title: FVB_left_rep1

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

country: Switzerland

institute: ETH Zurich

description: FVB_left_rep1 (TPM)

data_processing:
Trimmed RNA-Seq reads in FASTQ format were generated by GATC Biotech AG. RNA-Seq reads in FASTQ format were imported into the program CLC Genomics workbench 20 version 20.0.4 (QIAGEN Bioinformatics, QIAGEN Aarhus A/S) and aligned to the reference genome (Mouse GRCm39) in frame of the RNA Sequencing Workflow of CLC Genomics workbench 20.
The trimmed RNA-Seq reads in FASTQ format were mapped to the reference genome (Mouse GRCm39) in frame of the RNA Sequencing Workflow of CLC Genomics workbench 20. The following mapping settings were used: Mismatch count: 2; Insertion cost: 3; Deletion cost: 3; Length fraction: 0.8; Similarity fraction: 0.8; Maximum number of hits for a read: 10; Expression value: TPM. Gene and transcript annotations of the reference genome were added to the mapped reads. With these settings, read tracks and reports were generated. The processed data files show transcripts per million (TPM) for every transcript and every sample.
Assembly: Mouse GRCm39
Supplementary files format and content: Tab-separated text (txt) files show TPM values of each sample and transcript. The following tab-separated columns are presented in the processed data files: Name; Chromosome; Region; TPM; Gene name; Transcript length; Exons; Gene ID; Transcript ID; ENSEMBL; Biotype.
Supplementary files format and content: The matrix table shows TPM values of every transcript and every sample. The following tab-separated columns are included in the matrix table (Matrix_table_right_left_heart.txt): Name; Chromosome; Region; Gene name; Transcript length; Exons; Gene ID; Transcript ID; ENSEMBL; Biotype; TPM values of 16 samples.

source_name: left ventricular heart specimen

growth_protocol: After weaning at an age of 3-4 weeks, Tg-BBLN mice and non-transgenic FVB/N control mice were housed until the end of the observation period at an age of 3-4 months in groups of 2-4 mice under SPF conditions with a 12 h dark cycle in individually ventilated cages. All the mice had free access to food and water and were fed a standard rodent diet.

extract_protocol:
Right and left ventricular heart specimens were dissected from total hearts isolated from euthanized, male Tg-BBLN mice and non-transgenic FVB/N mice (age: 3-4 months). Dissected heart specimens were  rapidly frozen in liquid nitrogen. For RNA isolation, right and left heart specimens were pulverized under liquid nitrogen, and total RNA was isolated with the RNeasy midi kit (Qiagen).
RNA libraries were prepared for transcriptome sequencing by GATC Biotech AG, an Eurofins Genomics Company, using standard Illumina protocols in frame of the INVIEW Transcriptome Discover protocol. For library preparation, mRNA was fragmented, and random hexamer-primed cDNA synthesis was performed. Illumina paired-end read sequencing (2 x 150 bp) with guaranteed 30 million reads per sample was performed by the Genome Sequencer Illumina HiSeq, in the sequence mode HiSeq 4000.

value: left ventricular heart specimen

value: FVB/N

value: male

value: non-transgenic

tag: age

value: 3-4 months


title: D831C85_ChIP_p50_D2-24h_Bmori-v4_H4K20me1_rep1_Input

status: Public on Sep 17 2023

type: SRA

city: Paris

first: Héloïse

last: Muller

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: ChIP Input

library_source: genomic

data_processing:
Library were sequenced on Novaseq.
Adapter sequences were trimmedfrom reads using trimgalore.
ChIP-seq reads were aligned to our custom Bmori_v4 genome assembly using Bowtie2 v2.3.5.1. Only uniquely mapping reads with a mapping quality higher than 10 were retained.
To create ChIP-seq coverage plots, log2 IP/Input ratio files have been generated at 25pb resolution using bamCompare from deepTools and reformatted in the bigWig file format.
Assembly: Bmori_v4
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Bombyx mori

source_name: full embryo

growth_protocol: ~200 p50 diapaused eggs harvest after release 24h at 25°C

extract_protocol:
Eggs were placed in 1% formaldehyde before chorions were broken with a piston pellet to allow embryos fixation for 10 min. After quenching and cell lysis, embyo tissus were ruptured and chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HyperPrep  Library Preparation Kit complemented with Illumina TruSeq DNA UD Indexes. Libraries were amplified using 8-14 cycles on the thermocycler. Post amplification libraries were size selected at 250-600bp in length using SPRIselect beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity screenTapes.

tag: tissue

value: full embryo

tag: strain

tag: chip antibody

value: none (input)


title: D3-2

city: Harbin

first: Yu Jie

last: Chi

state: Heilongjiang

address: Hexing road, No.26; Xiangfang district

department: School of Forestry

country: China

institute: Northeast Forestry University

library_source: transcriptomic

data_processing:
Clean reads were obtained after quality control by removing reads containing an adapter and ploy-N, and low-quality reads from raw data through in-house Perl scripts. Q30, GC-content, and sequence duplication level of the clean data were calculated.
Hisat2 (https://daehwankimlab.github.io/hisat2/main/) was used to map the clean reads to the reference genome sequence of Trametes gibbosa (http://genome.jgi.doe.gov/Tragib1/Tragib1.home.html, Hage et al., 2021), then the mapped data were obtained. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome.
StringTie assembled transcripts of each sample according to the GFF files of the reference genome by using the mapped data reads. StringTie-merge merged all the transcripts from 15 samples, and a complete set of transcriptome information was obtained.
Quantification of gene expression levels was estimated by fragments per kilobase of transcript per million fragments mapped. Then, the transcriptome library qualities were assessed by the inserting segment length test, mRNA fragment randomness test, and sequencing data saturation test.
All the transcripts and genes were annotated as much as possible in eight databases, COG, KOG, eggNOG, GO, KEGG, NR, Pfam, and SwissProt, by using BLAST software to perform homologous sequence alignment to determine their function (Altschul et al., 1997).
Getorf software (v2.0, https://international.biocloud.net/zh/software/tools/detail/small/364) was used to predict Open Reading Frames (ORFs) in the predicted new transcripts (Yao et al., 2012). For known genes, the CDS region is directly extracted using GFF files. Based on the ORF length, log-likelihood score, and the alignment between the amino acid sequence and protein domain sequences in Pfam database, Getorf can identify the reliable and potential coding sequence (CDS) from transcripts.
Blastx software was used to annotate the genes in the databases of COG, KOG, eggNOG, KEGG, NR, and SwissProt, Hmmscan software was used in Pfam. And gene annotation in GO database was implemented by using Blast2GO software to associate with the annotation results in NR. The information of all of these genes is available on BMKCloud (https://international.biocloud.net/), and the gene retrieval and mining can be done on BMKCloud.
The screening and differential expression analysis of the DEGs between different two groups (including CK vs D3, D5, D7, and D11; D3 vs D5, D7, and D11; D5 vs D7, D11 d; and D7 vs D11) were also performed using BMKCloud by means of the DESeq R package (1.10.1) (Anders S et al.,2010; Wang et al., 2010) according to gene expression counts in the control group and the four poplar chip treatment groups.
The DESeq R package provides a statistical routine for determining differential gene expression using a model based on the negative binomial distribution, and can show that the counts of gene reads are different between different two groups. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate (FDR). Fold Change≥2 and FDR <0.01 found by DEseq2 were used as screening criteria to select DEGs.
GO function enrichment and significantly enriched pathways of DEGs were analyzed by statistical methods. GO enrichment analysis of the DEGs can screen out the GO terms and DEGs that are significantly related to specific biological functions, it was implemented by the GOseq R packages based Wallenius non-central hypergeometric distribution (Young et al, 2010), which can adjust for gene length bias in DEGs. KOBAS (Mao et al., 2005) software was used to test the statistical enrichment of DEGs in KEGG pathways. GO and KEGG annotation were performed on DEGs to obtain all GO terms and pathways participated by these DEGs.
The P-value of significance level of each GO term and pathway was calculated by using Fisher exact test of hypergeometric distribution. The FDR was obtained by correcting the results of multiple hypothesis tests, so as to select the GO terms and pathways significantly enriched by DEGs. In this study, the screening criteria both for significantly enriched GO terms and KEGG pathways were adjusted adjusted P-value <0.01 for Fisher exact test.
Genome_build: http://genome.jgi.doe.gov/Tragib1/Tragib1.home.html
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each gene and each sample
Supplementary_files_format_and_content: tab-delimited text file includes counts for each gene and each sample

molecule: total RNA

organism: Trametes gibbosa

source_name: Cultural mycelia

growth_protocol: The white-rot fungus L. gibbosa strain CB-1 was isolated from its fruiting body collected from Changbai Mountains in the province of Jilin, China, and maintained on potato dextrose agar (PDA) slants at 4℃ at Northeast Forestry University. For the inoculation of liquid cultures, the preserved strain was pregrown on PDA plates (9 cm) at 25℃ for 7–10 d. Five marginal inoculum plugs were taken using a 5-mm2 perforator and placed on 70 ml of Low-Nitrogen-Asparagine-Succinate (LNAS) medium supplemented with 5 ml of 15% sterilized glucose solution in a 250-ml Erlenmeyer flask.

extract_protocol:
The samples of frozen mycelia were sent to Beijing Biomarker Biotechnology Co., Ltd. The total RNA was extracted using the RNA extraction kit of Beijing Tiangen Biotech Co., Ltd., and corresponding methods.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was conducted using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First-strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After the adenylation of 3' ends of DNA fragments, NEBNext Adaptor with a hairpin loop structure was ligated to prepare for hybridization. To select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then, 3 μl USER Enzyme (NEB, USA) was used with size-selection. Subsequently, PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) Primer. Finally, PCR products were purified (AMPure XP system), and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina HiSeq Xten platform, and paired-end reads were generated.

treatment_protocol: After stationary cultures were incubated at 25℃ for 10 d, 75 bottles were divided into 5 groups，each group had 15 bottles, which were used as 3 biological replicates. In the first group, 15 bottles were randomly selected as the non-woody treated control group. In the other four groups, 60 bottles were supplemented with 2 g of lesser black poplar (Populus simonii × P. nigra) chips and were continuously incubated at 25℃ for 3, 5, 7, and 11 d. The mycelia of all bottles were harvested in the same way.

value: Cultural mycelia

tag: treatment

value: woody treatment 3d


title: Intermittent_hypoxia_TNF_Experiment3

city: TROMSOE

first: Casper

middle: Jan Elis

last: Wahlund

address: Hansine Hansens veg 18

department: Clinical Medicine

country: Norway

institute: UiT - The Arctic university of Norway

description:
EndoIHTNF3
sample_metadata.xlsx
salmon-merged.transcript_counts.csv
cpm.csv

data_processing:
Reads were pseudomapped to the human transcriptome (GRCh38.p13) using Salmon v1.5.1. Counts were combined and imported into R data downstream data analysis.
Transcripts were summed to gene level and filtered if 5 or less counts were detected in 3 samples, or less. Patient-level batch effects were corrected using ComBat implemented in the sva package
Differential gene expression was carried out in EdgeR using interaction between hypoxic condition and stimulant, where genes with fold change above 1.5 and p-value below 0.001 were considered significant
Selected genes were grouped into gene modules of similar expression by hierarchical clustering on correlation distance and "ward.D2” linkage, which were further used for gene set analysis using enrichR
Assembly: GRCh38
Supplementary files format and content: Metadata for each sample is supplied in an xlsx file
Supplementary files format and content: CPMs and merged transcripts are supplied in separate .csv files

organism: Homo sapiens

source_name: Peripheral venous blood

growth_protocol: Pooled donor endothelial cells were plated in gas-permeable bottom plates and cultured in endothelial growth media (Cell Applications) supplemented with 5% FBS. Five days after plating, the cells were fuly confluent, the media was changed and the plates were transferred to normoxic, hypoxic or intermittent hypoxic chambers.

extract_protocol:
Total RNA was  isolated using a miRNeasy kit according to manufacturer’s protocol
Libraries of cDNA were prepared by TruSeq RNA library kit (Illumina)

treatment_protocol: The endothelial cells were stimulated 48 hours in normoxia (17% O2), sustained hypoxia (1% O2) or intermittent hypoxia (1-17% O2) in absence or presence of 1 ng/ml TNF.

value: Peripheral venous blood

tag: cell type

tag: genotype

value: WT


title: cell,control,rep1

city: Fuzhou, Fujian, China

first: Jie

last: Liu

address: Shengli Clinical Medical College of Fujian Medical University, Department of Endoscopy, Fujian Provincial Hospital, Fuzhou, China

institute: Fujian Medical University

data_processing:
The mRNA is fragmented using a Fragmentation Buffer, and then the first strand of cDNA is synthesized using six base random primers.
Buffer, dNTPs, RNase H, and DNA polymerase I are added to synthesize the second strand of cDNA. Next, the resulting cDNA is then purified using a QiaQuick PCR kit and eluted with EB buffer.
End-repair is done and base A is added to the cDNA fragments, followed by sequencing connector ligation.
The target size fragments are recovered by agarose gel electrophoresis, and PCR amplification is carried out to complete the preparation of the entire library.
the constructed library is sequenced using the Illumina HiSeq2000 platform to obtain high-throughput sequencing data that can be used for downstream analysis.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: cell line

growth_protocol: cells maintained in a 37℃ incubator with 5% CO2

extract_protocol:
Total RNA is first extracted from the sample, and mRNA is enriched using magnetic beads with Oligo (dT).
RNA libraries for RNA-seg were usind SWARTER mRNASed ibrary prepared Prepkit fol owina manufacturer's protocols

treatment_protocol: Transfection plasmid

value: cell line

tag: cell line

value: tumor cell

value: mutant p53


title: Intermittent_hypoxia_TNF_Experiment2

description:
EndoIHTNF2
sample_metadata.xlsx
salmon-merged.transcript_counts.csv
cpm.csv


title: cell,control,rep2


title: D577C40_ChIP_p50_D2-24h_Bmori-v4_H3K9me3_rep2_IP

description: ChIP IP


title: D831C78_ChIP_p50_D2-24h_Bmori-v4_H3K9me3_rep1_IP

description: ChIP IP


title: D577C39_ChIP_p50_D2-24h_Bmori-v4_H3K9me3_rep2_Input

description: ChIP Input


title: CK1

value: non-woody control (Cultural mycelia were extracted directly from the cultures on LNAS liquid medium for 10 days)


title: D831C86_ChIP_p50_D2-24h_Bmori-v4_H4K20me1_rep1_IP

description: ChIP IP


title: Intermittent_hypoxia_CTRL_Experiment3

description:
EndoIHCTR3
sample_metadata.xlsx
salmon-merged.transcript_counts.csv
cpm.csv


title: Intermittent_hypoxia_CTRL_Experiment2

description:
EndoIHCTR2
sample_metadata.xlsx
salmon-merged.transcript_counts.csv
cpm.csv


title: D506-D492C29_ChIP_p50_D2-24h_Bmori-v4_H3K27me3_rep2_IP

description: ChIP IP


title: D330C100_ChIP_p50_D2-24h_Bmori-v4_H3K27me3_rep1_Input

description: ChIP Input


title: D831C77_ChIP_p50_D2-24h_Bmori-v4_H3K9me3_rep1_Input

description: ChIP Input


title: Sustained_hypoxia_TNF_Experiment1

description:
EndoHypTNF3
sample_metadata.xlsx
salmon-merged.transcript_counts.csv
cpm.csv


title: D330C101_ChIP_p50_D2-24h_Bmori-v4_H3K27me3_rep1_IP

description: ChIP IP


title: D330C102_ChIP_p50_D2-24h_Bmori-v4_H3K36me3_rep1_Input

description: ChIP Input


title: male, PFC, neighbor housed ethanol,  replicate 1

status: Public on Sep 18 2023

type: RNA

city: Richmond

first: JENNIFER

last: WOLSTENHOLME

state: VA

address: 1217 E Marshall Street, KMSB Rm 536

country: USA

institute: Virginia Commonwealth University

hyb_protocol: Labeled cDNA was hybridized to GeneChip Mouse Transcriptome Arrays (ClariomS)

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Each array was processed through quality control, normalization using Expression Console and the Transcriptome Analysis Center (TAC, Affymetrix)

label: biotin

organism: Mus musculus

source_name: brain tissue harvested on PND 57 after single or neighbor housing +/- 2BC

label_protocol: Biotinylated cRNA from PFC and NAc was reverse transcribed and labeled for microarray hybridization using standard kits and protocols from Affymetrix

growth_protocol: Male and females C57BL/6J mice (n = 4-5/group) were single or neighbor housed on PND 26. Half of the mice were given ethanol 2-BC drinking and half the mice were given two bottles of water from PND 29-52, as above. PFC and NAc were collected on PND 57 (n = 4-5/group) and flash frozen.

extract_protocol: Total RNA was isolated using STAT 60 Reagent (Tel-Test, Friendswood, TX, United States) and RNeasy mini kit (Qiagen, Valencia, CA, United States) according to the manufacturer’s protocol.

treatment_protocol: Prefrontal cortex (PFC) and Nucleus Accumbens (NAC) were collected on PND 57 and flsh frozen

tag: Sex

value: brain

tag: brain region

value: PFC

tag: group

value: neighbor housed ethanol


title: Sustained_hypoxia_TNF_Experiment2

description:
EndoHypTNF1
sample_metadata.xlsx
salmon-merged.transcript_counts.csv
cpm.csv


title: D506-D492C30_ChIP_p50_D2-24h_Bmori-v4_H3K36me3_rep2_IP

description: ChIP IP


title: D1221C17_ChIP_p50_D2-24h_Bmori-v4_H3K4me3_rep2_Input

description: ChIP Input


title: Sustained_hypoxia_CTRL_Experiment3

description:
EndoHypCTR3
sample_metadata.xlsx
salmon-merged.transcript_counts.csv
cpm.csv


title: D330C103_ChIP_p50_D2-24h_Bmori-v4_H3K36me3_rep1_IP

description: ChIP IP


title: Sustained_hypoxia_CTRL_Experiment2

description:
EndoHypCTR2
sample_metadata.xlsx
salmon-merged.transcript_counts.csv
cpm.csv


title: Sustained_hypoxia_CTRL_Experiment1

description:
EndoHypCTR1
sample_metadata.xlsx
salmon-merged.transcript_counts.csv
cpm.csv


title: D506-D492C27_ChIP_p50_D2-24h_Bmori-v4_H3K4me3_rep1_H3K36me3_rep2_H3K27me3_rep2_Input

description: ChIP Input


title: Normoxia_TNF_Experiment3

description:
EndoNormTNF3
sample_metadata.xlsx
salmon-merged.transcript_counts.csv
cpm.csv


title: Intermittent_hypoxia_TNF_Experiment1

description:
EndoIHTNF1
sample_metadata.xlsx
salmon-merged.transcript_counts.csv
cpm.csv


title: D506-D492C31_ChIP_p50_D2-24h_Bmori-v4_H3K4me3_rep1_IP

description: ChIP IP


title: Tim4KO_ID8_2

city: Trieste

first: Sonal

last: Joshi

state: Trieste

address: Localita Padriciano, 99

department: Cellular Immunology

country: Italy

institute: International Center for Genetic Engineering and Biotechnology

data_processing:
Fastq files coming from sequencing platform were merged and basic quality controls were performed with FASTQC and PRINSEQ tools. FASTQ files were aligned to the mm10 reference genome, reads were dereplicated for PCR duplicates and gene counts were generated using STAR v.2.5 using quantMode GeneCounts.
genome build:Mus musculus GRCm39.103 (GTF file) and Mus musculus GRCm39 DNA primary assembly fasta (sequence file).
Supplementary files format and content: tab delimited csv file contains raw counts for each sample.

source_name: Peritoneal cavity

growth_protocol: ID8ZGO were maintained in DMEM media supplemented with 4.5g/mL glucose (Invitrogen) and 10% fetal bovine serum (FBS, Euroclone) and Gentamicin (50ug/mL, Gibco) at 37°C in 5% CO2

extract_protocol:
RNA was extracted from sorted LPM using RNEasy micro kit (Qiagen)
Libraries were prepared with SMART-Seq mRNA LP kit (TAKARA) following manufacturer's protocols

treatment_protocol: ID8ZGO were injected intraperitoneally in 8-week old WT and Tim4KO female mice

value: Peritoneal cavity

value: Large Peritoneal macrophages

value: Tim4 KO

value: i.p injected ID8ZGO

value: female


title: D1221C18_ChIP_p50_D2-24h_Bmori-v4_H3K4me3_rep2_IP

description: ChIP IP

value: full embryo


title: Tim4KO_ID8_3


title: Tim4KO_ID8_1


title: Normoxia_TNF_Experiment2

description:
EndoNormTNF2
sample_metadata.xlsx
salmon-merged.transcript_counts.csv
cpm.csv


title: Intermittent_hypoxia_CTRL_Experiment1

description:
EndoIHCTR1
sample_metadata.xlsx
salmon-merged.transcript_counts.csv
cpm.csv


title: Normoxia_TNF_Experiment1

description:
EndoNormTNF1
sample_metadata.xlsx
salmon-merged.transcript_counts.csv
cpm.csv


title: Normoxia_CTRL_ Experiment3

description:
EndoNormCTR3
sample_metadata.xlsx
salmon-merged.transcript_counts.csv
cpm.csv


title: WT_ID8_3


title: Normoxia_CTRL_ Experiment2

description:
EndoNormCTR2
sample_metadata.xlsx
salmon-merged.transcript_counts.csv
cpm.csv


title: X2637LM

city: Guangzhou

first: Xiaoxue

last: Ren

state: Guangdong

address: 58 Zhong Shan Road 2, Guangzhou, China

institute: The First Affiliated Hospital of Sun Yat-Sen University

data_processing:
Short reads alignment procedure HISAT (27) was utilized for mapping reads to the human reference genome (GRCh38).
Assembly: GRCh38
Supplementary files format and content: Comma-Separated Values file

source_name: Bulk

extract_protocol:
Total RNAs were isolated using Trizol RNA extraction reagent (Ambion).
Fragmentation buffer was added for interrupting mRNA to short fragments. Taking these short fragments as templates, random hexamer-primer was used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNAse H and DNA polymerase I, respectively. Short fragments were purified with QIAQuick PCR extraction kit (Qiagen, Hilden, Germany) and resolved with EB buffer for end reparation and adding poly (A). After that, the short fragments were connected with sequencing adaptors. Then we selected suitable fragments as templates for PCR amplification based on agarose gel electrophoresis.

value: Liver cancer


title: Sustained_hypoxia_TNF_Experiment3

description:
EndoHypTNF2
sample_metadata.xlsx
salmon-merged.transcript_counts.csv
cpm.csv


title: X2512LM


title: X2580LM


title: Normoxia_CTRL_ Experiment1

description:
EndoNormCTR1
sample_metadata.xlsx
salmon-merged.transcript_counts.csv
cpm.csv


title: WT_ID8_2

data_processing:
Fastq files coming from sequencing platform were merged and basic quality controls were performed with FASTQC and PRINSEQ tools. FASTQ files were aligned to the mm10 reference genome, reads were dereplicated for PCR duplicates and gene counts were generated using STAR v.2.5 using quantMode GeneCounts.
Supplementary files format and content: tab delimited csv file contains raw counts for each sample.


title: X2429LM


title: X2422LM


title: X2385LM


title: X2390LM


title: PH6.0_2

city: Shanghai

first: Hai

last: Lin

state: Shanghai

address: No. 600, Yishan Road, Xuhui District

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Raw reads were filtered with Seqtk to remove adaptor sequence and low-quality sequence.
Genome mapping was performed by "splices mapping" algorithm in Hista2 (version:2.0.4).
Annotation genome used was GRCh38.p4 (hg38).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count and RPKM values for each Sample

source_name: HNEpC

growth_protocol: Cells were cultured in an airway epithelial cell basal medium (PromoCell, C-21060) with growth medium kit (PromoCell, C- 21160) in a 5% CO2 incubator at 37℃.

extract_protocol:
RNA was extracted using MagBeads Total RNA Extraction Kit（Cat#T02-096) following manufacturer's protocols.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: Cells were treated with 2mL 100 μg/ml LPS or same amount of normal culture medium for 24h.

value: HNEpC

value: nasal epithelial cell


title: Tim4KO_3


title: X2356LM


title: PH6.0_3


title: X2346LM


title: X2327LM


title: Tim4KO_1


title: PH6.0_1


title: X2281LM


title: Tim4KO_2


title: SHCC1765.T


title: PH7.4_2


title: WT_3

value: WT


title: SHCC1562.T


title: X2240LM


title: X2635LM


title: WT_2


title: SHCC1381.T


title: X2209LM


title: mCRC9.S5T


title: WT_ID8_1


title: WT_1


title: PH7.4_1


title: mCRC8.S7T


title: ATAC-seq of 3_naive,uninfected Calu-1 cells

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

country: Germany

institute: Berlin Institute of Health, Charité Medical University of Berlin

description:
3_naive_uninfected
Human lung cancer cells Calu-3, untreated, uninfected

data_processing:
Adapter sequences were removed using cutadapt v. 2.6
Reads were aligned to the human genome using the STAR aligner, v. 2.7.5a.
Peaks were identified using MACS v. 2.2.6
Differential binding was assessed using the R packages DiffBind, v. 3.0.15
Assembly: GRCh38 p7
Supplementary files format and content: output from MACS2 (narrowPeak format), peak_counts tsv file

growth_protocol: Calu-3 (ATCC HTB-55) were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% heat-inactivated fetal calf serum (FCS), 100 U/ml Penicillin-Streptomycin and 2mM L-glutamine (Gibco) (hereafter referred to as 10% DMEM) at 37°C/5% CO2. Unless stated otherwise, all cell cultures were maintained at 37°C/5% CO2.

extract_protocol:
ATACseq:Post-infection, ATAC-seq libraries were prepared from 50,000 cells per replicate using Illumina Tagment DNA Enzyme and Buffer Kit (#20034197 Illumina) according to the Omi-ATAC-seq protocol with minor optimizations. Briefly, 5 µl from the partially amplified barcoded fragments was subjected to SYBR Green qPCR in a LightCycler 480 System (Roche) using the FastStart Essential DNA Green Master Mix (Roche) according to the manufacturer’s protocol. Amplification was conducted for 20 cycles using a universal forward primer and the sample-specific barcoded reverse primers. Amplification curves from SYBR Green qPCR were generated and used to determine the number of cycles that give ⅓ of the maximum fluorescence.
Final library preparation was conducted by conventional PCR for 8-12 cycles. The amplified libraries were subjected to a single left-sided bead purification using the AMPure XP magnetic beads (Beckman Coulter). Libraries were sequenced on SP lane of NovaSeq 6000 System (Illumina) at the MDC/BIH Genomic Core Facility to generate 40 million 75-nucleotide paired-end reads per sample.

treatment_protocol: Calu-3 cells were treated with JQ-1 and DMSO, respectively, for 24 hours, infected with SARS-CoV-2 (MOI 0.1) under continuous treatment for another 24 hours. Uninfected but treated, and naïve Calu-3 cells were used as controls.

value: Human lung cancer

value: naive

tag: infection

value: uninfected


title: Splenocytes_Experiment_HTO

city: Jerusalem

first: Oren

last: Parnas

address: Faculty of Medicine, Ein-Kerem medical center

department: Immunology

country: Israel

institute: The Hebrew University of Jerusalem

library_source: other

data_processing:
cDNA Fastq files were aligned to mm10 library (Ensembl v98, also containing CROP-seq vector sequence) using Cellranger (v4.0.0). Each GEM was processed separately.
ADT, HTO, and GDO fastq files were quality filtered and trimmed using cutadapt (v3.4).
ADT, HTO, and GDO fastq files were aligned to reference by a modified version of CITE-seq-count (V1.4.3, see methods in paper).
Seurat (v4.0.5) was used to create an object with all relevant assays (cDNA, ADT, HTO and/or GDO). Cells with extremely high GDO counts or low cDNA counts were filtered out.
Normalization of individual assays, assignment of cells to samples, assignment of gene-KO to cells and other downstream analysis was performed as detailed in methods in the paper.

molecule: protein

source_name: Spleen

growth_protocol: BMDCs were extracted from the bone marrow and differentiated in a dish for 8 days, growth protocol and transduction protocol are described in detail in the paper. T cells were extracted from OT1 mice spleen and incubated for three days with BMDCs. Splenocyte were isolated from the spleen and CD11c were sorted. For the tumor experiment B16 cells were injected and 5 days later BMDCs were injected tumors were taken 10 days later.

extract_protocol:
To obtain BMDCs, femurs and tibia were removed, and BM was flushed. OT1 CD8+ T cells were isolated from the spleen of OT1 mice using EasySep™ Mouse CD8+ T Cell Isolation Kit (STEMCELL Technologies #19853). CD11c+ cells were isolated from the spleen using EasySep™ Mouse APC Positive Selection Kit II (STEMCELL Technologies #17667). B16 tumors were minced and digested using DMEM media supplemented with 2.5 mg/ml Collagenase D (Roche, #11088866001) and 0.2 mg/ml DNaseI (Roche, # 10104159001). Tumors were incubated in the water bath at 37 degrees while shaking for 10 min. After digestion samples were strained through 100-um filters and centrifuged at 1000 rpm at 4 degrees for 5 min. Cell pellets were resuspended in 1 ml of ACK lysing buffer (Gibco, #A100492-01), incubated for 5 min at RT, and washed twice with quenching buffer (PBS + 2% FCS).
According to 10x genomics Chromium single-cell V3 3′ protocol. For HTO, ADT and GDO amplification we used dial-up PCR.

value: Spleen

value: CD11c positive cells

value: CD11c-cre Cebpb (fl/fl) or control


title: mCRC6.S8T


title: ATAC-seq of 3_JQ-1,uninfected Calu-1 cells

description:
3_JQ-1_uninfected
Human lung cancer cells Calu-3, JQ1 treated, uninfected


title: mCRC6.S5T2


title: mCRC6.S5T1


title: ATAC-seq of 3_JQ-1,infected Calu-1 cells

description:
3_JQ-1_infected
Human lung cancer cells Calu-3, JQ1 treated, SARS-Cov-2 infected MOI 0.1


title: PH7.4_3


title: In-vivo_B16_Experiment_HTO

source_name: Tumor

value: Tumor

value: Tumor tissue

value: B6 mice


title: mCRC5.S5T


title: ATAC-seq of 3_DMSO,uninfected Calu-1 cells

description:
3_DMSO_uninfected
Human lung cancer cells Calu-3, DMSO treated, uninfected

value: DMSO


title: In-vivo_B16_Experiment_cDNA


title: Tcell_Experiment_HTO

value: T cells

value: OT1 mice


title: ATAC-seq of 3_DMSO,infected Calu-1 cells

description:
3_DMSO_infected
Human lung cancer cells Calu-3, DMSO treated, SARS-Cov-2 infected MOI 0.1


title: ATAC-seq of 2_naive,uninfected Calu-1 cells

description:
2_naive_uninfected
Human lung cancer cells Calu-3, untreated, uninfected


title: mCRC8.S4T


title: mCRC37.S6T


title: mCRC39.S3T


title: mCRC36.S8T


title: Tcell_Experiment_cDNA


title: mCRC35.S6T


title: ATAC-seq of 2_JQ-1,uninfected Calu-1 cells

description:
2_JQ-1_uninfected
Human lung cancer cells Calu-3, JQ1 treated, uninfected


title: mCRC4.S7T


title: Pertubation_Experiment_GDO

source_name: Bone marrow

value: Bone marrow

value: BMDCs

value: B6 Cas9


title: mCRC7.S6T

value: Liver cancer


title: ATAC-seq of 2_JQ-1,infected Calu-1 cells

description:
2_JQ-1_infected
Human lung cancer cells Calu-3, JQ1 treated, SARS-Cov-2 infected MOI 0.1


title: mCRC34.S5T


title: Splenocytes_Experiment_cDNA


title: ATAC-seq of 2_DMSO,uninfected Calu-1 cells

description:
2_DMSO_uninfected
Human lung cancer cells Calu-3, DMSO treated, uninfected


title: mCRC33.S6T


title: Pertubation_Experiment_ADT


title: mCRC31.S8T


title: Pertubation_Experiment_HTO


title: mCRC30.S7T


title: mCRC3.S8T


title: mCRC40.S5T


title: ATAC-seq of 2_DMSO,infected Calu-1 cells

description:
2_DMSO_infected
Human lung cancer cells Calu-3, DMSO treated, SARS-Cov-2 infected MOI 0.1


title: Pertubation_Experiment_cDNA


title: mCRC3.S6T


title: mCRC4.S8T


title: mCRC38.S5T


title: mCRC3.S5T


title: mCRC29.S4T


title: mCRC27.S5T


title: ATAC-seq of 1_JQ-1,uninfected Calu-1 cells

description:
1_JQ-1_uninfected
Human lung cancer cells Calu-3, JQ1 treated, uninfected


title: Cebpb+NR4_KO_Experiment_GDO


title: ATAC-seq of 1_JQ-1,infected Calu-1 cells

description:
1_JQ-1_infected
Human lung cancer cells Calu-3, JQ1 treated, SARS-Cov-2 infected MOI 0.1


title: mCRC29.S8T


title: mCRC26.S48T


title: Control_Experiment_GDO


title: mCRC25.S8T


title: mCRC25.S5T


title: Control_Experiment_ADT


title: ATAC-seq of 1_DMSO,infected Calu-1 cells

description:
1_DMSO_infected
Human lung cancer cells Calu-3, DMSO treated, SARS-Cov-2 infected MOI 0.1


title: ATAC-seq of 1_DMSO,uninfected Calu-1 cells

description:
1_DMSO_uninfected
Human lung cancer cells Calu-3, DMSO treated, uninfected


title: mCRC22.S7T1


title: Control_Experiment_HTO


title: mCRC22.S7T2


title: mCRC2.S5_8T


title: mCRC19.S5_8T


title: ATAC-seq of 1_naive,uninfected Calu-1 cells

description:
1_naive_uninfected
Human lung cancer cells Calu-3, untreated, uninfected


title: Control_Experiment_cDNA


title: mCRC21.S6T


title: RNA-Seq of naive, uninfected Calu-1 cells, rep1

description:
naive_mock_1
Human lung cancer cells Calu-3, untreated, SARS-Cov-2 infected MOI 0.1

data_processing:
Reads were aligned to a combined hg38 (Gencode v36) /SARS-CoV-2 (GenBank entry MN908947) reference using the STAR aligner v. 2.7.5 (Dobin et al., 2013) and quantified using featureCounts from the RSubread R package v1.22.2 (Liao Y, Smyth GK, Shi W, 2019.
Resulting count matrices were analysed using the DESEQ2 R package v1.38.3. Further analyses are described in the publication.
Assembly: hg38 (ENSEMBL v102)/SARS-CoV-2 (GenBank entry MN908947)
Supplementary files format and content: Tab-delimited file containing raw gene/feature integer counts.

extract_protocol:
Total RNA was isolated from 3x10^5 cells per replicate using Direct-Zol RNA Miniprep Kit (Zymo Research) according to the manufacturer's protocol and shipped in dry ice to the MDC/BIH Genomic Core RNAseq: Facility for quality assessment using TapeStation (Agilent Technologies)
Libraries were prepared using TrueSeq Stranded mRNA Kit to generate Illumina-compatible libraries by following the manufacturer’s protocol (Illumina). Libraries were sequenced on SP lane of NovaSeq 6000 System (Illumina) to generate 40 million 75-nucleotide paired-end reads per sample.


title: RNA-Seq of naive, uninfected Calu-1 cells, rep3

description:
naive_mock_3
Human lung cancer cells Calu-3, untreated, uninfected


title: RNA-Seq of naive, uninfected Calu-1 cells, rep2

description:
naive_mock_2
Human lung cancer cells Calu-3, untreated, uninfected


title: Cebpb+NR4_KO_Experiment_cDNA


title: mCRC17.S7T


title: ZM1_w2PBS

city: Worcester

first: Noah

middle: Jacob

last: Silverstein

state: Massachusetts

address: 373 Plantation, Biotech 2, suite 319

department: Molecular Medicine

institute: UMass Chan Medical School

description: 10X Genomics

data_processing:
The raw data were processed using Cell Ranger (10x Genomics, v3.1.0) within the DolphinNext Cell Ranger Pipeline (Revision 2) (Yukselen et al., 2020), and reads were aligned to both the mm10 and PR8 genomes.
Assembly: mm10 + GCF_000865725.1
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung, PR8 infection, paternal PBS

extract_protocol:
At 6 days post PR8 infection animals were sacrificed and perfused with 10ml cold PBS. Lungs were collected and single cell suspensions were prepared using the Miltenyi Biotec Lung Dissociation Kit (130-095-927) with the gentleMACS Octo Dissociator (130-095-937) following the manufacturer instructions.
Cells were loaded onto the Chromium Controller (10x Genomics) and single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3ʹ Reagent Kits v3 (10x Genomics) following the standard manufacturer protocols.

value: Lung

value: Male

value: paternal PBS

value: PR8 infection


title: mCRC18.S5_8T


title: mCRC16.S7T


title: WM5_w2FLU

description: 10X Genomics

source_name: Lung, PR8 infection, paternal PR8

value: paternal PR8


title: RNA-Seq of JQ1, uninfected Calu-1 cells, rep2

description:
jq1_mock_2
Human lung cancer cells Calu-3, JQ1 treated, SARS-Cov-2 infected MOI 0.1

value: Human lung cancer

value: uninfected


title: mCRC15.S6T


title: mCRC15.S5_8T


title: mCRC14.S6T


title: mCRC23.S7T


title: RM2_w1PBS

description: 10X Genomics


title: WM2_uninf

description: 10X Genomics

source_name: Lung, uninfected

value: Uninfected


title: RNA-Seq of JQ1, uninfected Calu-1 cells, rep3

description:
jq1_mock_3
Human lung cancer cells Calu-3, JQ1 treated, uninfected


title: mCRC15.S7T


title: RNA-Seq of JQ1, uninfected Calu-1 cells, rep1

description:
jq1_mock_1
Human lung cancer cells Calu-3, JQ1 treated, uninfected


title: mCRC14.S3T


title: RNA-Seq of JQ1, infected Calu-1 cells, rep3

description:
jq1_infect_3
Human lung cancer cells Calu-3, JQ1 treated, uninfected


title: LM6_w1FLU

description: 10X Genomics


title: mCRC13.S5T


title: LLM2_w2PBS

description: 10X Genomics


title: RNA-Seq of JQ1, infected Calu-1 cells, rep2

description:
jq1_infect_2
Human lung cancer cells Calu-3, JQ1 treated, SARS-Cov-2 infected MOI 0.1


title: mCRC1.S6T


title: HCC998T


title: mCRC1.S7T


title: HCC2143T


title: RNA-Seq of JQ1, infected Calu-1 cells, rep1

description:
jq1_infect_1
Human lung cancer cells Calu-3, JQ1 treated, uninfected


title: LLM1_uninf

description: 10X Genomics


title: HCC2137T


title: KM3_w1FLU

description: 10X Genomics


title: RNA-Seq of DMSO, uninfected Calu-1 cells, rep3

description:
dmso_mock_3
Human lung cancer cells Calu-3, DMSO treated, SARS-Cov-2 infected MOI 0.1


title: KKM1_w2PBS

description: 10X Genomics


title: RNA-Seq of DMSO, uninfected Calu-1 cells, rep2

description:
dmso_mock_2
Human lung cancer cells Calu-3, DMSO treated, uninfected


title: HCC2095T


title: HCC2105T


title: RNA-Seq of DMSO, uninfected Calu-1 cells, rep1

description:
dmso_mock_1
Human lung cancer cells Calu-3, DMSO treated, uninfected


title: HCC2086T


title: HCC2111T


title: JM3_w1PBS

description: 10X Genomics


title: mCRC10.S4_8T


title: RNA-Seq of DMSO, infected Calu-1 cells, rep3

description:
dmso_infect_3
Human lung cancer cells Calu-3, DMSO treated, SARS-Cov-2 infected MOI 0.1


title: HCC2071T


title: FFM2_w2FLU

description: 10X Genomics


title: mCRC13.S6T


title: RNA-Seq of DMSO, infected Calu-1 cells, rep2

description:
dmso_infect_2
Human lung cancer cells Calu-3, DMSO treated, uninfected


title: RNA-Seq of DMSO, infected Calu-1 cells, rep1

description:
dmso_infect_1
Human lung cancer cells Calu-3, DMSO treated, SARS-Cov-2 infected MOI 0.1


title: HCC2129T


title: HCC2056T


title: HCC2052T


title: HCC2053T


title: HCC2032T


title: EEM3_w2FLU

description: 10X Genomics


title: CM1_uninf

description: 10X Genomics


title: HCC2013T


title: EM2_w1FLU

description: 10X Genomics


title: Rep1_CDK12i_CDK9i_4h30min

city: Stockholm

first: Anniina

last: Vihervaara

address: Tomtebodavägen 23A, 17165 Solna, Sweden

department: Department of Gene Technology

country: Sweden

institute: Science for Life Laboratory, KTH Royal Institute of Technology

data_processing:
Adapters were removed using Fastp tool (Shifu Chen et al., 2018).
The reads were mapped to mm10-dm3 genome using Bowtie2 (Langmead et al., 2009) with parameters --end-to-end --ff
Mapped reads were processed to bed and bedgraph files.
Nascent transcription was quantified at promoter-proximal and genebody regions as described in Rabenius et al. (2022), STAR protocols 3, 101036.
DESeq2 (Love et al., 2014) was used to determine changes in transcription.
Assembly: hg38
Supplementary files format and content: bigWig files are provided for visualization of PRO-seq data for each sample. Two separate bigWig files are provided for plus (pl) and minus (mn) strand.
Library strategy: PRO-seq

molecule: nuclear RNA

growth_protocol: HCT116 cells were grown in McCoy's 5A medium (Merck) supplemented with 10% FBS, 100 U/ml penicillin/streptomycin and maintained at 37 °C in a humidified 5 % CO2 atmosphere.

extract_protocol:
Chromatin was isolated from HCT116 cells, after which precision run-on sequencing (PRO-seq) was performed as previously described in Mahat et al. (2016), Nat. Protocol 11, 1455–1476.
Libraries were constructed using TruSeq small-RNA adaptors as described in Mahat et al. (2016), Nat. Protocol 11, 1455–1476.

treatment_protocol: HCT116 cells were treated with three different inhibitors for either 1 h or 4 h 30min to inhibit CDK12 or CDK9. 3-MP-PP1 (5 µM) was used to inhibit CDK12 and NVP-2 (10 nM) was used to inhibit CDK9. DMSO treatment was used as a negative control. Two biological replicates were used for each condition.

value: Colorectal carcinoma cells

value: WT


title: HCC2094T


title: HCC2076T


title: Rep2_CDK12i_CDK9i_4h30min


title: Rep2_CDK12i_CDK9i_1h


title: HCC1986T


title: 3T3-L1-PolIISer2-shBRWD3-Induction

city: shanghai

first: Guosheng

last: Hu

state: shanghai

address: 2005 Songhu Road, Yangpu District, Shanghai

institute: fudan university

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the mm10 genome assembly using Bowtie version 2.2.6 with the default options.
The bigwig files were generated by using HOMER 4.9, in which the total tags are normalized to 1.00e+07.
Peaks are called by using Homer findPeaks script
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

growth_protocol: 3T3-L1 cells,obtained from American Type Culture Collection, were cultured in Medium B (Dulbecco’s modified Eagle’s medium (1 g/L glucose) supplemented with 10% (v/v) NCS (Thermo Fisher Scientific), 100 U/ml penicillin, and 100 mg/ml streptomycin) at 37C in an atmosphere of 8.8% CO2 and maintained in less than 50% confluence.

extract_protocol:
3T3-L1 preadipocytes with indicated treatments were used for ChIP-Seq analysis. For ChIP with anti-ELK1 antibodies, cells were fixed with 5mM DSG for 45 min at RT,then fixed with 1% formaldehyde for 15 min at RT.  For ChIP with anti-Pol II and anti-Pol II-S2P antibodies, cells were fixed with 1% formaldehyde for 15 min at RT. Fixation was stopped by adding glycine to a final concentration of 0.14 M and incubating at RT for 10 min, followed by two washes with cold PBS.    For each ChIP, 1×107 cells were resuspended in Buffer A (50 mM Hepes, pH7.6, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) supplemented with protease inhibitors (Roche), incubated on ice for 10 min, and spun at 1,000 g for 10 min at 4oC. Pellet (nuclear fractions) was washed twice with Buffer B (10 mM Tris, pH7.8, 200 mM NaCl, 1 mM EDTA and 1 mM EGTA) supplemented with protease inhibitors, and resuspended in 0.3 ml Buffer C (50 mM Tris, pH7.8, 10 mM EDTA and 1% SDS) supplemented with protease inhibitors. Chromatin was fragmented to 150-300 bp on a Bioruptor for 30 cycles of 30 s on and 30 s off. Chromatin lysates were then diluted 10-fold with Buffer D (20 mM Tris, pH7.8, 150 mM NaCl, 2 mM EDTA and 1% Triton X-100) supplemented with protease inhibitors, incubated with 5 μg anti-ELK1 (Abcam, ab32106),  5 μg anti-Pol II (Bethyl, A300-653A), 5 μg anti-Pol II-S2P (Abcam, ab5095), antibodies overnight at 4oC, and then immunoprecipitated with Protein G magnetic beads (Biorad, 161-4023) with rotation at 4oC for 4 hr. Immunoprecipitations were washed once with Buffer E (20 mM Tris, pH8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS and 1% Triton X-100) for 15 min at 4oC, once with Buffer E containing 400 mM NaCl for 15 min at 4oC, and twice with Buffer F (50 mM Tris, pH8.0, 1 mM EDTA). Formaldehyde crosslinked chromatin was reversed in Buffer G (50 mM Tris, pH8.0, 10 mM EDTA, 1% SDS) at 65oC overnight, and glutaraldehyde crosslinked chromatin was reversed in buffer G containing 1 mg/ml protease K at 65oC overnight as previously described51. DNA was isolated using Qiagen PCR product purification kit (#28104).
Library was generated using a KAPA Hyper Prep Kit (Roche, KK8503) following manufacturer’s instructions. Adaptors and primer sequences from Roche were used for library construction and amplification. After PCR amplification, the 250-450 bp fragments were purified using KAPA pure beads (Roche, KK8000) following manufacturer’s instructions.

treatment_protocol: On day 0 (2 days after confluence), 3T3-L1 preadipocytes were treated with Induction Medium (Dulbecco’s modified Eagle’s medium  (1 g/L glucose) supplemented with 10% (v/v) FCS, 100 U/ml penicillin, and 100 mg/ml streptomycin) containing 5 mg/ml insulin,  0.5 mM IBMX, 1 mM Dexamethasone and 1 mM pioglitazone.

value: 3T3-L1 preadipocytes harvested  with differentiation medium treatment

value: anti-Pol II-S2P (Abcam, ab5095)


title: HCC1990T


title: 3T3-L1-PolIISer2-shBRWD3-CTL

value: 3T3-L1 preadipocytes harvested  without differentiation medium treatment


title: FM6_w1PBS

description: 10X Genomics


title: HCC1982T


title: HCC2069T


title: Rep1_CDK12i_CDK9i_1h


title: 3T3-L1-PolIISer2-shCTL-Induction


title: HCC1988T


title: HCC1956T


title: Rep2_CDK9i_4h30min


title: HCC1978T


title: Rep1_CDK9i_4h30min


title: HCC1949T


title: HCC1954T


title: Rep2_CDK9i_1h


title: HCC1903T


title: 3T3-L1-PolII-shBRWD3-Induction

value: anti-Pol II (Bethyl, A300-653A)


title: 3T3-L1-PolII-shBRWD3-CTL


title: HCC1996T


title: Rep1_CDK9i_1h


title: HCC1901T


title: HCC1900T


title: 3T3-L1-PolII-shCTL-CTL


title: 3T3-L1-PolII-shCTL-Induction


title: rRNA Depleted totalRNA from heart, left ventricle from untreated SHR rats (rep 4, sequencing batch 2) [SHR_4_control_2]

city: Aurora

first: Laura

last: Saba

state: CO

address: 12850 E. Montview Blvd

department: Skaggs School of Pharmacy and Pharmaceutical Sciences

institute: University of Colorado Anschutz Medical Campus

description:
SHR_4_batch2
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.reconstruction.gtf
SHR_4_control_2

data_processing:
Cutadapt (v1.9.1) trim Illumina adapter, quality, and length, parameters: -q 20 -m 20
Remove rRNA reads by alignment with bowtie2(v2.3.4.3) to rRNA
genome Alignment Hisat2 (v2.1.0)
Stringtie (v1.3.5) reconstruction
Run Aptardi (v1.4) on each strain reconstructed GTF
Merge aptardi output reconstruction Stringtie(v1.3.5)
Run RSEM (v1.3.1) on reconstruction
Filter transcripts/genes from RSEM results if one third or more of samples have less than 1 read or  if the length of the mature RNA transcript was less than 200 nucleotides
Run RSEM(v1.3.1) on filtered reconstruction
Filter transcripts/genes from RSEM results if one third or more of samples have less than 1 read or  if the length of the mature RNA transcript was less than 200 nucleotides
Apply a regularized log transformation of expected read counts from RSEM (rlog function in DESeq2 package of R)
Remove technical artifacts including batch effects using Removal of Unwanted Variance  (RUVg) with empirically-derived controls (RUVSeq package in R)
Assembly: rn7.2
Supplementary files format and content: TSV batch corrected/normalized expression values
Supplementary files format and content: GTF of the reconstructed transcriptome

organism: Rattus norvegicus

source_name: heart

extract_protocol:
RNA was collected from the left ventricle of the heart using the RNeasy Plus Universal Midi kits for RNA sequencing (Qiagen, Valencia, CA, USA).
Libraries were constructed using the Illumina TruSeq Stranded TotalRNA Kit (Illumina, San Diego, CA, USA).
rRNA depleted stranded totalRNA

treatment_protocol: Tissue frozen in RNA later.

value: heart

value: SHR/OlaIpcv

tag: batch


title: rRNA Depleted totalRNA from heart, left ventricle from untreated SHR rats (rep 4, sequencing batch 3) [SHR_4_control_3]


title: HCC1887T

value: Liver cancer


title: ELK1-shBRWD3-Induction-3T3-L1

value: anti-ELK1 (Abcam, ab32106)


title: rRNA Depleted totalRNA from heart, left ventricle from untreated SHR rats (rep 4, sequencing batch 1) [SHR_4_control_1]


title: ELK1-shBRWD3-CTL-3T3-L1


title: rRNA Depleted totalRNA from heart, left ventricle from untreated SHR rats (rep 3, sequencing batch 1) [SHR_3]


title: HCC1877T


title: ELK1-shCTL-Induction-3T3-L1


title: Rep2_CDK12i_1h


title: Rep1_CDK12i_1h


title: HCC1874T


title: rRNA Depleted totalRNA from heart, left ventricle from untreated SHR rats (rep 2, sequencing batch 1) [SHR_2]


title: Rep2_DMSO_4h30min

value: DMSO


title: HCC1873T


title: ELK1-shCTL-CTL-3T3-L1


title: rRNA Depleted totalRNA from heart, left ventricle from untreated SHR rats (rep 1, sequencing batch 1) [SHR_1]


title: RNA-Seq-shELK1-Induction-3T3-L1

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Tophat version 2.1.1.
Genome_build: mm10

growth_protocol: 3T3-L1 cells,obtained from American Type Culture Collection, were cultured in Medium B (Dulbecco’s modified Eagle’s medium (1 g/L glucose) supplemented with 10% (v/v) NCS (Thermo Fisher Scientific), 100 U/ml penicillin, and 100 mg/ml streptomycin) at 37 C in an atmosphere of 8.8% CO2 and maintained in less than 50% confluence.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality.
RNA-Seq analysis of global gene expression profiling was conducted at Anoroad (Beijing, China). Briefly, 3 µg RNA pooled from 3 different samples of the same treatment was used to generate sequencing libraries using UltraTM RNA Library Prep Kit for Illumina (NEB, #7530L). Sequencing was performed at 125 bp/150 bp paired-end reads on an Illumina Hiseq platform. Paired-end clean reads were aligned to the reference genome using Tophat (v2.1.1). To quantify the expression level of each gene, Cuffdiff (v2.2.1) was used to count the reads numbers mapped to each gene, and genes with a FPKM greater than 0.5 in any group were kept for further analysis. Genes which were induced more than 1.5 fold after the induction were considered as immediate-early responsive genes (IEGs) during adipogenesis. In DDB1 or ELK1 knockdown cells, IEGs with an induction fold less than 67% of those in the control cells were defined as DDB1 and ELK1 downstream genes, respectively. Gene ontology analysis were performed using the cluster Profiler R package.

value: Cells were harvested at 1 hr after induction for differentiation.


title: HCC1946T


title: Rep1_DMSO_4h30min


title: rRNA Depleted totalRNA from heart, left ventricle from untreated  rats (rep 1, sequencing batch 3) [HXB7_1]

description:
HXB7_1_batch2
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.reconstruction.gtf
HXB7_1


title: HCC1824T


title: Rep2_DMSO_1h


title: Rep1_CDK12i_4h30min


title: Rep1_DMSO_1h


title: RNA-Seq-shELK1-CTL-3T3-L1

value: Cells were harvested at 0 hr after induction for differentiation.


title: HCC1803T


title: rRNA Depleted totalRNA from heart, left ventricle from untreated  rats (rep 1, sequencing batch 3) [HXB5_1]

description:
HXB5_1_batch2
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.reconstruction.gtf
HXB5_1


title: rRNA Depleted totalRNA from heart, left ventricle from untreated  rats (rep 1, sequencing batch 3) [HXB31_1]

description:
HXB31_1_batch2
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.reconstruction.gtf
HXB31_1


title: 293FT_OE_FOXP3_IP

city: Beijing

first: Jing

last: He

state: Beijing

address: Room D110, Medical Science Building, School of Medicine, Tsinghua University

department: School of Medicine

institute: Tsinghua University

data_processing:
Basecalls performed using CASAVA
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with fastp 0.20.0, then mapped to hg38 whole genome using hisat2 v2.1.0 with default parameters.
RNA-seq expression value Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated with exons from each transcript were merged to create one nonoverlapped meta-transcript.
ChIP-seq signal value Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using bamCoverage with parameters --binSize 10 --normalizeUsing RPKM --effectiveGenomeSize 2150570000 \--extendReads
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample's protein coding genes and lncRNA genes
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage

growth_protocol: In brief, undifferentiated hESCs were expanded on irradiated MEFs at 37℃ with 5% CO2 in hESC medium (KnockOut TM DMEM (Invitrogen, 10829018) with 20% knockout serum replacement (Invitrogen, 10828028) plus 1mM L-glutamine, 0.1mM nonessential amino acids, and 8 ng/ml recombinant human basic FGF (R&D systems)). 293FT cells were expanded with 5% CO2 in 293FT medium (DMEM high glucose with 10% FBS plus 1mM L-glutamine, 0.1mM nonessential amino acids, 1mM Sodium Pyruvate).

extract_protocol:
Total RNA was extracted using the TRIzol® Reagent (Life Technologies). Cells for ULI-ChIP were lysed in nuclear isolation buffer.
Libraries were prepared according to Illumina's instructions.RNA-Seq used the VAHTS mRNA-seq v2 Library Prep Kit (Vazyme NR611-02) for library construction. ChIP-Seq used the NEBNext® DNA Library Prep Kit and NEBNext® Multiplex Oligos for Illumina.

treatment_protocol: To differentiate hESCs into hPGCLCs, ~3×104 undifferentiated hESCs (~30% confluency in a six-well plate) were seeded onto one well of a six-well plate coated with Matrigel. Adherent differentiation began by treating the hESCs with differentiation medium (KODMEM supplemented with 10% FBS, 1mM L-glutamine, 0.1mM nonessential amino acids, 50 ng/ml BMP4 and BMP8a (R&D systems)) for 2 h at 37 ℃ with 5% CO2. This procedure was followed by transduction with lentiviral supernatant expressing DAZL-P2A-mCherry for 6 hours, then the differentiated hESCs were incubated with differentiation medium containing 50 ng/ml BMP4 and BMP8a for 12 days.

value: 293FT cells transfected FOXP3-P2A-mCherry plasmids and FACS for mCherry positive cells

value: anti-Flag tag(Sigma, Cat# F1804)

value: 293FT cells were transfected with p2k7-bsd-FOXP3-3xFLAG-P2A-mCherry plasmids by lipo2000, and FACS for mCherry strong positive cells 48 hours after transfection.


title: HCC1772T


title: RNA-Seq-shDDB1-CTL-3T3-L1


title: rRNA Depleted totalRNA from heart, left ventricle from untreated  rats (rep 1, sequencing batch 2) [HXB3_1]

description:
HXB3_1_batch1
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.reconstruction.gtf
HXB3_1


title: 293FT_OE_FOXP3_Input


title: RNA-Seq-shCTL-Induction-3T3-L1


title: LHX8_OE_rep2

data_processing:
Basecalls performed using CASAVA
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with fastp 0.20.0, then mapped to hg38 whole genome using hisat2 v2.1.0 with default parameters.
RNA-seq expression value Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated with exons from each transcript were merged to create one nonoverlapped meta-transcript.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample's protein coding genes

source_name: hESC

extract_protocol:
Total RNA was extracted using the TRIzol® Reagent (Life Technologies). Cells for ULI-ChIP were lysed in nuclear isolation buffer.
Libraries were prepared according to Illumina's instructions.RNA-Seq used the VAHTS mRNA-seq v2 Library Prep Kit (Vazyme NR611-02) for library construction.

value: differentiated cells derived from hESC

value: treated with BMP4 and BMP8a for 2 hours, then infect LHX8-P2A-GFP lentivirus for 6 hours, then culture in differentiation medium for 12 days


title: HCC1625T


title: HCC1864T


title: HCC1598T


title: LHX8_OE_rep1


title: rRNA Depleted totalRNA from heart, left ventricle from untreated  rats (rep 1, sequencing batch 2) [HXB25_1]

description:
HXB25_1_batch1
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.reconstruction.gtf
HXB25_1


title: HCC1534T


title: rRNA Depleted totalRNA from heart, left ventricle from untreated  rats (rep 1, sequencing batch 3) [HXB29_1]

description:
HXB29_1_batch2
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.reconstruction.gtf
HXB29_1


title: CDK9-shDDB1-Induction-3T3-L1

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the mm10 genome assembly using Bowtie version 2.2.6 with the default options.
The bigwig files were generated by using HOMER 4.9, in which the total tags are normalized to 1.00e+07.
Peaks are called by using Homer findPeaks script
Genome_build: mm10

extract_protocol:
3T3-L1 preadipocytes with indicated treatments were used for ChIP-Seq analysis. For ChIP with anti-DDB1 and anti-CDK9 antibodies, cells were fixed with 1% glutaraldehyde for 15 min at RT. For ChIP with anti-H3K27ac, anti-H3K9ac, anti-H3K4me3, anti-Pol II and anti-Pol II-S2P antibodies, cells were fixed with 1% formaldehyde for 15 min at RT. Fixation was stopped by adding glycine to a final concentration of 0.14 M and incubating at RT for 10 min, followed by two washes with cold PBS.    For each ChIP, 1×107 cells were resuspended in Buffer A (50 mM Hepes, pH7.6, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) supplemented with protease inhibitors (Roche), incubated on ice for 10 min, and spun at 1,000 g for 10 min at 4oC. Pellet (nuclear fractions) was washed twice with Buffer B (10 mM Tris, pH7.8, 200 mM NaCl, 1 mM EDTA and 1 mM EGTA) supplemented with protease inhibitors, and resuspended in 0.3 ml Buffer C (50 mM Tris, pH7.8, 10 mM EDTA and 1% SDS) supplemented with protease inhibitors. Chromatin was fragmented to 150-300 bp on a Bioruptor for 30 cycles of 30 s on and 30 s off. Chromatin lysates were then diluted 10-fold with Buffer D (20 mM Tris, pH7.8, 150 mM NaCl, 2 mM EDTA and 1% Triton X-100) supplemented with protease inhibitors, incubated with 3 μg anti-DDB1 (Abcam, ab109027), 5 μg anti-ELK1 (Abcam, ab32106), 5 μg anti-H3K9ac (Abcam, ab4441), 5 μg anti-H3K27ac (Abcam, ab4729), 5 μg anti-H3K4me3 (Abcam, ab8580), 5 μg anti-Pol II (Bethyl, A300-653A), 5 μg anti-Pol II-S2P (Abcam, ab5095), or 5 μg anti-CDK9 (CST, 2316s) antibodies overnight at 4oC, and then immunoprecipitated with Protein G magnetic beads (Biorad, 161-4023) with rotation at 4oC for 4 hr. Immunoprecipitations were washed once with Buffer E (20 mM Tris, pH8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS and 1% Triton X-100) for 15 min at 4oC, once with Buffer E containing 400 mM NaCl for 15 min at 4oC, and twice with Buffer F (50 mM Tris, pH8.0, 1 mM EDTA). Formaldehyde crosslinked chromatin was reversed in Buffer G (50 mM Tris, pH8.0, 10 mM EDTA, 1% SDS) at 65oC overnight, and glutaraldehyde crosslinked chromatin was reversed in buffer G containing 1 mg/ml protease K at 65oC overnight as previously described51. DNA was isolated using Qiagen PCR product purification kit (#28104).
Library was generated using a KAPA Hyper Prep Kit (Roche, KK8503) following manufacturer’s instructions. Adaptors and primer sequences from Roche were used for library construction and amplification. After PCR amplification, the 250-450 bp fragments were purified using KAPA pure beads (Roche, KK8000) following manufacturer’s instructions.

value: anti-CDK9 (CST, 2316s)


title: rRNA Depleted totalRNA from heart, left ventricle from untreated  rats (rep 1, sequencing batch 3) [HXB24_1]

description:
HXB24_1_batch2
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.reconstruction.gtf
HXB24_1


title: CDK9-shDDB1-CTL-3T3-L1


title: rRNA Depleted totalRNA from heart, left ventricle from untreated  rats (rep 1, sequencing batch 3) [HXB21_1]

description:
HXB21_1_batch2
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.reconstruction.gtf
HXB21_1


title: LNC1845_OE_H3K4me3

value: hPGCLCs derived from LNC1845 EF1A KI-hESC

value: EF1A promoter KI upstream of LNC1845 on chromosome 1 (heterozygote)

value: treated with BMP4 and BMP8a for 2 hours, then infect DAZL-P2A-mCherry lentivirus for 6 hours, then culture in differentiation medium for 12 days


title: LNC1845_OE_H3K27ac

value: hPGCLCs derived from LNC1845 EF1A KI-Hesc


title: RNA-Seq-shCTL-CTL-3T3-L1


title: HCC1515T


title: Rep2_CDK12i_4h30min

value: Colorectal carcinoma cells

value: WT


title: rRNA Depleted totalRNA from heart, left ventricle from untreated  rats (rep 1, sequencing batch 3) [HXB20_1]

description:
HXB20_1_batch2
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.reconstruction.gtf
HXB20_1

value: heart


title: CDK9-shCTL-Induction-3T3-L1

value: 3T3-L1 preadipocytes harvested  with differentiation medium treatment


title: HCC1507T

value: Liver cancer


title: CDK9-shCTL-CTL-3T3-L1

value: 3T3-L1 preadipocytes harvested  without differentiation medium treatment


title: HCC1505T


title: rRNA Depleted totalRNA from heart, left ventricle from untreated  rats (rep 1, sequencing batch 3) [HXB17_1]

description:
HXB17_1_batch2
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.reconstruction.gtf
HXB17_1


title: RNA-Seq-shDDB1-Induction-3T3-L1

value: Cells were harvested at 1 hr after induction for differentiation.


title: LNC1845_OE_Input DNA


title: LNC1845_KO_H3K4me3

value: hPGCLCs derived from LNC1845 KO-hESC

value: LNC1845 KO at its locus on chromosome 1 (homozygote)


title: HCC1422T


title: PolIISer2-shDDB1-Induction-3T3-L1

value: anti-Pol II-S2P (Abcam, ab5095)


title: rRNA Depleted totalRNA from heart, left ventricle from untreated  rats (rep 1, sequencing batch 2) [HXB13_1]

description:
HXB13_1_batch1
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.reconstruction.gtf
HXB13_1


title: 3T3-L1-PolIISer2-shCTL-CTL


title: LNC1845_KO_H3K27ac


title: rRNA Depleted totalRNA from heart, left ventricle from untreated  rats (rep 1, sequencing batch 3) [HXB1_1]

description:
HXB1_1_batch2
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.reconstruction.gtf
HXB1_1


title: HCC1329.P.T


title: PolIISer2-shCTL-Induction-3T3-L1


title: HCC1282T


title: LNC1845_KO_Input DNA


title: HCC1266T


title: Kras Ko placenta

city: Brussels

first: Patrick

last: Jacquemin

address: 75 Avenue Hippocrate

country: Belgium

institute: de Duve Institute

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation was made using Cell Ranger 6.1.2, using default parameters except 'include-introns' parameter that was included.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: e13.5 placenta

extract_protocol:
Sorted nuclei was used as the RNA source (see also below)
Library preparation from the sorted nuclei (see above) including reverse transcription, barcoding, cDNA amplification, and purification was performed according to Chromium 10x V3 protocols.

value: e13.5 placenta

value: Kras-/-


title: HCC1281T


title: control placenta

value: control (Kras+/+)


title: rRNA Depleted totalRNA from heart, left ventricle from untreated  rats (rep 1, sequencing batch 3) [BXH9_1]

description:
BXH9_1_batch2
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.reconstruction.gtf
BXH9_1


title: PolII-shDDB1-CTL-3T3-L1

value: anti-Pol II (Bethyl, A300-653A)


title: PolII-shDDB1-Induction-3T3-L1


title: rRNA Depleted totalRNA from heart, left ventricle from untreated  rats (rep 1, sequencing batch 3) [BXH8_1]

description:
BXH8_1_batch2
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.reconstruction.gtf
BXH8_1


title: WT_Input DNA

value: hPGCLCs derived from hESC


title: 293FT_FPM_rep2

description: 293FT_Con_and_FPM.coding.fpkm.txt,293FT_Con_and_FPM.lnc.fpkm.txt

value: 293FT cells transfected FOXP3-P2A-mCherry plasmids and FACS for mCherry positive cells

value: transfected FOXP3-P2A-mCherry plasmids and culture for 48 hours


title: HCC1256T


title: PolII-shCTL-Induction-3T3-L1


title: rRNA Depleted totalRNA from heart, left ventricle from untreated  rats (rep 1, sequencing batch 2) [BXH6_1]

description:
BXH6_1_batch1
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.reconstruction.gtf
BXH6_1


title: HCC1248T


title: PolII-shCTL-CTL-3T3-L1


title: 293FT_FPM_rep1


title: rRNA Depleted totalRNA from heart, left ventricle from untreated  rats (rep 1, sequencing batch 2) [BXH5_1]

description:
BXH5_1_batch1
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.reconstruction.gtf
BXH5_1


title: 293FT_Con_rep2

value: 293FT cells transfected empty plasmids

value: transfected empty plasmids and culture for 48 hours


title: WT_H3K4me3

value: WT

value: treated with BMP4 and BMP8a for 2 hours, then infect DAZL-P2A-mCherry lentivirus for 6 hours, then culture in differentiation medium for 12 days


title: HCC1226T

value: Liver cancer


title: rRNA Depleted totalRNA from heart, left ventricle from untreated BXH2 rats (rep 1, sequencing batch 3) [BXH2_1]

description:
BXH2_1_batch2
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.reconstruction.gtf
BXH2_1

value: heart


title: 293FT_Con_rep1


title: HCC1199T


title: WT_H3K27ac


title: rRNA Depleted totalRNA from heart, left ventricle from untreated BXH13 rats (rep 1, sequencing batch 3) [BXH13_1]

description:
BXH13_1_batch2
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.reconstruction.gtf
BXH13_1


title: H3K4ME3-CTL-3T3-L1

value: anti-H3K4me3 (Abcam, ab8580)

value: 3T3-L1 preadipocytes harvested  without differentiation medium treatment


title: PolIISer2-shCTL-CTL-3T3-L1


title: PolIISer2-shDDB1-CTL-3T3-L1


title: HCC1257T


title: LNC1845KO_rep2

description: hPGCLCs_coding.fpkm.txt, hPGCLCs_lnc.fpkm.txt

value: hPGCLCs derived from LNC1845 KO-hESC

value: LNC1845 KO at its locus on chromosome 1 (homozygote)


title: HCC1198T


title: rRNA Depleted totalRNA from heart, left ventricle from untreated BXH12 rats (rep 1, sequencing batch 3) [BXH12_1]

description:
BXH12_1_batch2
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.reconstruction.gtf
BXH12_1


title: H3K27AC-CTL-3T3-L1

value: anti-H3K27ac (Abcam, ab4729)


title: rRNA Depleted totalRNA from heart, left ventricle from untreated BXH11 rats (rep 1, sequencing batch 3) [BXH11_1]

description:
BXH11_1_batch2
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.reconstruction.gtf
BXH11_1


title: H3K9AC-CTL-3T3-L1

value: anti-H3K9ac (Abcam, ab4441)


title: control_rep2

value: DAZL-negative population derived from hESC


title: LNC1845KO_rep1


title: HCC1193T


title: rRNA Depleted totalRNA from heart, left ventricle from untreated BN-Lx rats (rep 4, sequencing batch 1) [BNLx_4]

value: BN-Lx/Cub


title: ES_rep2

value: hESC

value: untreated


title: HCC1180T


title: control_rep1


title: DDB1-shBRWD3-3T3-L1

value: anti-DDB1 (Abcam, ab109027)


title: rRNA Depleted totalRNA from heart, left ventricle from untreated BXH10 rats (rep 1, sequencing batch 2) [BXH10_1]

description:
BXH10_1_batch1
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.reconstruction.gtf
BXH10_1


title: DDB1-Induction-3T3-L1

value: 3T3-L1 preadipocytes harvested  with differentiation medium treatment


title: rRNA Depleted totalRNA from heart, left ventricle from untreated BN-Lx rats (rep 3, sequencing batch 1) [BNLx_3]


title: DDB1-CTL-3T3-L1


title: WT_rep2

value: hPGCLCs derived from hESC


title: ELK1-Induction-3T3-L1

extract_protocol:
3T3-L1 preadipocytes with indicated treatments were used for ChIP-Seq analysis. For ChIP with anti-DDB1 and anti-CDK9 antibodies, cells were fixed with 1% glutaraldehyde for 15 min at RT. For ChIP with anti-H3K27ac, anti-H3K9ac, anti-H3K4me3, anti-Pol II and anti-Pol II-S2P antibodies, cells were fixed with 1% formaldehyde for 15 min at RT.For ChIP with anti-ELK1 antibodies, cells were fixed with 5mM DSG for 45 min at RT,then fixed with 1% formaldehyde for 15 min at RT. Fixation was stopped by adding glycine to a final concentration of 0.14 M and incubating at RT for 10 min, followed by two washes with cold PBS.
For each ChIP, 1×107 cells were resuspended in Buffer A (50 mM Hepes, pH7.6, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) supplemented with protease inhibitors (Roche), incubated on ice for 10 min, and spun at 1,000 g for 10 min at 4oC. Pellet (nuclear fractions) was washed twice with Buffer B (10 mM Tris, pH7.8, 200 mM NaCl, 1 mM EDTA and 1 mM EGTA) supplemented with protease inhibitors, and resuspended in 0.3 ml Buffer C (50 mM Tris, pH7.8, 10 mM EDTA and 1% SDS) supplemented with protease inhibitors. Chromatin was fragmented to 150-300 bp on a Bioruptor for 30 cycles of 30 s on and 30 s off. Chromatin lysates were then diluted 10-fold with Buffer D (20 mM Tris, pH7.8, 150 mM NaCl, 2 mM EDTA and 1% Triton X-100) supplemented with protease inhibitors, incubated with 3 μg anti-DDB1 (Abcam, ab109027), 5 μg anti-ELK1 (Abcam, ab32106), 5 μg anti-H3K9ac (Abcam, ab4441), 5 μg anti-H3K27ac (Abcam, ab4729), 5 μg anti-H3K4me3 (Abcam, ab8580), 5 μg anti-Pol II (Bethyl, A300-653A), 5 μg anti-Pol II-S2P (Abcam, ab5095), or 5 μg anti-CDK9 (CST, 2316s) antibodies overnight at 4oC, and then immunoprecipitated with Protein G magnetic beads (Biorad, 161-4023) with rotation at 4oC for 4 hr. Immunoprecipitations were washed once with Buffer E (20 mM Tris, pH8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS and 1% Triton X-100) for 15 min at 4oC, once with Buffer E containing 400 mM NaCl for 15 min at 4oC, and twice with Buffer F (50 mM Tris, pH8.0, 1 mM EDTA). Formaldehyde crosslinked chromatin was reversed in Buffer G (50 mM Tris, pH8.0, 10 mM EDTA, 1% SDS) at 65oC overnight, and glutaraldehyde crosslinked chromatin was reversed in buffer G containing 1 mg/ml protease K at 65oC overnight as previously described51. DNA was isolated using Qiagen PCR product purification kit (#28104).

value: anti-ELK1 (Abcam, ab32106)


title: rRNA Depleted totalRNA from heart, left ventricle from untreated BN-Lx rats (rep 2, sequencing batch 1) [BNLx_2]


title: ES_rep1

value: WT


title: rRNA Depleted totalRNA from heart, left ventricle from untreated BN-Lx rats (rep 1, sequencing batch 1) [BNLx_1]


title: WT_rep1

value: treated with BMP4 and BMP8a for 2 hours, then infect DAZL-P2A-mCherry lentivirus for 6 hours, then culture in differentiation medium for 12 days


title: ELK1-CTL-3T3-L1


title: AP2-XII-1-KD-HA_AP2-XI-2-KD-Myc_IAA24h_replicate2

status: Public on Sep 16 2023

city: La Tronche

first: Christopher

last: Swale

address: Batiment Jean Roger

department: U1209 - Institute of Advanced Biosciences

institute: INSERM

description:
ATAC-SEQ-AP2-XII-1-KD-HA_AP2-XI-2-KD-MYC_IAA24h_merged-duplicates.bw
UTvsIAA24h-duplicate.deseq2.broadpeak.txt

data_processing:
Following the demultiplexing of raw reads by bcl2fastq V3, trimming, quality control, alignment to the ME49 reference genome (using bwa2) and duplicate read merging (using Picard) was performed by the nf-core ATAQ-SEQ pipeline (Ewels et al. 2020).
Quantitative analysis of UT vs IAA 24h conditions was performed by nf-core through a broad peak calling/annotation (MACS2) followed by HOMER to analyse peak distribution relative to gene features. Reads were counted on annotated peaks by featureCounts and counts were processed by DeSeq2 to generate global statistical analysis of peak intensities in between conditions using biological duplicates.
Assembly: Toxoplasma gondii genome (ME49 strain) file "ToxoDB-13.0_TgondiiME49_Genome.fasta" to upload at ToxoDB website : http://toxodb.org/common/downloads/release-13.0/TgondiiME49/fasta/data/
Supplementary files format and content: Data visualization:  Picard merged bam files were converted to bigWig file format using a bin size of 5 by bamCoverage (Deeptools).

organism: Toxoplasma gondii

source_name: intracellular parasites

growth_protocol: Toxoplasma gondii RHKU80 strains were maintained by serial passage Human foreskin fibroblast (HFF) monolayer under tachyzoite conditions in DMEM (Life) supplemented with 10% (vol/vol) FBS (Life) and 25 mM Hepes buffer, pH 7.2.

extract_protocol:
Nuclei preparation, permeabilization, Tn5 transposition and library preparation was prepared following precisely the Diagenode ATAC-SEQ kit protocol (C01080002)
Following the Tn5 reaction, libraries were amplified using the Diagenode 24 UDI kit 1 (ref 01011034) following standard protocol procedures.
Libraries were multiplexed and sequenced on a single Novaseq6000 lane by Fasteris (Genesupport SA) using 2*50 cycles, generating on average 27 million reads.

treatment_protocol: HFF cells were grown to confluence and infected with RHKU80  AP2-XII-1-mAID_AP2XI-2-mAID mAiD strains. Tn5 transposition was performed to quantify chromatin accessibility within this strain in both a condition left untreated (UT) and treated with IAA (indole-3-acetic acid) for 24 hours. Tn5 transposition was performed on approximately 100 000 intracellular tachyzoites after permeabilization using 0,02% Digitonin.

tag: dev. stage

value: tachyzoites

value: IAA treated for 24h


title: AP2-XII-1-KD-HA_AP2-XI-2-KD-Myc_IAA24h_replicate1


title: HCC1181T

value: Liver cancer


title: DDB1-shELK1-3T3-L1

value: 3T3-L1 preadipocytes harvested  without differentiation medium treatment


title: CRTC3 KO astrocyte_2hr_rep1

city: Seoul

first: Sukyoung

last: Park

address: 88, Olympic-ro 43-gil

country: South Korea

institute: Ulsan University

description:
Gene expression data from FSK treated for 2hr CRTC3 KO astrocyte cell
170512_10_KO_2_(MoGene-2_0-st).rma-gene-full-Signal

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Mouse. Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450.   2.0 ST Array at 45°C for 16hour

scan_protocol: GeneChips were scanned on a GCS3000 Scanner (Affymetrix).

data_processing:
Raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by AffymetrixGeneChip® Command Console® Software (AGCC). After importing CEL files, the data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Expression Console™ Software (EC). We exported the result with gene level RMA analysis and perfomed the differentially expressed gene (DEG) analysis
Signal values were computed using the Affymetrix® GeneChip™ Command Console software.

label: Biotin

source_name: FSK treated for 2hr in CRTC3 KO astorycte cell

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: Mixed glial cell cultured from mouse pups at postnatal day 1-3. After 2 weeks later, mixed glial cell incubated at 225rpm for 24hr in the shaking incubator. Floating microglia cells were remved and attached primary astrocyte cells were culture on plates for expeiments.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA purity and integrity were evaluated by ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA), Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: Astrocyte cell were treated vehicle(0.1% DMSO) or FSK 25uM for 0 and 2hr.

tag: strain background

value: CRTC3 KO

value: Primary astrocyte cell

value: FSK 25uM


title: AP2-XII-1-KD-HA_AP2-XI-2-KD-Myc_UT_replicate1

description:
ATAC-SEQ-AP2-XII-1-KD-HA_AP2-XI-2-KD-MYC_UT_merged-duplicates.bw
UTvsIAA24h-duplicate.deseq2.broadpeak.txt

value: untreated sample


title: AP2-XII-1-KD-HA_AP2-XI-2-KD-Myc_UT_replicate2


title: DDB1-shCTL-3T3-L1


title: GmMM-Input-br1

city: Davis

first: John

last: Harada

state: CA

address: One Shields Avenue

department: Plant Biology

institute: University of California

data_processing:
Basecalls performed using RTA version 1.12.4.2
Sequenced reads passing Illumina quality filter were aligned to the Glycine max genome (Wm82.a2.v1) using Bowtie v0.12.7 with parameters -v 2 -5 0 -3 0 -m 1 --best --strata
Reads from technical replicates were combined and peaks were identified for each biological replicates using MACS3, using default parameters and a q value threshold of 0.01.
Assembly: Wm82.a2.v1
Supplementary files format and content: NarrowPeak files generated by MACS3.

organism: Glycine max

source_name: embryos

growth_protocol: Soybean cv Williams 82 plants were grown in 2 gallon pots containing Ron’s mix (1 part coarse sand, 1 part compost, 1 part peat moss, 3 pounds/yard Dolomite) in UC Davis greenhouses at temperatures ranging 22-30°C and under 16 hour-days.

extract_protocol:
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp.  Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 2 ug of an antibody raised against the peptide CTEKGVIRKEPSLPRQ, or 3 ug of an antibody raised against CSGYAGNGKRDVGYPP,  corresponding to the amino acids 103-117 and 275-289 of GLYMA.13G153200, respectively.  Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.
ChIP and Input libraries were generated using Nugen Ovation Ultralow System V2, following the manufaturer's instructions and enriched by PCR using 15 cycles.  Libraries were size-selected by electrophoresis and purified using Qiagen MinElute gel purification kit

treatment_protocol: Mid-maturation stage embryos were dissected  from seeds weighing between 200 and 250 mg.  Tissues were crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10 mM Tris pH 8.0, 1mM EDTA pH 8.0) containing 1% formaldehyde, at room temperature, then quenched in 100 mM Glycine for 5 minutes.  Tissues were rinsed twice with deionized water and stored at -80C until use.

value: embryos

value: Williams 82

value: mid-maturation


title: GmMM-GLYMA.13G153200-ChIP-Ab2-br2

value: anti-peptide 2 GLYMA.13G153200


title: GmMM-GLYMA.13G153200-ChIP-Ab1-br2

value: anti-peptide 1 GLYMA.13G153200


title: GmMM-Input-br2


title: GmMM-GLYMA.13G153200-ChIP-Ab1-br1


title: GmMM-GLYMA.13G153200-ChIP-Ab2-br1


title: GmEM-Input-br2

extract_protocol:
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp.  Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 3 ug of an antibody raised against the peptide CSGYAGNGKRDVGYPP,  corresponding to the amino acids 275-289 of GLYMA.13G153200.  Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.
ChIP and Input libraries were generated using Nugen Ovation Ultralow System V2, following the manufaturer's instructions and enriched by PCR using 15 cycles.  Libraries were size-selected by electrophoresis and purified using Qiagen MinElute gel purification kit

treatment_protocol: Early maturation stage embryos were dissected from seeds measuring between 6 and 7 mm.  Tissues were crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10 mM Tris pH 8.0, 1mM EDTA pH 8.0) containing 1% formaldehyde, at room temperature, then quenched in 100 mM Glycine for 5 minutes.  Tissues were rinsed twice with deionized water and stored at -80C until use.

value: early maturation


title: GmEM-GLYMA.13G153200-ChIP-br2

value: anti-peptide GLYMA.13G153200


title: GmEM-Input-br1


title: GmEM-GLYMA.13G153200-ChIP-br1


title: WT astorycte_FSK 2hr_rep1

description:
Gene expression data from FSK treated for 2hr WT astrocyte cell
170512_13_WT_2_(MoGene-2_0-st).rma-gene-full-Signal

source_name: FSK treated for 2hr in WT astorycte cell

value: WT


title: GmCOT-Input-br3

extract_protocol:
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp.  Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 2 ug of an antibody raised against the peptide SRSQPQPQPLHPQYHH (corresponding to the amino acids 117-132 of GLYMA.04G093300), or 3 ug of antibody raised against the peptide CPEPRYQIRRTSSASF (corresponding to the amino acids 302-316 of GLYMA.06G314400).  Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.
ChIP and Input libraries were generated using Nugen Ovation Ultralow System V2, following the manufaturer's instructions and enriched by PCR using 15 cycles.  Libraries were size-selected by electrophoresis and purified using Qiagen MinElute gel purification kit

treatment_protocol: Cotyledon stage embryos were dissected from 3.5 to 4.5 mm seeds.  Tissues were crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10 mM Tris pH 8.0, 1mM EDTA pH 8.0) containing 1% formaldehyde, at room temperature, then quenched in 100 mM Glycine for 5 minutes.  Tissues were rinsed twice with deionized water and stored at -80C until use.

value: cotyledon stage


title: GmCOT_GLYMA.06G314400-ChIP-br3

value: anti-peptide GLYMA.06G314400


title: GmCOT-Input-br2


title: CRTC3 KO astrocyte_vehicle_rep1

description:
Gene expression data from vehicle treated CRTC3 KO astrocyte cell
170512_8_KO_0_(MoGene-2_0-st).rma-gene-full-Signal

source_name: Vehicle treated CRTC3 KO astrocyte cell

value: vehicle (0.1% DMSO)


title: GmCOT_GLYMA.06G314400-ChIP-br2


title: GmCOT-Input-br1


title: WT astrocyte_vehicle_rep1

description:
Gene expression data from vehicle treated WT astrocyte cell
170512_11_WT_0_(MoGene-2_0-st).rma-gene-full-Signal

source_name: Vehicle treated WT astrocyte cell


title: GmCOT_GLYMA.04G093300-ChIP-br2

value: anti-peptide GLYMA.04G093300


title: GmCOT_GLYMA.04G093300-ChIP-br1


title: Patient 14658, Lung tumor, Never-smoker, smoL19, MRE

city: St. Louis

first: Ting

last: Wang

address: 4515 McKinley Ave

department: Genetics

institute: Washington University in St. Louis

description:
smoL19_mCRF.bedGraph.gz
smoL19_mCRF.bedGraph.gz.tbi

data_processing:
Adapter trimming, read alignment to the hg19 genome with BWA, and methylQA post-processing were also performed as described the paper: "Li D, Zhang B, Xing X, Wang T. Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation. Methods. 2015;72(C):29–40".
methylCRF was performed on the 28 primary tumor and normal lung samples to estimate the methylation level at each CpG using MRE-seq and MeDIP-seq data. The methylCRF package was downloaded and installed from http://methylcrf.wustl.edu/. methylCRF was run using perl 5.14.4, R 3.3.0, and samtools 1.3.1.
M&M (R package methylMnM) was used to identify DMRs between samples using MRE-seq and MeDIP-seq data. First, the functions countcpgbin and countMREcpgbin were used to count the number of CpGs and restriction enzyme cut sites in 500bp bins across the genome (chromosomes 1-22, X, Y, and M; n=6,166,049 bins). Cut sites for the 4 enzymes used in MRE-seq were considered, and a blacklist file was provided (hg19 DAC Blacklisted Regions, e.g., wgEncodeDacMapabilityConsensusExcludable from the UCSC Genome Browser). Then, 500bp DMRs were identified using the read alignment bed files output by methylQA for MRE-seq and MeDIP-seq from two samples. The functions countMeDIPbin and countMREbin were used to produce normalized read counts per bin for each sample. Default values were used for MnM.test, MnM.qvalue, and MnM.selectDMR, and no PCR threshold was set. DMRs were identified between patient-matched normal lung and tumors from the same patient (n=11), between all pairs of normal samples (n=55), and between all normal-tumor sample pairs from different patients (n=176).
Assembly: hg19
Supplementary files format and content: mCRF bed files and index files were created and are available for each sample, dictating CpG methylation at individual loci.
Supplementary files format and content: DMR bed files and index files were created and are available for each patient where normal and primary data were collected and indicate regions showing differential methylation between the paired normal and primary.

source_name: NSCLC tumor

growth_protocol: Snap-frozen primary NSCLC tumor specimens were  collected from surgical remnants with patient consent under an IRB-approved protocol.

extract_protocol:
Genomic DNA was isolated using the Qiagen kit (56304).
MeDIP-seq and MRE-seq were generated using the protocol in the paper: "Li D, Zhang B, Xing X, Wang T. Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation. Methods. 2015;72(C):29–40". MRE-seq was performed with four enzymes: HpaII, SsiI, Hin6I, HpyCH4IV and a base offset of 3 was used during sequencing.

value: NSCLC tumor

value: Never-smoker