological Industries) and 1% penicillin/streptomycin (Gibco). Cells were grown in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using Trizol reagent and was further purified using Qiagen RNeasy Mini Kit according to the manufactures’ instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: OICR-9429 was  diluted at a stocking solution of 50mM in dimethyl sulfoxide (DMSO, Sigma), and DU145 and PC-3 cells were treated for 48h with 120µM and 150 μM  of OICR-9429，respectively.

value: prostate cancer

tag: inhibitor


title: IRIS, 15906

value: Male


title: not IRIS, 15908


title: Developing mouse embryo sections D11G01_S239


title: hiPSC line_11

value: induced pluripotent stem cell (iPSC) line


title: DU145_OICR-9429

source_name: prostate cancer cell line DU145


title: DU145_DMSO

value: Negetive control


title: IRIS, 15905


title: Developing mouse embryo sections D11G02_S335

value: E14 Mouse Embryo


title: IRIS, 15903

value: Mycobacterial


title: Developing mouse embryo sections D10G05_S46

value: Sagigital section


title: PC-3_DMSO


title: Developing mouse embryo sections D11G06_S143


title: hiPSC line_8


title: hiPSC line_9


title: Developing mouse embryo sections D10G02_S334


title: IRIS, 15902


title: Exp3 72h UL87HF Flavo Pro-seq

treatment_protocol:
Cells were treated with Flavo 1h and DMSO 72h during the final hours of infection before harvest.
HFF were infected with the indicated virus at an MOI of 1-3 for the indicated duration. Cells were treated with the indicated drugs (dTAG, Flavo, and/or PFA) or appropriate vehicle controls for the indicated times during the final hours of infection before harvest.

value: HFF

tag: infection

tag: infection duration

value: 72 hours

value: Flavo 1h and DMSO 72h


title: Developing mouse embryo sections D10G06_S142


title: hiPSC line_10


title: D458 shCDK7-3

city: Aurora

first: Rajeev

last: Vibhakar

state: CO

department: Pediatrics/Hematology/Oncology

institute: University of Colorado Anschutz Medical Campus

data_processing:
The reads were trimmed and clipped for quality control in Trimmomatic (v0.36).
Read quality was checked for each sample using FastQC v0.10.1.
High quality reads were then imported into STAR (v2.4.0.1) for alignment into BAM files.
The function summarizeOverlaps from the GenomicAlignments package (v1.16.0) was used to count the reads from BAM files.
DESeq2 (V1.30.0) was then used to get differential expression genes on the raw counts.
Genome_build: Alignment was initially to the transcriptome  GRCh38/hg38, and then to the genome GRCh38/hg38.
Supplementary_files_format_and_content: Raw read counts, log2FC

source_name: medulloblastom cell line D458

growth_protocol: D458 cell lines were cultured in DMEM (Gibco, Carlsbad, CA) supplemented with 10% FBS (Sigma-Aldrich), 1 mM sodium pyruvate (Gibco), 1× penicillin/streptomycin solution (Cellgro), and 1× L-glutamine (Cellgro). Cells were cultured at 37 °C with 95% air and 5% CO2.

extract_protocol:
Total RNA was isolated in triplicate from D458 cells treated with 10nM THZ1 or DMSO or shnull or shCDK7 in triplicate, using RNeasy Mini kit (Qiagen).
illumina TruSeq stranded mRNA

treatment_protocol: Cell lines were treated at 10nM THZ1 or DMSO for 48hrs before collection.  CDK7 stable knockdown cell lines were established using gene specific mission shRNAs (Cat# TRCN0000000595, TRCN0000000592, TRCN0000230910) or non-targeting control (Sigma-Aldrich).  HEK293FT cells were plated at 5x106 cells/10cm dish one day before transfection in complete media (DMEM, 10%FBS, 5% penicillin and streptomycin).  Lipofectamine 3000 (Thermo Fisher Scientific, Cat#L3000008) was diluted in Opti-MEM at a ratio of 1:16.6. P3000 was diluted at 1:25 in Opti-MEM along with 1g pMD2.G, 2 g psPAX2, and 1.2 g pLenti-shCDK7 expression vector. Both mixes were combined and incubated for 15 mins at room temperature. The mixture was added dropwise to HEK293FT cells in fresh media. 24 hours later the media was replaced with DMEM/2.5% FBS. Viral particles were collected at 48 hours in a 15 mL conical and centrifuged for 5 min at 500xg. Virus was then filtered through a 0.45 micron filter and stored in 1 mL aliquots at -80. To generate the stable knockdown cell lines, cells were plated at 5x105 in a 6-well dish in growth medium containing 8µg/mL polybrene. Viral particles were added with 8µg/mL polybrene and incubated for 7 hrs.  Transduced cells were disaggregated, grown, and selected with 1µg/mL puromycin for 14 days.  Transformants were confirmed by qRT-PCR and western blot.

tag: treatment

value: brain


title: hiPSC line_7


title: D458 shCDK7-1


title: D458 shNull-3

value: shNull


title: hiPSC line_6


title: Developing mouse embryo sections D10G01_S238


title: not IRIS, 15900

value: whole blood


title: IRIS, 15901

value: IRIS


title: IRIS, 15904


title: Developing mouse embryo sections D09G06_S141


title: hiPSC line_5


title: not IRIS, 15899

value: not IRIS


title: not IRIS, 15898

value: not Mycobacterial


title: Developing mouse embryo sections D09G05_S45


title: D458 shNull-1


title: hiPSC line_3


title: hiPSC line_2


title: D458 shCDK7-2


title: Developing mouse embryo sections D09G02_S333


title: D458 THZ2

value: THZ1 10nM


title: D458 THZ1


title: Developing mouse embryo sections D08G06_S140


title: IRIS, 15896


title: hiPSC line_1


title: D458 shNull-2


title: Developing mouse embryo sections D09G01_S237


title: D458-3

value: DMSO


title: D458-2


title: not IRIS, 15894

value: Male


title: D458-1


title: IRIS, 15895


title: OSC - Piwi-KD - HiC_rep1

city: Tokyo

first: Yuka

middle: W.

last: Iwasaki

address: 35 Shinanomachi, Shinjuku-ku,

department: Department of Molecular Biology

country: Japan

institute: Keio University School of Medicine

description: PIWImerge_40kb.ICEcor.Norm.ginteractions.tsv

library_source: genomic

data_processing:
Hi-C: HiCExplorer v3.3 software (Ramirez et al., 2018) was used for the calculation of HiC matrix, and GENOVA v1.0 was used for visualizing the results. Two replicates were performed per knockdown, and hicCorrelate was used to calculate correlation between replicate samples. Due to the high correlation between replicates, samples were combined by using hicSumMatrices for the further analysis. Bins of too low or high coverage were removed and the HiC matrix was iteratively corrected by ICE using hicCorrectMatrix. HiC matrix was further normalized between different knockdown samples using hicNormalize. TADs were defined using hicFindTADs function and matrixes were converted into ginteractions file using hicConvertFormat.
DamID-seq: Adapters were removed using cutadapt, and reads shorter than 50nt after adapter removal was discarded. damidseq_pipeline (Marshall and Brand, 2015) was used to map the reads to Drosophila melanogaster (dm3) genome, followed by normalization and background reduction. We used q-value cutoff 0 (to include multi-mapped reads), and fragment size of 300. Due to the high correlation of replicate samples, two replicate reads were merged for the further analysis. After mapping of DamID-seq reads to the genome, log2 ratio of LamDam/Dam was calculated and bedgraph file was generated using damidseq_pipeline.
ChIP-seq: For ChIP-seq analysis, adapters were removed from the reads using Cutadapt, and subsequent reads shorter than 50 nt were discarded. ChIP-seq reads were mapped to the Drosophila genome (dm3) using Bowtie 2.2.9 (Langmead and Salzberg, 2012) with the default parameters. MACS 1.4.2 (Zhang et al., 2008) was used for peak calling and generation of wig files.
Genome_build: dm3
Supplementary_files_format_and_content: Hi-C: ginteractions file (tsv format) generated using HiCExplorer v3.3 (Ramirez et al., 2018)
Supplementary_files_format_and_content: DamID-seq: bedgraph file generated using damidseq_pipeline v1.4.5 (Marshall and Brand, 2015)
Supplementary_files_format_and_content: ChIP-seq: wig file generated using MACS v1.4.2 (Zhang, 2008)

organism: Drosophila melanogaster

source_name: Ovarian Somatic Cells

growth_protocol: Ovarian somatic cells (OSCs) was established in the previous studies (Niki et al., 2006; Saito et al., 2009). OSCs were cultured in Shield and Sang M3 Insect Medium (Caisson Laboratories) supplemented with 10% fly extract, 10% fetal bovine serum, 0.6 mg/ml glutathione, and 10 μg/ml insulin.

extract_protocol:
Hi-C: Hi-C using OSCs were performed as described previously (Ulianov et al., 2016) with some minor modifications. OSCs were fixed with 1% formaldehyde for 10min, and stored at -80 degrees before usage. 5 x 10^5 cells were lysed and chromatin digested using 30G needle. Chromatin digestion was performed using HindIII restriction enzyme. Ends were filled with biotin-14-dCTP followed by blunt-end ligation. Proteins were reverse crosslinked form the cells, and DNA purification was performed. Biotin was removed from un-ligated ends and DNA was sonicated using covaris S220 (covaris). Sonicated DNA was used for biotin pull down by streptavidin conjugated to Dynabeads Streptavidin C1 beads (Invitrogen). Pulled-down DNA was used as the template to construct DNA library.
DamID-seq: Dam-ID-seq was performed as described previously (Pickersgill et al., 2006) with some modifications to analyze methylated sequences using deep-sequencing rather than microarray. DamID vectors were transfected into OSCs using Nucleofector, one day before cell harvest. pNDamMyc plasmid (van Steensel and Henikoff, 2000) was a kind gift from Dr. Bas van Steensel. Lamin was cloned into pNDamMyc vector as described previously (Pickersgill et al., 2006). Genome DNA precipitation, DpnI digestion, adapter ligation, DpnII digestion, PCR, and PCR cleanup was performed as described within “Van Steensel Lab version 28/08/2006” protocol. Obtained DNA was used as the template to prepare deep sequencing library.
ChIP-seq: ChIP was performed as described previously (Iwasaki et al., 2016). Briefly, OSCs (3×107) were fixed, lysed, and their nuclei were isolated using truChIP Chromatin Shearing Kits (Covaris), in accordance with the manufacturer’s instructions. DNA was sonicated to ~300 bases using Bioruptor (Cosmobio), and then diluted with ChIP buffer. DNA–protein complexes were incubated with antibody on Dynabeads-Protein G for 4 h, at 4 degrees. Beads were washed with ChIP buffer, high-salt lysis buffer, and wash buffer followed by TE. After reversing cross-linking for 12–16 h at 65 degrees, samples were treated with RNase for 30 min at 37 degrees and Proteinase K for 60 min at 55 degrees. DNA was then recovered.
DNA library was constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), in accordance with the manufacturer’s instructions.

treatment_protocol: For the transfection of siRNAs into OSCs, 200 pmol siRNA duplex was nucleofected into 3.0 × 10^6 cells using the Cell Line 96-well Nucleofector Kit SF (Lonza) and program DG150 of the 96-well Shuttle Device (Lonza). The siRNAs were transfected twice for 4-day KD, and once for 2-day KD. Co-transfection of siRNA and plasmid DNA was performed using the Cell Line Nucleofector Kit V (Lonza) and program T-029 of the Nucleofector II Device (Lonza).

value: Ovarian Somatic Cells

value: Piwi-KD


title: not IRIS, 15893


title: OSC - EGFP-KD - HiC_rep2

description: EGFPmerge_40kb.ICEcor.Norm.ginteractions.tsv

value: EGFP-KD


title: Developing mouse embryo sections D08G01_S236

value: E14 Mouse Embryo


title: not IRIS, 15892


title: IRIS, 15897


title: OSC - EGFP-KD - HiC_rep1


title: HBL1.DMF.20uM.48h.r3

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

country: Germany

institute: University of Münster

data_processing:
Sequenced reads of mRNA were aligned against the human transcriptome using HISAT2 [D. Kim, B. Langmead and S.L. Salzberg, HISAT: a fast spliced aligner with low memory requirements, Nat. Methods, vol. 12, no. 4, pp. 357–360, 2015.]
Gene and transcript annotations from RefSeq (GCF_000001405.38_GRCh38.p12_genomic.fna from ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/reference)
Aligned sequence counts were then aggregated for genes using RSEM [B. Li and C.N. Dewey, RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome, BMC Bioinformatics, vol. 12, p. 323, Aug. 2011.]
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: RSEM aggregation results on gene level as text files with 7 columns: gene_id transcript_id(s) length effective_length expected_count TPM FPKM

growth_protocol: RPMI-1640, 20 % FCS, Pen/Strep, Plasmocin

extract_protocol:
Qiagen RNeasy Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DMSO (control); 20 µM dimethyl fumarate in DMSO

tag: duration in hours

tag: replicate


title: HBL1.DMF.20uM.48h.r2


title: scRNAseq_ThrbPos_rep2

city: BOSTON

first: CHANGHEE

last: LEE

state: MA

address: 77 AVENUE LOUIS PASTEUR

department: Genetics

institute: Harvard Medical School

data_processing:
For 10X Chromium libraries, sequencing output was demultiplexed by Cell Ranger (version 3.0.0), then mapped with dropEst (Petukhov et al, Genome Biology 2018) pipeline
Quality score above 0.9 were filtered and then any cells more than 4,000 features filtered out for doublet removal and cells above 15% mitochondrial content removed
Genome_build: galGal5 (Ensembl, release 94, only protein coding and lincRNA with two additional transgenes MCHERRY and EGFP)
Supplementary_files_format_and_content: Seurat (v3.1.5) object with meta information; equivalent text file in market matrix format (MTX) with rownames (features) and colnames (barcodes)

organism: Gallus gallus

growth_protocol: Retina progenitor cells were cultured in DMEM with 10% FBS

extract_protocol:
Total RNA is extracted using Direct-zol RNA Kits (Zymo Research)
1ug of RNA is used to make the library using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

value: Retina Progentor Cell

tag: treatment/condition

value: ThrbPos


title: Developing mouse embryo sections D07G05_S43

value: Sagigital section


title: IRIS, 15891

tag: disease state

tag: iris condition

value: Mycobacterial

tag: gender

value: Female


title: not IRIS, 15890

tag: bmi


title: Developing mouse embryo sections D07G02_S331


title: Developing mouse embryo sections D07G06_S139


title: OSC - Piwi-KD - HiC_rep2

tag: cell line


title: HBL1.DMF.20uM.48h.r1


title: IRIS, 15889

tag: age


title: Developing mouse embryo sections D08G05_S44


title: HBL1.DMF.20uM.12h.r3


title: HBL1.DMF.20uM.24h.r1


title: JTL621_Auxin_NHS_8h_R4

city: Valhalla

first: Jian

last: Li

address: 15 Dana Road

institute: New York Medical College

description:
edgeR_depl-ctrl-germ-8h.tsv
edgeR_normcounts-germ-8h.tsv
Li_RNA_118

data_processing:
RNA-seq reads were mapped to Ensembl WBcel235 genome using RNA STAR (Dobin et al., 2013) with --alignIntronMax 120000 to set the intron size, and --outFilterMultimapNmax 200 to allow multi-mapped reads. All paired-end reads were trimmed to 50 bp to make downstream mapping and analyses consistent.
The mapped reads were then subject to FeatureCounts in Rsubread (Liao et al., 2019) for quantification with the setting -p -B -P -C -M -O --fraction –largestOverlap. The settings in STAR and FeatureCounts enabled proper quantification of those heat shock genes (e.g. hsp-70 and hsp-16s) that are duplicated in C. elegans genome.
Differential expression (DE) analyses were then done using edgeR (Robinson et al., 2010) with default settings except of using Likelyhood Ratio Test and filtering out those lowly expressed genes with CPM (counts per million) value less than 1 in more than 75% samples. For each time point, to control for effects by auxin and by insertion of AID:GFP to HSF-1, we pooled EtOH treated CA1199 and EtOH treated JTL621 with auxin treated CA1199 to calculate the expression levels in control condition, and then compare them to auxin treated JTL621. This analysis reports only DE genes caused by HSF-1 depletion (as HSF-1 depletion vs. control).
Genome_build: WS235/ce11

organism: Caenorhabditis elegans

growth_protocol: The HSF-1 AID animals (JTL621) and the corresponding control animals that only express TIR1 in the germline (CA1199) were synchronized by treatment of alkaline hypochlorite solution (bleach). Synchronized L1 larvae were grown on 10 cm normal NGM plates (~500 worms per plate) for 51 hr to develop into young adults.

extract_protocol:
RNA was extracted using 300 uL Trizol reagent. Worms were vortexed continuously for 20 minutes at 4°C and then went through one cycle of freeze-thaw to help release RNA. Following this, RNA was purified using Direct-zol RNA MiniPrep kit (Zymo Research) as per manufacturer’s instructions using on column DNase I digestion to remove genomic DNA.
Total RNAs were polyA enriched, and directional RNA-seq libraries were prepared using NEBNext Ultra II RNA library prep Kit.

treatment_protocol: For each condition, ~120 worms were transferred to either auxin or ethanol (EtOH) plates by picking, and kept for indicated time.

value: young adults

tag: tissue of tir1

value: germline

tag: strain

value: Auxin

tag: time


title: CA1199_EtOH_NHS_8h_R4

description:
edgeR_depl-ctrl-germ-8h.tsv
edgeR_normcounts-germ-8h.tsv
Li_RNA_115

value: EtOH


title: JTL621_EtOH_NHS_8h_R4

description:
edgeR_depl-ctrl-germ-8h.tsv
edgeR_normcounts-germ-8h.tsv
Li_RNA_117


title: Developing mouse embryo sections D07G01_S235

tag: genotype

tag: tissue

tag: sample type


title: JTL621_Auxin_NHS_8h_R3

description:
edgeR_depl-ctrl-germ-8h.tsv
edgeR_normcounts-germ-8h.tsv
Li_RNA_092


title: CA1199_Auxin_NHS_8h_R4

description:
edgeR_depl-ctrl-germ-8h.tsv
edgeR_normcounts-germ-8h.tsv
Li_RNA_116


title: HBL1.DMF.20uM.24h.r2


title: HBL1.DMF.20uM.12h.r2


title: IRIS, 15885

value: IRIS

value: Mycobacterial (CNS)

value: whole blood


title: IRIS, 15888

value: not Mycobacterial

value: Male


title: IRIS, 15887


title: JTL621_EtOH_NHS_8h_R3

description:
edgeR_depl-ctrl-germ-8h.tsv
edgeR_normcounts-germ-8h.tsv
Li_RNA_091


title: Developing mouse embryo sections D05G06_S137


title: Developing mouse embryo sections D06G06_S138


title: CA1199_Auxin_NHS_8h_R3

description:
edgeR_depl-ctrl-germ-8h.tsv
edgeR_normcounts-germ-8h.tsv
Li_RNA_090


title: IRIS, 15883


title: IRIS, 15886


title: not IRIS, 15880

value: not IRIS


title: HBL1.DMF.20uM.06h.r2


title: Developing mouse embryo sections D06G02_S330


title: HBL1.DMF.20uM.06h.r1


title: JTL621_EtOH_NHS_8h_R2

description:
edgeR_depl-ctrl-germ-8h.tsv
edgeR_normcounts-germ-8h.tsv
Li_RNA_059


title: HBL1.DMF.20uM.06h.r3


title: CA1199_Auxin_NHS_8h_R2

description:
edgeR_depl-ctrl-germ-8h.tsv
edgeR_normcounts-germ-8h.tsv
Li_RNA_058


title: HBL1.control.48h.r2

value: control


title: HBL1.DMF.20uM.24h.r3


title: HBL1.control.48h.r1


title: not IRIS, 15876


title: JTL621_Auxin_NHS_8h_R1

description:
edgeR_depl-ctrl-germ-8h.tsv
edgeR_normcounts-germ-8h.tsv
Li_RNA_028


title: CA1199_EtOH_NHS_8h_R2

description:
edgeR_depl-ctrl-germ-8h.tsv
edgeR_normcounts-germ-8h.tsv
Li_RNA_057


title: Developing mouse embryo sections D06G05_S42

value: E14 Mouse Embryo


title: HBL1.control.24h.r3


title: Developing mouse embryo sections D04G02_S328


title: Developing mouse embryo sections D05G05_S41


title: Developing mouse embryo sections D05G02_S329


title: not IRIS, 15879


title: Developing mouse embryo sections D06G01_S234


title: HBL1.DMF.20uM.12h.r1


title: IRIS, 15872


title: Developing mouse embryo sections D03G06_S135


title: not IRIS, 15878


title: IRIS, 15884


title: CA1199_EtOH_NHS_8h_R1

description:
edgeR_depl-ctrl-germ-8h.tsv
edgeR_normcounts-germ-8h.tsv
Li_RNA_025


title: JTL621_Auxin_NHS_8h_R2

description:
edgeR_depl-ctrl-germ-8h.tsv
edgeR_normcounts-germ-8h.tsv
Li_RNA_060


title: CA1199_EtOH_NHS_8h_R3

description:
edgeR_depl-ctrl-germ-8h.tsv
edgeR_normcounts-germ-8h.tsv
Li_RNA_089


title: IRIS, 15869


title: HBL1.control.48h.r3


title: Developing mouse embryo sections D04G06_S136

description:
Developing mouse embryo sections
sci-Space Slides 1-6
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell


title: Developing mouse embryo sections D05G01_S233


title: not IRIS, 15877


title: Developing mouse embryo sections D03G01_S231


title: Developing mouse embryo sections D04G05_S40


title: HBL1.control.24h.r2


title: not IRIS, 15875


title: Developing mouse embryo sections D04G01_S232


title: HBL1.control.06h.r3


title: IRIS, 15867


title: Developing mouse embryo sections D02G06_S134


title: CA1199_Auxin_NHS_8h_R1

description:
edgeR_depl-ctrl-germ-8h.tsv
edgeR_normcounts-germ-8h.tsv
Li_RNA_026


title: IRIS, 15870


title: HBL1.control.24h.r1


title: IRIS, 15871


title: JTL621_Auxin_NHS_24h_R3

description:
edgeR_depl-ctrl-germ-24h.tsv
edgeR_normcounts-germ-24h.tsv
Li_RNA_096


title: Developing mouse embryo sections D03G02_S327


title: HBL1.control.12h.r3


title: JTL621_EtOH_NHS_8h_R1

description:
edgeR_depl-ctrl-germ-8h.tsv
edgeR_normcounts-germ-8h.tsv
Li_RNA_027


title: HBL1.control.12h.r2


title: JTL621_Auxin_NHS_24h_R2

description:
edgeR_depl-ctrl-germ-24h.tsv
edgeR_normcounts-germ-24h.tsv
Li_RNA_064


title: CA1199_Auxin_NHS_24h_R3

description:
edgeR_depl-ctrl-germ-24h.tsv
edgeR_normcounts-germ-24h.tsv
Li_RNA_094


title: 5pcO2_r1_snRNA-seq

city: Ames

first: Geetu

last: Tuteja

address: 2106 Molecular Biology Building

department: Genetics, Development and Cell Biology

institute: Iowa State University

description: Replicate-1 of hESCs converted trophoblast cultured under 5 % O2 concentration condition

data_processing:
Library strategy: snRNAseq
Cellranger(v4.0.0) mkfastq: for adapter trimming and converting the basecalls
Cellranger (v4.0.0) counts: to align the reads on the pre-mRNA and create the read count matrices
Seurat (v3.3.22): for sample integration and vst normalization
Genome_build: GRCh38-2020-A (GRCh38)
Supplementary_files_format_and_content: text (MEX), filtered count matrices
Supplementary_files_format_and_content: text (tsv), filtered barcode tables
Supplementary_files_format_and_content: text (tsv), filtered feature tables
Supplementary_files_format_and_content: h5, raw feature bc matrices

source_name: Trophoblast nuclei

growth_protocol: hESCs (H1; WA01) originated from WiCell Research Institute, were cultured and maintained in Matrigel (BD Bioscience) coated 6-well tissue culture plates (Thermo Scientific) on mTeSR1 medium (Stemcell Technologies) under two different O2 concentration conditions (20 % and 5 %) at 37 °C.  The medium was replaced daily and cells (50,000/well) passaged approximately every 5–6 days. The cells were passaged several times to establish stable lines at both 20 % O2 and 5% O2 concentration conditions.

extract_protocol:
On day 8 of differentiation (cells cultured in BAP/DMEM/F12/KOSR for 3 days and AP/DMEM/F12/KOSR until day 8), each culture well was rinsed twice with DMEM/F12 (Thermo Scientific)  and the colonies partially dispersed by using gentle cell disassociation reagent (GDR) (Stemcell Technologies) (0.6 ml/well; 7 minutes (min)) at 37 °C. The colonies were fully dislodged from the substratum by gentle scraping and nuclei were isolated from the disassociated cells using the protocol provided by 10X genomics with minor modification. Briefly, 1 ml of chilled lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, and 0.1% Nonidet™ P40 Substitute in Nuclease-Free Water) was added to each well through a wide-bore pipet tip. After gently pipetting several times, the suspension was kept on ice for 5 min to achieve maximum lysis of cells and then centrifuged (500x g; 5 min at 4°C). The pellet was resuspended in 1 ml of nuclear wash and resuspension buffer (NWRB) (1X PBS with 1.0 % w/v bovine serum albumin) and 0.2U/μl RNase inhibitor (Roche, cat# 03335399001), cell debris was removed by filtration through a 40 µm Nylon cell strainer (Falcon), and recentrifuged as above. The supernatant solution was removed, and the final nuclear pellet suspended in 1ml of NWRB.
Libraries were constructed by following the manufacturer’s (10x Genomics) protocol with reagents supplied in 10x Genomics Chromium Next GEM Single Cell 3′ Kit v3.1.  Briefly, nuclear suspension concentration and viability (unbroken cells) were measured with an Invitrogen Countess II automated cell counter. Nuclear suspension (1000 nuclei per microliter), reverse transcription master mix, and partitioning oil were loaded on a Chromium Next GEM G chip with a nuclear capture target of 5,000 nuclei per library.  Post-Chromium controller GEMs were transferred to a PCR strip tube and reverse transcription performed on an Applied Biosystems Veriti thermal cycler at 53°C for 45 min.  cDNA was amplified for 14 cycles and purified using Axygen AxyPrep MagPCR Clean-up beads.  cDNA fragmentation, end-repair, A-tailing and ligation of sequencing adaptors was performed according to manufacturer specifications.  The final library was quantified with the Qubit HS DNA kit and the fragment size was analyzed using an Agilent Fragment Analyzer system.  Libraries were pooled and sequenced on an Illumina NovaSeq S1 flow cell with a goal to generate 50,000 reads per nucleus with a sequencing configuration of 28 base pair (bp) on read1 and 91 bp on read2.

treatment_protocol: After 24 h of passage in mTeSR1 medium, the cells were treated with DMEM/F12 medium containing knock-out serum replacement (KOSR) and low FGF2 (4 ng/ml) that had been conditioned by mouse embryonic fibroblast (MEFs) (conditioned medium + FGF2, or CM +FGF2). After the next 24 h, the conditioned medium was replaced with daily changes of DMEM/F12/KOSR medium minus FGF2 but containing BMP4 (10 ng/mL), A83-01 (1 μM), and PD1730740 (1 μM), so-called BAP treatment, for three days and then the same medium without BMP4 for the following four days (AP treatment).

tag: cell type

value: hESC-derived tropholast


title: Developing mouse embryo sections D02G01_S230


title: JTL621_EtOH_NHS_24h_R3

description:
edgeR_depl-ctrl-germ-24h.tsv
edgeR_normcounts-germ-24h.tsv
Li_RNA_095

tag: treatment


title: LACTB3

first: Yawen

last: Ma

address: No.833 Zhizaoju Road

department: ophthalmology

institute: Shanghai Ninth people's hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Clean data(clean reads) were obtained by removing reads containing adapter,reads containing ploy-Nand  low quality reads from raw data. Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two groups was performed using the DESeq2 R package(1.16.1).
ClusterProfiler R package was used to test the statistical enrichment of differential expression genes in KEGG pathways
Genome_build: GRCh38(hg38)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Melanoma

growth_protocol: MUM2B cells stably overexpressing empty vector or LACTB were cultured in RPMI 1640 medium with 10% FBS

extract_protocol:
RNA was harvested using Trizol reagent.
Sequencing libraries were generated using NEBNext UltraTM RNA Library PrepKit  with 1 ug of total RNA for the construction of sequencing libraries. The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: Cells were washed by PBS and collected

value: stable overexpression of  LACTB


title: 20pcO2_r2_snRNA-seq

description: Replicate-2 of hESCs converted trophoblast cultured under 20 % O2 concentration condition

value: BMP4 (10 ng/mL), A83-01 (1 μM), and PD1730740 (1 μM), so-called BAP treatment

value: hESCs (H1; WA01) originated from WiCell Research Institute


title: HBL1.control.12h.r1

tag: duration in hours


title: Developing mouse embryo sections D01G05_S37

value: Sagigital section


title: IRIS, 15868

value: Mycobacterial


title: Developing mouse embryo sections D02G05_S38


title: Developing mouse embryo sections D01G02_S325


title: 5pcO2_r2_snRNA-seq

description: Replicate-2 of hESCs converted trophoblast cultured under 5 % O2 concentration condition


title: HBL1.control.06h.r1

tag: replicate


title: EV2

value: stable overexpression of empty vector


title: Developing mouse embryo sections D03G05_S39


title: HBL1.control.06h.r2


title: Developing mouse embryo sections D02G02_S326


title: JTL621_EtOH_NHS_24h_R1

description:
edgeR_depl-ctrl-germ-24h.tsv
edgeR_normcounts-germ-24h.tsv
Li_RNA_031

value: young adults

value: germline


title: CA1199_EtOH_NHS_24h_R2

description:
edgeR_depl-ctrl-germ-24h.tsv
edgeR_normcounts-germ-24h.tsv
Li_RNA_061

value: EtOH


title: CA1199_EtOH_NHS_24h_R3

description:
edgeR_depl-ctrl-germ-24h.tsv
edgeR_normcounts-germ-24h.tsv
Li_RNA_093


title: EV1


title: CA1199_EtOH_NHS_24h_R1

description:
edgeR_depl-ctrl-germ-24h.tsv
edgeR_normcounts-germ-24h.tsv
Li_RNA_029


title: JTL621_Auxin_NHS_16h_R4

description:
edgeR_depl-ctrl-germ-16h.tsv
edgeR_normcounts-germ-16h.tsv
Li_RNA_112

value: Auxin


title: Developing mouse embryo sections D01G06_S133


title: 20pcO2_r1_snRNA-seq

description: Replicate-1 of hESCs converted trophoblast cultured under 20 % O2 concentration condition


title: LACTB2


title: Developing mouse embryo sections C12G06_S132


title: PAO1161 2504_2 RNA-seq

city: Warsaw

first: Joanna

last: Drabinska

state: Masovian

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics PAS

data_processing:
The raw data files were processed with the FASTQC program (ttp://www.bioinformatics.babraham.ac.uk/projects/fastqc)  to generate fastq files.
The sequenced reads were mapped with the use  of the TopHat program to the PAO1 reference genome (ASM676v1). The TopHat program was open with the fr-firststrand library preparation option  and in the no-novel-juncs mode.
The proportion of mapping reads to reference was counted (percentage). The amount of pair-end reads mapped for individual genes was counted with the use of HTseq with DNA strand distinction (–stranded=reverse). Gene annotations were assigned according to the description for the Pseudomonas aeruginosa genome from the (GCF_000006765.1_ASM676v1_genomic.gff) file.
The final results were prepared in the R environment (https://www.r-project.org/) with the use of DESeq2 (https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html) package.
Genome_build: ASM676v1
Supplementary_files_format_and_content: The tab-delimited text file "All_samples_raw_counts.txt' file contains raw counts for each sample.
Supplementary_files_format_and_content: The tab-delimited text file “PA2504-vs-PAO1161_deseq_all_genes_sorted_by_FDR.txt” contains DESeq2 processed data. It includes base mean, estimated fold change, log2 estimated fold change, not adjusted p-value, FDR adjusted p-value, standard error estimate, normalized counts for each sample, sequence ID (Seqid), start and end positions in genome, DNA strand (+ or -), gene ID, GeneBank ID and protein product description (“product”). The genesare sortedacording to the FDR adjusted p-value, from lowest to highest.

organism: Pseudomonas aeruginosa

source_name: bacterial cells

growth_protocol: The P. aeruginosa overnight L-broth cultures where dilutes 1:100 in fresh L-broth medium and were incubated in 37°C with vigorous shaking.

extract_protocol:
After 18 h of growth 1,5ml samples were taken from three independent biological replicates and immediately treated with RNAprotect Bacteria Reagent (Qiagen). RNA was isolated from the cell pellet with RNeasy Mini Kit (Qiagen). DNase I digestion using RapidOut DNA Removal Kit (Thermo Scientific) was applied to remove genomic DNA contamination. RNA quality and integrity were assessed with a Bioanalyzer (Agilent Technology), and concentration was estimated using a Nano Drop ND‐1000 spectrophotometer.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PA2504 deletant strain (PA2504)

value: stationary phase of growth of liquide bacterial culture


title: PAO1161 2504_3 RNA-seq


title: CA1199_Auxin_NHS_24h_R2

description:
edgeR_depl-ctrl-germ-24h.tsv
edgeR_normcounts-germ-24h.tsv
Li_RNA_062


title: CA1199_Auxin_NHS_24h_R1

description:
edgeR_depl-ctrl-germ-24h.tsv
edgeR_normcounts-germ-24h.tsv
Li_RNA_030


title: Developing mouse embryo sections C12G01_S228

description:
Developing mouse embryo sections
sci-Space Slides 1-6
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell


title: Developing mouse embryo sections C12G05_S36


title: dcatR rep 1

city: Seoul

first: Jung-Hye

last: Roe

address: 1 Gwanak-ro, Gwanak-gu

department: Biological sciences

country: South Korea

institute: Seoul National University

data_processing:
Adapter sequences were trimmed from raw read data using Trimmomatic v.0.36.
Processed reads were mapped to S. coelicolor A3(2) reference genome using Bowtie v.2.2.5.
Mapped read counts of each gene were calculated by featureCounts in the Subread package v.1.5.3.
Count was normalized and differential expression was assessed for features using DESeq2.
Genome_build: GCF_000203835.1
Supplementary_files_format_and_content: The tab-delimited text file includes normalized abundance measurements by DESeq2 of each genes on RefSeq NC_003888.3 (excluding pseudogenes), denoted by locus tag, for all samples.

organism: Streptomyces coelicolor

source_name: Streptomyces coelicolor A3(2) strain M145

growth_protocol: Spores were inoculated in YEME liquid media with 5 mM MgCl2 and 10% sucrose and were grown to OD600 of 0.4.

extract_protocol:
Total RNA was extracted by the modified Kirby mix method and was treated with DNase I. rRNA was removed using Ribo-Zero rRNA Removal Kit (Bacteria) (Illumina, USA) following the manufacturer's protocol.
RNA-Seq library was prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina, USA) following the manufacturer's protocol.

treatment_protocol: 25 μM hydrogen peroxide (H2O2) was treated at OD600 of 0.4 for 10 min.

value: catR mutant


title: EV3


title: PAO1161 WT_3 RNA-seq

value: wild type (WT)


title: Developing mouse embryo sections D01G01_S229


title: LACTB1


title: JTL621_EtOH_NHS_24h_R2

description:
edgeR_depl-ctrl-germ-24h.tsv
edgeR_normcounts-germ-24h.tsv
Li_RNA_063


title: PAO1161 2504_1 RNA-seq


title: CA1199_EtOH_NHS_16h_R4

description:
edgeR_depl-ctrl-germ-16h.tsv
edgeR_normcounts-germ-16h.tsv
Li_RNA_109


title: WT-HP rep 2

value: wild type

value: 25 uM H2O2, 10 minutes


title: PAO1161 WT_2 RNA-seq


title: JTL621_EtOH_NHS_16h_R4

description:
edgeR_depl-ctrl-germ-16h.tsv
edgeR_normcounts-germ-16h.tsv
Li_RNA_111


title: F8LHplus7

city: Milan

first: Giulia

middle: Maria

last: Scotti

state: Milan

address: Viale Rita Levi Montalcini, 1

department: National Facility for Data Handling and Analysis

country: Italy

institute: Fondazione Human Technopole

description:
Paired with corresponding F8LHplus2
counts_exp2.txt.gz

data_processing:
Low quality reads and Illumina adapters were trimmed using Trimmomatic (version 0.36)
Retained reads were mapped to the reference human genome, GRCh38, using STAR (version 2.5.3a)
Uniquely mapped reads were assigned to the corresponding genes using the featureCounts function in the Rsubread R package. Only reads mapped to exons were considered in the counting procedure. Genomic features were annotated according to Gencode basic annotations (Gencode version 26 for samples 1-20;  Gencode version 27 for samples 21-93)
Genome_build: UCSC hg38
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample

source_name: Uterine fluid derived Extracellular Vesicles

extract_protocol:
Endometrial tissue biopsies were obtained with the use of a Pipelle, immediately after UF sampling. Uterine fluid samples were obtained by lavage of the endometrial cavity with 2.5 of physiologic solution using a balloon hysterosonosonography catheter to avoid vaginal contamination. Extracellular vesicles were isolated- after mucus disgregation by vortexing- using standard ultracentrifugation protocol.  RNA was harvested using  RNase micro KIT of QIAGEN with DNAse treatment step in coloumn.
To compare the transcriptomic profile of tissues and UF-Evs (samples 1-20), cDNA libraries were generated from total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen GmbH, Vienna, Austria). To perform transcriptome sequencing on UF-EVs collected from fertile women and ART patients during the window of implantation (samples 21-93), cDNA libraries were prepared using the SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio Inc., Otsu, Shiga, Japan)

tag: population

value: Provenly fertile control women

tag: menstrual cycle phase

value: secretory

tag: mentrual cycle day (counted from the first day of menstrual bleeding and expressed as n or from the day of urinary lh surge detection and expressed an lh+n)

value: LH+7 (within window of implantation)


title: CA1199_Auxin_NHS_16h_R4

description:
edgeR_depl-ctrl-germ-16h.tsv
edgeR_normcounts-germ-16h.tsv
Li_RNA_110


title: Developing mouse embryo sections C12G02_S324

value: E14 Mouse Embryo


title: CA1199_Auxin_NHS_16h_R3

description:
edgeR_depl-ctrl-germ-16h.tsv
edgeR_normcounts-germ-16h.tsv
Li_RNA_106


title: F7LHplus2

description:
Paired with corresponding F7LHplus7
counts_exp2.txt.gz

value: Uterine fluid derived Extracellular Vesicles

value: LH+2 (pre-receptive phase)


title: WT rep 2


title: Developing mouse embryo sections C10G06_S130

value: Sagigital section


title: F9LHplus7

description:
Paired with corresponding F9LHplus2
counts_exp2.txt.gz


title: PAO1161 WT_1 RNA-seq


title: Developing mouse embryo sections C11G06_S131


title: F8LHplus2

description:
Paired with corresponding F8LHplus7
counts_exp2.txt.gz


title: REB206: UTI89 hsdS-MG1655 stat rep 3

city: Singapore

first: Swaine

state: Singapore

address: 60 Biopolis Street, Genome, #02-01

department: Medicine

country: Singapore

institute: National University of Singapore and Genome Institute of Singapore

data_processing:
Raw sequencing reads were mapped to their respective reference genomes: RefSeq accession GCF_000013265.1 for E. coli UTI89, GCF_000005845.2 for E. coli MG1655 and GCF_000007445.1 for E. coli CFT073 using BWA-MEM (version 0.7.10) with default parameters, then the resulting bam files were sorted and deduplicated using PicardTools v.2.2.2
HTseq was used to quantify sequencing reads mapping to predicted open reading frames (ORFs)
Ribosomal RNA (rRNA) and transfer RNA (tRNA) sequences (based on the corresponding Genbank RefSeq annotation) were filtered out of the data set.
R (version 2.15.1) was used for differential expression analysis, using the edgeR package (samples were normalized by TMM (trimmed median of means), common and tagwise dispersion factors were estimated using a negative binomial model, and then fold change values were calculated from these normalized counts)
Genome_build: RefSeq accession GCF_000013265.1 for E. coli UTI89, GCF_000005845.2 for E. coli MG1655 and GCF_000007445.1 for E. coli CFT073
Supplementary_files_format_and_content: Tab-delimited text files with normalized expression values, fold change, P-values, and FDR values.

organism: Escherichia coli UTI89

source_name: UTI89 hsdS-MG1655

growth_protocol: Stationary phase cells were obtained by propagating strains statically for two serial 24 hour passages at 37°C, with a 1:1000 dilution between passages (identical to the inoculum used for mouse infections). Log phase cells were obtained by diluting overnight cultures 1:100 in LB and growing to log phase (OD600 = 0.4 – 0.5) at 37°C with shaking.

extract_protocol:
RNA extraction with the Qiagen RNAEasy Mini Kit; ribosomal depletion with the Ribo Zero rRNA removal kit
RNA libraries were prepared using the ScriptSeq v2 RNA-seq library preparation kit

tag: growth condition

value: stationary phase


title: JTL621_EtOH_NHS_16h_R3

description:
edgeR_depl-ctrl-germ-16h.tsv
edgeR_normcounts-germ-16h.tsv
Li_RNA_107

value: young adults

value: germline


title: dcatR rep 2


title: Developing mouse embryo sections C11G05_S35


title: Developing mouse embryo sections C11G01_S227


title: F7LHplus7

description:
Paired with corresponding F7LHplus2
counts_exp2.txt.gz


title: F9LHplus2

description:
Paired with corresponding F9LHplus7
counts_exp2.txt.gz


title: REB204: UTI89 hsdS-MG1655 stat rep 2


title: JTL621_Auxin_NHS_24h_R1

description:
edgeR_depl-ctrl-germ-24h.tsv
edgeR_normcounts-germ-24h.tsv
Li_RNA_032

value: Auxin


title: JTL621_Auxin_NHS_16h_R2

description:
edgeR_depl-ctrl-germ-16h.tsv
edgeR_normcounts-germ-16h.tsv
Li_RNA_104


title: REB202: UTI89 hsdS-MG1655 stat rep 1


title: Developing mouse embryo sections C10G01_S226


title: JTL621_Auxin_NHS_16h_R3

description:
edgeR_depl-ctrl-germ-16h.tsv
edgeR_normcounts-germ-16h.tsv
Li_RNA_108


title: WT-HP rep 1


title: Developing mouse embryo sections C09G06_S129


title: F15LHplus7

description:
Paired with corresponding F15LHplus2
counts_exp2.txt.gz


title: F14LHplus2

description:
Paired with corresponding F14LHplus7
counts_exp2.txt.gz


title: Developing mouse embryo sections C11G02_S323

description:
Developing mouse embryo sections
sci-Space Slides 1-6
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell


title: REB200: UTI89 hsdS-MG1655 log rep 3

value: log phase


title: F16LHplus7

description:
Paired with corresponding F16LHplus2
counts_exp2.txt.gz


title: Developing mouse embryo sections C09G05_S33


title: WT rep 1


title: Developing mouse embryo sections C09G01_S225


title: JTL621_Auxin_NHS_16h_R1

description:
edgeR_depl-ctrl-germ-16h.tsv
edgeR_normcounts-germ-16h.tsv
Li_RNA_100


title: Developing mouse embryo sections C10G02_S322


title: F16LHplus2

description:
Paired with corresponding F16LHplus7
counts_exp2.txt.gz


title: JTL621_EtOH_NHS_16h_R1

description:
edgeR_depl-ctrl-germ-16h.tsv
edgeR_normcounts-germ-16h.tsv
Li_RNA_099

value: EtOH


title: CA1199_Auxin_NHS_16h_R1

description:
edgeR_depl-ctrl-germ-16h.tsv
edgeR_normcounts-germ-16h.tsv
Li_RNA_098


title: CA1199_EtOH_NHS_16h_R3

description:
edgeR_depl-ctrl-germ-16h.tsv
edgeR_normcounts-germ-16h.tsv
Li_RNA_105


title: REB203: UTI89 wt stat rep 8

source_name: UTI89 wt

value: wt


title: Developing mouse embryo sections C08G05_S32


title: Developing mouse embryo sections C08G02_S320


title: REB201: UTI89 wt stat rep 7


title: JTL621_EtOH_NHS_16h_R2

description:
edgeR_depl-ctrl-germ-16h.tsv
edgeR_normcounts-germ-16h.tsv
Li_RNA_103


title: F15LHplus2

description:
Paired with corresponding F15LHplus7
counts_exp2.txt.gz


title: Developing mouse embryo sections C10G05_S34


title: F14LHplus7

description:
Paired with corresponding F14LHplus2
counts_exp2.txt.gz


title: JTL621_Auxin_2h_HS_R3

description:
Li_RNA_088
edgeR_JTL621(germ)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_JTL621(germ)_2h.tsv

data_processing:
RNA-seq reads were mapped to Ensembl WBcel235 genome using RNA STAR (Dobin et al., 2013) with --alignIntronMax 120000 to set the intron size, and --outFilterMultimapNmax 200 to allow multi-mapped reads.
The mapped reads were then subject to FeatureCounts in Rsubread (Liao et al., 2019) for quantification with the setting -p -B -P -C -M -O --fraction –largestOverlap. The settings in STAR and FeatureCounts enabled proper quantification of those heat shock genes (e.g. hsp-70 and hsp-16s) that are duplicated in C. elegans genome.
Differential expression (DE) analyses were then done using edgeR (Robinson et al., 2010) with default settings except of using Likelyhood Ratio Test and filtering out those lowly expressed genes with CPM (counts per million) value less than 1 in more than 75% samples.
Genome_build: WS235/ce11

growth_protocol: The HSF-1 AID animals (JTL611 and JTL621) and the corresponding control animals that only express TIR1 (CA1200 and CA1199) were synchronized by treatment of alkaline hypochlorite solution (bleach). Synchronized L1 larvae were grown on 10 cm normal NGM plates (~500 worms per plate) for 51 hr to develop into young adults.

treatment_protocol: Worms were transferred to either auxin or ethanol (EtOH) plates, and kept for 2 hours. Following this, worms were either directly collected or subjected to heat shock performed in a water bath pre-heated to 34°C. For heat shock, NGM plates were wrapped with parafilm and submerged for 30 min.

value: Auxin;HS


title: JTL621_EtOH_2h_HS_R3

description:
Li_RNA_087
edgeR_JTL621(germ)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_JTL621(germ)_2h.tsv

value: EtOH;HS


title: REB197: UTI89 wt log rep 8


title: CA1199_Auxin_NHS_16h_R2

description:
edgeR_depl-ctrl-germ-16h.tsv
edgeR_normcounts-germ-16h.tsv
Li_RNA_102


title: F12LHplus2

description:
Excluded from analysis because of missing paired LHplus7 sample
counts_exp2.txt.gz


title: JTL621_Auxin_2h_NHS_R3

description:
Li_RNA_084
edgeR_JTL621(germ)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_JTL621(germ)_2h.tsv

value: Auxin;NHS


title: CA1199_EtOH_NHS_16h_R2

description:
edgeR_depl-ctrl-germ-16h.tsv
edgeR_normcounts-germ-16h.tsv
Li_RNA_101


title: JTL621_EtOH_2h_NHS_R3

description:
Li_RNA_083
edgeR_JTL621(germ)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_JTL621(germ)_2h.tsv

value: EtOH;NHS


title: REB198: UTI89 hsdS-MG1655 log rep 2


title: REB196: UTI89 hsdS-MG1655 log rep 1


title: Developing mouse embryo sections C07G02_S319

description:
Developing mouse embryo sections
sci-Space Slides 1-6
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell

data_processing:
Basecalls performed using bcl2fastq version 2.20
Poly-dT adapters were trimmed using Trimmomatic and aligned to mm10 using STAR. Mapped reads were then deduplicated and assigned to a gene (GENCODE vM15 - mouse). UMIs were enumerated for each cell/gene combination and finally a count matrix was made.
Count matrix was loaded into Monocle3 for further analysis
Genome_build: mm10
Supplementary_files_format_and_content: Count Matrix (matrix marker file- .mtx), Cell Metadata (tab separated values- .tsv), Gene Metadata (tab separated values- .tsv)


title: SC13M

city: Madrid

first: Odei

last: Barreñada

address: C/ Ramiro de Maeztu 9

country: Spain

institute: CIB Margarita Salas - CSIC

description: Total RNA < 100 bp length

data_processing:
Illumina Casava1.7 software used for base-calling.
The raw sequences obtained from short RNA sequencing were trimmed to eliminate the adapters, discarding sequences under 28 Phred score using Trim Galore script (http://www.bioinformatics.babraham.ac.uk/projects/trim_ galore/). Trimmed sequences quality was assessed by FastQC software (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) ensuring the correct processing of the trimming. Clean sequences were collapsed using the FASTX-Toolkit suite (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Additionally, to enrich in the most representative sequences all the sequences under 10 counts per million (CPM) were discarded
By Bowtie aligner the two types of sncRNAs, miRNAs and piRNAs, were identified using miRBase version 22.1 (Kozomara et al., 2019) allowing 2 mismatches  and by a custom piRNA-IPdb allowing 1 mismatch (Larriba and del Mazo, 2018) from https://odbt.github.io/ respectively
Genome_build: mm39
Supplementary_files_format_and_content: Tab-delimited text files include raw count values for each Sample

source_name: Somatic gonadal cell, Male, E13.5

growth_protocol: Pathogen-free (SPF), temperature (22°C ± 1°C), humidity (50%-55%). All animals were housed on a 12 h light/dark cycles with ad libitum access to food and water.

extract_protocol:
Mus musculus CD1 strain was used as animal model. PGCs and somatic gonadal cells were isolated from embryos obtained from pregnant females at E11.5, E12.5 and E13.5. At E11.5 and E12.5, male and female gonads are morphologically indistinguishable at early stages of development. To sex embryos at E11.5 and E12.5, we isolated and stored individually each set of gonads in PBS at 4ºC. Sex was identified in each single embryo by PCR of DNA, obtained from the heads, using primers to identify the presence of Sry gene and Jarid1d (a single band for XX and a double band for XY). After sexing the embryos, the mesonephros was removed before the purification of germ and somatic cells. PGCs and somatic cells were purified using a paramagnetic technology according to Brieño-Enriquez et al. 2015. Briefly, groups of about 80 gonads were incubated in 0.25% trypsin-EDTA during 15 minutes at 37ºC, washed followed by incubation with PGC-specific antibodies (anti-CD15) bound to paramagnetic-microbeads. Finally, PGCs were isolated from somatic stromal cells by a magnetic column (miniMAcs) and stained both separated fractions with the naphtol AS-MX/ FAST-RED (Sigma-Aldrich) (PGC specific) to determine the level of enrichment of cell populations. In all cases, the enrichment of the PGCs was 93-96%. Similarly, the purity of somatic cells was over 90% in all samples. RNA libraries were prepared for sequencing using standard Illumina protocols.
Libraries were prepared according to Illumina's instructions
RNA-seq (size fractioning)

value: Gonad

value: somatic gonadal cell

tag: gender

value: Male


title: REB205: UTI89 wt stat rep 9

last: Chen


title: Developing mouse embryo sections C06G06_S126

first: Sanjay

last: Srivatsan

institute: University of Washington

extract_protocol:
Nuclei were extracted with a permeabilization buffer, sonicated and fixed. cDNA molecules within nuclei are extracted after tagmentation through the use of denaturants.
3' end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis, tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it, a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.

value: E14 Mouse Embryo


title: JTL621_EtOH_2h_HS_R2

description:
Li_RNA_055
edgeR_JTL621(germ)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_JTL621(germ)_2h.tsv


title: REB199: UTI89 wt log rep 9


title: Developing mouse embryo sections C07G01_S223


title: SC12M

description: Total RNA < 100 bp length

source_name: Somatic gonadal cell, Male, E12.5


title: SC12F

description: Total RNA < 100 bp length

source_name: Somatic gonadal cell, Female, E12.5

value: Female


title: CA1199_EtOH_NHS_16h_R1

description:
edgeR_depl-ctrl-germ-16h.tsv
edgeR_normcounts-germ-16h.tsv
Li_RNA_097


title: JTL621_EtOH_2h_NHS_R2

description:
Li_RNA_051
edgeR_JTL621(germ)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_JTL621(germ)_2h.tsv


title: Developing mouse embryo sections C09G02_S321

source_name: E14 saggital sections 8-10um thick

value: Sagigital section


title: JTL621_Auxin_2h_HS_R1

description:
Li_RNA_024
edgeR_JTL621(germ)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_JTL621(germ)_2h.tsv


title: Developing mouse embryo sections C07G05_S31


title: SC11F

description: Total RNA < 100 bp length

source_name: Somatic gonadal cell, Female, E11.5


title: Developing mouse embryo sections C06G01_S222


title: REB195: UTI89 wt log rep 7


title: Developing mouse embryo sections C07G06_S127


title: Developing mouse embryo sections C08G06_S128


title: SC13F

description: Total RNA < 100 bp length

source_name: Somatic gonadal cell, Female, E13.5


title: JTL611_EtOH_2h_HS_R3

description:
Li_RNA_071
edgeR_JTL611(soma)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_JTL611(soma)_2h.tsv

value: soma


title: JTL621_Auxin_2h_NHS_R2

description:
Li_RNA_052
edgeR_JTL621(germ)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_JTL621(germ)_2h.tsv

value: young adults


title: PGC12M

description: Total RNA < 100 bp length

source_name: Primordial Germ Cell, Male, E12.5

value: Primordial germ cell


title: PGC13M

description: Total RNA < 100 bp length

source_name: Primordial Germ Cell, Male, E13.5


title: Developing mouse embryo sections C06G05_S30


title: JTL611_Auxin_2h_NHS_R3

description:
Li_RNA_068
edgeR_JTL611(soma)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_JTL611(soma)_2h.tsv


title: Developing mouse embryo sections C04G06_S124


title: Developing mouse embryo sections C06G02_S318


title: JTL621_Auxin_2h_NHS_R1

description:
Li_RNA_020
edgeR_JTL621(germ)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_JTL621(germ)_2h.tsv

value: germline


title: JTL621_Auxin_2h_HS_R2

description:
Li_RNA_056
edgeR_JTL621(germ)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_JTL621(germ)_2h.tsv


title: Postpubertal TG Stem Cell 10X

city: Bryan

first: Robin

last: Fuchs-Young

state: TX

address: 8441 Riverside Pkwy

department: Molecular Cellular Medicine

institute: Texas A&M University Health Science Center

description: RFY7BTG_matrix.mtx, RFY7BTG_genes.tsv, RFY7BTG_barcodes.tsv

data_processing:
DESeq2 was used to normalize read data and generate gene expression matrices
Read processing performed using Cell Ranger 3.1.0 with default parameters
Quality control and downstream analyses performed using the Cell Ranger Single Cells software
Filtering was performed as follows:  Libraries with <200 and >6000 genes detected were excluded.  RNA spike-in controls and cells with a percentage of total reads that aligned to the mitochondrial genomes >10% were also removed.
Seurat was used to normalize read data and identify clusters
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression matrix with log-normalized data for every gene and sample

source_name: MaSCs

extract_protocol:
Mammary epithelial cells were sorted by flow cytometry and prepared in HBSS with 2% FBS at a concentration of 1000 cells/µl
10X libraries were prepared using a 10X Genomics Chromium platform following the Single Cell 3' manufacturer's protocol recommended by the manufacturer

value: ICR

value: Mammary gland

value: 10 weeks old


title: SC11M

description: Total RNA < 100 bp length

source_name: Somatic gonadal cell, Male, E11.5


title: Developing mouse embryo sections C08G01_S224

city: Seattle

address: 3720 15TH Ave NE Genome Sciences S Foefe Bldg


title: PGC12F

description: Total RNA < 100 bp length

source_name: Primordial Germ Cell, Female, E12.5


title: JTL621_EtOH_2h_NHS_R1

description:
Li_RNA_019
edgeR_JTL621(germ)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_JTL621(germ)_2h.tsv


title: JTL611_Auxin_2h_HS_R2

description:
Li_RNA_040
edgeR_JTL611(soma)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_JTL611(soma)_2h.tsv

value: Auxin;HS


title: Postpubertal WT Stem Cell 10X

description: RFY6BWT_matrix.mtx, RFY6BWT_genes.tsv, RFY6BWT_barcodes.tsv

value: wild type


title: PGC11F

description: Total RNA < 100 bp length

source_name: Primordial Germ Cell, Female, E11.5


title: Developing mouse embryo sections C05G06_S125


title: Postpubertal TG Stem Cell C1 Biological Replicate 3

description: 08102016_biological replicate 3_all_log_transformed_counts.txt

data_processing:
Base calls performed using NextSeq 500
Quality of raw reads was checked by FASTQC.  Sequencing reads were checked for sequencing adapters and primers and low quality bases were trimmed using the FastX toolkit.  Trimmed reads were mapped to mm10 using STAR 2.5.3a.
Filtering was performed as follows:  Samples with <70% sequence alignment were excluded.  Cells showing numbers of genes detected or mapping rates that were below two times the standard deviation were filtered out.  Cells with low Actb expression were also filtered out.
HTSeq was used to generate raw read counts per gene
DESeq2 was used to normalize read data and generate gene expression matrices
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression matrix with log-normalized data for every gene and sample

extract_protocol:
Mammary epithelial cells from abdominal/inguinal mammary glands were isolated using gentle collagenase/hyaluronidase according to the manufacturer's protocol (cat# 07919; Stem Cell Technologies, Vancouver, BC, Canada)
Nextera XT libraries were prepared using the Nextera XT DNA Sample Preparation Kit and the Nextera XT Index Kit following the manufacturer's protocol


title: JTL611_EtOH_2h_NHS_R3

description:
Li_RNA_067
edgeR_JTL611(soma)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_JTL611(soma)_2h.tsv


title: Developing mouse embryo sections C03G02_S315


title: Postpubertal WT Stem Cell C1 Biological Replicate 3


title: Developing mouse embryo sections C05G02_S317


title: F6LHplus7

description:
Excluded from analysis because of missing paired LHplus2 sample
counts_exp2.txt.gz

value: Uterine fluid derived Extracellular Vesicles

value: Provenly fertile control women

value: secretory

value: LH+7 (within window of implantation)


title: Developing mouse embryo sections C04G05_S28

description:
Developing mouse embryo sections
sci-Space Slides 1-6
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell


title: JTL621_EtOH_2h_HS_R1

description:
Li_RNA_023
edgeR_JTL621(germ)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_JTL621(germ)_2h.tsv

value: EtOH;HS


title: PGC13F

description: Total RNA < 100 bp length

source_name: Primordial Germ Cell, Female, E13.5

value: Gonad


title: Developing mouse embryo sections C04G01_S220

value: E14 Mouse Embryo


title: JTL611_EtOH_2h_NHS_R2

description:
Li_RNA_035
edgeR_JTL611(soma)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_JTL611(soma)_2h.tsv

value: EtOH;NHS


title: Developing mouse embryo sections C05G01_S221

value: Sagigital section


title: Developing mouse embryo sections C02G05_S26


title: JTL611_EtOH_2h_NHS_R1

description:
Li_RNA_005
edgeR_JTL611(soma)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_JTL611(soma)_2h.tsv

value: young adults

value: soma


title: JTL611_EtOH_2h_HS_R2

description:
Li_RNA_039
edgeR_JTL611(soma)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_JTL611(soma)_2h.tsv


title: Developing mouse embryo sections C04G02_S316


title: F4LHplus7

description:
Paired with corresponding F4LHplus2
counts_exp2.txt.gz


title: PGC11M

description: Total RNA < 100 bp length

source_name: Primordial Germ Cell, Male, E11.5

value: Primordial germ cell

value: Male


title: JTL611_Auxin_2h_HS_R3

description:
Li_RNA_072
edgeR_JTL611(soma)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_JTL611(soma)_2h.tsv


title: Developing mouse embryo sections C05G05_S29


title: CA1200_Auxin_2h_HS_R3

description:
Li_RNA_070
edgeR_CA1200(soma)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_CA1200(soma)_2h.tsv


title: F5LHplus2

description:
Paired with corresponding F5LHplus7
counts_exp2.txt.gz

source_name: Uterine fluid derived Extracellular Vesicles

value: LH+2 (pre-receptive phase)


title: Developing mouse embryo sections C03G05_S27


title: Postpubertal TG Stem Cell C1 Biological Replicate 2

description: 05272016_biological replicate 2_all_log_transformed_counts.txt

value: ICR

value: Mammary gland

value: 10 weeks old


title: Developing mouse embryo sections C03G01_S219


title: F4LHplus2

description:
Paired with corresponding F4LHplus7
counts_exp2.txt.gz

value: Uterine fluid derived Extracellular Vesicles


title: JTL611_Auxin_2h_NHS_R2

description:
Li_RNA_036
edgeR_JTL611(soma)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_JTL611(soma)_2h.tsv

value: Auxin;NHS


title: Postpubertal WT Stem Cell C1 Biological Replicate 2

value: wild type


title: Developing mouse embryo sections C01G05_S25


title: KY_Mononuclear

city: Lexington

first: Kevin

last: Murach

state: KY

address: 900 South Limestone CTW 445

department: Physical Therapy

institute: University of Kentucky

data_processing:
Ai9_tdTomato.fasta and Ai9_tdTomato.gtf were concatenated to the ENSEMBL GRCm38 genome and assembly (release 99) and then prepared using Cell Ranger (v3.1.0) mkref and mkgtf (--attribute=gene_biotype:protein_coding).
FASTQ files were analyzed using the Cell Ranger count pipeline (--expect-cells 10000) to generate the raw count matrices.
BAM files from Cell Ranger were used as input to Velocyto (0.17.17) to generate spliced, unpliced, and ambiguous count matrices.
Count matrices from Cell Ranger and Velcoyto were processed with Seurat, with features being in less than 10 cells and, cells with less than 250 features being discarded. Processed count matrices were exported from Seurat as CSV files.
Genome_build: GRCm38
Supplementary_files_format_and_content: Count matrices are formatted with columns as cells, rows as features, and values as raw read counts.

source_name: pooled plantaris muscles

extract_protocol:
Plantaris muscles were harvested and dissociated mechanically and enzymatically to yield a mononuclear cell suspension. Cells were loaded onto 10X Chromium controller and Chromium Single Cell Gene Expression Solution was used for generating 3'-droplet-based RNA-seq libraries.
scRNA-seq libraries were prepared using the standard Chromium Single Cell 3' v3 kit protocols.

tag: genotype/variation

tag: overload

value: 14 day


title: JTL611_Auxin_2h_HS_R1

description:
Li_RNA_008
edgeR_JTL611(soma)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_JTL611(soma)_2h.tsv

tag: age

tag: tissue of tir1

value: Auxin;HS


title: Developing mouse embryo sections C03G06_S123


title: JTL611_Auxin_2h_NHS_R1

description:
Li_RNA_006
edgeR_JTL611(soma)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_JTL611(soma)_2h.tsv

tag: strain


title: E12_cortex_scRNA-seq

city: Paris

first: Matthieu

middle: X.

last: Moreau

address: 102-108 Rue de la Santé

country: France

institute: Institute of Psychiatry and Neuroscience of Paris, INSERM U1266

data_processing:
Raw sequencing reads were processed to counts matrix with Cell Ranger (version 2.1.1) using the mouse genome mm10 as reference
Genome_build: mm10

source_name: E12.5 mouse cortex

extract_protocol:
Four wild-type E12.5 embryos obtained from two distinct litters were collected in ice-cold HBSS. The PSB region (see Fig. 1A) was dissected on both hemispheres and dissociated using the Neural Tissue Dissociation Kit (P) (Miltenyi Biotec) and a gentleMACS Octo Dissociator with Heaters following the manufacturer’s instructions. Cell clumps and debris were removed by two consecutive rounds of centrifugation 3 minutes at 200xg and filtration through 30 µm cell strainers (Miltenyi Biotec). Additional mechanical dissociation and removal of cell multiplets was achieved by gentle pipetting up and down 5 times using a P200 pipette and Gel Saver tips (QSP), followed by filtration through a 10 µm cell strainer (pluriSelect). Assessment of cell viability and counting were achieved using a MACSQuant flow cytometer (Miltenyi Biotec) in the presence of 7-AAD. The absence of dead cells, debris or doublets in the cell suspension was crosschecked using a hemocytometer and trypan blue staining. Approximatively 10,000 cells were loaded on a 10X Genomics Chromium Controller for partioning. The entire procedure, from the sacrifice of the pregnant female until loading the controller, was achieved in two hours
A single-cell barcoded cDNA library was prepared using a Chromium Single Cell 3’ Library and Gel Bead Kit v2 according to the manufacturer’s instructions

value: embryonic cortex

tag: embryonic age

value: Wildtype C57BL/6J


title: Developing mouse embryo sections C02G06_S122

tag: genotype

tag: tissue

value: E14 Mouse Embryo


title: E17.5 WT3 (scRNA-seq)

city: Los angeles

first: Xue

last: Liu

state: CA

address: AHSP A9404, 127 S. San Vicente Blvd

institute: Cedars-Sinai Medical Center

data_processing:
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp
We used Cell Ranger version 1.3.1 (10x Genomics) to process raw sequencing data and Cell Ranger R kit version 3.0.0 and Seurat suite version 3.0.0 for downstream analysis.
For clustering, principal-component analysis was performed for dimension reduction.
Top 10 principal components (PCs) were selected by using a permutation based test implemented in Seurat and passed to t-SNE for clustering visualization. sSeq version 1.0.0 integrated in the Cell Ranger R kit was used for modeling the gene expression with negative binomial distribution to identify genes whose expression was enriched in specific clusters. The Benjamini-Hochberg procedure was used for correcting errors of multiple testing.
Supplementary_files_format_and_content: h5

source_name: embryonic mouse lung and trachea single cells

extract_protocol:
Isolated tissues were taken immediately to a sterile laminar flow tissue culture hood where they were, rinsed in fresh PBS and then minced finely using a scissors in a 100mm2 Petri dish. The minced lung tissue was then suspended in a digestion media containing 0.125% vol/vol Trypsin-EDTA (#25300056, Gibco, Thermo Fisher Scientific, Waltham, MA, USA), 1mg/ml Bovine Serum Albumin (#15260037, Gibco, Thermo Fisher Scientific, Waltham, MA, USA), 100 U/ml DNase 1 (#DN25, Sigma Aldrich, St. Louis, MO, USA), 1 mg/ml Collagenase IV (#LS004209, Worthington Biochemical, Lakewood, NJ, USA) and transferred a tissue culture incubator at 37C for 30 minutes. At 10-minute intervals the lung digestion solution was titurated 10 times using a 10 ml glass pipette. Following the incubation period, the supernatant and remaining tissue was passed through a 100 um strainer into a 50ml tube. The strainer was washed with Dulbecco’s Modified Eagle Medium (#11995065, Gibco, Thermo Fisher Scientific, Waltham, MA, USA) containing 10% vol/vol fetal bovine serum (#SH3062601, HyClone, GE Healthcare, Chicago, IL USA). The tube was then centrifuged at 1600 rpm for 10 minutes at 4C and the pellet resuspended in Hank’s Buffered Saline Solution (#14175095, Gibco, Thermo Fisher Scientific, Waltham, MA, USA) containing 0.2 mM EGTA, 10mM HEPES (#15630106, Gibco, Thermo Fisher Scientific, Waltham, MO, USA), 2% vol/vol FBS and 1% vol/vol antibiotic-antimycotic (#15240062, Gibco, Thermo Fisher Scientific, Waltham, MA, USA) referred to hereafter as HBSS+. Red blood cells were preferentially lysed by treating the isolated cells with 1X RBC lysis buffer (# 00-4333-57, eBiosceinces, Thermo Fisher Scientific, Waltham, MA, USA) for 45 seconds, followed by immediate dilution in 20 ml HBSS+. Cells were centrifuged again and resuspended in fresh HBSS+ prior to florescence-activated cell sorting (FACS).
mRNA from single cells sorted from lung into lysis plates was reverse transcribed to complementary DNA (cDNA) and amplified as previously described. Library preparation and sequencing were performed as described previously. Sequencing libraries for cDNA from single cells were prepared as per the Single Cell 3′ v2 Reagent Kits User Guide (10x Genomics, Pleasanton, CA, USA). Cellular suspensions were loaded on a Chromium Controller instrument (10x Genomics) to generate single-cell Gel Bead-In-EMulsions (GEMs). GEM-reverse transcription (RT) was performed in a Veriti 96-well thermal cycler (Thermo Fisher Scientific, Waltham, MA, USA). GEMs were collected and the cDNA was amplified and purified with SPRIselect Reagent Kit (Beckman Coulter, Brea, CA, USA). Indexed sequencing libraries were constructed using Chromium Single-Cell 3′ Library Kit for enzymatic fragmentation, end-repair, A-tailing, adapter ligation, ligation cleanup, sample index PCR, and PCR cleanup. The barcoded sequencing libraries were quantified by quantitative PCR using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems, Roche Holding AG, Basel, Switzerland). Sequencing libraries were loaded on a NextSeq500 (Illumina, San Diego, CA, USA) with a custom sequencing setting (26bp for Read 1 and 98bp for Read 2) to obtain a sequencing depth of ~200K reads per cell.

tag: mouse lung cells

value: E17.5 WT lung single cells


title: CA1200_EtOH_2h_HS_R2

description:
Li_RNA_037
edgeR_CA1200(soma)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_CA1200(soma)_2h.tsv

value: young adults

tag: treatment

value: EtOH;HS


title: Developing mouse embryo sections C01G01_S217

tag: sample type

value: Sagigital section


title: JTL611_EtOH_2h_HS_R1

description:
Li_RNA_007
edgeR_JTL611(soma)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_JTL611(soma)_2h.tsv

value: soma


title: CA1200_EtOH_2h_HS_R3

description:
Li_RNA_069
edgeR_CA1200(soma)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_CA1200(soma)_2h.tsv


title: F5LHplus7

description:
Paired with corresponding F5LHplus2
counts_exp2.txt.gz

value: Provenly fertile control women

value: secretory

value: LH+7 (within window of implantation)


title: Developing mouse embryo sections B12G06_S120

description:
Developing mouse embryo sections
sci-Space Slides 1-6
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell


title: CA1200_EtOH_2h_NHS_R2

description:
Li_RNA_033
edgeR_CA1200(soma)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_CA1200(soma)_2h.tsv

value: EtOH;NHS


title: E17.5 WT1 (scRNA-seq)


title: Developing mouse embryo sections B12G05_S24


title: Developing mouse embryo sections C02G02_S314


title: Developing mouse embryo sections B12G02_S312


title: CA1200_Auxin_2h_HS_R1

description:
Li_RNA_004
edgeR_CA1200(soma)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_CA1200(soma)_2h.tsv


title: tdt_parental

value: tdT


title: Developing mouse embryo sections C02G01_S218


title: Postpubertal WT Stem Cell C1 Biological Replicate 1

description: 05162016_biological replicate 1_all_log_transformed_counts.txt

value: ICR

value: Mammary gland

value: 10 weeks old


title: Postpubertal TG Stem Cell C1 Biological Replicate 1


title: E12_G4ko_ATAC_rep2

city: Boston

first: William

middle: T

last: Pu

address: 300 Longwood Ave

institute: Children's Hospital Boston

description: EC ATAC-seq

data_processing:
GATA4 bioChIP-seq:  Bowtie v1.1.1, m=1
GATA4 bioChIP-seq:  MACS2 v2.2.4, p 1e-5
GATA4 bioChIP-seq:  bamCoverage 3.3.1 --normalizeUsing RPKM --binSize 10 --smoothLength 20 -e 150
Genome_build: GATA4 bioChIP-seq:  mm10
Supplementary_files_format_and_content: GATA4 bioChIP-seq:  bigWig files represent reads per 1000 bp per 1 M reads.
Supplementary_files_format_and_content: GATA4 bioChIP-seq:  peak text files
ATAC-seq:  Bowtie v.2.2.9 (alignment)
ATAC-seq:  MACS2 v2.2.4 (peak-calling)
ATAC-seq:  bamCoverage 3.3.1 --normalizeUsing RPKM --binSize 10 --smoothLength 20 (create signal file)
Genome_build: ATAC-seq:  mm10
Supplementary_files_format_and_content: ATAC-seq:  bigWig files represent reads per 1000 bp per 1 M reads.
Supplementary_files_format_and_content: ATAC-seq:  peak text files
EC RNA-seq:  Star v2.7.3a (alignment)
EC RNA-seq:  featureCounts v1.6.3 -T 4 -s 1 (read counting)
Genome_build: EC RNA-seq: mm10
Supplementary_files_format_and_content: EC RNA-seq:  read counts per gene

source_name: E12.5 ventricular apex

extract_protocol:
GATA4 bioChIP-seq:  For each bioChIP-seq of GATA4, 15-20 E12.5 heart ventricles were harvested and crosslinked in 1% formaldehyde in PBS for 10 minutes at room temperature. Chromatin was fragmented using a microtip sonicator (Qsonica, S-3000) at 65% amplitude for 8 minutes. GATAfb and bound chromatin was pulled down by incubation with streptavidin beads (ThermoFisher Scientific, Cat#11206D)
GATA4 bioChIP-seq:   Libraries were constructed using the KAPA HyperPrep ChIP-seq library preparation kit (Roche, cat# 07962347001). Sequencing (75 nt single end) was performed on an Illumina NextSeq 500.
EC ATAC-seq:  For ATAC-seq of Tie2-Cre cell lineages, E12.5 Rosa26fsTrap;Tie2Cre mouse heart ventricles were dissected in ice cold PBS and dissociated to single cells with Neonatal Cardiomyocyte Isolation kit (Cellutron, cat#nc-6031). 40K GFP+ cells were sorted (BD FACSMelody) for each ATAC-seq library sample. For ATAC-seq of Cdh5(Pac)-CreERT2 labeled, Gata4 mutant and control cell lineages, 1mg tamoxifen dissolved in sunflower seed oil was administered to pregnant mice by gavage to induce the activity of Cre at E9.5. E12.5 heart ventricles were dissected in ice cold PBS and dissociated to single cells with the Neonatal Cardiomyocyte Isolation kit (Miltenyi). 20K GFP+ cells were sorted (BD FACSMelody) for each ATAC-seq library sample.
EC ATAC-seq:  The optimized-ATACSeq (omni-ATACSeq) libraries were generated from purified cells using the author’s recommended lysis steps and transposition protocol
EC ATAC-seq:  optimized-ATACSeq (omni-ATACSeq)
EC RNA-seq:  E12.5 Rosa26fsTrap;Tie2Cre mouse heart ventricles were dissected in ice cold PBS and dissociated to single cells with Neonatal Cardiomyocyte Isolation kit (Cellutron, cat#nc-6031). 60K GFP+ cells were sorted (BD FACSMelody) for each RNA sample.
EC RNA-seq:  RNA was prepared with RNeasy Micro Kit (Qiagen, Cat#74004). The polyadenylated RNA was purified by binding to oligo (dT) magnetic beads (ThermoFisher Scientific, 61005).
EC RNA-seq:  RNA-seq libraries were prepared with ScriptSeq v2 kit (Illumina, SSV 21106) according to the manufacturer’s instructions.

value: E12.5 ventricular apex

tag: lineage selectivity

value: FACS sorted using Cdh5CreER activated Rosa26mTmG reporter


title: Developing mouse embryo sections B11G06_S119


title: pax7_tdt

value: 4 day


title: Developing mouse embryo sections B11G05_S23

value: E14 Mouse Embryo


title: CA1200_EtOH_2h_NHS_R3

description:
Li_RNA_065
edgeR_CA1200(soma)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_CA1200(soma)_2h.tsv


title: EUF21

description:
Excluded from analysis due to low coverage/quality
counts_exp2.txt.gz

value: Uterine fluid derived Extracellular Vesicles

tag: population

value: Women undergoing ART and transfer of an euploid blastocyst


title: CA1199_Auxin_2h_HS_R3

description:
Li_RNA_086
edgeR_CA1199(germ)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_CA1199(germ)_2h.tsv

value: young adults

value: germline

value: Auxin;HS


title: EUF30

tag: menstrual cycle phase


title: Developing mouse embryo sections B11G02_S311

value: Sagigital section


title: EUF29

value: secretory

tag: mentrual cycle day (counted from the first day of menstrual bleeding and expressed as n or from the day of urinary lh surge detection and expressed an lh+n)


title: CA1200_Auxin_2h_NHS_R3

description:
Li_RNA_066
edgeR_CA1200(soma)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_CA1200(soma)_2h.tsv

value: soma

value: Auxin;NHS


title: EUF23

value: LH+7 (within window of implantation)


title: CA1200_Auxin_2h_HS_R2

description:
Li_RNA_038
edgeR_CA1200(soma)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_CA1200(soma)_2h.tsv


title: Developing mouse embryo sections C01G02_S313


title: CA1199_EtOH_2h_HS_R3

description:
Li_RNA_085
edgeR_CA1199(germ)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_CA1199(germ)_2h.tsv

value: EtOH;HS


title: pax7_dta


title: EUF19


title: CA1199_Auxin_2h_NHS_R3

description:
Li_RNA_082
edgeR_CA1199(germ)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_CA1199(germ)_2h.tsv


title: E12_CM_ATAC_rep2

source_name: cardiomyocytes

tag: cell type

value: E12.5 cardiomyocytes


title: Developing mouse embryo sections C01G06_S121

source_name: E14 saggital sections 8-10um thick


title: EUF25


title: CA1199_EtOH_2h_NHS_R3

description:
Li_RNA_081
edgeR_CA1199(germ)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_CA1199(germ)_2h.tsv

value: EtOH;NHS


title: WT_Input_4

city: Gothenburg

first: Ayman

last: Osman

address: Medicinaregatan 1F

department: Laboratory medicine

country: Sweden

institute: Gothenburg University

data_processing:
Fastq files were aligned to hg38 reference genome using BWA.
Mapped bam files were used for peak calling by MACS2. Minimum FDR (q-value) cutoff for peak detection was set to 0.01
To visualize the peaks, ChIP signals (bigwig) were generated by bamcompare tool from deepTools using signal extraction scaling (SES) method, and the background signal were subtracted from ChIP signal.
Differential binding analysis was performed using DiffBind R/Bioconductor package. Motifs analysis were performed using (findMotifsGenome.pl) program from HOMER. Search for known motifs followed by de novo motif discovery were performed.
The DDIT3 microarray expression data was combined with DDIT3 ChIP-seq data using binding and expression target analysis (BETA) software to examine the effect of DDIT3 on regulation of gene. BETA basic was used with the following parameters: --da 500 -d 150000 -c 0.5 -g hg19.
Genome_build: hg38
Supplementary_files_format_and_content: BED

source_name: HT1080 cell line

growth_protocol: Human parental fibrosarcoma cell line HT1080 and transfected clones were cultured at 37oC and 5% CO2 in RPMI 1640 medium supplemented with 2 mM L-glutamine, 50 U/ml penicillin, 50 g/ml streptomycin and 8% FCS (all Invitrogen). G418 (200 g/ml, Invitrogen) was added to the transfected cell clones to ensure stable expression of EGFP constructs in the cell population.

extract_protocol:
For chromatin immunoprecipitation, we used the iDeal ChIP-seq kit for Transcription Factors (Diagenode, cat No: C01010170). For cross-linking proteins with DNA, formaldehyde (37%) was mixed with Fixation Buffer (Diagenode), to a final concentration of 11% and added to the cultured cells medium in a proportion of 1:10, and incubated with gentle shaking at room temperature for 15 minutes. The reaction was stopped by adding glycine (1:10) for 5 minutes with gentle shaking at room temperature. The cells were collected by scraping and lysed with lysis buffers from Diagenode. chromatin was sheared by sonication using Bioruptor Pico sonication device (Diagenode, Belgium) (7 cycles, 30 seconds ON, 30 seconds OFF).
Chip-seq grade antibodies (H3K27ac #C15410196, H3K27me3 #C15410195, CTCF #C15410210, Diagenode), (DDIT3 #2895, Cell Signaling Technology) mixed with magnetic beads (Diagenode) were added to 250 µl of sheared chromatin and incubated under constant rotation at 4 ⁰C overnight. A volume of 2.5 µl was treated in the same but without antibody and used as input. The beads were washed with washing buffers from (Diagenode) and elution buffer was added and samples were incubated overnight at 65 ⁰C. for DNA purification  IPure beads v2 (Diagenode) were used. The beads were washed with washing buffers from (Diagenode), then resuspended with buffer C (Diagenode) and kept for further analysis.
Library preparation was performed by (Diagenode, Belgium). ChIP’d DNA was quantified using QuBit HS ds DNA kit. Libraries were prepared using IP-Star® Compact Automated System (Diagenode Cat# B03000002) from input and ChIP’d DNA using MicroPlex Library Preparation Kit v2 (12 indices) (Diagenode Cat# C05010013). Optimal library amplification was assessed by qPCR using KAPA SYBR® FAST (Sigma-Aldrich) on LightCycler® 96 System (Roche) and by using High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Agilent). Libraries were then purified (double-size selected) using Agencourt® AMPure® XP (Beckman Coulter) and quantified using Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854). Finally their fragment size was analised by High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Agilent).
Libraries were pooled and sequenced with Illumina technology with single-end reads of 50bp length. Sequencing was performed by (Diagenode, Belgium).

value: fibrosarcoma cell line

tag: oncogene transfection

value: WT

tag: antibody

value: Input


title: E12_CM_ATAC_rep1


title: CA1200_Auxin_2h_NHS_R1

description:
Li_RNA_002
edgeR_CA1200(soma)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_CA1200(soma)_2h.tsv


title: E12_G4ko_ATAC_rep3

description: EC ATAC-seq

value: E12.5 ventricular apex

value: FACS sorted using Cdh5CreER activated Rosa26mTmG reporter


title: CA1200_EtOH_2h_HS_R1

description:
Li_RNA_003
edgeR_CA1200(soma)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_CA1200(soma)_2h.tsv


title: Developing mouse embryo sections B10G05_S22

value: E14 Mouse Embryo


title: E17.5 WT2 (scRNA-seq)

value: E17.5 WT lung single cells


title: E12_G4het_ATAC_rep4

description: EC ATAC-seq


title: CA1199_Auxin_2h_HS_R2

description:
Li_RNA_054
edgeR_CA1199(germ)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_CA1199(germ)_2h.tsv

value: young adults

value: germline


title: E12_G4het_ATAC_rep3

description: EC ATAC-seq


title: Developing mouse embryo sections B12G01_S216

value: Sagigital section


title: E12_CM_RNA_rep1

description:
stranded RNA-seq
E12_ECvsCM_featurecounts.txt
E12_CM_1


title: E12_CM_RNA_rep2

description:
stranded RNA-seq
E12_ECvsCM_featurecounts.txt
E12_CM_2


title: CA1199_Auxin_2h_NHS_R2

description:
Li_RNA_050
edgeR_CA1199(germ)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_CA1199(germ)_2h.tsv


title: E12_G4ko_ATAC_rep4

description: EC ATAC-seq


title: E12_G4het_ATAC_rep2

description: EC ATAC-seq


title: Developing mouse embryo sections B09G06_S117

description:
Developing mouse embryo sections
sci-Space Slides 1-6
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell


title: CA1200_Auxin_2h_NHS_R2

description:
Li_RNA_034
edgeR_CA1200(soma)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_CA1200(soma)_2h.tsv


title: DDIT3_Input_4


title: WT_CTCF_2

value: CTCF


title: Developing mouse embryo sections B11G01_S215


title: Developing mouse embryo sections B10G01_S214


title: WT_H3K27me3_2


title: Developing mouse embryo sections B10G02_S310


title: E12_CM_RNA_rep3

description:
stranded RNA-seq
E12_ECvsCM_featurecounts.txt
E12_CM_3


title: Developing mouse embryo sections B10G06_S118


title: Developing mouse embryo sections B09G02_S309


title: CA1199_Auxin_2h_HS_R1

description:
Li_RNA_022
edgeR_CA1199(germ)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_CA1199(germ)_2h.tsv

value: Auxin;HS


title: CA1199_EtOH_2h_HS_R2

description:
Li_RNA_053
edgeR_CA1199(germ)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_CA1199(germ)_2h.tsv


title: WT_H3K27ac_2


title: CA1199_EtOH_2h_NHS_R2

description:
Li_RNA_049
edgeR_CA1199(germ)_Auxin_HS-EtOH_HS.tsv
edgeR_normcounts_CA1199(germ)_2h.tsv


title: E12_EC_ATAC_rep3

description: EC ATAC-seq

value: FACS sorted using Tie2Cre activated Rosa26fsTRAP reporter


title: E12_EC_RNA_rep2

description:
EC RNA-seq
stranded RNA-seq
E12_ECvsCM_featurecounts.txt
E12.5_Tie2_RNASeq_rep2


title: E12_EC_RNA_rep1

description:
EC RNA-seq
stranded RNA-seq
E12_ECvsCM_featurecounts.txt
E12.5_Tie2_RNASeq_rep1


title: DDIT3_H3K27ac_1


title: E12_EC_ATAC_rep2

description: EC ATAC-seq