title: RRBS-seq of RNA from from pig-470

description:
metilene.5.Obese_Lean.3-3.out.tsv
metilene.5.Obese_Lean.5-5.out.tsv
RRBS-470


title: RRBS-seq of RNA from from pig-436

status: Public on Dec 05 2019

type: SRA

city: Copenhagen

first: Christian

last: Anthon

address: Thorvaldsensvej 57

country: Denmark

institute: University of Copenhagen

description:
metilene.5.Obese_Lean.3-3.out.tsv
metilene.5.Obese_Lean.5-5.out.tsv
RRBS-436

library_source: genomic

data_processing:
RRBS: The raw reads were cleaned for quality and adapters using and in-house tools removing TrueSeq adapters and clipping read tails of phred quality less than 20. The reads were mapped to the pig genome version 10.2 using bismark v 0.10 (Krueger and Andrews, 2011) with standard parameters except using bowtie 2 v2.1.0 for the mapping option of bismark (Langmead and Salzberg, 2012). The mapped reads were analyzed using Metilene v 0.2-7 requiring at least five pigs in both the obese and lean groups (–X 5 –Y 5)
mDNAcap:  The raw reads were trimmed for quality and adapters using trimmomatic V0.22 (Bolger et al., 2014) (quality trimming by phred quality of 20) The cleaned reads were mapped to the pig genome version 10.2 using segemehl V0.1.4 (Hoffmann et al., 2009) and the following parameters: accuracy 95%, and minimum mapping size 18. The mapped reads were analyzed with diffReps V1.55.4 using the G-test and default values for all remaining parameters
RNAseq: The raw reads were cleaned for quality and adapters using and in-house tools removing TrueSeq adapters and clipping read tails of phred quality less than 20 The reads were mapped to the pig transcriptome using the STAR aligner v2.3.1 (Dobin et al., 2013) with the following options and data: pig genome version 10.2, ensembl annotation version 70 and with intron-motifs [XS:A] tags in the SAM output. The aligned reads were assigned to transcripts of the ensembl version 70 annotation with cufflinks version 2.2.0 (Trapnell et al., 2013). The subsequent differential expression analysis was performed with cuffdiff from the cufflinks package and was based on the Ensembl v70 annotation. Standard options were used for the cufflinks programs in all cases. All further analysis was done using the annotation from ensemble v81.
Supplementary_files_format_and_content: [RNAseq]  fpkm_tracking.tsv, gene_exp.diff.tsv (1=obese, q2=lean)
Supplementary_files_format_and_content: [MeDIP-seq]  data_all.gt.Obese_lean.*.tsv (Treatment=obese, control=lean)
Supplementary_files_format_and_content: [RRBS-seq]  metilene.*.tsv

molecule: genomic DNA

organism: Sus scrofa

source_name: Adipocytes

extract_protocol:
DNA was extracted from the mature adipocytes using the Epicenter kit (Illumina), and total RNA was isolated from the mature adipocytes according to the protocol described in (Cirera, 2013) using TriReagent and included a DNAse treatment step.
RNA libraries were prepared for sequencing using Truseq lib prep kit from Illumina together with RiboZero Gold  using 0.5ug of total RNA as input. mRRBS libraries were prepared as described in Boyle (2012) using 200ng DNA as input. MeDiP libraries were prepared from 1.1ug DNA, fragmented in a bioruptor and methylated DNA fragments were enriched using MethylMiner Methylated DNA Enrichment KIt (cat#ME10025). Sequencing libraries were generated according to the low Input TruSeq library preparation protocol.

treatment_protocol: Mature adipocytes were isolated from approx. 15 g of the retroperitoneal adipose tissue from each animal, treated with 0.2% collagenase and filtered through a 200-um nylon filter.

tag: cell type

value: adipocyte

tag: Sex

value: F

tag: phenotype

value: obese


title: RRBS-seq of RNA from from pig-539

description:
metilene.5.Obese_Lean.3-3.out.tsv
metilene.5.Obese_Lean.5-5.out.tsv
RRBS-539


title: RRBS-seq of RNA from from pig-433

description:
metilene.5.Obese_Lean.3-3.out.tsv
metilene.5.Obese_Lean.5-5.out.tsv
RRBS-433

value: M


title: RRBS-seq of RNA from from pig-411

description:
metilene.5.Obese_Lean.3-3.out.tsv
metilene.5.Obese_Lean.5-5.out.tsv
RRBS-411


title: RRBS-seq of RNA from from pig-434

description:
metilene.5.Obese_Lean.3-3.out.tsv
metilene.5.Obese_Lean.5-5.out.tsv
RRBS-434

value: lean


title: RRBS-seq of RNA from from pig-435

description:
metilene.5.Obese_Lean.3-3.out.tsv
metilene.5.Obese_Lean.5-5.out.tsv
RRBS-435


title: RRBS-seq of RNA from from pig-410

description:
metilene.5.Obese_Lean.3-3.out.tsv
metilene.5.Obese_Lean.5-5.out.tsv
RRBS-410


title: RRBS-seq of RNA from from pig-407

description:
metilene.5.Obese_Lean.3-3.out.tsv
metilene.5.Obese_Lean.5-5.out.tsv
RRBS-407


title: RRBS-seq of RNA from from pig-402

description:
metilene.5.Obese_Lean.3-3.out.tsv
metilene.5.Obese_Lean.5-5.out.tsv
RRBS-402


title: RRBS-seq of RNA from from pig-308

description:
metilene.5.Obese_Lean.3-3.out.tsv
metilene.5.Obese_Lean.5-5.out.tsv
RRBS-308


title: RRBS-seq of RNA from from pig-401

description:
metilene.5.Obese_Lean.3-3.out.tsv
metilene.5.Obese_Lean.5-5.out.tsv
RRBS-401


title: MeDIP-seq of DNA from pig-577

description:
data_all.gt.Obese_lean.diffReps.tsv
data_all.gt.Obese_lean.diffReps.hotspot.tsv
meDIP-577


title: E06_MS099_065 (SingleCell054)

status: Public on Jan 29 2020

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: Cynomolgus Embryo at E06

library_source: transcriptomic

data_processing:
library strategy: SC3-seq
Samples were sequenced on NextSeq and SOLiD sequencers with the read length are 76 and 50 bases.
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-e 0.1 -q 20 -n 2 -O 1 -m 30 -a CTCGAGGGCGCGCCGGATCC -g CTCGAGGGCGCGCCGGATCC -a AAAAAAAAAAAAAAAAAAAA -a TTTTTTTTTTTTTTTTTTTT". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the Cynomolgus monkey genome Macfac5.0 and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the “—no-coverage-search” option.
Mapped reads on the genome and the ERCC were separated, and the reads on the genome were converted into the expression levels by cufflinks-2.2.0 using the “—compatible-hits-norm”,  “—max-mle-iterations 50000", “—no-length-correction” and “—library-type fr-secondstrand” options and macfas5.0 reference gene annotations with extended TTSs. For the reference gene annotations used in cufflinks, we extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Genome_build: macfas5.0
Supplementary_files_format_and_content: tab-delimited text file includes RPM values for each Sample

molecule: total RNA

organism: Macaca fascicularis

source_name: Cynomolgus Embryo at E06

growth_protocol:
For cultivation of CMK6 and CMK9 cyESCs, they were cultured with conventional hESC medium [DMEM/F12 supplemented with 20% (vol/vol) of KSR, 1 mM of sodium pyruvate, 2 mM of GlutaMax, 0.1 mM of non-essential amino acids, 0.1 mM of 2-mercaptoethanol, 1000 U/ml of ESGRO mouse LIF, and 4 ng/ml of recombinant human bFGF] on mouse embryonic feeders (MEFs).
For cultivation in 656BTAG42 cells under undifferentiated state, it was cultured in AITS medium containing 20ng/mL bFGF and 2.5nM IWR1

extract_protocol:
For single cell isolation from cy pre-implantation embryos, a whole embryo was incubated with 0.25% trypsin/PBS  for around 10 min at 37℃, then dissociated into single cells by repeated pipetting, and dispersed in 0.1 mg/ml of PVA/PBS  for preparation of single-cell cDNAs.
For single cell isolation from cy post-implantation embryos, the implantation site was dissected out from the uterus and the embryonic fragment containing the epiblast (EPI), amnion, hypoblast, and yolk sac endoderm was isolated manually. The fragment was incubated with 0.25% trypsin/PBS for around 10 min at 37℃, then dissociated into single cells by repeated pipetting, and dispersed in 0.1 mg/ml of PVA/PBS.
For single cell isolation from cyESCs, cells were first detached as clumps with CTK solution, incubated in 0.25% trypsin/PBS (Sigma-Aldrich) for around 10 min at 37℃, and dispersed into single cells in 1% (vol/vol) KSR/PBS containing 10 M of the ROCK inhibitor Y-27632. Cells under feeder-free condition were directly incubated in TrypLE Select for around 5 min at 37℃, and dispersed into single cells in 1% (vol/vol) KSR/PBS containing 10 uM of the ROCK inhibitor Y-27632.
For single cell isolation from cyPGCLCs, the cells dissociated with TryPLE select were collected by cell sorting.
For SC3-seq analysis, cDNA synthesis / amplification from single cells and library construction from the cDNAs were performed as described previously [Nakamura et al. 2015, NAR, 43, e60].

treatment_protocol: For cyPGCLCs, undifferentiated ESCs were dissociated and replated to low-adherent V-bottom plates to form aggregates with BMP4 (200 ng/ml), SCF (100 ng/ml), EGF (50 ng/ml), LIF(1000U/ml), and Y27632 (10µM) in GMEM containing 15% KSR or Advanced RPMI1640 containing B27, until the harvest day.

tag: cell line

value: not applicable

value: embryo

tag: developmental stage


title: MeDIP-seq of DNA from pig-584

description:
data_all.gt.Obese_lean.diffReps.tsv
data_all.gt.Obese_lean.diffReps.hotspot.tsv
meDIP-584


title: RRBS-seq of RNA from from pig-572

description:
metilene.5.Obese_Lean.3-3.out.tsv
metilene.5.Obese_Lean.5-5.out.tsv
RRBS-572


title: MeDIP-seq of DNA from pig-529

description:
data_all.gt.Obese_lean.diffReps.tsv
data_all.gt.Obese_lean.diffReps.hotspot.tsv
meDIP-529


title: MeDIP-seq of DNA from pig-525

description:
data_all.gt.Obese_lean.diffReps.tsv
data_all.gt.Obese_lean.diffReps.hotspot.tsv
meDIP-525


title: MeDIP-seq of DNA from pig-572

description:
data_all.gt.Obese_lean.diffReps.tsv
data_all.gt.Obese_lean.diffReps.hotspot.tsv
meDIP-572


title: MeDIP-seq of DNA from pig-539

description:
data_all.gt.Obese_lean.diffReps.tsv
data_all.gt.Obese_lean.diffReps.hotspot.tsv
meDIP-539


title: MeDIP-seq of DNA from pig-524

description:
data_all.gt.Obese_lean.diffReps.tsv
data_all.gt.Obese_lean.diffReps.hotspot.tsv
meDIP-524


title: MeDIP-seq of DNA from pig-503

description:
data_all.gt.Obese_lean.diffReps.tsv
data_all.gt.Obese_lean.diffReps.hotspot.tsv
meDIP-503


title: MeDIP-seq of DNA from pig-473

description:
data_all.gt.Obese_lean.diffReps.tsv
data_all.gt.Obese_lean.diffReps.hotspot.tsv
meDIP-473


title: MeDIP-seq of DNA from pig-470

description:
data_all.gt.Obese_lean.diffReps.tsv
data_all.gt.Obese_lean.diffReps.hotspot.tsv
meDIP-470


title: MeDIP-seq of DNA from pig-436

description:
data_all.gt.Obese_lean.diffReps.tsv
data_all.gt.Obese_lean.diffReps.hotspot.tsv
meDIP-436


title: MeDIP-seq of DNA from pig-434

description:
data_all.gt.Obese_lean.diffReps.tsv
data_all.gt.Obese_lean.diffReps.hotspot.tsv
meDIP-434


title: MeDIP-seq of DNA from pig-522

description:
data_all.gt.Obese_lean.diffReps.tsv
data_all.gt.Obese_lean.diffReps.hotspot.tsv
meDIP-522


title: MeDIP-seq of DNA from pig-433

description:
data_all.gt.Obese_lean.diffReps.tsv
data_all.gt.Obese_lean.diffReps.hotspot.tsv
meDIP-433


title: MeDIP-seq of DNA from pig-413

description:
data_all.gt.Obese_lean.diffReps.tsv
data_all.gt.Obese_lean.diffReps.hotspot.tsv
meDIP-413


title: MeDIP-seq of DNA from pig-435

description:
data_all.gt.Obese_lean.diffReps.tsv
data_all.gt.Obese_lean.diffReps.hotspot.tsv
meDIP-435


title: MeDIP-seq of DNA from pig-411

description:
data_all.gt.Obese_lean.diffReps.tsv
data_all.gt.Obese_lean.diffReps.hotspot.tsv
meDIP-411


title: MeDIP-seq of DNA from pig-410

description:
data_all.gt.Obese_lean.diffReps.tsv
data_all.gt.Obese_lean.diffReps.hotspot.tsv
meDIP-410


title: RRBS-seq of RNA from from pig-413

description:
metilene.5.Obese_Lean.3-3.out.tsv
metilene.5.Obese_Lean.5-5.out.tsv
RRBS-413


title: MeDIP-seq of DNA from pig-402

description:
data_all.gt.Obese_lean.diffReps.tsv
data_all.gt.Obese_lean.diffReps.hotspot.tsv
meDIP-402


title: MeDIP-seq of DNA from pig-407

description:
data_all.gt.Obese_lean.diffReps.tsv
data_all.gt.Obese_lean.diffReps.hotspot.tsv
meDIP-407


title: MeDIP-seq of DNA from pig-401

description:
data_all.gt.Obese_lean.diffReps.tsv
data_all.gt.Obese_lean.diffReps.hotspot.tsv
meDIP-401


title: RRBS-seq of RNA from from pig-321

description:
metilene.5.Obese_Lean.3-3.out.tsv
metilene.5.Obese_Lean.5-5.out.tsv
RRBS-321


title: MeDIP-seq of DNA from pig-321

description:
data_all.gt.Obese_lean.diffReps.tsv
data_all.gt.Obese_lean.diffReps.hotspot.tsv
meDIP-321


title: MeDIP-seq of DNA from pig-308

description:
data_all.gt.Obese_lean.diffReps.tsv
data_all.gt.Obese_lean.diffReps.hotspot.tsv
meDIP-308


title: totalRNA-seq from pig-577

description:
gene_exp.diff.tsv
totalRNA-577


title: totalRNA-seq from pig-572(B)

description:
gene_exp.diff.tsv
totalRNA-573


title: totalRNA-seq from pig-572

description:
gene_exp.diff.tsv
totalRNA-572


title: totalRNA-seq from pig-525

description:
gene_exp.diff.tsv
totalRNA-525


title: totalRNA-seq from pig-529

description:
gene_exp.diff.tsv
totalRNA-529


title: totalRNA-seq from pig-524

description:
gene_exp.diff.tsv
totalRNA-524


title: totalRNA-seq from pig-473

description:
gene_exp.diff.tsv
totalRNA-473


title: totalRNA-seq from pig-433

description:
gene_exp.diff.tsv
totalRNA-433


title: totalRNA-seq from pig-413

description:
gene_exp.diff.tsv
totalRNA-413


title: totalRNA-seq from pig-407

description:
gene_exp.diff.tsv
totalRNA-407


title: totalRNA-seq from pig-402

description:
gene_exp.diff.tsv
totalRNA-402


title: WT_Smad4ChIP_rep2

status: Public on Apr 08 2019

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

country: USA

institute: Rutgers, the State University of New Jersey

data_processing:
FastQC (version 0.11.3) was used to check the quality of raw sequencing reads (fastq)
Alignment: RNA-seq: TopHat2, version 2.1.0; ATAC-seq and ChIP-seq: Bowtie2, version 2.2.6
RNA-seq: Gene and transcript level computation done with CuffQuant, version 2.2.1
RNA-seq: Normalized abundance measurements generated by CuffNorm, version 2.2.1, calculate FPKM values using quartile normalization
RNA-seq: CuffDiff, version 2.2.1, geometric normalization, per-condition dispersion
ATAC-seq and ChIP-seq: Deeptools bamCoverage (v2.4.2, duplicate reads ignored, RPKM normalized and extended reads) was used to generate bigwig files from bam files.
ATAC-seq and ChIP-seq: Model-based Analysis of ChIP-Seq (MACS 1.4.1) was used for peak calling and to generate bed files from aligned reads. Shiftsize parameter was used for MACS based on the fragment size of Pippin Prep.
scRNA-seq: Read 1 is 26 bp to incorporate the UMIs and cell barcodes, read 2 is 98 bp for the transcript information. Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using the 10X Genomics’ cellranger mkfastq command. Subsequence UMI and cell barcode de-convolution was performed using 10X Genomics’ cellranger count command to generate the final digital gene expression matrices, t-SNE plot, and cloupe files.
Genome_build: mm9 (ChIP-seq); mm10 (scRNA-seq)

organism: Mus musculus

source_name: WT duodenum epithelium

extract_protocol:
Freshly harvested duodenum was flushed with cold PBS, opened longitudinally, cut into 1 cm pieces, and then rotated in 3 mM EDTA in PBS at 4 °C. The tissue was then violently shaken to release the epithelium from underlying muscular tissue. The intestine pieces were discard and the supernatant was collected as whole epithelium fraction. Standard procedures were used for ChIP on mouse duodenum epithelial cells. Briefly, cells were isolated by 3mM EDTA/PBS and then cross-linked 2 mM DSG (Thermo 20593) for 45 min, and then further cross-linked in 1% formaldehyde for 20 min at room temperature. Cells were washed with ice-cold PBS, resuspended with lysis buffer (1% SDS, 10 mM EDTA pH 8.0, 50 mM Tris pH 8.0, and protease inhibitor cocktails), and further incubated at room temperature for 10 min. Cell lysates were sonicated using a Diagenode Bioruptor to generate 200 bp to 500 bp fragments, as determined by agarose gel electrophoresis. The supernatant of lysates were diluted in binding buffer (20 mM Tris pH 8.0, 2 mM EDTA pH 8.0, 150 mM NaCl, 1% Triton X-100, and protease inhibitor cocktails) and incubated with Smad4 (20 μl, Cell signaling #46535, lot 2) antibody coupled to Dynabeads (Invitrogen) at 4°C overnight. The final concentration of SDS in the sonicates for mouse SMAD4 ChIP is 0.167%. The immunoprecipitates were washed 5 times and rotated at 4°C with RIPA buffer (50 mM HEPES pH 7.6, 1 mM EDTA pH 8.0, 0.7% Na-deoxycholate, 1% NP-40, and 0.5 M LiCl) and a quick wash of TE buffer (0.1 mM EDTA pH 8.0 and 10 mM Tris pH 8.0). To recover the DNA, the samples were incubated overnight in reverse cross-linking buffer (1% SDS and 0.1 M NaHCO3) at 65 °C. The DNA was purified by QIAquick PCR Purification Kit (QIAGEN) and quantified with Picogreen (Life Technologies). ChIP enrichment was confirmed with qPCR for putative targets prior to library preparation.
Rubicon Genomics ThruPLEX DNA-seq Kit (Illumina)

tag: tissue

value: duodenum epithelium

tag: genotype

value: WT

tag: chip antibody

value: Smad4 (Cell signaling #46535, lot 2)


title: Hnf4αɣDKO_H3K27ac_MNaseChIP_rep2

description: Hnf4alphagammaDKO_H3K27ac_MNaseChIP_rep2.bw

data_processing:
FastQC (version 0.11.3) was used to check the quality of raw sequencing reads (fastq)
Alignment: RNA-seq: TopHat2, version 2.1.0; ATAC-seq and ChIP-seq: Bowtie2, version 2.2.6
RNA-seq: Gene and transcript level computation done with CuffQuant, version 2.2.1
RNA-seq: Normalized abundance measurements generated by CuffNorm, version 2.2.1, calculate FPKM values using quartile normalization
RNA-seq: CuffDiff, version 2.2.1, geometric normalization, per-condition dispersion
ATAC-seq and ChIP-seq: Deeptools bamCoverage (v2.4.2, duplicate reads ignored, RPKM normalized and extended reads) was used to generate bigwig files from bam files.
ATAC-seq and ChIP-seq: Model-based Analysis of ChIP-Seq (MACS 1.4.1) was used for peak calling and to generate bed files from aligned reads. Shiftsize parameter was used for MACS based on the fragment size of Pippin Prep.
Genome_build: mm9/hg19

source_name: Hnf4αɣDKO_duodenum epithelium

extract_protocol:
Freshly harvested duodenum was flushed with cold PBS, opened longitudinally, cut into 1 cm pieces, and then rotated in 3 mM EDTA in PBS at 4 °C. The tissue was then violently shaken to release the epithelium from underlying muscular tissue. The intestine pieces were discard and the supernatant was collected as whole epithelium fraction. For MNase-ChIP, mouse duodenum epithelial cells were resuspended in a digestion buffer (50 mM Tris-HCl pH7.6, 1 mM CaCl2, 0.2% Triton X-100, 5 mM Na butyrate, and protease inhibitor cocktails) and treated with micrococcal nuclease (MNase, Sigma #N3755) at 0.67 U/ml for 5 min at 37°C. The reaction was terminated by adding 5 mM EDTA in 10 mM Tris, pH7.6, and samples were dialyzed in chromatin RIPA buffer (10 mM Tris, pH7.6, 1 mM EDTA, 0.1% SDS, 0.1% Na-deoxycholate, 1% Triton X-100) before overnight IP at 4°C with Histone H3K27Ac (Abcam ab4729, lot #GR184332-2) antibody. IP material was subsequently handled as described above for conventional ChIP of sonicated genomic DNA (a final concentration of 0.13% SDS in the sonicates).
Rubicon Genomics ThruPLEX DNA-seq Kit (Illumina)

treatment_protocol: Mice were injected i.p. with tamoxifen (50mg/kg/day)  for 3 consecutive days and were sacrificed 1 day after last injection.

tag: treatment

value: tamoxifen 50mg/kg/day


title: WT_Smad4ChIP_rep1


title: Hnf4αɣDKO_H3K27ac_MNaseChIP_rep1

description: Hnf4alphagammaDKO_H3K27ac_MNaseChIP_rep1.bw


title: WT_H3K27ac_MNaseChIP_rep2

source_name: WT_duodenum epithelium

treatment_protocol: Mice were injected i.p. with oil (vehicle for tamoxifen) for 3 consecutive days and were sacrificed 1 day after last injection.

value: oil vehicle


title: WT_H3K27ac_MNaseChIP_rep1


title: WT_Hnf4ɣChIP_rep1

extract_protocol:
Freshly harvested duodenum was flushed with cold PBS, opened longitudinally, cut into 1 cm pieces, and then rotated in 3 mM EDTA in PBS at 4 °C. The tissue was then violently shaken to release the epithelium from underlying muscular tissue. The intestine pieces were discard and the supernatant was collected as whole epithelium fraction. Standard procedures were used for ChIP on mouse duodenum epithelial cells. Briefly, cells were isolated by 3mM EDTA/PBS and then cross-linked in 1% formaldehyde for 10 min at 4°C and then for 35 or 50 min at room temperature. Cells were washed with ice-cold PBS, resuspended with lysis buffer (1% SDS, 10 mM EDTA pH 8.0, 50 mM Tris pH 8.0, and protease inhibitor cocktails) and further incubated at room temperature for 10 min. Cell lysates were sonicated using a Diagenode Bioruptor to generate 200 bp to 500 bp fragments, as determined by agarose gel electrophoresis. The supernatant of lysates were diluted 8-fold in binding buffer (20 mM Tris pH 8.0, 2 mM EDTA pH 8.0, 150 mM NaCl, 1% Triton X-100, and protease inhibitor cocktails) and incubated with 6 ug of Hnf4α (Santa Cruz sc-6556 X, lot #B1015) or Hnf4ɣ (Santa Cruz sc-6558 X, lot #F0310) antibody coupled to Dynabeads (Invitrogen) at 4°C overnight. The immunoprecipitates were washed 5 times and rotated at 4°C with RIPA buffer (50 mM HEPES pH 7.6, 1 mM EDTA pH 8.0, 0.7% Na-deoxycholate, 1% NP-40, 0.5M LiCl) and a quick wash with TE buffer (0.1 mM EDTA pH 8.0 and 10 mM Tris pH 8.0). The DNA was recovered by incubating overnight in reverse cross-linking buffer (1% SDS, 0.1 M NaHCO3) at 65 °C. The DNA was purified by QIAquick PCR Purification Kit (QIAGEN) and quantified by using Picogreen (Life Technologies). ChIP enrichment was confirmed with qPCR for putative targets prior to library preparation.
Rubicon Genomics ThruPLEX DNA-seq Kit (Illumina)


title: WT_Hnf4ɣChIP_rep2


title: WT_Hnf4αChIP_rep1


title: Hnf4αɣDKO_rep3

description: HNF4_gene_exp_Cuffdiff_percondition.diff

extract_protocol:
RNAs were extracted from duodenum epithelia of the indicated genotypes (Wild type, Villin-CreERT2; Hnf4αf/f, Hnf4ɣCrispr/Crispr and Villin-CreERT2; Hnf4αf/f; Hnf4ɣCrispr/Crispr) one day following 2 or 3 consecutive days of tamoxifen injection. Uninjected Villin-CreERT2; Hnf4αf/f mice served as WT control. After flushing the freshly harvested duodenum with cold PBS, the epithelia was dissociated from underlying mesenchyme by incubating with 3 mM EDTA/PBS at 4°C as described previously (Perekatt, 2014). The epithelial cells were washed with PBS, and pelleted to remove excess PBS prior to addition of TRIzol for RNA extraction according to manufacturer’s protocols.
Illumina TruSeq RNA Library Prep kit v2


title: Hnf4αɣDKO_rep2


title: Hnf4αɣDKO_rep1

treatment_protocol: Mice were injected i.p. with tamoxifen (50mg/kg/day)  for 2 consecutive days and were sacrificed 1 day after last injection.


title: WT_rep3


title: WT_Hnf4αChIP_rep2


title: WT_rep1

treatment_protocol: Mice were injected i.p. with oil (vehicle for tamoxifen) for 2 consecutive days and were sacrificed 1 day after last injection.


title: WT_rep2


title: si-Pias4_rep2

status: Public on Mar 05 2019

city: Beijing

first: Yangming

last: Wang

address: 5 Yiheyuan Road

department: Institute of Molecular Medicine

country: China

institute: Peking University

description:
replicate2
si-Pias4_FPKM.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR v2.6.0
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks v2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample in txt file

molecule: polyA RNA

source_name: Embryonic stem cell

growth_protocol: Mouse ESCs were cultured on 0.1% gelatin-coated plates in serum medium and leukemia inhibitory factor (1,000 unit /ml).

extract_protocol:
For RNA-seq, cells were treated with TRIzol and followed with phase seperation, RNA precipitation and RNA wash. Finally, RNA were dissolved in DEPC water.
For RNA-seq, total RNA was subjected to two rounds of purification using poly-T oligo-attached magnetic beads before the synthesis of double-stranded (ds) cDNA. The ds cDNA was ligated to adaptors and sequenced with illumina Hiseq2000 platform.

tag: genotype/variation

value: Pias4 knock down

value: Mouse embryonic stem cell

tag: strain

value: 3.5 days


title: Macrophage, HFD, Ly6c- / Cd9+, rep5

status: Public on Jun 04 2018

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

description:
featureCount.ATM.Cd9_vs_Lc.txt
ATM_Cd9_r5

data_processing:
Bulk RNA-seq reads were aligned to UCSC mm9 genome using STAR aligner. Raw read counts were measured within RefSeq genes using featureCounts.
Genome_build: mm9
Supplementary_files_format_and_content: Raw tag count by featureCount

source_name: eWAT macrophage

growth_protocol: All experiments used male age-matched C57BL/6J mice housed at four or five animals per cage. High-fat diet studies were conducted by feeding mice a purified-ingredient diet composed of 60:20:20 kcal percentage of fat:carbohydrate:protein (Research Diets, D12492)

extract_protocol:
For bulk RNA-seq of sort-purified cell populations, libraries were prepared using the SMARTer Stranded RNA-seq kit (Clontech) and TruSeq RNA library prep kit (Illumina). For bulk RNA-seq of adipose tissue, total RNA was isolated from snap-frozen tissue samples. Tissues were mechanically homogenized in 500μL TRIzol (Life Technologies) in a TissueLyser (Qiagen) for 4 min, at a frequency of 22s−1. After homogenization, samples were centrifuged at 4°C and homogenates transferred to a fresh tube for RNA extraction with chloroform. Aqueous chloroform fractions were mixed with equal volumes of 70% ethanol/30% water and RNA further purified with RNeasy Mini spin columns (Qiagen) and oncolumn DNase-digestion (Qiagen). One microgram of purified DNase-treated total RNA from biological replicates was processed with a Ribo-Zero Magnetic rRNA removal kit (Epicentre, MRZH11124).
Bulk adipose RNA libraries were prepared using a TruSeq Stranded Total RNA Library Prep Gold (Illumina, 200020599) and standard Illumina protocol.

treatment_protocol: [ex-vivo macrophages] Epididymal white adipose tissue (eWAT) depots were isolated from mice. Adipose samples were placed in 1 mL of DMEM and individual depots were finely minced under sterile conditions with a razorblade prior to digestion in 5 mL DMEM with 6 mg/1 mL collagenase D (Roche) or 3 mg/1 mL collagenase IV (Gibco) at 37° C in a shaking incubator for 30 min. Cells were pelleted at 700g and adipocyte fraction removed. After resuspension of the stromal fraction in 5mL of MACS buffer (1x PBS, 2% calf serum, 25 mM HEPES, 2 mM EDTA) for cell sorting, cells were purified through a 100 μm filter (Falcon), pelleted at 700g, and re-suspended in 1 mL of RBC lysis buffer (0.15 M NH4Cl, .01 M NaHCO3, 0.0013 M EDTA) for 5 minutes at room temperature. Cells were washed again in MACS buffer prior to staining for sorting.  [BMDM] Bone marrow cells were isolated under sterile conditions and cultured in the presence of mCSF at a density of 5x106 cells/10 mL of complete media for a period of six days. On day six of culture, cells were re-plated at a density of 3x106 cells and cultured for a period of 24 hours in the presence of BSA (control), LPS (5 ng/mL), or IL-4 (10 ng/mL).  [Adoptive Transfer] 75-125K cells were sort-purified from obese, CD45.2+ donors and transferred via intraperitoneal injection three times over the course of one week into lean, CD45.1+ recipients. Recipient mice were allowed to rest 24-48 hours prior to sacrifice for subsequent eWAT RNA-seq.

tag: condition

value: High fat diet

value: Epididymal white adipose tissue (eWAT)

value: adipose tissue macrophage (ATM)

tag: cell sorting

value: Ly6c- / Cd9+


title: Macrophage, HFD, Ly6c- / Cd9+, rep2

description:
featureCount.ATM.Cd9_vs_Lc.txt
ATM_Cd9_r2


title: Macrophage, HFD, Ly6c- / Cd9+, rep1

description:
featureCount.ATM.Cd9_vs_Lc.txt
ATM_Cd9_r1


title: Macrophage, HFD, Ly6c- / Cd9+, rep3

description:
featureCount.ATM.Cd9_vs_Lc.txt
ATM_Cd9_r3


title: Ik1 wild-type 24h DOX rep2

status: Public on Feb 06 2017

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor and low-quality sequences, then mapped to hg19 reference genome using tophat2 (Kim et al., 2013 PMID: 23618408) with parameters  -p 16 --no-coverage-search, also -G parameter was used in conjunction with the Gencode annotation gtf file (gencode.v23.annotation.gtf)
Uniquely mapped reads were counted using Htseq-counts version v0.6.0 with the parameters -m union -r pos -i gene_name -a 10 --stranded=yes
Genome_build: hg19
Supplementary_files_format_and_content: matrix of normalized HTSeq-counts

organism: Homo sapiens

source_name: PDX2 Ik6 pre-B ALL + TET-Ik1

growth_protocol: Single cell suspensions were prepared from in vitro cell cultured cells.

extract_protocol:
RNA was isolated using TRI Reagent (Molecular Research Center, Inc.) followed by purification with an RNeasy kit (Qiagen), or direct isolation by RNA-isolation kit (Qiagen and Macherey-Nagel), with on-column RNase-free DNase I treatment. 1 ug of total RNA was depleted of rRNA using RiboErase (KAPA Biosystems).
RNA libraries were prepared for sequencing using the Kapa Biosystems Kapa Stranded RNA-seq library kit

treatment_protocol: Cell suspensions were either untreated or treated with doxycycline (DOX) for the indicated time, prior to sorting cells based on GFP signal

tag: cell-line

value: pre-B ALL xenograft

tag: induction time

value: 24 hour


title: Ik1 wild-type 24h DOX rep1


title: GFP control 24h DOX rep2

source_name: PDX2 Ik6 pre-B ALL + TET-empty vector

value: empty vector


title: human fetal kidney isolate GW 17 weeks 5 days negative

status: Public on Sep 16 2016

city: Los Angeles

first: Brendan

middle: H

last: Grubbs

state: CA

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

institute: University of Southern California

description:
01Sep15_hFK_topTable_DE_rpkm_annotated.xls
gencode_v22_ERCC.gtf.gz
hFK_17_5_negative

data_processing:
Data was assayed for quality using FastQC
Adapters identified as over-represented sequences in fastqc output were trimmed and data was trimmed for quality with Trimmomatic using the command 'java trimmomatic-0.32.jar SE {data_file}.fastq {data_file}_trimmed.fq ILLUMINACLIP:/opt/Trimmomatic-0.32/adapters/{fastqc determined adapters}.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36'
Trimmed data was aligned to the reference genome using the short read aligner STAR with the following command, '/STAR --runMode alignReads --runThreadN 12 --genomeDir ${MET2}/genomes/gencode_hg38_ERCC_star --genomeLoad NoSharedMemory --readFilesIn {data_file}_trimmed.fq --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outFileNamePrefix {data_file}_gencode_ERCC_star.'
Read counts were normalized using the R/Bioconductor package RUVSeq using the RUVg protocol with spike-in probes (ERCC) followed by RUVg with Empirically determined non-differentially expressed genes using EdgeR
Statistical analysis of differential gene expression was performed with the GLM procedure in the R/Bioconductor package EdgeR using RUV normalized data.
Genome_build: Gencode version 22
Supplementary_files_format_and_content: Excel Sheet of RPKM, read counts, statistics, and annotation

source_name: fetal kidney

growth_protocol: Cells were isolated by Fluorescence Activated Cell Sorting  following labeling with fluorescent RNA probes

extract_protocol:
Illumina TruSeq poly A
Illumina standard

treatment_protocol: trizol reagent

tag: time

value: Growth week 17 and 5 days

value: human fetal kidney


title: WT_input DNA

extract_protocol:
Freshly harvested duodenum was flushed with cold PBS, opened longitudinally, cut into 1 cm pieces, and then rotated in 3 mM EDTA in PBS at 4 °C. The tissue was then violently shaken to release the epithelium from underlying muscular tissue. The intestine pieces were discard and the supernatant was collected as whole epithelium fraction. Standard procedures were used for ChIP on mouse duodenum epithelial cells. Briefly, cells were isolated by 3mM EDTA/PBS and then cross-linked in 1% formaldehyde for 10 min at 4°C and then for 35 or 50 min at room temperature. Cells were washed with ice-cold PBS, resuspended with lysis buffer (1% SDS, 10 mM EDTA pH 8.0, 50 mM Tris pH 8.0, and protease inhibitor cocktails) and further incubated at room temperature for 10 min. Cell lysates were sonicated using a Diagenode Bioruptor to generate 200 bp to 500 bp fragments, as determined by agarose gel electrophoresis. The DNA was recovered by incubating overnight in reverse cross-linking buffer (1% SDS, 0.1 M NaHCO3) at 65 °C. The DNA was purified by QIAquick PCR Purification Kit (QIAGEN) and quantified by using Picogreen (Life Technologies).
Rubicon Genomics ThruPLEX DNA-seq Kit (Illumina)

value: duodenum epithelium


title: human fetal kidney isolate GW 17 weeks 5 days positive

description:
01Sep15_hFK_topTable_DE_rpkm_annotated.xls
gencode_v22_ERCC.gtf.gz
hFK_17_5_positive


title: GFP control 24h DOX rep1


title: si-NC_rep2

description:
replicate2
si-Pias4_FPKM.txt

value: control


title: 14H023

status: Public on Jul 09 2015

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

description: Sample 260

data_processing:
Basecalls performed using CASAVA 1.8.2
Sequenced reads were masked for sequencing adapters and mapped to the reference genome using CASAVA 1.8.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CASAVA 1.8.2
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. Columns are: Chromosome, Start location, Stop location, Gene, RPKM, base count.

source_name: acute myeloid leukemia

extract_protocol:
TriZol + RNeasy mini Kit (Qiagen, #74106)
TruSeq RNA Stranded Sample Preparation (Illumina)

value: Blood

value: acute myeloid leukemia (AML) cells


title: human fetal kidney isolate GW 17 weeks 2 days negative

description:
01Sep15_hFK_topTable_DE_rpkm_annotated.xls
gencode_v22_ERCC.gtf.gz
hFK_17_2

value: Growth week 17 and 2 days


title: human fetal kidney isolate GW 17 negative (single)

description:
01Sep15_hFK_topTable_DE_rpkm_annotated.xls
gencode_v22_ERCC.gtf.gz
hFK_17_0_negative

value: Growth week 17 and 0 days


title: human fetal kidney isolate GW 17 negative (paired-end)


title: human fetal kidney isolate GW 17 weeks 2 days positive

description:
01Sep15_hFK_topTable_DE_rpkm_annotated.xls
gencode_v22_ERCC.gtf.gz
hFK_17_2_positive


title: human fetal kidney isolate GW 17 positive (paired-end)

description:
01Sep15_hFK_topTable_DE_rpkm_annotated.xls
gencode_v22_ERCC.gtf.gz
hFK_17_0_positive


title: 14H020

description: Sample 259

value: Bone marrow


title: MPP1_R1

status: Public on Aug 25 2014

city: Heidelberg

first: Christoph

last: Plass

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center

description: bisulfite converted genomic DNA

data_processing:
Basecalling was performed using Ilumina Real-Time Analysis (RTA) Software 1.13.48.
Sequencing reads were trimmed for adapter sequence (SeqPrep v0.4 ) and then mapped with BWA (bwa-0.6.1-tpx) with default parameters except the quality threshold for read trimming ( -q) of 20 and the Smith-Waterman for the unmapped mate disabled (-s).
Duplicate reads were removed using Picard (version 1.61) and reads with alignment scores less than 1 were filtered before subsequent analysis.
At each cytosine position, reads that maintain the cytosine status were considered methylated, and the reads that have cytosine converted to thymine were considered unmethylated.
Only bases with Phred-scaled quality score of ≥20 were considered. The first 9 bp of the second read and last 9 bp before the adapter in the first read were excluded from methylation calling.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include CpG coordinates, the numbers of methylated cytosines and the coverage at the CpG postion, as well as smoothed methylation level estimates using bsseq (version 0.8.0; default parameters)

source_name: primary murine hematopoietic multipotent progenitor cells

extract_protocol:
Genomic DNA was isolated using the QIAamp DNA Micro Kit (Qiagen, Germany) and polyacryl precipitation carrier (Molecular Research Center Inc., Cincinnati, OH, USA).
Tagmentation-based whole-genome bisulfite sequencing (TWGBS) was performed as recently published (Wang et al., Nat. Prot., 2013). We used 8-30 ng genomic mouse DNA as input.


title: MPP1_R2

description: bisulfite converted genomic DNA


title: HSC_R3

description: bisulfite converted genomic DNA

source_name: primary murine hematopoietic stem cells


title: Macrophage, HFD, Ly6c- / Cd9+, rep4

description:
featureCount.ATM.Cd9_vs_Lc.txt
ATM_Cd9_r4


title: MPP2_R1

description: bisulfite converted genomic DNA


title: MPP2_R2

description: bisulfite converted genomic DNA


title: MPP1_R3

description: bisulfite converted genomic DNA


title: MPP2_R3

description: bisulfite converted genomic DNA


title: HSC_R2

description: bisulfite converted genomic DNA


title: HSC_R1

description: bisulfite converted genomic DNA


title: human fetal kidney isolate GW 17 positive (single)