title: ChIP_seq_FL_WT_Input_for_H3K27me3

data_processing:
ATAC data was mapped to mm10 using Bowtie2 (Langmead & Salzberg, 2012; Langmead et al., 2009) with standard settings. Tag directories with reads mapped to the mitochondrial chromosome filtered out and UCSC BedGraph files normalized to 10M total mapped reads were created using the HOMER platform (Heinz et al, 2010) (makeTagDirectory, makeUCSCfile). BedGraph files were up-loaded to the UCSC-genome browser (Kent et al, 2002) for visualization. Abundance of ATAC-tags on defined peak positions was analyzed in HOMER using the annotatePeaks.pl command with normalization to 10M mapped reads. When used for differential binding analysis, annotatePeaks.pl command with the -noadj option was used followed by processing with edgeR. Reads from OMNI-ATAC data were trimmed using TrimGalore and mapped to mm10 (Gencode build GRCm38.p5) with Bowtie2 (v. 2.3.5) (Langmead & Salzberg, 2012). PCR duplicates were removed with Picard MarkDuplicates (v. 2.21.4) and files were further filtered for mapq score of 10 using Samtools (v. 1.9). BigWig files from the mapq score 10 filtered bam file was generated using bamCoverage (v.3.3.1) from the deepTools suite (Ramirez et al, 2016). Peak calling from the mapq10 filtered bam file was performed using the Kundaje lab ATAC-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL792NWO/) with MACS2 and IDR (irreproducible discovery rate) threshhold set to 0.05 and 0.1, respectively. Samtools was used to remove mitochondrial reads prior to peak calling. From the processed duplicate, the Optimal peak set was used for downstream analysis. Aditionally, Tag directories with reads mapped to the mitochondrial chromosome filtered out were created using the HOMER platform (v. 4.10; 4.11) (Heinz et al., 2010).
ChIP-seq: Reads were aligned to mouse reference genome mm10 using Bowtie2 (Langmead et al., 2009). If not indicated, further analyzes were performed using the HOMER package (Heinz et al., 2010). ChIP-peaks/regions from single samples ChIPs were identified using findPeaks.pl with the –style factor parameter for TF-peaks and –style histone for histone ChIPs. Identified peaks were normalized to input controls. When duplicate or more ChIPs  were  available, transcription factor peaks were identified with findPeaks.pl against a matched control sample using the settings “-P .1 -LP .1 -poisson .1 -style factor”. Transcription factor peak reproducibility was determined by a HOMER adaptation of the IDR (Irreproducibility Discovery Rate) package (Li QB, 2011) (Karmel A. 2015. homer-idr: Second pass updated) according to (https://sites.google.com/site/anshulkundaje/projects/idr). Motif enrichment analysis was performed with the findMotifsGenome.pl command of the HOMER package. Overlapping peaks between samples were identified using mergePeaks.pl (default parameters). Tag density plots and heat maps were created with annotatePeaks.pl (–hist or –hist & -ghist respectively), normalizing data to 10 million mapped reads per experiment, and visualized using Excel or by hierarchical clustering in Cluster3 (de Hoon et al, 2004) followed by Java Treeview (Saldanha, 2004). UCSC genome browser was used for visualization of BedGraph files (Kent et al., 2002). To create Violin-plots, peak positions were annotated using annotatePeaks.pl normalizing data to 10 million mapped reads per experiment. Prior to log transformation a small number was added to all normalized read values and Log2 values were exported to Prism for visualization and statistics.  For H3K27me3 ChIP, reads were trimmed with Trim-galore in paired-end mode (Babraham Bioinformatics) and mapped to the mm10 genome (Gencode version GRCm38) with Bowtie2 (2.3.5) (Langmead & Salzberg, 2012). Bam-files were generated using Samtools v.1.9 (Li et al, 2009) and PCR duplicates were removed with Picard MarkDuplicates (2.21.4) followed by a filtration of read för MAPQ-score ³ 10 using Samtools. BigWig files from the MAPQ-score filtered bam files were generated using bamCoverage (v.3.3.1) from the deepTools suite (Ramirez et al., 2016). Tag directories as above and genomic regions enriched for H3K27me3 signal were identified using findPeaks.pl (Heinz et al., 2010) with the –style histone parameter and normalized to their respective inputs.
Cut and Run Reads were trimmed with Trim-galore in paired-end mode (Babraham Bioinformatics) and mapped to the mm10 genome (Gencode version GRCm38) with Bowtie2 (2.3.5) (Langmead & Salzberg, 2012). Bam-files were generated using Samtools v.1.9 (Li et al., 2009) and PCR duplicates were removed with Picard MarkDuplicates (2.21.4) followed by a filtration of read för MAPQ-score ³ 10 using Samtools. Peaks were called from the filtered bam-file using MACS2 callpeak (Zhang et al, 2008) with default settings, using the Normal IgG as the control. Subsequently, the bam-files were used to generate HOMER Tag directories with makeTagDirectory (Heinz et al., 2010) .
PLAC-seq: To maximize interaction calling, fastq-files containing both read 1 and read 2 with their counter parts from the replicates were combined for a total of 460M (230-238)  Trim Galore trimmed paired-end reads per sample. Reads were trimmed in pair-end mode with Trim Galore (0.6.4)(--paired --fastqc --clip_R1 10 --clip_R2 10 --three_prime_clip_R1 3 --three_prime_clip_R2 3) (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Trimmed paired fastq reads were preprocessed through the HiC-Pro pipeline (v2.11.1) (Servant et al, 2015), using Bowtie2 (2.3.5) (Langmead & Salzberg, 2012; Langmead et al, 2009) for alignment against mm10 (GRCm38) reference genome, assigning mapped reads to a mm10 MboI restriction map followed by removal of PCR duplicates with Picard tools MarkDuplicates (2.21.4) (https://broadinstitute.github.io/picard/) and subsequently the generation of a list of valid interaction read pairs. Single-end sequenced fastq files from the 230-238 H3K4me3 ChIP-seq were used as inputs for the generation of interaction anchor points. Bias corrected significant interactions (FDR ≤ 0.05) between anchor points and other anchor points/non-anchor-points  (peak-to-all) were identified for the 230-238 H3K4me3 PLAC-sequence data with the FitHiChIP pipeline (v. 6.0) (Bhattacharyya et al, 2019) using the HiC-Pro valid pairs and identified ChIP-anchors as input files with following settings: GCSize (size of the window upstream and downstream the restriction site used to calculate the GC content)=200, MappSize (size of the window upstream and downstream the restriction site used to calculate the mappability)=500, BINSIZE (Size of the bins in bases, for detecting the interactions)=5000, LowDistThr (Lower distance threshold of interaction between two segments)=10000, UppDistThr (Upper distance threshold of interaction between two segments)=3000000, BiasCorrection with Coverage specific bias. FitHiChIP was used to merge adjacent loops. Interactions were uploaded and visualized on the WashU EpiGenome. Interaction anchor points were annotated against mm10 with a custom bash script utilizing the HOMER annotation database (annotatePeaks.pl). Annotated interactions files were further processed in R as follows: We defined anchor-points spanning one bin size (5 kb) surrounding TSS as a TSS-annotated bin. Interactions lacking a TSS in either anchor-point or interactions containing a TSS in both anchor-points were filtered out. After this filtration step 40179 (57.5%) TSS-distal interactions remained. The distally located anchor-points were subsequently assigned to their connected TSS. Since our PLAC-seq analysis is limited to a 5 kb resolution, we used a 10 kb cutoff (distance from TSS to the middle of a 5 kb bin) for identification of distal interactions. Contrasting this, ATAC-peaks located within a 7.5 kb window from the TSS were proximity annotated to the closest gene.
Genome_build: mm10
Supplementary_files_format_and_content: txt-files describing ChIP-and-ATAC-seq data annotated at indicated position

source_name: Wt Fetal liver

value: Wt


title: RIT1M90I_YAP5SA_3

status: Public on May 31 2021

type: SRA

city: Seattle

first: Alice

last: Berger

state: WA

address: 1100 Fairview Ave N

country: USA

institute: Fred Hutchinson Cancer Center

library_source: transcriptomic

data_processing:
Illumina NovaSeq reads were aligned by STAR v2.5.3a in 2-pass mode to BAM files.
Picard tools v.1.114 used mark duplicate reads, add read group info, and reorder BAMs.
BAMs are indexed using samtools v.0.1.19
FeatureCounts from Subread v.1.5.3 was used to quantify gene transcripts and generate raw counts file
EdgeR v.3.30.3 was used to normalize read counts and obtain CPM and RPKM values.
CPM values were used to filter the gene list  down to the 12,887 genes with average log2CPM >0.1 across all samples. RPKM values were converted into TPM values.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: counts_all.txt is a tab-separated values file with the quantified read counts from FeatureCounts. Each row is a gene transcript. The first six columns describe the gene, and each of the remaing columns correspond to a sample.
transcript_quants_log2TPM.csv is a comma-separated values file of the log2 of TPM values. Each row is a gene transcript and each column is a sample.

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
Direct-zol RNA Miniprep plus (Zymo Research)
Illumina TruSeq kit for 50bp paired-end reads, poly-A selection, non-strand-specific

tag: cell line

value: SALE

tag: cell type

value: lung epithelial

tag: treatment (lentiviral transduction)

value: RIT1 M90I + YAP1 5SA


title: ChIP_seq_FL_EKO_Input_for_H3K27me3

city: Lund

first: Mikael

last: Sigvardsson

address: Sölvegatan 19

country: Sweden

institute: Lund University

description:
Annotate-WT_EKO_histone_ChIP_andH3K27Ac_CnR_on_ATAC-peaks_WT-enriched-genes-OpenWTandEKO-NOT-Promoter.txt
Annotate-WT_EKO_histone_ChIP_andH3K27Ac_CnR_on_ATAC-peaks_WT-enriched-genes-OpenWTandEKO-Promoter.txt
Annotate-WT_EKO_histone_ChIP_andH3K27Ac_CnR_on_ATAC-peaks_WT-enriched-genes-OpenWTnotEKO-NOT-Promoter.txt
Annotate-WT_EKO_histone_ChIP_andH3K27Ac_CnR_on_ATAC-peaks_WT-enriched-genes-OpenWTnotEKO-Promoter.txt

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Ebf1-KO Fetal liver

growth_protocol: Fetal liver cells were purified from wild-type, Ebf1 deficient, E2A deficient or Pax5 deficient fetuses, and expanded on OP9 stromal cells in Opti-MEM supplemented with 10% heat-inactivated fetal calf serum, 25mM HEPES, 50μg/ml Gentamicin, 50μM β-mercaptoethanol, 10ng/ml KIT ligand, 10ng/ml Fms-like tyrosine kinase 3 ligand, and 10ng/ml Interleukin-7. Murine pre-B cell line, 230-238 cells were maintained in RPMI1640 supplimented with 10% heat-inactivated fetal calf serum, 25mM HEPES, 50μg/ml Gentamicin, and 50μM β-mercaptoethanol. Infection: Retronectin coated 24-well plates were pre-inkubated with 500ul viral supernatant. Cells were harvested,  resuspended 500ul media and added to 500μl of virus supernatant. Polybrene was added to supernatant at concentration of 0.5μg/ml. Spin-infection was performed at 1800xg, for 90min at 32°C.

extract_protocol:
ATAC-seq: Cells were washed in ice cold PBS prior to Assay for Transposase Accessible Chromatin (ATAC-seq) as described in (Buenrostro et al, 2013) or for 230-238 cells as described in (Corces et al, 2017). Cells for transcriptions factor ChIP were fixed at RT in 1 mg/ml DSG (ThermoFisher Scientific) in PBS for 30 min followed by additional 10 min after addition of formaldehyde up to 1%. Cells for histone modification ChIP were fixed in 1% formaldehyde for 10 min at RT. The reactions were quenched by addition of 1/10 volume of 0.125M glycine and the cells were washed in PBS. Nuclei were isolated by 10 min incubation in Nuclei Isolation buffer (50 mM Tris-pH 8.0, 60 mM KCl, 0.5% NP40) + protease inhibitor cocktail (PIC) (Roche) on ice. Pelleted nuclei were dissolved in Lysis buffer (0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8)) + PIC and sonicated on a Bioruptor (Diagenode). Sonication was followed by pelleting of debris and the supernatant was transferred to new tube and chromatin was diluted 5X in Dilution Buffer (1% Triton, 2mM EDTA, 150 mM NaCl, 20 mM Tris-HCl (pH 8) + PIC) for transcription factor ChIP and in HBSS (Lonza, Verviersa, Belgium) +PIC and 2X RIPA buffer (20 mM Tris–HCl, pH 7.5, 2 mM EDTA, 2% Triton X-100, 0.1% SDS, 0.2% Sodiumdeoxycholate, 200 mM NaCl + PIC) for histone modification ChIPs. Cut&Run was performed similar to (Skene et al, 2018) with minor changes using one million FL Wt or Ebf1-/- cells per sample and 2 ug of the following antibodies: rabbit polyclonal aH3K27ac (Abcam, ab4729, Lot GR3231937-1), and polyclonal Normal Rabbit IgG (Millipore 12-370, Lot 3109265). PLAC-seq was carried out similar to previously reported (Okuyama et al, 2019) with minor modifications. Cells that had been cross-linked with 1% formaldehyde for 5 min (Covaris sonication) or 10 min (Bioruptor sonication) were thawed on ice for 5 min, re-suspended in ice cold lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2% NP-40, 1x Roche protease inhibitors – 11697498001 (PIC), and subsequently processed for PLAC-seq.
ChIP-Seq: Libraries were constructed using Illumina Truseq Nano DNA library preparation kit or by addition of Bioo-scientiffic Nextflex barcodes following standard procedures. Libraries were run on the Illumina NexSeq500. Cut&Run libraries for sequencing was essentially prepared as previously descried for ChIP-sequencing (Okuyama et al., 2019) with two modifications: 1) Prior to adapter ligation all purification steps were carried out using Zymo Research ChIP DNA Clean and Concentrator to not lose fragments smaller than 100 nt and 2) size-selection with Ampure XP beads was performed after adapter ligation with a targeted mean fragment size of 150-300 bp. Libraries were paired-end sequenced on an Illumina Nextseq 500 (read-length: 2 × 38 bp).   ATAC-seq library preparation was as described in (Buenrostro et al, 2013) or for 230-238 cells as described in (Corces et al, 2017).   PLAC-seq was carried out similar to previously reported (Okuyama et al, 2019) with minor modifications. NEXTflex DNA barcode ligation  (BIOO scientific) was performed using the Fast-link ligation kit (Epicenter, LK0750H). PLAC-seq libraries were subject to 2X 75 cycles of paired-end sequencing on a NextSeq500.

treatment_protocol:
Cultured in Optimem +10% FBS, 25mM HEPES, 50μg/ml Gentamicin, 50μM β-mercaptoethanol FL, KL, IL7 on OP9
FL-Ebf1-KO cells transduced with pMiG-Ebf1-ER constructs were treated with 1mM of Tamoxifen (4OHT) for indicated times prior to processing by ATAC-seq.

tag: strain background

tag: genotype / variation

value: ProB

tag: chip (antibody)


title: CutNRun_seq_FL_Ebf1KO_a_IgG

data_processing:
Library strategy: CUT&RUN
ATAC data was mapped to mm10 using Bowtie2 (Langmead & Salzberg, 2012; Langmead et al., 2009) with standard settings. Tag directories with reads mapped to the mitochondrial chromosome filtered out and UCSC BedGraph files normalized to 10M total mapped reads were created using the HOMER platform (Heinz et al, 2010) (makeTagDirectory, makeUCSCfile). BedGraph files were up-loaded to the UCSC-genome browser (Kent et al, 2002) for visualization. Abundance of ATAC-tags on defined peak positions was analyzed in HOMER using the annotatePeaks.pl command with normalization to 10M mapped reads. When used for differential binding analysis, annotatePeaks.pl command with the -noadj option was used followed by processing with edgeR. Reads from OMNI-ATAC data were trimmed using TrimGalore and mapped to mm10 (Gencode build GRCm38.p5) with Bowtie2 (v. 2.3.5) (Langmead & Salzberg, 2012). PCR duplicates were removed with Picard MarkDuplicates (v. 2.21.4) and files were further filtered for mapq score of 10 using Samtools (v. 1.9). BigWig files from the mapq score 10 filtered bam file was generated using bamCoverage (v.3.3.1) from the deepTools suite (Ramirez et al, 2016). Peak calling from the mapq10 filtered bam file was performed using the Kundaje lab ATAC-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL792NWO/) with MACS2 and IDR (irreproducible discovery rate) threshhold set to 0.05 and 0.1, respectively. Samtools was used to remove mitochondrial reads prior to peak calling. From the processed duplicate, the Optimal peak set was used for downstream analysis. Aditionally, Tag directories with reads mapped to the mitochondrial chromosome filtered out were created using the HOMER platform (v. 4.10; 4.11) (Heinz et al., 2010).
ChIP-seq: Reads were aligned to mouse reference genome mm10 using Bowtie2 (Langmead et al., 2009). If not indicated, further analyzes were performed using the HOMER package (Heinz et al., 2010). ChIP-peaks/regions from single samples ChIPs were identified using findPeaks.pl with the –style factor parameter for TF-peaks and –style histone for histone ChIPs. Identified peaks were normalized to input controls. When duplicate or more ChIPs  were  available, transcription factor peaks were identified with findPeaks.pl against a matched control sample using the settings “-P .1 -LP .1 -poisson .1 -style factor”. Transcription factor peak reproducibility was determined by a HOMER adaptation of the IDR (Irreproducibility Discovery Rate) package (Li QB, 2011) (Karmel A. 2015. homer-idr: Second pass updated) according to (https://sites.google.com/site/anshulkundaje/projects/idr). Motif enrichment analysis was performed with the findMotifsGenome.pl command of the HOMER package. Overlapping peaks between samples were identified using mergePeaks.pl (default parameters). Tag density plots and heat maps were created with annotatePeaks.pl (–hist or –hist & -ghist respectively), normalizing data to 10 million mapped reads per experiment, and visualized using Excel or by hierarchical clustering in Cluster3 (de Hoon et al, 2004) followed by Java Treeview (Saldanha, 2004). UCSC genome browser was used for visualization of BedGraph files (Kent et al., 2002). To create Violin-plots, peak positions were annotated using annotatePeaks.pl normalizing data to 10 million mapped reads per experiment. Prior to log transformation a small number was added to all normalized read values and Log2 values were exported to Prism for visualization and statistics.  For H3K27me3 ChIP, reads were trimmed with Trim-galore in paired-end mode (Babraham Bioinformatics) and mapped to the mm10 genome (Gencode version GRCm38) with Bowtie2 (2.3.5) (Langmead & Salzberg, 2012). Bam-files were generated using Samtools v.1.9 (Li et al, 2009) and PCR duplicates were removed with Picard MarkDuplicates (2.21.4) followed by a filtration of read för MAPQ-score ³ 10 using Samtools. BigWig files from the MAPQ-score filtered bam files were generated using bamCoverage (v.3.3.1) from the deepTools suite (Ramirez et al., 2016). Tag directories as above and genomic regions enriched for H3K27me3 signal were identified using findPeaks.pl (Heinz et al., 2010) with the –style histone parameter and normalized to their respective inputs.
Cut and Run Reads were trimmed with Trim-galore in paired-end mode (Babraham Bioinformatics) and mapped to the mm10 genome (Gencode version GRCm38) with Bowtie2 (2.3.5) (Langmead & Salzberg, 2012). Bam-files were generated using Samtools v.1.9 (Li et al., 2009) and PCR duplicates were removed with Picard MarkDuplicates (2.21.4) followed by a filtration of read för MAPQ-score ³ 10 using Samtools. Peaks were called from the filtered bam-file using MACS2 callpeak (Zhang et al, 2008) with default settings, using the Normal IgG as the control. Subsequently, the bam-files were used to generate HOMER Tag directories with makeTagDirectory (Heinz et al., 2010) .
PLAC-seq: To maximize interaction calling, fastq-files containing both read 1 and read 2 with their counter parts from the replicates were combined for a total of 460M (230-238)  Trim Galore trimmed paired-end reads per sample. Reads were trimmed in pair-end mode with Trim Galore (0.6.4)(--paired --fastqc --clip_R1 10 --clip_R2 10 --three_prime_clip_R1 3 --three_prime_clip_R2 3) (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Trimmed paired fastq reads were preprocessed through the HiC-Pro pipeline (v2.11.1) (Servant et al, 2015), using Bowtie2 (2.3.5) (Langmead & Salzberg, 2012; Langmead et al, 2009) for alignment against mm10 (GRCm38) reference genome, assigning mapped reads to a mm10 MboI restriction map followed by removal of PCR duplicates with Picard tools MarkDuplicates (2.21.4) (https://broadinstitute.github.io/picard/) and subsequently the generation of a list of valid interaction read pairs. Single-end sequenced fastq files from the 230-238 H3K4me3 ChIP-seq were used as inputs for the generation of interaction anchor points. Bias corrected significant interactions (FDR ≤ 0.05) between anchor points and other anchor points/non-anchor-points  (peak-to-all) were identified for the 230-238 H3K4me3 PLAC-sequence data with the FitHiChIP pipeline (v. 6.0) (Bhattacharyya et al, 2019) using the HiC-Pro valid pairs and identified ChIP-anchors as input files with following settings: GCSize (size of the window upstream and downstream the restriction site used to calculate the GC content)=200, MappSize (size of the window upstream and downstream the restriction site used to calculate the mappability)=500, BINSIZE (Size of the bins in bases, for detecting the interactions)=5000, LowDistThr (Lower distance threshold of interaction between two segments)=10000, UppDistThr (Upper distance threshold of interaction between two segments)=3000000, BiasCorrection with Coverage specific bias. FitHiChIP was used to merge adjacent loops. Interactions were uploaded and visualized on the WashU EpiGenome. Interaction anchor points were annotated against mm10 with a custom bash script utilizing the HOMER annotation database (annotatePeaks.pl). Annotated interactions files were further processed in R as follows: We defined anchor-points spanning one bin size (5 kb) surrounding TSS as a TSS-annotated bin. Interactions lacking a TSS in either anchor-point or interactions containing a TSS in both anchor-points were filtered out. After this filtration step 40179 (57.5%) TSS-distal interactions remained. The distally located anchor-points were subsequently assigned to their connected TSS. Since our PLAC-seq analysis is limited to a 5 kb resolution, we used a 10 kb cutoff (distance from TSS to the middle of a 5 kb bin) for identification of distal interactions. Contrasting this, ATAC-peaks located within a 7.5 kb window from the TSS were proximity annotated to the closest gene.
Genome_build: mm10
Supplementary_files_format_and_content: txt-files describing ChIP-and-ATAC-seq data annot

value: Normal Rabbit IgG Polyclonal Antibody control [12-370 Sigma-Aldrich]


title: RIT1M90I_YAP5SA_1


title: PCGF1_ERT2-Cre_Pcgf1Control_ES_rep1

city: Tsurumi-ku,Yokohama

first: Hiroki

last: Sugishita

state: Kanagawa

address: 1-7-22, Suehiro-cho

department: IMS

country: Japan

institute: RIKEN

description:
ERT2-Cre;Pcgf1f/f
PCGF1_ERT2-Cre_Pcgf1Control_ES.bw

data_processing:
Sequencing was performed with 75 bp single-end read by NextSeq500 (run by Kazusa DNA Research Institute) or 50bp single-end read by HiSeq1500 (run in RIKEN-IMS NGS facility).
The data were mapped onto UCSC-mm9 from illumina igenome. Generated sam format file combine to bam format file using samtools view (version 1.3.1). Then, PCR duplicate and multiple aligned reads are removed.
For bigwig generation, bam format files were processed by deeptools bamCoverage. The data of CpG island and TSS are derived from UCSC mm9.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: ES

growth_protocol: Embryonic stem cells (ESCs) were cultured with LIF (1U: Laboratory made), SU5402 (Altair corporation), PD184352 (Altair corporation) and CHIR99021 (Altair corporation) on MEF. For Embryoid Body (EB) formation, ESCs were cultured without LIF, SU5402, PD184352, CHIR99021 for 2 days on low attach culture dish. For epiblast stem cell (EpiSC) establishment, Embryoid Body (day2) are dispersed. And the cells were cultured on MEF with ActivinA (Peprotech), bFGF (Wako) and IWP-2 (Wako) on MEF in F12 medium (Gibco) 1%KSR (Gibco).

extract_protocol:
10^6-10^7 cells were cross-linking by 1% formaldehyde for 10 min at room temperature. Cross-linked cells were washed once with PBS, added swelling buffer (0.1% NP-40, 1 mM DTT in PBS) and chilled on ice for 10 minutes. After centrifuge, pellets were suspended with RIPA buffer (10 mM Tris-HCl pH8.0, 1mM EDTA, 140 mM NaCl, 1%Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate), and then were sonicated by using a BioRuptor sonicator (Diagenode). After sonication, DNA concentration is measured with Qubit 1x dsDNA HS Assay Kit (Thermo, cat. Q33230). On the other hand, protein A/G beads were prepared as washed twice with beads blocking buffer and suspended with beads blocking buffer with approximately 5 µg of antibody and incubated at 4ºC for more than 2 hours. Then, antibody attached beads were washed twice with beads blocking buffer and the chromatin samples were added to those antibody-attached-beads. After overnight incubation at 4ºC, chromatin samples bound beads were washed with RIPA for 6 times, RIPA high salt buffer(10 mM Tris-HCl pH8.0, 1mM EDTA, 500 mM NaCl, 1%Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate) twice, LiCl buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Sodium Deoxycholate) twice and TE twice. The chromatins were eluted with elution buffer (10 mM Tris-HCl pH8.0, 5 mM EDTA, 300 mM NaCl, 0.1 % SDS) overnight at 65ºC and treated with RNase for 30 min for 37°C and further incubation with Proteinase K for 1 hour at 37ºC. Then DNA samples were purified and used for further ChIP-qPCR or ChIP-seq.
ChIP-seq libraries were prepared by using NEBNext Ultra II FS DNA prep kit (NEB E7805) following manufacturer’s instruction.

tag: tamoxifen treatment

value: without 4-OHT

tag: genotype

value: embryonic stem cell

tag: antibody

value: PCGF1 (Laboratory made)

tag: replicate


title: ChIP_seq_FL_EKO_aH3K27me3_rep2

value: Rabbit anti H3K27me3 polyclonal IgG [07-449, Millipore]


title: ChIP_seq_FL_EKO_aH3K27me3_rep1


title: CutNRun_seq_FL_Wt_a_IgG


title: ChIP_seq_FL_WT_aH3K27me3_rep2


title: YAP5SA_3

value: YAP1 5SA


title: ChIP_seq_FL_WT_aH3K27me3_rep1


title: YAP5SA_2


title: RIT1-M90I_3

value: RIT1 M90I


title: YAP5SA_1


title: ChIP-seq-Ebf1-KO-Input-for-H3K4me2


title: RIT1-M90I_2


title: ChIP-seq-Ebf1-KO-H3K4me2

value: Rabbit anti  H3K4me2 polyclonal IgG [07-030, Millipore]


title: CutNRun_seq_FL_Wt_a_H3K27Ac

value: Rabbit anti H3K27ac polyclonal IgG [ab4729, Abcam]


title: ChIP_seq_Wt_Input_for_H3K4me2


title: ChIP-seq-Wt-H3K4me2


title: RIT1M90I_YAP5SA_2


title: ChIP_seq_Ebf1KO_Input_for_H3K4me3


title: RIT1-M90I_1


title: SALE_parental 1

value: parental control


title: ChIP_seq_WT_Input_for_H3K4me3


title: ChIP_seq_Ebf1KO_a_H3K4me3_rep2

value: Rabbit anti H3K4-Me3 polyclonal (Millipore, 07-473)


title: SALE_parental 3


title: ChIP_seq_WT_a_H3K4me3_rep2


title: SALE_parental 2


title: ChIP_seq_Ebf1KO_a_H3K4me3_rep1


title: H1975 Input DNA ChIP

city: Utrecht

first: Stefan

last: Prekovic

address: Universiteitsweg 100

department: CMM

country: Netherlands

institute: UMC Utrecht

data_processing:
Sequences were generated by the Illumina Hiseq 2500 genome analyzer (using 65bp reads) in case of RNA and ChIP seq, while for 4C MiSeq was used, subsequently sequences  were processed by the Illumina pipeline.
For RNA sequencing data was aligned to hg38 using TopHat and Differential expression (DE) was performed using optimized DESeq2 pipeline.
For ChIP sequencing reads were aligned to the Human Reference Genome (hg19) using BWA version 0.5.9. Reads with a BWA alignment quality score less than 20 were removed. Peaks were called MACS peak caller version 2 (Zhang Y et al. Genome Biol 2008;9(9):R137). MACS2 was run with the default parameters.
For 4C sequencing the alignment of the sequencing reads was done using bowtie2 with default parameters. We use samtools to filter for mapped reads with a minimum mapping quality score of 1. Next we extract from the reference genome all possible 4C capture sequences (in FASTA format) with the exact same length as the observed 4C captures from the sequencing run. We map and filter these reference capture sequences with the same parameters as the observed 4C reads using bowtie2 and samtools. In subsequent analysis we only include the thus mappable 4C fragment ends.
Genome_build: Hg38 (RNA seq), Hg19 (ChIP seq)

source_name: Lung cancer cell line

growth_protocol: A549 mentained in DMEM/F12 + 10%FCS + 1%P/S. H2122/H1944/H1975/H460 mentained in RPMI + 10%FCS + 1%P/S.

extract_protocol:
Chromatin immunoprecipitations (ChIP) were performed as described (Stelloo et al. Oncogene 2018). For each ChIP 5 μg of GR antibody  prebound to protein G beads were used.
Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303 KAPA biosystems kit).

treatment_protocol: Cells were serum starved for 3 days, subsequently the cells either remained untreated or were treated for 2 (ChIP and 4C) or 8 (RNA seq) hours with hydrocortisone and processed for downstream analysis.

tag: chip antibody

tag: treatment

value: Vehicle


title: H460 Input DNA ChIP


title: H2122 Input DNA ChIP


title: ChIP-seq-Ebf1-KO-Input-for-BRG1-EP300

description:
Annotate_230238-ebf1-chip_WT_EKO_BRG1_EP300_PolII_ChIP_n1_on_WT_enriched_Ebf1-bound_ATAC_peaks_WT_AND_EKO_acc.txt
Annotate_230238-ebf1-chip_WT_EKO_BRG1_EP300_PolII_ChIP_n1_on_WT_enriched_Ebf1-bound_ATAC_peaks_WT_NOT_EKO_acc.txt


title: ChIP-seq-Ebf1-KO-EP300

value: Rabbit anti-EP300 polyclonal IgG [sc-585, Santa Cruz, Dallas, TX]


title: H1944 Input DNA ChIP


title: ChIP-seq-Wt-Input-for-BRG1-EP300

value: Wt


title: H460 Hydrocortisone Rep 2 GR-ChIP-seq

value: GR Ab

value: Hydrocortisone (2,75 μM)


title: ChIP-seq-Ebf1-KO-BRG1

value: ProB

value: Rabbit anti-BRG1/Smarca4 polyclonal IgG [07-478 Millipore, Billerica, MA ]


title: ChIP-seq-Wt-EP300

value: PolII antibodies?


title: ChIP-seq-Wt-BRG1


title: A549 Input DNA ChIP


title: H460 Vehicle Rep 2 GR-ChIP seq


title: H2122 Hydrocortisone Rep 2 GR-ChIP-seq


title: H2122 Vehicle Rep 2 GR-ChIP seq


title: A549 Hydrocortisone Rep 2 GR-ChIP-seq


title: ChIP_seq_WT_a_H3K4me3_rep1


title: ChIP_seq_FL_EKO_a_IKZF1

value: Rabbit anti-Ikzf1 polyclonal IgG [ab26083, Abcam]


title: ChIP_seq_FL_EKO_a_Fli1

value: Rabbit anti-Fli1 polyclonal IgG [ab15289, Abcam, Cambridge, UK]


title: H1975 Hydrocortisone Rep 1 GR-ChIP-seq


title: A549 Vehicle Rep 2 GR-ChIP seq


title: H1975 Vehicle Rep 1 GR-ChIP seq


title: H1944 Hydrocortisone Rep 1 GR-ChIP-seq


title: H460 Hydrocortisone Rep 1 GR-ChIP-seq


title: ChIP_seq_FL_Wt_input_for_Fli1_IKZF1

description:
annotate_Wt-Fli1_peaks.txt
annotate_Wt-IKZF1_peaks.txt


title: ChIP_seq_FL_Wt_a_IKZF1


title: ChIP_seq_FL_Wt_a_Fli1


title: ChIP_seq_Input_for_Ebf1_KO_a_PolII


title: ChIP_seq_Ebf1_KO_a_RNAPolII

value: Mouse anti-POLII monoclonal IgG [39097 (102660) Active Motif]


title: H1944 Vehicle Rep 1 GR-ChIP seq


title: ChIP_seq_Input_for_WT_a_PolII


title: ATAC_seq_FL_Wt_rep3

description: Annotation_E2A-KO_n3_EKO_n3_PKO_n3_WT_n6_ATAC_on_WT_enriched_gene_ATAC_Peaks.txt


title: ChIP_seq_WT_a_RNAPolII


title: ATAC_seq_FL_Wt_rep2


title: H2122 Hydrocortisone Rep 1 GR-ChIP-seq


title: A549 Vehicle Rep 1 GR-ChIP seq


title: H2122-p57-ko Hydrocortisone Rep 2 mRNA seq

description: raw_counts_dexamethasone WTvsKO.csv

molecule: total RNA

extract_protocol:
RNA was extracted using the AllPrep DNA/RNA universal kit (Qiagen) according to the manufacturer’s instruction with Qiagen’s QIAcube robot. Samples with a RIN>8 were considered for library preparation.
Libraries were generated with the Illumina TruSeq RNA Library Preparation kit (RS-122-2001/2, Illumina Inc.) and sequenced on a HiSeq 2500 (using 65bp reads)

tag: crispr cell line features

value: CRISPR p57-knockout

tag: grna


title: ChIP_seq_FL_EKO_input_for_Fli1_IKZF1


title: H2122 Vehicle Rep 1 GR-ChIP seq


title: ATAC_seq_FL_E2AKO_rep3

source_name: E2A-KO Fetal liver


title: ATAC_seq_EKO_EbfER_72h_4OHT_rep2

description:
Annotate_Tam_addition_ATAC_on_WT_enriched_Ebf1_bound_ATAC_closed_EKO.txt
Annotate_Tam_addition_ATAC_on_WT_enriched_Ebf1_bound_ATAC_open_EKO.txt

treatment_protocol:
Cultured in Optimem +10% FBS, 25mM HEPES, 50μg/ml Gentamicin, 50μM β-mercaptoethanol FL, KL, IL7 on OP9, treated with 4OHT for indicated times prior to processing for ATAC-seq
FL-Ebf1-KO cells transduced with pMiG-Ebf1-ER constructs were treated with 1mM of Tamoxifen (4OHT) for indicated times prior to processing by ATAC-seq.

value: Ebf1-KO, transfected with a pMiG-Ebf1ER  vector


title: H2122-p57-ko Vehicle Rep 2 mRNA seq

description: raw_counts_dexamethasone WTvsKO.csv


title: ATAC_seq_FL_Wt_rep1


title: ATAC_seq_EKO_Ebf1ER_24h_4OHT_rep2


title: H2122-p57-ko Hydrocortisone Rep 1 mRNA seq

description: raw_counts_dexamethasone WTvsKO.csv


title: A549 Hydrocortisone Rep 1 GR-ChIP-seq


title: ATAC_seq_EKO_Ebf1ER_24h_4OHT_rep1


title: ATAC_seq_FL_E2AKO_rep1


title: H2122-NT Hydrocortisone Rep 2 mRNA seq

description: raw_counts_dexamethasone WTvsKO.csv

value: CRISPR control (non-targeting)


title: H460 Hydrocortisone Rep 2 mRNA seq


title: ATAC_seq_FL_E2AKO_rep2


title: ATAC_seq_EKO_Ebf1ER_72h_4OHT_rep1


title: ATAC_seq_EKO_Ebf1ER_0h_4OHT_rep2


title: H1975 Hydrocortisone Rep 2 mRNA seq


title: H460 Vehicle Rep 2 mRNA seq


title: H2122-NT Vehicle Rep 2 mRNA seq

description: raw_counts_dexamethasone WTvsKO.csv


title: Sample6: MDMXC462A NPC scRNA-seq

city: Boston

first: Zhi-Min

last: Yuan

state: Massachusetts

address: 677 Huntington Ave.

department: Environmental Sciences

institute: Harvard University

data_processing:
10X Genomics' CellRanger pipeline
R Bioconductor package Seurat standard differential analysis
Genome_build: mm10 (pre-mRNA)
Supplementary_files_format_and_content: Final data format for the processed datais attached as an R data file (corrected for batch effects).
Supplementary_files_format_and_content: FASTQ files are uploaded for samples 1-6, which were run in duplicate (names are identical, but appended to avoid conflict in file name).

source_name: liver

growth_protocol: C57BL/6J wild-type (WT) (The Jackson Laboratory, Stock No: 000664) and hepatocyte-specific MdmxC462A-knockin (Mdmx-KI) mice were used in the present study. Mdmx-KI mice were obtained by crossing MdmxC462A-floxed mice (the 11th exon of the Mdmx gene was floxed by two loxP sites) (Kuser-Abali et al., 2018) with albumin-Cre mice (The Jackson Laboratory, Stock No: 003574) on a C57BL/6J background. PCR-based genotyping was performed using the primer pairs listed in Supplementary Table 1. All mice were housed under a specific pathogen-free condition with a 12-h light/dark cycle. 7–10-week-old male mice were used for the experiments. All animal procedures were conducted in accordance with the Guidelines for the Care and Use of Laboratory Animals and were approved by the Harvard Medical Area Animal Care and Use Committee.

extract_protocol:
Liver nuclei were isolated for single cell analysis using the Nuclei PURE Prep kit (Sigma Aldrich) following manufacturer’s instructions. Isolated nuclei were stored at -80oC in nuclei PURE storage buffer (provided within the kit) until library preparation.
Libraries were prepared using NextSeq 500/550 kit following Illumina’s recommended protocol. The diluted denatured libraries were loaded onto a sequencing cartridge and then sequenced on the Illumina NextSeq 500.

treatment_protocol: Carbon tetrachloride (CCl4) (Sigma Aldrich) was delivered at 1 mg/kg (1:3 in corn oil) (Sigma-Aldrich) by a single intraperitoneal injection.

tag: strain

value: Neural progenitor cells

tag: scrna-seq

value: scRNA-Seq (10X Genomics)

value: acetaminophen treatment


title: Sample5: MDMXC462A NPC scRNA-seq


title: H1944 Vehicle Rep 2 mRNA seq

value: Vehicle


title: H2122 Hydrocortisone Rep 2 mRNA seq


title: ATAC_seq_EKO_Ebf1ER_6h_4OHT_rep2


title: H460 Vehicle Rep 1 GR-ChIP seq


title: Sample4: MDMXC462A NPC scRNA-seq


title: H2122-p57-ko Vehicle Rep 1 mRNA seq

description: raw_counts_dexamethasone WTvsKO.csv


title: H2122-NT Hydrocortisone Rep 1 mRNA seq

description: raw_counts_dexamethasone WTvsKO.csv


title: H2122-NT Vehicle Rep 1 mRNA seq

description: raw_counts_dexamethasone WTvsKO.csv


title: H2122 Vehicle Rep 2 mRNA seq


title: ATAC_seq_EKO_Ebf1ER_6h_4OHT_rep1


title: H1975 Vehicle Rep 2 mRNA seq


title: ATAC_seq_EKO_Ebf1ER_0h_4OHT_rep1


title: ATAC_omni_seq_230-238_rep1

description: Omni_230238_mapq10_IDR.mm10_annotated.txt

source_name: 230-238 murine Progenitor B celline

treatment_protocol:
Cultured in RPMI1640 + UltraGlutamine +10% FBS, 20mM HEPES, 50ug/ml Gentamicin and 50uM β-ME.
FL-Ebf1-KO cells transduced with pMiG-Ebf1-ER constructs were treated with 1mM of Tamoxifen (4OHT) for indicated times prior to processing by ATAC-seq.

value: cell line

value: Abelson transformed Progenitor B cell-line


title: ATAC_omni_seq_230-238_rep2


title: H1944 Hydrocortisone Rep 2 mRNA seq


title: RNA_3XNeg_Cort_Rep4

city: Cambridge

first: Li-Huei

last: Tsai

state: MA

address: 43 Vassar St

department: Brain and Cognitive Sciences

institute: MIT

data_processing:
To eliminate nucleotides that are part of the template-switching oligo, as per the manufacturer’s instructions (SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian; v1 or v2; Takara), the first three nucleotides of the first sequencing read (Read 1) for kit v1 or the first three nucleotides of the second sequencing read (Read 2) for kit v2 were trimmed with Trimmomatic. Trimmed reads were then aligned to the mouse genome GRCm38 (mm10) with HISAT2 using default parameters. Picard MarkDuplicates was used to remove duplicate reads and the remaining reads sorted and indexed with SAMtools. Read counts aligning to the entire gene body (exons and introns) of each gene were generated using featureCounts.
genome build: mm10
processed data files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: hippocampus

extract_protocol:
Tissue was dissociated with a motorized pestle (Argos Technologies) in 0.3-0.5mL in ice cold PBS treated with protease and phosphatase inhibitors (cOmplete & PhosSTOP; Roche). For RNA isolation, RNAse inhibitors where added to all buffers (RiboLock (Thermo Scientific) or SUPERaseIn (Invitrogen); 1:100 for homogenization, 1:1000 for buffers with BSA, and 1:10,000 for other buffers). Dissociated brain tissue was fixed in 10 mL of 1% Methanol-free Paraformaldehyde (16%; Electron Microscopy Sciences) for 10 minutes before quenching with 0.25M Tris-HCl pH 8. Homogenate was centrifuged for 15 minutes 2000 RCF 4°C (utilized for subsequent nuclei centrifugation) and the supernatant aspirated. Nuclei were released by resuspending in NF1 buffer (0.5% Triton X-100, 0.1M Sucrose, 5mM MgCl2, 1mM EDTA) and dounce-homogenized with a loose pestle for 30 strokes, then filtered with 70uM cell strainers (Falcon). Nuclei were centrifuged  resuspended in 1mL 0.5% BSA in PBS (IgG-Free, Protease-Free; Jackson ImmunoResearch). Nuclei were stained in Eppendorf tubes with the relevant antibodies rocking for 30-60 minutes at 4°C. For neuron and glia isolation, nuclei were stained with NeuN AF488 (1:1000; clone MAB377X; Millipore). For neuron and glial subtype isolation nuclei were stained with NeuN AF488 (1:1000; clone MAB377X; Millipore), GFAP AF647 (1:200; clone GA5; Cell Signaling Technology), and PU.1 PE (1:200; clone 9G7; Cell Signaling Technology). Finally, to help gate for singlet nuclei, 1:1000 DAPI (Sigma-Aldrich) was added to the buffer to just prior to flow cytometry. Nuclei were then isolated with BD FACSAria (BD Biosciences) cell sorter into 1% BSA PBS with inhibitors. To decrosslink the nuclei, the RecoverAll Total Nucleic Acid Isolation Kit for FFPE (Thermo Fisher Scientific) was utilized following the manufacturer’s instructions. Briefly, nuclei were resuspended in 200uL digestion buffer with 4 uL protease (an equal volume of protease K (NEB) was substituted if the manufacturer provided protease was exhausted) for 15 minutes at 50C, then 15 minutes at 80C. To isolate the RNA and eliminate most DNA prior to DNAase treatment, 800uL TRIzol LS (Invitrogen) was added, mixed well, and incubated for 5 minutes at room temperature before proceeding with isolation, or freezing at -80C. 215uL Chloroform was added to the solution and vortexed vigorously for 30 seconds before adding to a 5Prime Phase Lock Gel Heavy tube (Quantabio) and centrifuged for 15 minutes at 12,000g at 4C, before transfer to an eppendorf tube. An equal volume of 100% ethanol, 800uL, was added immediately and mixed well before proceeding to RNA isolation with the Direct-zol RNA Microprep Kit (Zymo Research). DNase treatment and RNA Isolation proceeded according to the manufacturer’s instructions before elution in 6-20uL water. For library preparation, RNA concentration and quality was assessed with a Fragment Analyzer (Agilent), yielding a RNA fragment distribution concentrated between approximately 200bp to 6000bp.
RNA-Seq libraries were generated with the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian (v2; Takara) according to the manufacturer’s instructions. Because the RNA was already partially degraded during the fixation and decrosslinking procedure, the RNA fragmentation time was 90 seconds. Paired end sequencing was performed with a NextSeq500 (Illumina).

treatment_protocol: For corticosterone treatment, Corticosterone:HBC complex (Sigma-Aldrich) was dissolved in saline and administered at 2mg/Kg IP, an equal volume of saline for control, followed by euthanasia 30 minutes later.

tag: tissue

value: hippocampus

tag: age

value: 4 month

value: corticosterone


title: RNA_3XNeg_Cort_Rep3

tag: cell type


title: Sample3: wildtype NPC scRNA-seq

value: wildtype


title: RNA_3XNeg_Sal_Rep4

value: saline


title: A549 Vehicle Rep 2 mRNA seq


title: H460 Hydrocortisone Rep 1 mRNA seq

value: Hydrocortisone (2,75 μM)


title: H1944 Vehicle Rep 1 mRNA seq


title: H460 Vehicle Rep 1 mRNA seq


title: Sample2: wildtype NPC scRNA-seq


title: Sample1: wildtype NPC scRNA-seq


title: Patient C30

type: RNA

city: Olsztyn

first: Marcin

middle: P.

last: Mycko

address: Warszawska 30

department: Department of Neurology

country: Poland

institute: University of Warmia and Mazury in Olsztyn

description: Total RNA from each sample was treated with RNase R to enrich circular RNA. The enriched circular RNA was reverse transcribed with random primers containing a T7 promoter. The cRNA was linearly amplified and Cy3 labeled by in vitro T7 polymerase transcription using Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The microarray slides were scanned with an Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package.

source_name: peripheral blood mononuclear cells

growth_protocol: ex vivo peripheral blood mononuclear cells

extract_protocol: Total RNA was extracted from PBMC using mirVana™ miRNA Isolation Kit (Life Technologies).

tag: disease state

value: healthy control

value: peripheral blood mononuclear cells (PBMC)


title: RNA_3XNeg_Cort_Rep1


title: RNA_3XNeg_Cort_Rep2


title: Patient C25

label_protocol: Total RNA from each sample was treated with RNase R to enrich circular RNA. The enriched circular RNA was reverse transcribed with random primers containing a T7 promoter. The cRNA was linearly amplified and Cy3 labeled by in vitro T7 polymerase transcription using Arraystar Super RNA Labeling protocol (Arraystar, Inc.).


title: Patient C27


title: RNA_3XNeg_Sal_Rep2


title: H1975 Hydrocortisone Rep 1 mRNA seq


title: H2122 Vehicle Rep 1 mRNA seq


title: RNA_PU.1_Cort_Rep4

value: microglia - PU.1+


title: A549 Hydrocortisone Rep 2 mRNA seq


title: H1975 Vehicle Rep 1 mRNA seq


title: H1944 Hydrocortisone Rep 1 mRNA seq


title: RNA_3XNeg_Sal_Rep3


title: A549 Hydrocortisone Rep 1 mRNA seq


title: A549 Vehicle Rep 1 mRNA seq


title: RNA_PU.1_Cort_Rep3


title: Patient C29


title: Patient C21


title: Patient C28


title: RNA_PU.1_Cort_Rep2


title: Patient B19

value: multiple sclerosis remission


title: RNA_PU.1_Cort_Rep1


title: Patient C26


title: RNA_PU.1_Sal_Rep3


title: Patient B11


title: Patient B20


title: H2122 Hydrocortisone Rep 1 mRNA seq


title: Patient C23


title: H3K4me3_P7Wt-1_ChIP

city: Indianapolis

first: Nathan

middle: J

last: VanDusen

state: IN

department: Pediatrics

institute: Indiana University School of Medicine

data_processing:
Adapters were removed and reads trimmed by quality score.
Reads were aligned to the mouse genome by Bowtie2.
RPKM normalized bigwig files were generated using Deeptools.
Read in each TSS interval were quantified using Bedtools.
Genome_build: mm10
Supplementary_files_format_and_content:  H3K4me3_ChIP-seq.txt: tab delimited text, max RPKM for each TSS interval. Bigwig files: RPKM normalized genome browser file for each sample.

source_name: P7 ventricles

growth_protocol: In vivo growth

extract_protocol:
Ventricles homogenized at P7
KAPA Hyper Prep Kit

value: P7 ventricles

value: WT

value: postnatal day 7

tag: sample  type

value: H3K4me3 ChIP

value: high dose AAV9-TnT-Cre


title: RNA_3XNeg_Sal_Rep1


title: Patient B14


title: Patient C24


title: Patient A10

value: multiple sclerosis relapse


title: Patient C22


title: RNA_GFAP_Cort_Rep4

value: astrocyte - GFAP+


title: RNA_GFAP_Cort_Rep3

value: hippocampus


title: Patient B12


title: Patient A8


title: RNA_PU.1_Sal_Rep4

value: 4 month


title: Patient B18


title: Patient B15


title: 118_Malaria

city: Marburg

first: Wilhelm

last: Bertrams

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

country: Germany

institute: Philipps University Marburg

description: Malaria patient

data_processing:
Raw Ct data are shown in Matrix non-normalized. U6 snRNA (average of 4 values) was used for normalization in Matrix normalized, yielding deltaCt values.
Fold changes were calculated with the the ddCt method (2^-ddCt)

label: FAM/NFQ-MGB

source_name: PBMC (blood leukocyte)

label_protocol: RNA was reverse transcribed with the Life Technologies miR RT kit wiith megaplex primers. Reverse transcribed RNA was then run on a TLDA plate with FAM-labelled primers

extract_protocol: Total RNA was isolated by cell lysis in Trizol and subsequent phenol/chloroform precipitation

treatment_protocol: PBMCs were isolated from patients suffering from Malaria or from healthy donors. RNA was extracted from these samples.

tag: condition

value: malaria


title: Patient A9


title: RNA_GFAP_Sal_Rep4


title: RNA_PU.1_Sal_Rep2


title: Patient B17


title: 116_Malaria

description: Malaria patient


title: 99_Malaria

description: Malaria patient


title: RNA_PU.1_Sal_Rep1


title: Patient A1


title: Patient A2


title: Patient A7


title: RNA_GFAP_Sal_Rep1


title: Patient B16


title: Patient A5


title: RNA_GFAP_Cort_Rep2

value: corticosterone


title: Patient A6


title: ERT2-Cre_Pcgf1_Mutant_ES_rep5

data_processing:
Sequencing was performed with either 75 bp single-end read by NextSeq500 (run by Kazusa DNA Research Institute) or 50 bp single-end read by HiSeq1500 (run in RIKEN-IMS NGS facility).
The data were mapped onto UCSC-mm9 from illumina igenome and counted the reads on exon using STAR (version 2.5.2b: --outSAMtype BAM SortedByCoordinate), and the counted reads are normalized to TPM(Transcripts Per Million).
Each gene reads on exon were normalized by DESeq2 for fold change and p-value calculation.
Genome_build: mm9
Supplementary_files_format_and_content: tpm values

extract_protocol:
Total RNA was extracted using simplyRNA Tissue Kit (Promega).
Sequencing libraries were generated according to NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) protocol.

value: with 4-OHT

value: embryonic stem cell


title: Patient A4


title: ERT2-Cre_Pcgf1_Mutant_EB_rep4

source_name: EB

value: embryoid body


title: RNA_GFAP_Sal_Rep2

value: saline


title: ERT2-Cre_Pcgf1_Control_EB_rep5

value: without 4-OHT


title: RNA_GFAP_Cort_Rep1


title: gH2AX_mPFC_CFC30_Rep3

data_processing:
ChIP-Seq reads were aligned to the mouse genome GRCm38 (mm10) with Bowtie2 with default parameters. Picard MarkDuplicates was used to remove duplicate reads. Poorly aligned reads were then filtered out (MAPQ> 10) and the remaining reads sorted and indexed with SAMtools. SAMtools was used to down sample ChIP replicates to an equivalent number of reads before merging. Peaks were called with MACS2 using a broad-cutoff of 0.00001. To get peaks more representative of the underlying signal, peaks were recalled with MACS2 using --broad-cutoff 0.1, and bedtools intersect was used to get the overlap with more stringently called peaks. Bedtools intersect was then used to annotate peaks overlapping genes with a minimum of 50% overlap with the GRCm38.93 (mm10) GTF annotation file, with manual inspection of genome browser tracks for correction. MACS2 was used to make read normalized (-SPMR) LogLR signal tracks and these were converted to the BigWig file format with bedGraphToBigWig.
genome build: mm10
processed data files format and content: BigWig files were generated with bedGraphToBigWig
processed data files format and content: peak bed file

source_name: medial prefrontal cortex

extract_protocol:
Tissue was dissociated with a motorized pestle (Argos Technologies) in 0.3-0.5mL in ice cold PBS treated with protease and phosphatase inhibitors (cOmplete & PhosSTOP; Roche). Dissociated brain tissue was fixed in 10 mL of 1% Methanol-free Paraformaldehyde (16%; Electron Microscopy Sciences) for 10 minutes before quenching with 0.25M Tris-HCl pH 8. Homogenate was centrifuged for 15 minutes 2000 RCF 4°C and the supernatant aspirated. Nuclei were released by resuspending in NF1 buffer (0.5% Triton X-100, 0.1M Sucrose, 5mM MgCl2, 1mM EDTA) and dounce-homogenized with a loose pestle for 30 strokes, then filtered with 70uM cell strainers (Falcon). Nuclei were centrifuged for 15 minutes 2000 RCF 4°C and the supernatant aspirated. Pelleted nuclei were combined from three different animals’ hippocampi or mPFC and were then lysed by the addition of 400 μl LB3 (1mM EDTA pH 8, 0.5mM EGTA pH 8, 10 mM Tris pH 8, 0.5% Sarkolsyl solution), split into 2 tubes, and sonicated on ‘HIGH’ for 30-40 cycles (30” on and 30” off) in a Bioruptor bath sonicator (Diagenode). The IP was prepared by diluting 15-30ug of the chromatin into 1% Triton X-100, 0.1 % sodium deoxycholate, 1 mM EDTA plus protease and phosphatase tablets and preclearing with Protein A Dynabeads (Life Technologies) blocked with BSA. Then 5 ug anti-gH2AX (ab2893; Abcam) was added and the chromatin rotated overnight. BSA blocked Protein A Dynabeads (Life Technologies) were added and rocked for 4 hours before 4 washes with RIPA buffer (50 mM HEPES, pH 7.6, 10 mM EDTA, 0.7 % sodium Deoxycholate, 1 % NP-40, 0.5 M LiCl) and one wash with T50E10 buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA) before resuspending beads in  T50E10S1 buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) and heating to 65C for 15 minutes to elute DNA. After transferring to a new tube, DNA was decrosslinked by leaving at 65C for 5 hours to overnight. DNA was treated with Proteinase K (NEB) and RNAse (Roche) before purification with phenol:chloroform:isoamyl-alcohol 1 Phase (VWR), 5Prime Phase Lock Gel Heavy tube (Quantabio), and glycogen (sigma Aldrich) to facilitate DNA pelleting. Resuspended DNA was then used for library preparation.
Library preparation proceeded with a HyperPrep Kit (Kapa Biosystems) and NEXTFLEX DNA Barcodes (Perkin Elmer), with size selection performed with Agencourt AMPure XP (Beckman Coulter). Libraries were sequenced on the Illumina HiSeq2000.

treatment_protocol: Mice were subjected to contextual fear conditioning (CFC) and ten or thirty minutes after placement in the context, mice were euthanized. Naïve mice remained in their home cages prior to euthanasia.

value: medial prefrontal cortex

value: Contextual Fear Conditioning - 30 minutes

value: Anti-gamma H2A.X (phospho S139; ab2893; Abcam)


title: Patient A3

value: peripheral blood mononuclear cells (PBMC)


title: ERT2-Cre_Pcgf1_Mutant_ES_rep4


title: gH2AX_mPFC_CFC30_Rep4


title: RNA_NeuN_Cort_Rep1

value: Neuron - NeuN+


title: RNA_GFAP_Sal_Rep3


title: ERT2-Cre_Pcgf1_Control_ES_rep4


title: 111_Malaria

description: Malaria patient


title: ERT2-Cre_Pcgf1_Mutant_EB_rep5


title: RNA_NeuN_Sal_Rep3


title: ERT2-Cre_Pcgf1_Mutant_EB_rep3


title: RNA_NeuN_Sal_Rep4


title: gH2AX_mPFC_CFC30_Rep1


title: gH2AX_mPFC_Naive_Rep3

value: Naïve


title: RNA_NeuN_Sal_Rep1


title: 88_Malaria

description: Malaria patient


title: ERT2-Cre_Pcgf1_Mutant_ES_rep3


title: 78_Malaria

description: Malaria patient


title: Patient B13

value: multiple sclerosis remission


title: ERT2-Cre_Pcgf1_Control_ES_rep3


title: RNA_NeuN_Cort_Rep4


title: ERT2-Cre_Pcgf1_Mutant_EB_rep2


title: RNA_HIP_Glia_CFC30_Rep4

value: Glia - NeuN-


title: RNA_HIP_Glia_CFC30_Rep3

value: hippocampus


title: ERT2-Cre_Pcgf1_Control_EB_rep2


title: ERT2-Cre_Pcgf1_Mutant_ES_rep2


title: ERT2-Cre_Pcgf1_Control_ES_rep2


title: gH2AX_HIP_CFC30_Rep3

source_name: Hippocampus

value: Hippocampus

value: 4 month


title: RNA_NeuN_Cort_Rep3

value: corticosterone


title: ERT2-Cre_Pcgf1_Control_EB_rep4


title: 75_Malaria

description: Malaria patient

value: malaria


title: gH2AX_HIP_Naive_Rep2


title: RNA_NeuN_Cort_Rep2


title: RNA_HIP_Glia_CFC10_Rep3

value: Contextual Fear Conditioning - 10 minutes


title: ERT2-Cre_Pcgf1_Control_EB_rep1

value: embryoid body


title: ERT2-Cre_Pcgf1_Mutant_ES_rep1

value: with 4-OHT

value: embryonic stem cell


title: RNA_HIP_Glia_CFC10_Rep1


title: ERT2-Cre_Pcgf1_Control_ES_rep1

value: without 4-OHT


title: gH2AX_mPFC_CFC30_Rep2

value: medial prefrontal cortex

value: Contextual Fear Conditioning - 30 minutes


title: RNA_NeuN_Sal_Rep2

value: saline


title: GATA4/6-Control-S06

description:
mRNA RNA-seq
GATA_RNA-seq

data_processing:
Adapters were removed and reads trimmed by quality score.
Reads were aligned to the mouse genome by TopHat.
Counts for each gene were collected with HTSeq-Count.
Differential expression was assessed with DESeq.
Genome_build: mm10
Supplementary_files_format_and_content: GATA_RNA-seq.txt: tab delimited text, DESeq comparison of gene expression between groups.

source_name: FACS sorted P6 CMs

growth_protocol: In vivo maturation

extract_protocol:
Hearts were dissociated at P6. GFP+ CMs were collected by FACS. RNA extraction by Trizol.
Epicentre ScriptSeq-v2

value: FACS sorted P6 CMs

value: postnatal day 6

tag: sample type

value: Control (GFP+)

value: AAV-TnT-Cre


title: gH2AX_mPFC_Naive_Rep4

value: Naïve

value: Anti-gamma H2A.X (phospho S139; ab2893; Abcam)


title: RNA_HIP_Glia_Naive_Rep4

value: hippocampus

value: 4 month

value: Glia - NeuN-


title: GATA4/6-Control-S05

description:
mRNA RNA-seq
GATA_RNA-seq


title: gH2AX_mPFC_Naive_Rep2


title: gH2AX_mPFC_Naive_Rep1


title: RNA_HIP_Glia_CFC30_Rep2


title: ERT2-Cre_Ring1aKO_Ring1bControl_Control_EB_rep2

tag: tamoxifen treatment


title: gH2AX_HIP_CFC30_Rep2

value: Hippocampus


title: ERT2-Cre_Ring1aKO_Ring1bControl_Mutant_ES_rep2

tag: genotype


title: RNA_HIP_Glia_Naive_Rep1


title: gH2AX_HIP_CFC30_Rep1


title: RNA_HIP_Glia_CFC30_Rep1


title: ERT2-Cre_Ring1aKO_Ring1bControl_Control_ES_rep2


title: RNA_HIP_Glia_CFC10_Rep4

value: Contextual Fear Conditioning - 10 minutes


title: ERT2-Cre_Ring1aKO_Ring1bControl_Mutant_EB_rep1

value: with 4-OHT

value: embryoid body


title: ERT2-Cre_Pcgf1_Control_EB_rep3

value: without 4-OHT


title: gH2AX_HIP_Naive_Rep3


title: ERT2-Cre_Pcgf1_Mutant_EB_rep1


title: gH2AX_HIP_Naive_Rep1


title: RNA_HIP_Glia_CFC10_Rep2


title: ERT2-Cre_Ring1aKO_Ring1bControl_Control_ES_rep1

value: embryonic stem cell


title: RNA_HIP_Glia_Naive_Rep3


title: ERT2-Cre_Ring1aKO_Ring1bControl_Mutant_EB_rep2


title: RNA_HIP_NeuN_CFC10_Rep3

value: Neuron - NeuN+


title: GATA4/6-Control-S04

description:
mRNA RNA-seq
GATA_RNA-seq


title: RNA_HIP_Glia_Naive_Rep2


title: GATA4/6-KO-S03

description:
mRNA RNA-seq
GATA_RNA-seq

value: GATA4/6-KO (GFP+)


title: TY1_ERT2-Cre_Pcgf1Mutant_ES_rep1

data_processing:
Sequencing was performed with 75 bp single-end read by NextSeq500 (run by Kazusa DNA Research Institute) or 50bp single-end read by HiSeq1500 (run in RIKEN-IMS NGS facility).
The data were mapped onto UCSC-mm9 from illumina igenome. Generated sam format file combine to bam format file using samtools view (version 1.3.1). Then, PCR duplicate and multiple aligned reads are removed.
For bigwig generation, bam format files were processed by deeptools bamCoverage. The data of CpG island and TSS are derived from UCSC mm9.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

tag: antibody


title: RNA_HIP_NeuN_CFC30_Rep4

value: Contextual Fear Conditioning - 30 minutes


title: RNA_HIP_NeuN_CFC30_Rep3


title: GATA4/6-KO-S02

description:
mRNA RNA-seq
GATA_RNA-seq

value: FACS sorted P6 CMs

value: postnatal day 6


title: activated+T007

city: Hefei

first: Sicheng

last: Fu

address: Huangshan road

country: China

institute: USTC

data_processing:
Frist at all, we use FastQC performs basic statistics on the quality of the raw reads. Then,those read sequences produced by the Illumina pipeline in FASTQ format were pre-processed through Trimmomatic software which can be summarized as below:(1) Remove low-quality reads: The reads that mean quality value less than 20 were removed.(2) Remove the reads that contain more than 15 percent N bases.(3) Remove adapters. Remove the reads that alignment with the adapter sequence.(4) Drop reads blow the 18 bases long after trimming.(5) The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last,we use FastQC performs basic statistics on the quality of the clean reads.
Index of the reference genome was built using BWA v0.7.12 and clean reads were aligned to the reference genome using BWA mem v 0.7.12.
After mapping reads to the reference genome, we used the MACS2 version 2.1.0 (model-based analysis of ChIP-seq) (Zhang et al., 2008) peak finding algorithm to indentify regions of IP enrichment over background. A q value threshold of enrichment of 0.05 was used for all data sets. Then, the distribute of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: iNKT cells

growth_protocol: To expand iNKT cells in vitro, splenocytes from Va14 Tg mice were cultured with 100 U/ml human recombinant IL-2 and 100 ng/ml aGC for 3 days, then were cultured for another 7 days with only 100 U/ml human recombinant IL-2.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select DNA fragments of preferentially 150~200 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-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer.At last,PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Expanded iNKT cells were activated by immobilized anti-CD3 plus anti-CD28 in the presence or absence of T007 (2 mg/ml)

value: PPAR-gamma1+2 (Abcam, ab41928)


title: ctrl


title: Isolated Corticotropes 24h after eNampt administration 4

city: Poznań

last: Ruciński

state: Wielkopolska

address: Święcickiego 6

department: Histology and Embryology

institute: Poznań University of Medical Sciences

description: Gene expression data from isolated rat corticotropes 24h after eNampt administration

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 20 hr at 45C on GeneChip™ Rat Gene 2.1 ST Array Strip (cat. 902126). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Obtained cell files were submied to bioconductor and R programing lenguage. Each CEL file was merged with a description file.  In order to correct background, normalize, and summarize results, we used the Robust Multiarray Averaging (RMA) algorithm.

label: biotin

organism: Rattus norvegicus

source_name: Pituitary gland of 21-day old Wistar rats

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ng total RNA (GeneChip™ WT Pico Kit (cat: 902622))

growth_protocol:
Pituitary glands were isolated by sterile surgical tools after decapitation of the rats. Treated with collaganese and subjected into the cell culture. The corticotropic cells were separated from the culture by the means of CELLection™ Biotin Binder Kit (Thermo Fisher Scientific - Invitrogen, lot:11533D). For the cell separation the anti CRHR1 antibody was used (Alomone Labs, ACR050AN0150) with secondary biotin-labeled antibody (Abcam, Cambridge, UK, anti-IgG ab6720).
The cells were cultured in DMEM/F12 (without phenol red) medium supplemented with 10% FBS (Fetal Bovine Serum), 1x AA solution (Sigma‑Aldrich; Merck KGaA, A5955) and 0.05 µg/l FGF (Thermo-Fisher Catalogue number: 1263344C).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The cells were treated with eNampt, CRH or Il-6 for 24h.

value: Pituitary Gland

tag: cells

value: Isolated Corticotropes


title: TY1_ERT2-Cre_Pcgf1Mutant_EB_rep1

tag: replicate


title: RNA_HIP_NeuN_Naive_Rep4

value: hippocampus

tag: treatment

value: Naïve


title: ERT2-Cre_Ring1aKO_Ring1bControl_Control_EB_rep1


title: RNA_HIP_NeuN_CFC30_Rep2

value: 4 month


title: activated

tag: chip antibody


title: GATA4/6-KO-S01

description:
mRNA RNA-seq
GATA_RNA-seq

value: AAV-TnT-Cre


title: ERT2-Cre_Ring1aKO_Ring1bControl_Mutant_ES_rep1


title: RNA_HIP_NeuN_CFC10_Rep2

value: Contextual Fear Conditioning - 10 minutes


title: RNA_HIP_NeuN_CFC10_Rep4


title: TY1_ERT2-Cre_Pcgf1Mutant+hPCGF1TY1_ES_rep2

value: with 4-OHT


title: RNA_HIP_NeuN_Naive_Rep2


title: RNA_HIP_NeuN_Naive_Rep1


title: RNA_HIP_NeuN_CFC30_Rep1


title: RNA_mPFC_NeuN_CFC30_Rep3

extract_protocol:
Tissue was dissociated with a motorized pestle (Argos Technologies) in 0.3-0.5mL in ice cold PBS treated with protease and phosphatase inhibitors (cOmplete & PhosSTOP; Roche). For RNA isolation, RNAse inhibitors where added to all buffers (RiboLock (Thermo Scientific) or SUPERaseIn (Invitrogen); 1:100 for homogenization, 1:1000 for buffers with BSA, and 1:10,000 for other buffers). Dissociated brain tissue was fixed in 10 mL of 1% Methanol-free Paraformaldehyde (16%; Electron Microscopy Sciences) for 10 minutes before quenching with 0.25M Tris-HCl pH 8. Homogenate was centrifuged for 15 minutes 2000 RCF 4°C (utilized for subsequent nuclei centrifugation) and the supernatant aspirated. Nuclei were released by resuspending in NF1 buffer (0.5% Triton X-100, 0.1M Sucrose, 5mM MgCl2, 1mM EDTA) and dounce-homogenized with a loose pestle for 30 strokes, then filtered with 70uM cell strainers (Falcon). Nuclei were centrifuged  resuspended in 1mL 0.5% BSA in PBS (IgG-Free, Protease-Free; Jackson ImmunoResearch). Nuclei were stained in Eppendorf tubes with the relevant antibodies rocking for 30-60 minutes at 4°C. For neuron and glia isolation, nuclei were stained with NeuN AF488 (1:1000; clone MAB377X; Millipore). For neuron and glial subtype isolation nuclei were stained with NeuN AF488 (1:1000; clone MAB377X; Millipore), GFAP AF647 (1:200; clone GA5; Cell Signaling Technology), and PU.1 PE (1:200; clone 9G7; Cell Signaling Technology). Finally, to help gate for singlet nuclei, 1:1000 DAPI (Sigma-Aldrich) was added to the buffer to just prior to flow cytometry. Nuclei were then isolated with BD FACSAria (BD Biosciences) cell sorter into 1% BSA PBS with inhibitors. To decrosslink the nuclei, the RecoverAll Total Nucleic Acid Isolation Kit for FFPE (Thermo Fisher Scientific) was utilized following the manufacturer’s instructions. Briefly, nuclei were resuspended in 200uL digestion buffer with 4 uL protease (an equal volume of protease K (NEB) was substituted if the manufacturer provided protease was exhausted) for 15 minutes at 50C, then 15 minutes at 80C. To isolate the RNA and eliminate most DNA prior to DNAase treatment, 800uL TRIzol LS (Invitrogen) was added, mixed well, and incubated for 5 minutes at room temperature before proceeding with isolation, or freezing at -80C. 215uL Chloroform was added to the solution and vortexed vigorously for 30 seconds before adding to a 5Prime Phase Lock Gel Heavy tube (Quantabio) and centrifuged for 15 minutes at 12,000g at 4C, before transfer to an eppendorf tube. An equal volume of 100% ethanol, 800uL, was added immediately and mixed well before proceeding to RNA isolation with the Direct-zol RNA Microprep Kit (Zymo Research). DNase treatment and RNA Isolation proceeded according to the manufacturer’s instructions before elution in 6-20uL water. For library preparation, RNA concentration and quality was assessed with a Fragment Analyzer (Agilent), yielding a RNA fragment distribution concentrated between approximately 200bp to 6000bp.
RNA-Seq libraries were generated with the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian (v1; Takara) according to the manufacturer’s instructions. Because the RNA was already partially degraded during the fixation and decrosslinking procedure, the RNA fragmentation time was 90 seconds. Paired end sequencing was performed with a NextSeq500 (Illumina).

value: medial prefrontal cortex


title: TY1_ERT2-Cre_Pcgf1Mutant+hPCGF1TY1_EB_rep2

value: embryoid body


title: S8D_replicate

city: Kolkata

first: BIDYUT

last: ROY

state: West bengal

address: 203 bt road

department: human genetics unit

country: India

institute: indian statistical institute

data_processing:
Basecalls performed using CASAVA version 1.4
RRBS reads were aligned to the hg38 genome assembly using DMAP pipeline.
Data were filtered using the following specifications- Adapter removal and end trimming of last two bases were performed with Trim Galore program (Phred Score≥28).
Good quality reads, checked by FASTQC, were mapped to the human reference genome (hg38) using Bismark (with default setting of 2 mismatches in a seed region of 28 nucleotides).
Diffmeth program of the DMAP package [with fragments with at least 2 CpG sites, covered by ≥10 reads, was used. MspI fragments were used as the unit of differential methylation analysis. Proportion of methylation was calculated from the ratio of total number of methylated CpGs in all reads divided by the total number of CpGs in a read. Pair-wise Fisher’s exact test, followed by Benjamini-Hochberg correction, was performed for each fragment from each pair of tissues to get differentially methylated regions (DMR) for each sample pair.
Genome_build: hg38
Supplementary_files_format_and_content: identgeneloc files generated where each row is a DMR or differentially methylated region in that particular sample,column with label "R" represents methylation frequency in normal and column with label "S" represents methylation frequency in cancer followed by genomic location and name of the annotated gene for that DMR

source_name: Buccal Mucosa

extract_protocol:
Qiagen Tissue DNA kit was used to isolate DNA from the tissue samples as per the manufacturer’s protocol
As per the protocol provided by Chatterjee A et al (PMID: 23193365). Briefly, 2.5µg of DNA was digested with 80U of MspI followed by end repair and A-tailing with clean up step. After ligation to methylated adapters, small fragments of DNA were removed by AMPure XP beads.  Fragments of size 160-340bps (i.e. 40-220bps DNA + 120bp adapters) were extracted from 3% Nusieve gel using Qiaquick gel extraction kit. DNA samples were then treated for bisulfite conversion and clean-up. Libraries were prepared by13 cycles of PCR followed by size selection (160-340bps) from gel and, finally, assessed for quality using a Bioanalyzer and Kapa Kit.

value: Cancer Tissue

value: Technical replicate of S8D


title: Isolated Corticotropes 24h after eNampt administration 3


title: Isolated Corticotropes 24h after eNampt administration 2


title: S8N_replicate

value: Adjacent Normal Tissue

value: Technical replicate of S8N


title: Isolated Corticotropes 24h after Il-6 administration 4

description: Gene expression data from isolated rat corticotropes 24h after IL-6 administration


title: RNA_HIP_NeuN_CFC10_Rep1

value: Neuron - NeuN+


title: Isolated Corticotropes 24h after CRH administration 3

description: Gene expression data from isolated rat corticotropes 24h after CRH administration


title: RNA_mPFC_NeuN_CFC30_Rep2

value: Contextual Fear Conditioning - 30 minutes


title: RNA_HIP_NeuN_Naive_Rep3


title: TY1_ERT2-Cre_Pcgf1Mutant+hPCGF1TY1_EB_rep1


title: Isolated Corticotropes 24h after eNampt administration 1


title: S11N_replicate

value: Technical replicate of S11N


title: RING1B_ERT2-Cre_Pcgf1Mutant_EB_rep1

value: RING1B (Laboratory made)


title: TY1_ERT2-Cre_Pcgf1Mutant+hPCGF1TY1_ES_rep1

value: embryonic stem cell


title: RING1B_ERT2-Cre_Pcgf1Mutant_EB_rep2


title: Isolated Corticotropes 24h after Il-6 administration 3

value: Pituitary Gland

value: Isolated Corticotropes


title: S9D_replicate

value: Technical replicate of S9D


title: RING1B_ERT2-Cre_Pcgf1Control_EB_rep1

value: without 4-OHT


title: S9N_replicate

value: Technical replicate of S9N


title: S11D_replicate

value: Technical replicate of S11D


title: S16D


title: RING1B_ERT2-Cre_Pcgf1Control_EB_rep2


title: RING1B_ERT2-Cre_Pcgf1Mutant_ES_rep2

value: with 4-OHT


title: Isolated Corticotropes 24h after CRH administration 1


title: RING1B_ERT2-Cre_Pcgf1Control_ES_rep2


title: Isolated Corticotropes 24h after Il-6 administration 1


title: RNA_mPFC_NeuN_CFC30_Rep1

value: medial prefrontal cortex

value: 4 month


title: S7N_replicate

value: Technical replicate of S7N


title: RNA_mPFC_NeuN_CFC10_Rep3

value: Contextual Fear Conditioning - 10 minutes


title: S7D_replicate

value: Cancer Tissue

value: Technical replicate of S7D


title: S16N

value: Adjacent Normal Tissue


title: S15D


title: S15N


title: H1944 Hydrocortisone Rep 2 4C

data_processing:
Library strategy: 4C
Sequences were generated by the Illumina Hiseq 2500 genome analyzer (using 65bp reads) in case of RNA and ChIP seq, while for 4C MiSeq was used, subsequently sequences  were processed by the Illumina pipeline.
For RNA sequencing data was aligned to hg38 using TopHat and Differential expression (DE) was performed using optimized DESeq2 pipeline.
For ChIP sequencing reads were aligned to the Human Reference Genome (hg19) using BWA version 0.5.9. Reads with a BWA alignment quality score less than 20 were removed. Peaks were called MACS peak caller version 2 (Zhang Y et al. Genome Biol 2008;9(9):R137). MACS2 was run with the default parameters.
For 4C sequencing the alignment of the sequencing reads was done using bowtie2 with default parameters. We use samtools to filter for mapped reads with a minimum mapping quality score of 1. Next we extract from the reference genome all possible 4C capture sequences (in FASTA format) with the exact same length as the observed 4C captures from the sequencing run. We map and filter these reference capture sequences with the same parameters as the observed 4C reads using bowtie2 and samtools. In subsequent analysis we only include the thus mappable 4C fragment ends.
Genome_build: Hg38 (RNA seq), Hg19 (ChIP seq)

extract_protocol:
The 4C procedure was performed according to the published protocol (van de Werken et al., 2012, Nature Methods (PMID 22961246)).
The 4C library constuction was performed according to the published protocol (van de Werken et al., 2012, Nature Methods (PMID 22961246)).

tag: viewpoints

value: Viewpoint CDKN1C and Viewpoint CERES enhancer

value: Hydrocortisone (2,75 μM)


title: RNA_mPFC_NeuN_CFC10_Rep2

tag: strain

value: Neuron - NeuN+


title: Isolated Corticotropes 24h after Il-6 administration 2

value: Pituitary Gland


title: RING1B_ERT2-Cre_Pcgf1Mutant_ES_rep1

value: embryonic stem cell

value: RING1B (Laboratory made)


title: Isolated Corticotropes 24h after CRH administration 2

value: Isolated Corticotropes


title: Isolated Corticotropes 24h after CRH administration 4


title: Isolated Corticotropes - control sample 3

description: Gene expression data from isolated rat corticotropes, control sample


title: RNA_mPFC_NeuN_Naive_Rep2

value: Naïve


title: RNA_mPFC_NeuN_CFC10_Rep1


title: RING1B_ERT2-Cre_Pcgf1Control_ES_rep1

value: without 4-OHT


title: H1944 Vehicle Rep 2 4C

value: Vehicle


title: RNA_mPFC_NeuN_Naive_Rep3

value: medial prefrontal cortex


title: Isolated Corticotropes - control sample 4


title: ESCs, BRD7-ChIP-4h

city: hangzhou

first: kuang

last: junqi

address: No.18 Shilongshan Road

institute: westlake University

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
The ChIP-seq datasets were aligned to the mouse Genome mm10 using Bowtie2 (version 2.2.5) with the parameters --very-sensitive --end-to-end --no-unal.
Bowtie2 SAM output files were converted to sorted BAM files using SAMtools. Multiple mapped reads were discarded. When multiple reads mapped to the same genomic position, only one read were retained.
The samtools and bedtools suites were used to generate bigwig files for visualization in the IGV browser.
Peaks were called using MACS2 software with the default parameters.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files

source_name: mouse embryonic stem cells (mESCs)

growth_protocol: Mouse ESCs were cultured on feeder free with mESC-2i medium (DMEM, 15%FBS, NEAA, GlutaMAX, PD0325901, Chir99021, LIF).

extract_protocol:
Protein-DNA complexes were isolated with antibody and Tn5-proteinA/G.
The ChIP DNA library for sequencing was constructed with NovoNGS CUT&Tag 2.0 High-Sensitivity Kit for Illumina (novoprotein) according to manufacturer’s instructions.

treatment_protocol: Treated with 2µg/ml doxycycline.

value: OG2 transgenetic mouse embryonic stem cells (OG2ES)

value: treated with doxycycline for 4h

value: BRD7 (Proteintech, 51009-2-AP)


title: ESCs, PBRM1-ChIP-8h

value: treated with doxycycline for 8h

value: PBRM1 (Bethyl, A301-591A)


title: ESCs, BRD7-ChIP-8h


title: H2122 Hydrocortisone Rep 2 4C


title: ESCs, PBRM1-ChIP-4h


title: RNA_mPFC_Glia_CFC30_Rep2

value: 4 month

value: Contextual Fear Conditioning - 30 minutes

value: Glia - NeuN-


title: ESCs, PBRM1-ChIP-0h

value: no doxycycline


title: RNA_mPFC_NeuN_Naive_Rep1

value: Neuron - NeuN+


title: S13D

value: Cancer Tissue


title: S14D


title: S14N

value: Adjacent Normal Tissue


title: H2122 Vehicle Rep 2 4C

value: Viewpoint CDKN1C and Viewpoint CERES enhancer


title: RNA_mPFC_Glia_CFC10_Rep3

value: Contextual Fear Conditioning - 10 minutes


title: Isolated Corticotropes - control sample 2

value: Pituitary Gland

value: Isolated Corticotropes


title: ESCs, BRD7-ChIP-0h


title: RNA_mPFC_Glia_CFC30_Rep1

value: medial prefrontal cortex


title: A549 Vehicle Rep 2 4C

value: Vehicle


title: Isolated Corticotropes - control sample 1


title: RNA_mPFC_Glia_CFC30_Rep3


title: S13N


title: RNA_mPFC_Glia_CFC10_Rep1


title: ESCs, SS18-ChIP-0h

value: OG2 transgenetic mouse embryonic stem cells (OG2ES)


title: A549 Hydrocortisone Rep 2 4C

value: Hydrocortisone (2,75 μM)


title: S11N

description:
This sample is also known as S26N in GSE101547 study
none


title: H2122 Hydrocortisone Rep 1 4C


title: H2122 Vehicle Rep 1 4C


title: Mouse lung WSNdelNS1-2

city: Hong Kong

first: Honglin

last: Chen

address: Rm 5-19, 5/F, Lab block, 21 Sassoon Road, Pokfulam

department: Department of Microbiology

country: Hong Kong

institute: The University of Hong Kong

description:
WSNdelNS1-2
Infected with WSN mutant virus. The WSN-dNS1 virus has no expression of NS1 from the NS gene.

data_processing:
Raw data was aligned and counts were obtained using the CellRanger count function (v6.0.1)
Cells were filtered out if more than 5% of reads mapped to mitochondrial genes or had more than 5000 or less than 200 genes expressed
Samples were intergrated using Seurat using the SCTransform method for normalization.
Cell-typing was performed manually through the identification of key markers matched to the CellMarker database (http://biocc.hrbmu.edu.cn/CellMarker/) using the FindAllMarkers function from Seurat (v4.0)
Genome_build: mmc9
Supplementary_files_format_and_content: Supplementary files include markers for intial clusters and metadata generated from Seurat. Both files are in CSV format. Clusters in marker.csv are represented under the 'seurat_clusters' column in the seurat_metadata.csv file.

source_name: Mouse lung

growth_protocol: Mice were infected for 24 hours.

extract_protocol:
The lung tissue was dissociated into single-cell suspensions by enzymatic degradation using Lung Dissociation Kit (mouse) (Miltenyi Biotech) according to the manufacturer's protocol, followed by mechanical dissociation using gentleMACS™ Dissociators (Miltenyi Biotech).  Low quality single cells were then depleted by MACS® Separation using Dead Cells Removal kit (Miltenyi Biotech).
Single cells suspension were then loaded into a Chromium Single Cell Chip G (10x Genomics) according to the manufacturer’s instructions for co-encapsulation with barcoded Gel Beads at a target capture rate of ~5,000 individual cells per sample.

value: BALB/c

tag: viral strain

value: WSN (delNS1 mutant)

tag: dose


title: Mouse lung WSNdelNS1-1

description:
WSNdelNS1-1
Infected with WSN mutant virus. The WSN-dNS1 virus has no expression of NS1 from the NS gene.


title: ESCs, SS18-ChIP-4h

value: treated with doxycycline for 4h


title: RNA_mPFC_Glia_CFC10_Rep2

tag: tissue

tag: age

value: 4 month


title: S11D

description:
This sample is also known as S26D in GSE101547 study
none


title: H1944 Hydrocortisone Rep 1 4C

source_name: Lung cancer cell line


title: A549 Hydrocortisone Rep 1 4C


title: RNA_mPFC_Glia_Naive_Rep3

value: Naïve

tag: cell type

value: Glia - NeuN-


title: A549 Vehicle Rep 1 4C


title: TG19-0361_TU3

city: Durham

first: Chaitanya

middle: R

last: Acharya

state: NC

address: 203 Research Drive,Medical Sciences Research Building, Suite 433

department: Dept. of Surgery

institute: Duke University

description:
Nulliparous, 16 weeks, metaplastic
SRRs represent multiple libraries that were concatenated for the UMI.tsv files

data_processing:
fastq files were aligned to version 79 of mouse reference genome GRCm38 using Illumina's BaseSpace.
BAM files resulting from the alignments were summarized to genes.
Unique Molecular Identifier (UMI) matrix of gene counts was obtained from demultiplexing cellular barcodes were further processed using Seurat R package (version 3.0.2).
Genome_build: version 79 of mouse reference genome GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include UMI values for each tumor sample.

source_name: Mammary tumor

extract_protocol:
Tumor harvest protcol: Mammary glands from mMTV-Cre/HER2 Crainbow mice were harvest between 15 and 20 weeks and digested to obtain a single cell suspension.
Single cell isolation: ddSEQ Single-Cell Isolator (Biorad 12004336) was used to capture single cells according to manufacturer’s protocol.
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
Library preparation was performed using a compatible SureCell™ WTA 3’ Library Prep Kit (Illumina, 220014279).

tag: background strain

value: FVBN

value: mammary tumor

value: p95 HER2

tag: phenotype

value: metaplastic/invasive

value: untreated


title: S9N

value: Adjacent Normal Tissue


title: RNA_mPFC_Glia_Naive_Rep2


title: S10D

value: Cancer Tissue


title: TG19-0361_TU2

description:
Nulliparous, 16 weeks,  metaplastic
SRRs represent multiple libraries that were concatenated for the UMI.tsv files

value: d16 HER2


title: RNA_mPFC_Glia_Naive_Rep1

value: medial prefrontal cortex


title: Mouse lung WSN-2

description:
WSN-2
Infected in WSN wildtype strain

value: Wildtype (WSN, H1N1)


title: S10N


title: S8N


title: TG19-0370

description:
Nulliparous, 15 weeks, metaplastic
SRRs represent multiple libraries that were concatenated for the UMI.tsv files


title: TG19-0184

description:
Multiparous, 16 weeks, solid/nodular
SRRs represent multiple libraries that were concatenated for the UMI.tsv files

value: unknown

value: solid nodular


title: Mouse lung WSN3M-2

description:
WSN3M-2
Infected with WSN mutant virus. The WSN-3M mutant expresses a form of NS1 that has a three-point mutation at positions R148A, E152A, E153A at the nuclear-localization signal site (NLS) on the NS gene. This encodes a NS1 protein that is unable to translocate into the nucleus thus NS1 is confined to the cytoplasm

value: BALB/c

value: WSN (3M mutant)


title: TG19-0183

description:
Multiparous, 16 weeks, mixed
SRRs represent multiple libraries that were concatenated for the UMI.tsv files

value: Mixed


title: S9D


title: S12D

description:
This sample is also known as S25D in GSE101547 study
none


title: TG19-0360

description:
Nulliparous, 17 weeks, metaplastic
SRRs represent multiple libraries that were concatenated for the UMI.tsv files


title: S12N

description:
This sample is also known as S25N in GSE101547 study
none


title: ESCs, SS18-ChIP-8h

value: OG2 transgenetic mouse embryonic stem cells (OG2ES)

value: treated with doxycycline for 8h


title: Wt; Sal/Alt rep3

city: Denver

first: Rafeul

last: Alam

state: Colorado

address: 1400 Jackson Street

department: Medicine

institute: National Jewish Health

data_processing:
(ATAC) in Rag-/- (illumina high-seq) samples  ATAC-seq reads were trimmed of adapters and poor sequence by skewer-0.2.2 (Jiang et al., 2014) and then quality control was assessed with fastqc-0.11.5 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Bam files were generated by mapping to the mm10 mouse genome with Bowtie2-2.3.2 (Langmead and Salzberg, 2012) with max fragment length set to    –X 2000. The resulting Bam files are filtered for ChrM, PCR duplicates and the ATAC-seq Blacklist from Encode (https://www.encode.org/files/ENCFF299EZH/@@download/ENCFF299EZH.bed.gz) using picardtools-2.12.1 (http://broadinstitute.github.io/picard/) and samtools1.5 (Li et al., 2009). Peaks were called for each sample using MACS-2.1.1 (Zhang et al., 2008) with -B --SPMR --nomodel --nolambda --call-summits options. A bed file of peak summits +/-200bp was generated using bedtools2-2.26.0 (Quinlan and Hall, 2010) slopbed tool and using bedops-2.4.14 (Neph et al., 2012) merged across samples to create a common reference peak list. A count table of the number of fragments intersecting each reference peak was then generated with Bedtools2 multiBamCov tool for each sample and imported into R-3.4.2 where differential peak calling was performed using EdgeR-3.20.9 (Robinson et al., 2010). Significant differential peaks were determined as those with relative peak fragment counts between different exposed ILC2 groups differing by >2 fold and padj<0.05. Peaks were annotated by Homer-4.8 (http://homer.ucsd.edu/homer/index.html) annotatePeaks.pl with nearest gene and genomic location.  Homer (findMotifsGenome.pl) was used to determine enriched motifs in the defined peaks of each data-set. Peaks were visualized with the genome using the Integrated Genome Viewer IGV-2.3.97.
(ATAC) in WT (illumina nova-seq) samples same as above but trimmed to 50bp
Genome_build: (ATAC) assembly: mm10
Supplementary_files_format_and_content: (ATAC) tab delimited raw counts file
(RNA-Seq) We trimmed and culled raw demultiplexed cDNA reads in FASTQ files using Cutadapt, trimming poly A tails and 5’ and 3’ ends with q < 20 and removing any reads shorter than 25 base pairs. We then aligned trimmed reads to the GRCm38 mouse genome with GSNAP, setting “max-mismatches=0.05” and accounting for both known Ensembl splice sites and SNPs.
(RNA-Seq) We quantified gene expression using HTSeq with “stranded=yes”, “mode=intersection-nonempty”, and “t=gene” and then summed the number of unique molecular identifiers (UMIs) for each gene across runs for each cell to obtain a UMI count matrix that we used for all downstream analysis.
Genome_build: (RNA-Seq) assembly: GRCm38
Supplementary_files_format_and_content: (RNA-Seq) "expressionMatrix" text files contain expression count tables that include all samples in the original fastq files. All sample names include the sequencing barcode (after the underscore)

source_name: Lung

growth_protocol: After flow sorting cells were kept in RPMI1640@ 37°C in 5% CO2 incubator

extract_protocol:
50,000 viable cells were resuspended in 50ul lysis buffer (0.01% Digitonin, 0.1% NP-40, 0.1% Tween-20, 10mM Tris-HCl pH=7.4,10mM NaCl and 3mM MgCl2.) and incubated on ice for 3min. Lysis buffer was washed out by adding 1mL Resuspending buffer (0.1% Tween-20, 10mM Tris-HCl pH=7.4,10mM NaCl and 3mM MgCl2.) and invert tubes for 3 times. Nuclei were centrifuged at 500 x g for 10 min at 4˚C. All supernatant was carefully aspirated. Transposase reaction was performed by Nextera DNA Library Preparation kit from Illumina (San Diego, CA, USA.) Transposed DNA was isolated by MiniElute PCR Purification Kit from Qiagen(Valencia, CA, USA).
Libraries were made by PCR. Real-time PCR was performed to determine PCR cycle number by calculating one-third of maximum fluorescent intensity. Primers are listed on Buenrostro et al. (2013) and synthesized by Integrated DNA technologies (Coralville, IA, USA) All libraries were sequenced using 2x50 bps reads on Hiseq 2500 from Illumina (San Diego, CA, USA.)

value: Saline (Sal) sensitized and Alt challenged

value: Lung ILCs:Flow sorted CD45+Lin-NK1.1-CD25+ICOS+ cells


title: COVID_46

type: genomic

city: Madison

first: Andy

last: Madrid

state: Wisconsin

address: 600 Highland Ave

department: Neurological Surgery

institute: University of Wiconsin - Madison

description:
blood from COVID-19 patient
C46

hyb_protocol: hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions

scan_protocol: arrays were imaged using BeadArray Readerusing standard recommended settings

data_processing:
minfi
matrix_processed.csv = average beta
matrix_signal_intensities.csv = unmethylated and methylated signal intensities

label: Cy5 and Cy3

label_protocol: standard illumina protocol

extract_protocol: genomic DNA from whole blood tissue was extracted using the GeneJET whole blood kit according to the manufacturer's recommendations

tag: Sex

value: M

tag: race

value: W

tag: death

tag: covid status

value: blood


title: COVID_71

description:
blood from COVID-19 patient
C71

value: H


title: TG19-0182

description:
Multiparous,  17 weeks, solid/nodular
SRRs represent multiple libraries that were concatenated for the UMI.tsv files

value: FVBN

value: mammary tumor

tag: genotype

value: untreated


title: Mouse lung WSN3M-1

description:
WSN3M-1
Infected with WSN mutant virus. The WSN-3M mutant expresses a form of NS1 that has a three-point mutation at positions R148A, E152A, E153A at the nuclear-localization signal site (NLS) on the NS gene. This encodes a NS1 protein that is unable to translocate into the nucleus thus NS1 is confined to the cytoplasm

tag: replicate


title: H1944 Vehicle Rep 1 4C

value: Viewpoint CDKN1C and Viewpoint CERES enhancer

tag: treatment

value: Vehicle


title: S8D

value: Cancer Tissue


title: Mouse lung WSN-1

description:
WSN-1
Infected in WSN wildtype strain

value: BALB/c

value: Wildtype (WSN, H1N1)


title: Wt; Sal/Alt rep1


title: COVID_59

description:
blood from COVID-19 patient
C59


title: Mouse lung Mock-1

description:
Mock-1
Uninfected/mock control

value: Uninfected


title: Mouse lung Mock-2

description:
Mock-2
Uninfected/mock control


title: NONCOVID_24

description:
blood from non-COVID-19 patient
NC24

value: F


title: WT; Alt/Alt rep3

value: Alternaria (Alt) sensitized and Alt challenged


title: TG19-0393-2

value: p95 HER2

value: metaplastic/invasive


title: WT; Alt/Alt rep2

value: Lung ILCs:Flow sorted CD45+Lin-NK1.1-CD25+ICOS+ cells


title: WT; Alt/Alt rep1


title: COVID_22

description:
blood from COVID-19 patient
C22

value: M


title: COVID_34

description:
blood from COVID-19 patient
C34

value: O

value: blood


title: S6D


title: S4D

description:
This sample is also known as S19D in GSE101547 study
S4_sig_mirna.txt


title: Wt; Sal/Alt rep2

value: Saline (Sal) sensitized and Alt challenged


title: S7N

value: Adjacent Normal Tissue


title: COVID_100.1

description:
blood from COVID-19 patient
C100.1

value: W


title: S4N

description:
This sample is also known as S19N in GSE101547 study
S4_sig_mirna.txt


title: COVID_58

description:
blood from COVID-19 patient
C58

value: H


title: TG19-0181

description:
Multiparous, 17 weeks, mixed
SRRs represent multiple libraries that were concatenated for the UMI.tsv files

value: FVBN

value: mammary tumor

value: unknown

value: Mixed

value: untreated


title: TG19-0393-4

description:
Nulliparous, 17 weeks,  metaplastic
SRRs represent multiple libraries that were concatenated for the UMI.tsv files

value: d16 HER2


title: ERT2-Cre_Ring1aPM_Ring1bCPM_Mutant_EB_rep2

tag: tamoxifen treatment

value: with 4-OHT

value: embryoid body


title: S7D

value: Cancer Tissue


title: ERT2-Cre_Ring1aPM_Ring1bCPM_Control_EB_rep2

value: without 4-OHT


title: S3D

description:
This sample is also known as S7D in GSE101547 study
S3_sig_mirna.txt


title: S5D


title: S3N

description:
This sample is also known as S7N in GSE101547 study
S3_sig_mirna.txt


title: BL_NC_Rep2

city: Hangzhou

first: Kun

last: Zhang

address: 866 Yuhangtang Rd

institute: Zhejiang University

description: normalized abundance measurements_BL.txt

data_processing:
Reads were trimmed to remove the bases with low quality and adapter sequences
The trimmed reads were assigned directly to transcripts and counted with Salmon software
Gene expression level was quantified and normolized by Salmon(v0.14.1)
Differentially expressed genes between NC and Snf2h_KD group were selected by DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Text files include normalized counts by DESeq2 for each sample

source_name: embryo

extract_protocol:
Total RNA extraction was performed using Picopure RNA isolation kit (Life Technologies, Grand Island, NY, USA) based on the manufacturer's manual.
mRNAs separation was achieved using oligo(dT)25 beads. Sequencing libraries were constructed with NEB Next Ultra RNA Library Prep Kit for Illumina (New England Biolabs) according to the instruction. In brief, mRNAs were fragmented followed by reverse transcription. The cDNA library underwent end repair, poly(A)-tailing, adaptor ligation, and PCR amplification for 12–15 cycles to prepare sequencing libraries.

value: embryo

value: blastocyst


title: COVID_70

description:
blood from COVID-19 patient
C70

value: M

value: blood


title: S6N

value: Adjacent Normal Tissue


title: NONCOVID_12

description:
blood from non-COVID-19 patient
NC12

value: W


title: TG19-0165B

description:
Nulliparous, 20 weeks, metaplastic
SRRs represent multiple libraries that were concatenated for the UMI.tsv files

value: p95 HER2

value: metaplastic/invasive


title: BL_Snf2h_KD_Rep2


title: TG19-0167B

description:
Nulliparous, 21 weeks, solid/nodular
SRRs represent multiple libraries that were concatenated for the UMI.tsv files

value: FVBN

value: mammary tumor

value: solid nodular


title: S5N


title: COVID_09

description:
blood from COVID-19 patient
C9

value: F

value: A


title: ERT2-Cre_Ring1aPM_Ring1bCPM_Control_EB_rep1


title: MO_Snf2h_KD_Rep1

description: normalized abundance measurements_MO.txt

value: morula


title: COVID_45

description:
blood from COVID-19 patient
C45

value: O


title: BL_Snf2h_KD_Rep1


title: MO_Snf2h_KD_Rep2


title: COVID_21

description:
blood from COVID-19 patient
C21


title: ERT2-Cre_Ring1aPM_Ring1bCPM_Mutant_ES_rep2

source_name: ES

value: with 4-OHT

value: embryonic stem cell


title: S2D

description:
This sample is also known as S2D in GSE101547 study
S2_sig_mirna.txt

value: Cancer Tissue


title: NONCOVID_11

description:
blood from non-COVID-19 patient
NC11


title: S2N

description:
This sample is also known as S2N in GSE101547 study
S2_sig_mirna.txt


title: S1N


title: ERT2-Cre_Ring1aPM_Ring1bCPM_Mutant_EB_rep1

value: embryoid body


title: ERT2-Cre_Ring1aPM_Ring1bCPM_Control_ES_rep2

value: without 4-OHT


title: S1D


title: COVID_69

description:
blood from COVID-19 patient
C69

value: blood


title: ERT2-Cre_Ring1aPM_Ring1bCPM_Mutant_ES_rep1


title: COVID_44

description:
blood from COVID-19 patient
C44

value: M

value: H


title: NONCOVID_23

description:
blood from non-COVID-19 patient
NC23

value: W


title: sRNA mutant_triple ovaries

first: Daniel

last: Gebert

state: Cambridgeshire

address: Downing Street

department: Department of Genetics

country: United Kingdom

institute: University of Cambridge

description:
Size-selected small RNA
4N adaptors at 5' and 3' ends

data_processing:
Small RNA sequencing reads were quality-filtered and trimmed with Trim-Galore, applying standard settings.
For cross-sample normalization, trimmed reads were mapped to the complete set of mature miRNA sequences of D. melanogaster (miRBase; Kozomara and Griffiths-Jones, 2011) with bowtie (Langmead et al., 2009), reporting all best valid alignments without mismatches. In parallel, trimmed reads were mapped to the combined set of non-coding RNA, protein-coding, and pseudogene sequences (FlyBase) allowing two mismatches and retaining unmatched reads in the size range of 23-29 nt. Filtered reads were then mapped to the D. melanogaster genome (dm3) using bowtie and allowing either perfect unique matches or all best valid alignments without mismatches.
dm3
bedgraph files generated by bowtie, samtools, bedtools

organism: Drosophila melanogaster

source_name: ovaries

extract_protocol:
Total RNA from dissected adult ovaries was isolated using Trizol reagent (Invitrogen) and quantified using Qubit (Invitrogen).
Small RNA-sequencing analysis was performed on 10 µg of total RNA using the NEBNext® Small RNA Library Prep Set for Illumina® and with an initial 2S rRNA depletion step as previously described (Li et al., 2009).
Libraries were multiplexed using the NEBNext® Multiplex Oligos for Illumina® and sequenced in single-end, 50-nt-long reads on an Illumina HiSeq 2500.

value: ovaries

value: adult

value: 20A(p)-delta; 38C-delta, 42AB-delta


title: MO_NC_Rep2

value: embryo


title: ERT2-Cre_Ring1aPM_Ring1bCPM_Control_ES_rep1

last: Sugishita

institute: RIKEN


title: COVID_57

description:
blood from COVID-19 patient
C57

value: F


title: ERT2-Cre_Pcgf6_Control_EB_rep2


title: MO_NC_Rep1


title: LTi

city: Braunschweig

first: Michael

last: Beckstette

state: Lower Saxony

address: Inhoffenstrase 7

department: Molecular Infection Biology

institute: Helmholtz Centre for Infection Research

data_processing:
Illumina RTA3 was used for basecalling.
All libraries have been assessed for sufficient sequencing quality and potential adapter contamination using programs FastQC (Babraham Bioinformatics; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), trim_galore and cutadapt. To avoid potential methylation bias due to insufficient end-repair reaction, from both reads (R1/R2) the first 10 bases at the 5' as well as the 3' end have been trimmed after adapter removal and trimming of low-quality ends with a Phred score below 20. Reads, which are shorter than 20 nucleotides after trimming have been discarded.
Quality controlled libraries have been mapped against the mouse reference genome (version: GRCm38, w/o gonosomes) using the bisulfite short read mapping software BSMAP. In order to accurately measure the methylation levels of cytosines inside CpG context genome-wide and obtain corresponding coverage information, methylation level calling has taken only properly paired unique read pair mappings (methratio.py parameters: --unique, --paired,--remove-duplicate) into account.
The reliable detection of DMRs even in the absence of replicates was performed with the software tool metilene. We considered for the detection process only CpG motifs with a coverage of at least five that are present in at least one sample. In addition, a DMR has to contain at least three CpG's with a distance between two CpGs of at most 200 nucleotides and a total length of the region of at least 300. Further on, to be classified as DMR, the difference in mean methylation (i.e., mean over all CpG's of a region) of a region between two compared samples/conditions has to be greater or equal 25 percent and the adjusted P-value from the 2D-KS test has to be at most 0.1
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: *,methout.txt: CSV formatted file with methylation values for all CpGs for each sample as generated by  BSMAp/methratio.py; *metilene_DMRs.csv.gz: Differentially methylated regions for each pairwise comparison (generated by metilene)

source_name: Lymphoid tissue inducer cells

extract_protocol:
Lymph nodes were removed and meshed through a sieve. Genomic DNA was prepared from ILC subpopulations sorted by FACS. Genomic DNA was converted by bisulfite and subjected to library preparation.
The bislufite converted DNA was fragmented by sonication and served as input for library preparation by using the Accel-NGS Methyl-Seq DNA Library Kit.

value: Innate lymphoid cells

value: lymph node

tag: marker


title: ERT2-Cre_Pcgf6_Mutant_EB_rep2

city: Tsurumi-ku,Yokohama

first: Hiroki

address: 1-7-22, Suehiro-cho


title: sRNA 20ApD_38CD ovaries

description: Size-selected small RNA

tag: strain

value: 20A(p)-delta; 38C-delta


title: ILC1

source_name: Innate lymphoid cells 1


title: BL_NC_Rep1

value: blastocyst


title: ERT2-Cre_Pcgf6_Control_ES_rep2

value: embryonic stem cell


title: ERT2-Cre_Pcgf6_Mutant_ES_rep2

value: with 4-OHT


title: COVID_08

description:
blood from COVID-19 patient
C8

value: AA