title: NSC input spike-in

first: zhiguo

last: zhang

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

description: spike-in Drosophila reference chromatin

data_processing:
For the spike-in H3K27me3 ChIP-seq, the sequencing reads were aligned to a combined hg19/dm6 or h19/sf9 genome and reads were separated into each organism post-alignment. For other normal ChIP-seq, paired-end reads were aligned to the human genome (hg19) using the Bowtie2 software. For the further analysis, the consistent pair reads were used.
The genome-wide read coverage was calculated by BEDTools and in-house Perl programs.
ChIP-seq peaks were identified by MACS2 with the parameter of broad peak calling and the p value cutoff is set to 1 x 10-5.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated, scores represent the normalization reads density.

source_name: whole cell

growth_protocol: SF7761 and SF8628 cell lines from patients harboring the histone H3.3 K27M mutation were obtained from Hashizume et al. (2012). NSCs (N7800-100) were purchased from Invitrogen and cultured and maintained in NSC medium (A10509-01, StemPro NSC SFM, Invitrogen).

extract_protocol:
Frozen tissues were cut, divided into 50 mg aliquots, and stored in tubes at -80°C. The frozen tissues were homogenized on ice for 15–30 seconds in 500 μL 1X PBS using a tissue grinder (ACTGene). Tissue homogenates or cultured cells were cross-linked with 1% formaldehyde (final concentration) for 10 min and quenched with 125 mM glycine for 5 min at room temperature and washed once with TBS. The pellets were resuspended in cell lysis buffer (10 mM Tris-HCl, pH7.5, 10 mM NaCl, 0.5% NP-40) and incubated on ice for 10 min. Lysates were divided into two aliquots and washed with MNase digestion buffer (20 mM Tris-HCl, pH7.5, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2). After re-suspending in 500 μL MNase digestion buffer containing a proteinase inhibitor cocktail (Sigma), the lysates were incubated in the presence of 1,000 units of MNase (NEB, Ipswich, MA, Cat.# M0247S) at 37 °C for 20 min with continuous mixing in thermal mixer (Fisher Scientific, Pittsburgh, PA). After adding the same volume of sonication buffer (100 mM Tris-HCl, pH8.1, 20 mM EDTA, 200 mM NaCl, 2% Triton X-100, 0.2% sodium deoxycholate), the lysates were sonicated for 15 min (30 secs on / 30 secs off) using Bioruptor Twin (UCD-400) (Diagenode) and centrifuged at 21,130 x g for 10 min. The supernants were collected and the chromatin content was estimated by the Qubit assay (Invitrogen). For the normalization of ChIP efficiency, S2 or Sf9 chromatin was added. The chromatin was then incubated with 5 µg of rabbit monoclonal anti-Ezh2 antibody (Cell Signaling, Cat.# 5246), 5 µg of rabbit monoclonal anti-H3K27me3 antibody (Cell Signaling, Cat.# 9733), 2 µg of rabbit polyclonal anti-H3K27M antibody (Millipore, Cat.# abe419), or 5 µg of mouse monoclonal anti-Jarid2 antibody (Novus, Cat.# NB100-2214) on a rocker overnight. Protein G-magnetic beads (30 μl, Life Technologies) were added for 3 hours incubation. The beads were extensively washed with ChIP buffer (50 mM Tris-HCl, pH8.1, 10 mM EDTA, 100 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), high salt buffer (50 mM Tris-HCl, pH8.1, 10 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), LiCl buffer (10 mM Tris-HCl, pH8.0, 0.25 M LiCl2, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA), and TE buffer. Bound chromatin was eluted and reverse-crosslinked at 65°C overnight. DNAs were purified using Min-Elute PCR purification kit (Qiagen) after the treatment of RNase A and proteinase K.
ChIP-seq libraries were prepared from 10 ng ChIP and input DNA using the Ovation ultralow DR Multiplex kit (NuGEN). The ChIP-seq libraries were sequenced to 51 base pairs from both ends on an Illumina HiSeq 2000 instrument in the Mayo Clinic Center for Individualized Medicine Medical Genomics Facility.

tag: media

value: DMEM

tag: cell cycle stage

value: asynchronization

tag: chip antibody


title: 20dpc_C4

status: Public on Jul 03 2018

type: SRA

city: Delhi

first: Beena

last: Pillai

address: Mathura Road

country: India

institute: IGIB

library_source: transcriptomic

data_processing:
The quality of RNA sequencing reads were checked using FastQC followed by adapter trimming by Trimmomatic (default parameters) .
The data was then de novo assembled using Trinity package (Grabherr et al., 2011). to align reads to the reference. To get a common reference, all the samples were assembled together in a single assembly using Trinity.
The assemblies were annotated using Trinotate pipeline (https://trinotate.github.io/).
Denovo RNA seq differential expression analysis was done using reference made by Trinity and Tuxedo pipeline.
Genome_build: To get a common reference, all the samples were assembled together in a single assembly using Trinity and annotated by Trinotate.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Eisenia fetida

source_name: Three segments anterior to the cut, 20days after cutting

growth_protocol: Eisenia fetida earthworms were procured from farmers engaged in vermicomposting and then maintained in a culture in the laboratory at around 22oC with moderate humidity.

extract_protocol:
The regenerated tissue and the tissue adjacent to it, termed control, were collected separately. RNA was isolated using the Trizol method. Briefly, the tissues were frozen in liquid nitrogen, homogenized using a mortar and pestle in the presence of 1ml Trizol reagent and transferred to a microfuge tube. Phase separation was done by adding 200uL chloroform and centrifugation at 10,000g. The aqueous phase was collected and equal volume of isopropanol was added to precipitate RNA. Pellet was collected by centrifugation at 10,000g, followed by repeated 70% ethanol washes. The RNA was then air dried and dissolved in nuclease-free water
Approximately, 1ug of RNA was taken per sample and RNA sequencing libraries were made using TruSeq v2 Library Prep Kit as per manufacturer's protocol. Briefly, the RNA was polyA selected using OligodT magnetic beads followed by shearing into 200-500bp fragments. This sheared RNA was then used to generate cDNA. The cDNA was end-repaired to blunt ends . These blunt ends were then A-tailed i.e. a "A" overhang was added so as to ligate the adapters in the next step. The adapter ligated cDNA was then amplified by PCR and purified by AMPure XP beads. This library was then quality checked and sequenced on Illumina HiSeq 2500. For small RNA sequencing, total RNA was isolated from bodywall and sequenced on the illumina platform. ~800ng of Total RNA was used as the starting material. Briefly, 3’ adaptors were ligated to the   specific 3’OH group of microRNAs followed by 5’ adaptor ligation. The ligated products were  reverse transcribed with Superscript III Reverse transcriptase by priming with Reverse   transcriptase primers. The cDNA was enriched and barcoded by PCR (15 cycles) and   cleaned using Polyacrylamide gel. The library was size selected in the range of 140 – 160 bp   followed by overnight gel elution and salt precipitation using Glycogen, 3M Sodium Acetate and absolute ethanol. The precipitate was re-suspended in Nuclease free water. The prepared library was quantified using Qubit Fluorometer, and validated for quality on High Sensitivity Bioanalyzer Chip (Agilent).

treatment_protocol: Earthworms were cut transversely at approximately two thirds of the body length (60 +/- 6 segments) and allowed to regenerate for 15, 20 or 30 days . At 15, 20 and 30 days post cut (dpc), the regenerated tissue (15R,20R and 30R) and the adjacent tissue (15C, 20C and 30C) were collected.  Samples from non-regenerating worms were collected from the 60th+3segments (control) on day0. One set of samples (sample 22-24) are segments 60-posterior end collected on day0.

tag: number of worms

value: pooled from 50 worms

tag: type of tissue

value: Tissue adjacent to Regenerated tissue 20days post cut


title: NSC H3K27me3 ChIP-seq spike-in

status: Public on Jul 02 2018

city: New York

state: NY

country: USA

institute: Columbia University

description: spike-in Drosophila reference chromatin

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

value: Cell Signaling, Cat.# 9733

value: NSC


title: SF8628 H3K27me3 spike-in

description: spike-in Drosophila reference chromatin


title: SF8628 input spike-in

description: spike-in Drosophila reference chromatin


title: Pontine K27me3 spike-in

description: spike-in SF9 cells reference chromatin

source_name: tissue

value: frozen tissue

value: Pontine


title: H3.3K27M#1 H3K27Me3 ChIP-seq repeat 2

description:
k128
spike-in Drosophila reference chromatin

data_processing:
For the spike-in ChIP-seq, the sequencing reads were aligned to a combined mm9/dm6 genome and reads were separated into each organism post-alignment. For the further analysis, the consistent pair reads were used.
The genome-wide read coverage was calculated by BEDTools and in-house Perl programs.
ChIP-seq peaks were identified by MACS2 with the parameter of broad peak calling and the p value cutoff is set to 1 x 10-5.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigwig files were generated, scores represent the normalization reads density.

organism: Mus musculus

growth_protocol: mESC were cultured in DMEM with Lif added.

extract_protocol:
Cultured cells were cross-linked with 1% formaldehyde (final concentration) for 10 min and quenched with 125 mM glycine for 5 min at room temperature and washed once with TBS. The pellets were resuspended in cell lysis buffer (10 mM Tris-HCl, pH7.5, 10 mM NaCl, 0.5% NP-40) and incubated on ice for 10 min. Lysates were divided into two aliquots and washed with MNase digestion buffer (20 mM Tris-HCl, pH7.5, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2). After re-suspending in 500 μL MNase digestion buffer containing a proteinase inhibitor cocktail (Sigma), the lysates were incubated in the presence of 1,000 units of MNase (NEB, Ipswich, MA, Cat.# M0247S) at 37 °C for 20 min with continuous mixing in thermal mixer (Fisher Scientific, Pittsburgh, PA). After adding the same volume of sonication buffer (100 mM Tris-HCl, pH8.1, 20 mM EDTA, 200 mM NaCl, 2% Triton X-100, 0.2% sodium deoxycholate), the lysates were sonicated for 15 min (30 secs on / 30 secs off) using Bioruptor Twin (UCD-400) (Diagenode) and centrifuged at 21,130 x g for 10 min. The supernants were collected and the chromatin content was estimated by the Qubit assay (Invitrogen). For the normalization of ChIP efficiency, S2 or Sf9 chromatin was added. The chromatin was then incubated with 5 µg of rabbit monoclonal anti-Ezh2 antibody (Cell Signaling, Cat.# 5246), 5 µg of rabbit monoclonal anti-H3K27me3 antibody (Cell Signaling, Cat.# 9733), 2 µg of rabbit polyclonal anti-H3K27M antibody (Millipore, Cat.# abe419), or 5 µg of mouse monoclonal anti-Jarid2 antibody (Novus, Cat.# NB100-2214) on a rocker overnight. Protein G-magnetic beads (30 μl, Life Technologies) were added for 3 hours incubation. The beads were extensively washed with ChIP buffer (50 mM Tris-HCl, pH8.1, 10 mM EDTA, 100 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), high salt buffer (50 mM Tris-HCl, pH8.1, 10 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), LiCl buffer (10 mM Tris-HCl, pH8.0, 0.25 M LiCl2, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA), and TE buffer. Bound chromatin was eluted and reverse-crosslinked at 65°C overnight. DNAs were purified using Min-Elute PCR purification kit (Qiagen) after the treatment of RNase A and proteinase K.
ChIP-seq libraries were prepared from 10 ng ChIP and input DNA using the Ovation ultralow DR Multiplex kit (NuGEN). The ChIP-seq libraries were sequenced to 76 base pairs from single end on an Illumina HiSeq 2000 instrument in the Mayo Clinic Center for Individualized Medicine Medical Genomics Facility.

tag: strain/background

value: H3.3K27M mES


title: SF7761 input spike-in

description: spike-in Drosophila reference chromatin


title: H3.3K27M#2 ESC input repeat 2

description:
k135
spike-in Drosophila reference chromatin


title: H3.3K27M#1 Ezh2 ChIP-seq repeat 2

description:
k126
spike-in Drosophila reference chromatin

value: Cell Signaling, Cat.# 5246


title: H3.3K27M#2 H3.H3K27M ChIP-seq repeat 2

description:
k129
spike-in Drosophila reference chromatin

value: Millipore, Cat.# abe419


title: Pontine input spike-in

description: spike-in SF9 cells reference chromatin


title: H3.3K27M#1 H3.H3K27M ChIP-seq repeat 2

description:
k125
spike-in Drosophila reference chromatin


title: H3.3K27M#2 Ezh2 ChIP-seq repeat 2

description:
k130
spike-in Drosophila reference chromatin


title: 0dpc_3

source_name: Three segments around the 60th segment (from anterior)

value: Tissue collected immediately after cutting for regeneration experiment.


title: H3.3K27M#2 H3K27Me3 ChIP-seq repeat 2

description:
k132
spike-in Drosophila reference chromatin


title: H3.3K27M#1 ESC input repeat 2

description:
k134
spike-in Drosophila reference chromatin


title: Gliosis K27me3 spike-in

description: spike-in SF9 cells reference chromatin

value: Gliosis


title: Gliosis input spike-in

description: spike-in SF9 cells reference chromatin


title: WT ESC H3.H3K27M ChIP-seq repeat 2

description:
k121
spike-in Drosophila reference chromatin


title: WT ESC Ezh2 ChIP-seq repeat 2

description:
k122
spike-in Drosophila reference chromatin


title: SF8628 EZH2 ChIP-seq repeat 2


title: NSC H3.3K27M ChIP-seq


title: SF8628 H3.3K27M ChIP-seq repeat 2


title: SF8628 EZH2 ChIP-seq repeat 1


title: SF7761 H3K27me3 spike-in

description: spike-in Drosophila reference chromatin


title: H3.3K27M#2 H3K27Me3 ChIP-seq repeat 1

description:
k120
spike-in Drosophila reference chromatin


title: H3.3K27M#2 H3.H3K27M ChIP-seq repeat 1

description:
k119
spike-in Drosophila reference chromatin


title: H3.3K27M#2 ESC input repeat 1

description:
k116
spike-in Drosophila reference chromatin


title: WT ESC input repeat 2

description:
k133
spike-in Drosophila reference chromatin


title: SF7761 H3.3K27M ChIP-seq repeat 2


title: SF7761 H3.3K27M ChIP-seq repeat 1


title: H3.3K27M#2 Ezh2 ChIP-seq repeat 1

description:
k117
spike-in Drosophila reference chromatin


title: H3.3K27M#1 H3.H3K27M ChIP-seq repeat 1

description:
k114
spike-in Drosophila reference chromatin


title: H3.3K27M#1 H3K27Me3 ChIP-seq repeat 1

description:
k115
spike-in Drosophila reference chromatin


title: H3.3K27M#1 Ezh2 ChIP-seq repeat 1

description:
k112
spike-in Drosophila reference chromatin


title: SF8628 H3.3K27M ChIP-seq repeat 1


title: WT ESC H3K27Me3 ChIP-seq repeat 1

description:
k110
spike-in Drosophila reference chromatin

value: mES


title: WT ESC Ezh2 ChIP-seq repeat 1

description:
k107
spike-in Drosophila reference chromatin


title: SF8628 input


title: SF7761 input


title: atra-rarb

city: Buffalo

first: AC

last: CHANG

address: Elm and Carlton

institute: RPCI

data_processing:
Sequencing was carried out by running 100 cycles on Illumina HiSeq 2000 according to the manufacturer’s instructions. Image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8). Aligned reads were used for peak calling of the ChIP regions using MACS V1.4.0.
Statistically significant ChIP-enriched regions (peaks) were identified by comparison to a Poisson background model, using a p-value threshold of 10-4. The peaks in samples were annotated by the nearest gene using the newest UCSC RefSeq database.
Genome_build: hg19
Supplementary_files_format_and_content: text

source_name: human mammary epithelial cells

growth_protocol: Human mammary epithelial cells MCF12A were purchased from ATCC and cultured in DMEM-F12 Cell Growth Medium with horse serum.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cells were treated with ATRA or vehicle DMSO for 24 hrs

tag: cell line

tag: antibody

value: RARb

tag: treatment

value: ATRA


title: mock-5hmc

value: DMSO


title: atra-5hmc


title: WT ESC H3.H3K27M ChIP-seq repeat 1

description:
k109
spike-in Drosophila reference chromatin

value: DMEM


title: mock-rarb


title: H3.3K27M#1 ESC input repeat 1

description:
k111
spike-in Drosophila reference chromatin

value: asynchronization


title: WT ESC H3K27Me3 ChIP-seq repeat 2

description:
k124
spike-in Drosophila reference chromatin


title: WT ESC input repeat 1

description:
k106
spike-in Drosophila reference chromatin


title: atra-tet2


title: mock-tet2


title: 2012-07-26_256Cell

city: Cambridge

first: Guo-Liang

last: Chew

state: MA

address: 16 Divinity Ave BL 1019

department: Dept of Molecular and Cellular Biology

institute: Harvard University

data_processing:
Aligned using Tophat2, with supplied transcript junctions from Ensembl 72
Timecourse quantified with Cufflinks on Ensembl 72 transcripts
Genome_build: danRer7/Zv9
Supplementary_files_format_and_content: genes.fpkm_tracking from cufflinks for gene expression quantification at loci level (FPKM)

molecule: polyA RNA

organism: Danio rerio

source_name: Whole embryos

growth_protocol: ~100 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995

extract_protocol:
Total RNA was isolated using the standard TRIzol (Invitrogen) protocol. Genomic DNA was removed by DNase treatment. Two rounds of PolyA+-RNA purification were performed for each sample.
Strand-specific libraries for 76-bp paired-end sequencing were prepared according to a modified UTP-method (Parkhomchuk et al. 2009), as detailed by Levin et al. (2010).
Libraries were sequenced on the Illumina HiSeq 2000

treatment_protocol: Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen

tag: developmental stage

value: 256 cells

tag: strain

value: TL/AB


title: 2012-07-26_Dome

description: Strand-specific libraries for 76-bp paired-end sequencing

value: Dome


title: 2012-07-26_5dpf

value: 5 days post fertilization


title: 2012-07-26_Shield

value: Shield


title: 2012-07-26_28hpf

value: 28 hours post fertilization


title: 2012-07-26_Bud

value: Bud


title: ORG_HFmedium_DF_1

city: Utrecht

first: Onur

last: BASAK

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: cells from cultured organoids

data_processing:
Paired end reads were aligned to the transcribed regions on the canis lupus (dog) genome using bwa. Since no reliable fully annotated transcriptome of dog was available, ncbi gff annotation (version 103) was used to build the transcriptome file using the CanFam3.1 genome build as a reference. Paired end reads obtained by CEL-seq2 were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were also included and distributed to the matching target loci. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the total number of reads for every transcript.
Genome_build: CanFam3.1
Supplementary_files_format_and_content: *.csv: Comma separated data file listing all genes (rows) and the number of sequenced transcripts for all samples. Column names indicate the GeneID and primer number of the sample. The first column lists the official gene symbol.

organism: Canis lupus familiaris

source_name: RNA from bulk cells of organoids, from hair follicles, mid-term in culture, 7 days after culture, differentiation medium, replicate 1

extract_protocol:
Cells were sorted into Trizol (Life Technologies) and total RNA was isolated according to the manufacturer’s instructions, with the following alterations. RNA was precipitated overnight at -20 °C, with 2.5ug GlycoBlue (Life Technologies).
RNA was processed using the previously described CEL-seq2 technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

tag: cell type

tag: protocol

tag: passages


title: ORG_noNR_HFmedium_DF_1

description: cells from cultured organoids

source_name: RNA from bulk cells of organoids, from hair follicles, mid-term in culture, 7 days after culture, without Noggin and R-Spondin-1, differentiation medium, replicate 1


title: ORG_noNR_minusF_HFmedium_DF_1

description: cells from cultured organoids

source_name: RNA from bulk cells of organoids, from hair follicles, mid-term in culture, 7 days after culture, without Noggin, R-Spondin-1 and Forskolin, differentiation medium, replicate 1


title: ORG_EFA83_HFmedium_2

description: cells from cultured organoids

source_name: RNA from bulk cells of organoids, from hair follicles, mid-term in culture, 7 days after culture, with Tgf-beta inhibitor, replicate 2


title: ORG_noNR_HFmedium_DF_2

description: cells from cultured organoids

source_name: RNA from bulk cells of organoids, from hair follicles, mid-term in culture, 7 days after culture, without Noggin and R-Spondin-1, differentiation medium, replicate 2


title: 2012-07-26_2-4Cell

value: 2-4 cells


title: ORG_HFmedium_DF_2

description: cells from cultured organoids

source_name: RNA from bulk cells of organoids, from hair follicles, mid-term in culture, 7 days after culture, differentiation medium, replicate 2


title: ORG_HFmedium_2

description: cells from cultured organoids

source_name: RNA from bulk cells of organoids, from hair follicles, mid-term in culture, 7 days after culture, replicate 2


title: Testis4-RNAseq

city: Barcelona

first: Dafni

last: Anastasiadi

address: Pg. Marítim de la Barceloneta 37-49

department: Renewable Marine Resources

country: Spain

institute: Institute of Marine Sciences-CSIC

description:
FoldChange.csv
Testis-GeneExpression.csv

data_processing:
RRBS raw reads were quality trimmed by the Timmomatic v. 0.32 with the following parameters SLIDINGWINDOW:4:15 MAXINFO:20:0.50 MINLEN:18
Trimmed reads were aligned to the reference genome dicLab v1.0c using BSMAP v. 2.90 in RRBS mode with the following parameters -D C-CGG -w 100 -v 0.08 -r 1 -p 4 -n 0 -s 12 -S 0 -f 5 -q 0 -u -V 2
Methylation calling was performed by the methratio.py python script that accompanies BSMAP.
Supplementary_files_format_and_content: Output of methratio.py was converted using awk to methylkit input. Tab-delimited files contain the coverage and the frequency of Cs (methylated cytosines) and of Ts (unmethylated cytosines) per CpG (chromosome, base, strand) covered
RNA-seq reads were aligned with the GEMtools RNAseq pipeline v1.7 which is based on the GEM mapper. The pipeline aligns the reads in a sample in three phases, mapping against the reference genome (dicLab v1.0c), against a reference transcriptome (COMBINED ANNOTATION track) and against a de novo transcriptome, generated from the input data to detect new junction sites. After mapping, all alignments were filtered to increase the number of uniquely mapped reads. The filtering criteria included a minimum intron length of 20 bp, a maximum exon overlap of 5 bp and a filter step against a reference annotation.
The TMM method was used for gene expression normalization and the EdgeR method was used for differential expression analysis.
The link of the published genome to verify:    http://seabass.mpipz.mpg.de/ and the information of the publication:    Tine M et al. Nat. Commun. 2014;5:5770.
The annotation used for the RNA-seq data is based on the "NEW_COMBINED_ANNOTATION" of the sea bass genome browser that can be found in the server: http://seabass.mpipz.mpg.de/DOWNLOADS/
Supplementary_files_format_and_content: For each tissue, one comma-separated file is provided with the copy million number per transcript ID as annotated in the COMBINED ANNOTATION track of the genome
Supplementary_files_format_and_content: Comma-separated file with differential gene expression data containing log2FoldChange values and statistics including p-adjusted values
Supplementary_files_format_and_content: dicLab v1.0c (June 2012)
Supplementary_files_format_and_content: Muscle-GeneExpression.csv: counts per milion
Supplementary_files_format_and_content: Testis-GeneExpression.csv: counts per milion
Supplementary_files_format_and_content: FoldChange.csv: differential expression

organism: Dicentrarchus labrax

source_name: D. labrax testis

growth_protocol: Tissues dissected on boat from wild fish caught in the sea by speargun

extract_protocol:
Trizol RNA extraction
mRNA-Seq sample preparation kit (Illumina Inc., Cat. # RS-122-2001x2)

treatment_protocol: Samples stored in RNAlater immediately after dissection and kept at -80 until DNA/RNA extraction

tag: tissue

value: testis


title: ORG_HFmedium_1

description: cells from cultured organoids

source_name: RNA from bulk cells of organoids, from hair follicles, mid-term in culture, 7 days after culture, replicate 1


title: Testis3-RNAseq


title: ORG_noNR_minusF_HFmedium_DF_2

description: cells from cultured organoids

source_name: RNA from bulk cells of organoids, from hair follicles, mid-term in culture, 7 days after culture, without Noggin, R-Spondin-1 and Forskolin, differentiation medium, replicate 2


title: Testis2-RNAseq


title: ORG_HFearly_2

description: cells from cultured organoids

source_name: RNA from bulk cells of organoids, from hair follicles, early in culture, 7 days after culture, replicate 2

value: early in culture, 7 days after culture


title: ORG_HFearly_1

description: cells from cultured organoids

source_name: RNA from bulk cells of organoids, from hair follicles, early in culture, 7 days after culture, replicate 1


title: ORG_EFA83_HFmedium_1

description: cells from cultured organoids

source_name: RNA from bulk cells of organoids, from hair follicles, mid-term in culture, 7 days after culture, with Tgf-beta inhibitor, replicate 1


title: ORG_EFA83_IFEmedium_1

description: cells from cultured organoids

source_name: RNA from bulk cells of organoids, from  interfollicular epidermis, mid-term in culture, 7 days after culture, with Tgf-beta inhibitor, replicate 1


title: Testis1-RNAseq


title: 2012-07-26_1KCell

value: 1k cells


title: Muscle4-RNAseq

description:
FoldChange.csv
Muscle-GeneExpression.csv

source_name: D. labrax muscle

value: muscle


title: Muscle5-RNAseq


title: ORG_EFA83_HFearly_3

description: cells from cultured organoids

source_name: RNA from bulk cells of organoids, from hair follicles, early in culture, 7 days after culture, with Tgf-beta inhibitor, replicate 3


title: ORG_EFA83_HFearly_1

description: cells from cultured organoids

source_name: RNA from bulk cells of organoids, from hair follicles, early in culture, 7 days after culture, with Tgf-beta inhibitor, replicate 1


title: ORG_EFA83_IFEearly_1

description: cells from cultured organoids

source_name: RNA from bulk cells of organoids, from interfollicular epidermis, early in culture, 7 days after culture, with Tgf-beta inhibitor, replicate 1


title: IFE_2

description: tissue

source_name: RNA from the interfollicular epidermis, replicate 2

value: interfollicular epidermis


title: Muscle2-RNAseq


title: Testis3-RRBS

extract_protocol:
Phenol-Chlorofrom DNA extraction
Custom RRBS library preparation with 100 ng of DNA, as in Klughammer et al., Cell 2015


title: Muscle3-RNAseq


title: IFE_1

description: tissue

source_name: RNA from the interfollicular epidermis, replicate 1


title: whole_skin_2

description: tissue

source_name: RNA from the whole skin, replicate 2

value: whole skin


title: whole_skin_1

description: tissue

source_name: RNA from the whole skin, replicate 1


title: HF_1

description: tissue

source_name: RNA from a mixture of anagen and telogen phase hair follicles, replicate 1


title: Testis2-RRBS


title: Testis5-RNAseq


title: Muscle2-RRBS


title: Muscle1-RRBS


title: 24hpf Hi-C (Nextseq 500)

status: Public on Jul 01 2018

first: Robin H.

last: van der Weide

state: Utrecht

description: TruSeq libraries prepared from 3C template

data_processing:
Raw sequence data was mapped and processed using HiC-Pro v2.9 (Servant et al., 2015).
Genome_build: danRer10
Supplementary_files_format_and_content: Hi-C summary files contain the genomic position and strand of the two pairs of a Hi-C ligation

source_name: Zebrafish 24hpf

extract_protocol:
Carefully staged embryo’s were dechorionated, deyolked and made single cell in three consecutive steps. First embryos were dounched and spun down at 500 rcf at 4 degrees. The precipitant was thereafter incubated in 2 ml of TRIPLE (life, Cat# 12605-010) for 5 min at RT after which 10% end concentration FBS was added. This solution was filtered using a 100uM cell strainer (Sigma, Cat# CLS431752-50EA and cells was spun down at 500 rcf at 4 degrees to collect the single cells.
These cells were subsequently processed following the standard 4C protocol using DPNII as the restriction enzyme (and CSP6I as the second restion enzyme in the case of 4C-Seq). Successful digestion and ligation was confirmed using the agilent TAPEStation.We omitted the usual biotin incorporation and enrichment step due to the low amounts of DNA obtained from the early developmental stages. Instead we generated paired-end deep-sequencing libraries suitable for illumina sequencing after shearing the 3C template to 500-900bp and computationally filtered for ligation events.

value: embryo


title: 8hpf Hi-C (Nextseq 500)

source_name: Zebrafish 8hpf

value: 80% epiboly


title: Testis1-RRBS

source_name: D. labrax testis


title: LMP_Replicate2

city: Austin

first: Joseph

middle: D

last: Dekker

state: TX

address: 2506 Speedway Blvd, NMS 1.264

department: Molecular Biosciences

institute: University of Texas at Austin

description: Gene expression data in LMP cells

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 whole genome using tophat.
For RNA-seq, *.fpkm_tracking files from Cufflinks containing FPKM values are provided.
We used three different sample data to normalize to control sample.
For LLP1.fpkm_tracking, LLP1 is normalized to LMP1/2/3:
q1 is from LLP1 normalized to LMP1
q2 is from LLP1 normalized to LMP2
q3 is from LLP1 normalized to LMP3
q4 is from LLP1 normalized internally
For LLP2.fpkm_tracking, LLP2 is normalized to LMP1/2/3.
For LLP3.fpkm_tracking, LLP3 is normalized to LMP1/2/3.
Genome_build: mm9
Supplementary_files_format_and_content: *.fpkm_tracking files from Cufflinks containing FPKM values

source_name: Mouse CMP derived plasmacytoid dendritic cells

growth_protocol: Cells were freshly isolated and sorted from mouse bone marrow before placed in Trizol for total RNA extraction

extract_protocol:
For RNA-seq, total RNAs were extracted using Rneasy plus mini kit (Qiagen).
RNA-sequencing libraries were generated using library prep kits (NEB) according to the manufacturer’s instructions.

value: Myeloid derived plasmacytoid dendritic cells


title: LMP_Replicate1

description: Gene expression data in LMP cells


title: 2.3hpf Hi-C (Nextseq 500)

source_name: Zebrafish 2.3hpf


title: 4hpf Hi-C (Nextseq 500)

source_name: Zebrafish 4hpf


title: LLP_Replicate3

description: Gene expression data in LLP cells

source_name: Mouse CLP derived plasmacytoid dendritic cells

value: Lymphoid derived plasmacytoid dendritic cells


title: LMP_Replicate3

description: Gene expression data in LMP cells


title: ORG_EFA83_HFearly_2

description: cells from cultured organoids

source_name: RNA from bulk cells of organoids, from hair follicles, early in culture, 7 days after culture, with Tgf-beta inhibitor, replicate 2


title: LLP_Replicate2

description: Gene expression data in LLP cells


title: shRNA_KYSE70

city: Beijing

first: Yuan

last: Li

address: Panjiayuannanli No.17

country: China

institute: National cancer center/cancer hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human genome (hg19) using TopHat v2.0.9.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene.And then Reads Per Kilobase of exon model per Million mapped reads,(RPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: esophageal squamous cell carcinoma cells_NMR_knockdown_KYSE70

growth_protocol: Human ESCC cell lines KYSE70 and KYSE450 were cultured at 37 ℃ in an atmosphere of 5% CO2 in RMPI 1640 (Hyclone) supplemented with 10% FBS (Gibco), penicillin, and streptomycin (Thermo Fisher).

extract_protocol: Total RNA from each sample was extracted with Trizol (Thermo Fisher), quality control for total RNA was assessed using NanoPhotometer® spectrophotometer, Qubit® 2.0 Fluorometer, and Agilent 2100 bioanalyzer. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For knockdown of NMR, the recombined plasmid and the packing plasmid mixture (Invitrogen) were co-transfected into HEK 293T cells using Lipofectamine 3000 (Invitrogen). The supernatant containing lentivirus was collected and used to infect ESCC cell lines; For overexpression of NMR, plasmid vectors PCDNA3.1 were transfected into ESCC cancer cells using Lipofectamine 3000 (Invitrogen) according to the manufacturer’s instructions.

value: esophagus


title: Muscle1-RNAseq

source_name: D. labrax muscle


title: shcon_KYSE450

source_name: esophageal squamous cell carcinoma cells_knockdown_control_KYSE450


title: HF_2

description: tissue

source_name: RNA from a mixture of anagen and telogen phase hair follicles, replicate 2


title: Muscle3-RRBS


title: NMR_KYSE450

source_name: esophageal squamous cell carcinoma cells_NMR_overexpression_KYSE450


title: shRNA_KYSE450

source_name: esophageal squamous cell carcinoma cells_NMR_knockdown_KYSE450


title: LLP_Replicate1

description: Gene expression data in LLP cells


title: shcon_KYSE70

source_name: esophageal squamous cell carcinoma cells_knockdown_control_KYSE70


title: BM1108_mouse_10_allograft_untreated

first: Tamas

last: Gonda

address: 630 West 168th Street

department: Department of Medicine, Division of Digestive and Liver Diseases

description: 1 month allograft tumors  from untreated cultured KPC tumor cells , paradigm II

data_processing:
Base calling using (RTA, Illumina, San Diego, CA, USA)
conversion of BCL to FASTQ format (bcl2fastq version 1.8.4)
adaptor trimming
alignment using Tophat version 2.0.4
Genome_build: USCS/mm9
Supplementary_files_format_and_content: FPKM matrix with gene ID, TSS ID and locus coordinates

source_name: subcutaneous allograft

growth_protocol: For paradigm I and II, KPC cells were cultured in DMEM media, 10% FBS, 1% penicillin/streptomycin

extract_protocol:
RNA was isolated using Trizol reagent (Invitrogen, MA, USA)
Poly-A pull-down was used to enrich for mRNAs, and libraries were prepared using the Illumina TruSeq RNA kit

treatment_protocol: 1uM, 5 uM or 10uM DAC during 3 consecutive days or 3 times every 48h

tag: model

value: KPC derived tumor cells allografted in syngeneic host mice

tag: genotype

value: none before SC injection

tag: rin

value: subcutaneous allograft


title: BM9819_mouse_11_KPC_cutltured_DAC_5uM

description: cultured KPC tumor epithelial cells, paradigm I

source_name: cultured KPC tumor epithelial cells

value: KPC transgenic model

value: 5 uM DAC 3 consecutive days

value: cultured KPC tumor epithelial cells


title: BM9820_mouse_11_KPC_cutltured_DAC_10uM

value: 10 uM DAC 3 consecutive days


title: BM1106_mouse_9_allograft_untreated


title: NMR_KYSE70

source_name: esophageal squamous cell carcinoma cells_NMR_overexpression_KYSE70


title: BM1107_mouse_10_allograft_DAC

description: 1 month allograft tumors  from pre-treated cultured KPC tumor cells, paradigm II

value: 1uM DAC, 3 consecutive days before SC injection


title: CON_KYSE450

source_name: esophageal squamous cell carcinoma cells_control_KYSE450


title: CON_KYSE70

source_name: esophageal squamous cell carcinoma cells_control_KYSE70


title: BM1102_mouse_7_allograft_untreated


title: BM1104_mouse_8_allograft_untreated


title: BM1103_mouse_8_allograft_DAC


title: BM9818_mouse_11_KPC_cutltured_control


title: green sector

city: Pingtung County

first: Chi-Chu

last: Tsai

address: 2-6 Dehe Rd., Dehe Village, Changjhih Township

department: Crop Improvement Section

country: Taiwan

institute: Kaohsiung District Agricultural Research and Extension Station

data_processing:
Illumina Casava v1.8.2 software was used for basecalling.
Sequenced reads were trimmed for low-quality sequence using ConDeTri v2.0 with default parameters.
Trimmed reads from both samples were combined and de novo assembled using Oases v0.2 with defalut parameters. The longest contigs or the contigs with the highest confidence score from each loci were picked as unigenes.
Differential expression analysis was performed to obtain FPKMs (Fragments Per Kilobase of transcript per Million mapped reads) of each sample using Tophat and Cufflinks softwares against the unigenes.
Unigenes with over two-fold FPKM changes and with P<0.01 were picked to perform GO and KEGG analysis.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample and a FASTA file of assembled transcripts.

organism: Phalaenopsis aphrodite subsp. formosana

growth_protocol: Plants are grown in sphagnum moss and cultivated in green house.

extract_protocol:
Total RNA was extracted by Trizol® Reagent (Invitrogen, USA), and followed by RNeasy Mini Kit (Qiagen, Germany). RNA purified was quantified at OD260 by using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 nano labchip kit (Agilent Technologies, USA).
RNA libraries were prepared for sequencing using TruSeq RNA Library Preparation Kit v2 with standard Illumina protocols

tag: phenotype

value: variegation mutant

value: leaf


title: yellow sector

data_processing:
Illumina Casava v1.8.2 software was used for basecalling.
Sequenced reads were trimmed for low-quality sequence using ConDeTri v2.0 with default parameters.
Trimmed reads from both samples were combined and de novo assembled using Oases v0.2 with defalut parameters. The longest contigs or the contigs with the highest confidence score from each loci were picked as unigenes.
Differential expression analysis was performed to obtain FPKMs (Fragments Per Kilobase of transcript per Million mapped reads) of each sample using Tophat and Cufflinks softwares against the unigenes.
Unigenes with over two-fold FPKM changes and with P<0.01 were picked to perform GO and KEGG analysis.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample and a FASTA file of assembled transcripts..


title: BM1101_mouse_7_allograft_DAC


title: Fetal Sample 3

city: Darlinghurst

first: Aaron

last: Statham

state: NSW

address: 384 Victoria St

department: Cancer Department

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
Raw read pairs were aligned to the human genome (hg19) using bwa-meth, a bisulfite aware wrapper for the bwa-mem aligner.
Read pairs with identical strand, start and end positions were considered PCR duplicates and removed from downstream analysis using MarkDuplicates from the Picard toolset.
BisSNP v0.82.2 was then used to extract the methylation status of each CpG site in each sample which was then transformed into a "bigTable" of counts of methylation and coverage per-sample per-CpG site.
Unmethylated regions (UMR) and lowly methylated regions (LMR) were called using the MethylSeekR Bioconductor package using default settings and PMD filtering disabled.
DNA methylation valleys (DMV) were called using the aaRon R package (http://github.com/astatham/aaRon).
Differentially methylated regions between the fetal and lamb PRAT were called using the bsseq bioconductor package, with a t-stat cutoff of 4, minimum absolute methylation difference of >=0.1 and minimum number of CpG sites of >=3.
Genome_build: Ovis_aries Oar_v3.1.74
Supplementary_files_format_and_content: BED; Tab separated values - containing co-ordinates of each CpG site with a count of methylation reads "C" and total sequencing coverage "cov" per CpG-site, per-sample.

organism: Ovis aries

source_name: Perirenal adipose tissue

growth_protocol: Tissues for this study were provided by Janna L Morrison and Isabella C McMillen from Sansom Institute for Health Research, The University of South Australia, Adelaide, 4001, SA, Australia.  All procedures involving animals were carried out with approval from the University of Adelaide Animal Ethics Committee.  Animals were maintained on 100% maintenance energy requirement diets and  cared for humanely as a research flock according to strict animal ethics guidelines. The  ewes for the fetal samples were housed from 110 dpc (days post conception (dpc); term, 150 d) in pens for two weeks before sampling. The pregnant ewes were maintained on a diet that provided 100% of their maintenance energy requirements. Three pregnant ewes were humanely euthanased with an intravenous overdose of sodium pentobarbitone (8.2 g Lethobarb, Virbac Pty ltd, Peakhurst, NSW, Australia) and the uterus removed and fetuses tissue collected at 132±1 dpc. Three ewes were allowed to deliver at term and the lambs were reared with ewes until weaning. At ~89±7 d after birth, lambs were humanely euthansed (as described) and tissues collected.

extract_protocol:
Genomic DNA from perirenal adipose tissue (n=3 animals /gp) was purified by first pulverizing frozen tissue in liquid N2, and then resuspending the samples in 10 volumes of tissue lysis buffer (10 mM Tris base (pH 8), 100 mM NaCl, 25 mM EDTA (pH 8), 0.5% SDS, Proteinase K (100 µ/ml)) and incubating at 55oC (4 h, gentle mixing). The lysate was clarified (2,000 xg, 5 min) and soluble material extracted by emulsifying in an equal volume of Tris-saturated (pH 8.0) phenol/chloroform/isoamyl alcohol (25:1:1) followed by centrifugation (2,000 xg, 10 min). The aqueous phase was introduced into 100% isopropanol with gentle swirling and the DNA clot was collected, semi-dried and resuspended in 10 mM Tris (pH 8.0). DNA concentrations were determined using a Nanodrop spectrophotometer (Agilent Technologies, Santa Clara, CA, USA) and used for subsequent Bisulphite conversion and sequencing.
Whole genome bisulfite sequencing libraries were prepared following Illumina’s “Whole-Genome Bisulfite sequencing for Methylation Analysis” protocol. Briefly, DNA (1ug) was sheared to 150-300bp by sonication with a Covaris S2. Library preparation was performed for each sample using the Illumina Paired-end DNA Sample Prep Kit according to the manufacturer’s protocol - fragments were end-repaired and an adenine added to the 3’ end before ligation of Illumina TruSeq adaptors.  A gel was used to purify and size select the ligated products, followed by treatment with sodium bisulfite (Clark et al 2006, Nat Prot). Adaptor-ligated bisulfite treated DNA was enriched through 10 cycles of PCR using PfuTurboCx Hotstart DNA polymerase (Stratagene). Library quality was assessed with the Agilent 2100 Bioanalyzer using the High-sensitivity DNA kit (Agilent, CA, USA). DNA was quantified using the KAPA Library Quantification kit by quantitative PCR (KAPA Biosystems). One lane of paired-end 100bp sequencing was performed for each library on the Illumina HiSeq 2500 platform using Truseq v3 cluster kits and SBS kits.

treatment_protocol: No treatment was applied to the  animals.

tag: breed

value: pure bred merino

value: 132 day old fetus

value: perirenal adipose tissue

value: wild type

tag: age

value: Fetal (Brown adipose tissue)


title: Lamb Sample 2

value: 89 day old lamb

value: Lamb (White adipose tissue)


title: Fetal Sample 2


title: BM878_mouse_6_KPC_HOP_PBS

description: in vivo model, paradigm III

source_name: Head of pancreas

value: PBS, 3 times every 48h

value: Head of pancreas


title: BM730_mouse_4_KPC_HOP_PBS

description: in vivo model, paradigm III


title: BM663_mouse_1_KPC_HOP_DAC

description: in vivo model, paradigm III

value: 1uM DAC, 3 times every 48h


title: BM726_mouse_3_KPC_HOP_DAC

description: in vivo model, paradigm III

value: KPC transgenic model


title: Fetal Sample 1


title: THP1_input

city: Kuopio

first: Carsten

last: Carlberg

address: Yliopistonranta 1D

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description: ChIP-seq

data_processing:
Alignment to hg19 using Bowtie v1.1 Parameters -n 1 -k 1 -m 1 -l 32 -t -q best
tdf created by igvtools count -z 5 -e 150
Genome_build: hg19
Supplementary_files_format_and_content: tdf

source_name: THP-1 input

growth_protocol: THP-1 cells were grown in RPMI 1640 medium, supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin at 37°C

extract_protocol:
Cells were grown in culture as mentioned above, after which they were crosslinked with formaldehyde, lysed and the DNA was extracted. Then, ChIP was performed
ChIP DNA was sent to EMBL and the library was prepared there according to their protocol

treatment_protocol: Cells were treated with100 nM of 1,25(OH)2D3 (Sigma-Aldrich) or solvent (0.1% ethanol)

tag: treatment protocol


title: BM667_mouse_2_KPC_HOP_DAC

description: in vivo model, paradigm III


title: THP1_H3K27ac_rep3_0

description: ChIP-seq

source_name: THP-1 24h after EtOH treatment, 3rd replicate H3K27ac

value: 24h with EtOH


title: BM1105_mouse_9_allograft_DAC

value: KPC derived tumor cells allografted in syngeneic host mice

value: subcutaneous allograft


title: THP1_H3K27ac_rep3_24

description: ChIP-seq

source_name: THP-1 24h after 1,25D treatment, 3rd replicate H3K27ac


title: Lamb Sample 3


title: Lamb Sample 1


title: Pelota rep5

city: Godollo

first: Daniel

last: Silhavy

state: US and Canada only

address: Szent-Gyorgyi 4

department: Agricultural Biotechnology Intsitute

country: Hungary

institute: National Agricultural Research and Innovation Cen.

data_processing:
Read alignment (TopHat v2.1.1)
Differential Gene Expression (Cufflinks suite v2.2.1)
Genome_build: Solgenomics Niben v1.0.1
Supplementary_files_format_and_content: gene_exp.diff, miR_target_cover_pub.xlsx
Supplementary_files_format_and_content: gtf files were generated using Stringtie v1.3.3b software including the assembled transcript structures and FPKM values.

organism: Nicotiana benthamiana

source_name: N. benthamiana_Pelota

growth_protocol: Seeds of wild type Nicotiana benthamiana plants were germinated directly on Jiffy pellets (Jiffy-7 44mmm; Jiffy International AS, Norway), and then seedling were transferred to soil. Tobacco plants were grown in a greenhouse. After VIGS-treatment N. benthamiana plants were kept in a growth chamber at 23°C under 14/10 h light/dark conditions.

extract_protocol:
Total RNA was extracted from 100 mg of leaf tissue (White and Kaper, 1989). Briefly, the homogenized plant materials were resuspended in 600 μL of extraction buffer (0.1 M glycine-NaOH, pH 9.0, 100 mM NaCl, 10 mM EDTA, 2% SDS, and 1% sodium lauroylsarcosine) and mixed with an equal volume of phenol. The aqueous phase was treated with equal volumes of phenol and chloroform, precipitated with ethanol, and resuspended in sterile water.
Libraries were prepared from total RNA samples with Illumina® Ribo-Zero™ rRNA Removal (Plant Leaf) and ScriptSeq™ v2 RNASeq Library Preparation Kits.

treatment_protocol: Virus-induced gene silencing (VIGS) was used to transiently silence Pelota. N. benthamiana plants were infected with Tobacco Rattle Virus VIGS vector containing a segment from the Pelota or from the PDS gene (called Pelota and control silenced plants, respectively).

tag: genotype/variation

value: Pelota-silenced


title: THP1_H3K27ac_rep2_0

description: ChIP-seq

source_name: THP-1 24h after EtOH treatment, 2nd replicate H3K27ac


title: THP1_H3K27ac_rep1_0

description: ChIP-seq

source_name: THP-1 24h after EtOH treatment, 1st replicate H3K27ac


title: THP1_H3K27ac_rep1_24

description: ChIP-seq

source_name: THP-1 24h after 1,25D treatment, 1st replicate H3K27ac


title: Control rep6

source_name: N. benthamiana_control-silenced

value: Control-silenced


title: Control rep5

value: leaf


title: THP1_H3K4me3_rep3_0

description: ChIP-seq

source_name: THP-1 24h after EtOH treatmentt, 3rd replicate H3K4me3


title: BM731_mouse_5_KPC_HOP_PBS

description: in vivo model, paradigm III


title: THP1_H3K4me3_rep2_0

description: ChIP-seq

source_name: THP-1 24h after EtOH treatment, 2nd replicate H3K4me3


title: THP1_H3K4me3_rep1_0

description: ChIP-seq

source_name: THP-1 24h after EtOH treatment, 1st replicate H3K4me3


title: THP1_H3K4me3_rep1_24

description: ChIP-seq

source_name: THP-1 24h after 1,25D treatment, 1st replicate H3K4me3


title: Pelota rep6


title: shNT_rep3 RNA-seq

city: Irvine

first: Jiejun

last: Shi

state: CA

address: 5270 California Ave

department: School of Medicine

institute: University of California Irvine

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to the hg19 genome using Bowtie2 v2.1.0; RNA-seq reads were aligned to hg19 genome using tophat v2.0.10
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq wig files were generated using MACS-1.4.2; Scores represent the ChIP-seq tag numbers; RNA-seq htseq file include differential significance across treatment and control and the tag numbers in all samples

growth_protocol: Human WI38, IMR90 and HEK 293T cells (ATCC) were maintained in DMEM (Cellgro) supplemented with 10% fetal bovine serum (Sigma). The human lung cancer cell lines A549, NCI-H1299, NCI-H1355, NCI-H1972, and NCI-H1993 were maintained in RPMI-1640 supplemented with 10% fetal bovine serum.

extract_protocol:
mRNA was prepared using the RNeasy Plus kit (Qiagen) and reverse-transcribed using the First Strand Synthesis kit (Invitrogen). Libraries were prepared using the Illumina TruSeq RNA Library Prep kit following the manufactory manual.
Samples were sequenced using the Illumina Solexa Hiseq 2500.

treatment_protocol: For infections, cells were incubated with viral supernatants in the presence of 8 µg/ml polybrene; after 48 hours, the infected cells were selected with puromycin (1.5 µg/ml) for pLKO clones or blasticidin (10 µg/ml) for pCDH clones for 3-4 days before experiments.

tag: cell line

value: NIH H1299

value: non-small cell lung cancer

value: control vector


title: shGAS41_rep2 RNA-seq

value: GAS41 Knock Down


title: shNT_rep1 RNA-seq


title: shGAS41_rep1 RNA-seq


title: H1299_shNT_H3K27ac ChIP-seq

extract_protocol:
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20.
Samples were sequenced using the Illumina Solexa Hiseq 2500.

tag: antibody

value: Abcam, Ab4729


title: shGAS41_rep3 RNA-seq

tag: treatment


title: shNT_rep2 RNA-seq


title: H1299_shGAS41_H2AZ ChIP-seq

value: Abcam, Ab4174


title: H1299_shNT_H2AZ ChIP-seq


title: THP1_H3K27ac_rep2_24

description: ChIP-seq

source_name: THP-1 24h after 1,25D treatment, 2nd replicate H3K27ac


title: THP1_H3K4me3_rep3_24

description: ChIP-seq

source_name: THP-1 24h after 1,25D treatment, 3rd replicate H3K4me3


title: H1299_shNT_H3K14ac ChIP-seq

value: Millipore, 07-353


title: H1299_GAS41 ChIP-seq

value: Santa Cruz, sc-393708


title: Pelota rep4


title: SC1034_mRNA

city: Berkeley

first: Jungwoo Wren

last: Kim

address: Barker Hall, Room 416

department: Molecular and Cell Biology

institute: UC Berkeley

description: processed data: hDA.txt

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequences were processed and trimmed using Greg Hannon's fastx_toolkit setup and rRNA depleted, aligned following a protocol from Ingolia NT. Nature Protocols (2012).  Tophat (2.0.11) with Bowtie2 (2.2.2) was used.
Counted reads were processed by DESeq (1.20), and translation efficiency was calculated.
(LRRK2 knockout set 1 ribosome profiling data are aligned reads as the original fastq became unavailable to access)
Genome_build: mm9, hg19
Supplementary_files_format_and_content: tab-delimited text files with DESeq processed expression levels and translation efficiency

source_name: Parkinson's Disease patient-derived dopamine neurons

extract_protocol:
Mouse samples: samples were dissected and frozen in dry ice, and homogenized and processed. hDA samples: samples were lysed on the culture plates, incubated in refrigerated rotator and processed.
Libraries were prepared for sequencing using previously published ribosome profiling protocol.

value: iPSC-differentiated dopamine neurons

value: Differentiation day 60

value: G2019S LRRK2


title: THP1_H3K4me3_rep2_24

description: ChIP-seq

source_name: THP-1 24h after 1,25D treatment, 2nd replicate H3K4me3


title: SC1055_mRNA

description: processed data: hDA.txt

source_name: control dopamine neurons

value: wild-type


title: Control rep4


title: SC1034_ribo

description: processed data: hDA.txt

data_processing:
Library strategy: Ribosome profiling
Illumina Casava 1.8 software used for basecalling.
Sequences were processed and trimmed using Greg Hannon's fastx_toolkit setup and rRNA depleted, aligned following a protocol from Ingolia NT. Nature Protocols (2012).  Tophat (2.0.11) with Bowtie2 (2.2.2) was used.
Counted reads were processed by DESeq (1.20), and translation efficiency was calculated.
(LRRK2 knockout set 1 ribosome profiling data are aligned reads as the original fastq became unavailable to access)
Genome_build: mm9, hg19
Supplementary_files_format_and_content: tab-delimited text files with DESeq processed expression levels and translation efficiency


title: SC1041_mRNA

description: processed data: hDA.txt


title: Activated primary CD4+ T cells from humans

city: HOUSTON

first: Aviva

middle: P

last: Aiden

address: 2205 MARONEAL ST

institute: BCM

data_processing:
Library strategy: HiC-Seq
Data was processed using the Juicer pipeline (Durand et al, Cell Systems 2016)
Genome_build: Hg19
Supplementary_files_format_and_content: .hic file containing matrix data for the HiC contact map. This map can be visualized in Juicebox either the downloadable or web-based version (http://aidenlab.org/juicebox/) (Durand et al, Cell Systems 3(1), 2016)

growth_protocol: Blood samples were collected from healthy donors, and CD4+ T cells were isolated using CD4 microbeads

extract_protocol:
CD4+ T cells were isolated from whole blood by negative selection using RosetteSep human CD4+ T cell enrichment cocktail (STEMCELL Technologies Inc., Vancouver, BC) and RosetteSep density medium gradient centrifugation. At each time point, cells were further purified by a second step positive selection with CD4+ Dynabeads (Invitrogen #11145D, Life Technologies).
Libraries were constructed using the in situ HiC protocol described in Rao & Huntley, Cell 2014

treatment_protocol: CD4+ T cells were isolated from whole blood by negative selection using RosetteSep human CD4+ T cell enrichment cocktail (STEMCELL Technologies Inc., Vancouver, BC) and RosetteSep density medium gradient centrifugation. Isolated CD4+ T cells were placed in freezing container at -80°C for overnight, and then moved into a liquid nitrogen tank for long-term storage. On the day of activation, CD4+ T cells were thawed in a 37°C water bath, counted and resuspended in RPMI-1640 supplemented with 10% FCS, and plated at 50,000 cells per well in a 96 well round-bottom plate. Cells were stimulated for 48 hours with beads conjugated with anti-CD3 and anti-CD28 antibodies (Dynabeads, Invitrogen #11131D, Life Technologies) at a cell:bead ratio of 1:1. At each time point, cells were further purified by a second step positive selection with CD4+ Dynabeads (Invitrogen #11145D, Life Technologies).

value: Activated primary CD4+ T cells


title: SC1014_mRNA

description: processed data: hDA.txt


title: SC1015_ribo

description: processed data: hDA.txt


title: SC1055_ribo

description: processed data: hDA.txt


title: H1299_shNT_H3K4me3 ChIP-seq

value: Abcam, Ab8580


title: SC1014_ribo

description: processed data: hDA.txt


title: SC1041_ribo

description: processed data: hDA.txt


title: SC1015_mRNA

description: processed data: hDA.txt


title: SC1007_mRNA

description: processed data: hDA.txt


title: SC1007_ribo

description: processed data: hDA.txt


title: Input_SKBR3

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: Cancer Research UK, Cambridge Institute

data_processing:
Single-end 36 bp reads were generated on the Illumina Hi-Seq and aligned to the human genome version GRCh37 using BWA version 0.5.9
Reads were filtered by removing those with a BWA alignment quality score less than 15.
A further filtration was carried out by removing reads falling into the ‘blacklist’ regions identified by ENCODE (27) or in regions found to have high signals in cell-line-specific  input samples as determined by the Bioconductor package GreyListChIP (http://www.bioconductor.org/packages/release/bioc/html/GreyListChIP.html)
Peaks were then called using MACS version 1.4.1 (14) for HER2 data and Sicer version 1.1 (28) for the histone mark data.
Genome_build: GRCh37
Supplementary_files_format_and_content: bed/text

source_name: SKBR3 breast cancer cell line

growth_protocol: SKBR3 cells were grown in McCoys 5A Glutamax, supplemented with 10% FBS.  BT474 cells were grown in RPMI-1640, supplemented with 10% FBS.  T47D cells were grown in DMEM, supplemented with 10% FBS.

extract_protocol:
ChIPexo, Serandour et al, 2013. PMID: 24373287
above (in samples section)
ChIPexo, Serandour et al, 2013. PMID: 24373287, ChIPseq, Schmidt et al, 2009. PMID: 19275939

treatment_protocol: Cells were treated, without any serum deprivation, for 3 hours with vehicle (H2O) or EGF (100ng/ml, Sigma-Aldrich, St Louis, MO, USA).

tag: chip antibody


title: H3K4me1_ChIPseq_SKBR3_Rep1

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275939
above (in samples section)
ChIPexo, Serandour et al, 2013. PMID: 24373287, ChIPseq, Schmidt et al, 2009. PMID: 19275939

value: Asynchonous cells


title: H3K4me1_ChIPseq_BT474_Rep1

source_name: BT474 breast cancer cell line


title: HER2_ChIPexo_vehicle_SKBR3

description: ChIPexo

value: Asynchonous cells, vehicle (H2O)


title: H3K4me1_ChIPseq_BT474_Rep2


title: H3K4me1_ChIPseq_SKBR3_Rep2


title: Young rep3

city: Gwangju

first: Tae Hoon

last: Lee

address: 300 Yongbong-Dong

department: School of Dentistry

country: South Korea

institute: Chonnam National University

data_processing:
Illumina Casava1.7 software used for basecalling.
Reference genome sequence data from Homo sapiens were obtained from the University of California Santa Cruz Genome Browser Gateway (assembly ID: hg19). The reference genome index was built using the Bowtie2-build component of Bowtie2 (ver. 2.0) and SAMtools (ver. 0.1.18). Tophat2 (ver. 2.0) was applied to map the reads obtained from our tissue samples to the reference genome.
The fragments per kilobase of transcript per million mapped reads (FPKM) values were used to estimate the expression level of each gene. The FPKM data were normalized by the quantile method, log2-transformed, and median-centered across genes and samples.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Samples..

source_name: Gingiva

extract_protocol:
Gingival tissues were removed, flash frozen on dry ice, and RNA was isolated using RNeasy kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) was used with 4 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: Female

value: Gingiva


title: Young rep1


title: Old rep3


title: Old rep1


title: RNAseq_Veh_Rep 6

data_processing:
Single-end 40BP reads generated on the Illumina HiSeq were aligned to the human genome version GRCh37.64 using TopHat version 2.0.4
Read counts were then obtained using HTSeq-count version 0.5.3p9 (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Read counts were then normalised and tested for differential gene expression using the Bioconductor package DESeq2 (30) version 1.8.1.
Multiple testing correction was applied using the Benjamini-Hochberg method.
Genes were selected as differentially expressed such that FDR <0.01.
Genome_build: GRCh37.64
Supplementary_files_format_and_content: Veh_V_EGF_DESeq_Results.txt

growth_protocol: SKBR3 cells were grown in McCoys 5A Glutamax, supplemented with 10% FBS.  BT474 cells were grown in RPMI-1640, supplemented with 10% FBS.

extract_protocol:
RNA was extracted using Qiagen RNeasy kit
RNAseq libraries were prepared using Illumina’s TruSeq mRNA Stranded Sample prep kit


title: HER2_ChIPexo_EGF_BT474

description: ChIPexo

value: HER2 (Santa Cruz sc-284, Lots I2717/K0711)

value: Asynchonous cells, treated with EGF (100ng/ml) for 3 hours


title: Input_BT474


title: Old rep2


title: HER2_ChIPexo_vehicle_BT474

description: ChIPexo


title: RNAseq_EGF_Rep 5


title: RNAseq_Veh_Rep 3


title: RNAseq_Veh_Rep 5


title: RNAseq_EGF_Rep 4


title: RNAseq_EGF_Rep 6


title: RNAseq_EGF_Rep 3


title: RNAseq_Veh_Rep 4


title: HER2_ChIPexo_EGF_SKBR3

description: ChIPexo


title: Tolerant_male_RNASeq

city: New Delhi

first: Prakash

middle: Chand

last: Sharma

state: Delhi

address: Sector 16-C, Dwarka

department: University School of Biotechnology

institute: GGS indraprastha University

description: Each spreadsheet of processed file contains genes differentially expressed in samples as compared to Tolerant male (as reference).

data_processing:
Base calling by Illumina Casava1.8 software.
The raw RNA-seq Fastq files were trimmed by for quality assurance by running perl script of IlluQC.pl of NGSQC Toolkit_v.2.2.
All reads from the five sample libraries were mapped together onto the reference genome of rat using large gap read mapper from CLC Genomics Workbench 6.02 to extend annotations.
Reads from individual library samples were aligned using RNA-seq analysis tool of same workbench to this newly annotated genome.
The differential gene expression was analyzed using normalized expression values based on exon based model RPKM (reads per kilo base per million) (Mortazavi et al. 2008).
Kal’s test was carried out for calculating differential gene expression in terms of proportional fold change of quantile based normalized data and Benjamini and Hochberg (1995) method to calculate FDR corrected p-values to control false positives (record with FDR < 0.05 was considered as significant).
Genome_build: RGSC_3.4
Supplementary_files_format_and_content: Each .xlsx processed data file contains spreadsheets having list of differentially expressed genes with proportional fold change > 2 or <-2 and FDR value below 0.05. The information on location of each differentially expressed transcript is given by the chromosome number, start and end region. Each spreadsheet's name symbolises the DEGs in one sample compared to other. For example, Sus(M) vs Con(M) has gene differentially expressed in Susceptible male as compared to control male.

organism: Rattus norvegicus

source_name: lung tissue_hypoxia_tolerant_male

growth_protocol: Rats were reared on daily standard nutritional diet and sterile water, at a temperature of 24±2ºC with day and night routine cycles of 12 hours each under hygienic disease free conditions.

extract_protocol:
Total RNA was extracted from lung tissue samples of control, susceptible male, normal male, tolerant male and female rats using TriReagent and its quality control analysis by Agilent 2100 Bioanalyser
RNA libraries were prepared for sequencing using standard Illumina TruSeq SBS kit v5-GA protocols

treatment_protocol: Rats screened for gasping time (time taken for arrival of first gasp during acute hypobaric hypoxia exposure) and divided into designated groups of susceptible, normal and tolerant animals. After acclimatization of a week, all the groups were exposed to simulated acute hypobaric hypoxia in a decompression chamber for one hour at 9144 m and 24°C. Relative humidity was maintained at 40-50% with airflow around 2 L/min inside the chamber.

value: lung

tag: strain

value: Sprague Dawley

tag: gasping time

value: first gasp observed in more than 45 minutes

tag: sample details

value: Tolerant male (designated as (Tol(M))

value: male


title: RNAseq_EGF_Rep 1


title: Susceptible_RNASeq

description: Each spreadsheet of processed file contains genes differentially expressed in samples as compared to susceptible male (as reference).

source_name: lung tissue_hypoxia_susceptible

tag: tissue

value: first gasp observed in less than 5 minutes

value: Susceptible male (designated as Sus(M))


title: RNAseq_Veh_Rep 1


title: Tolerant_female_RNASeq

source_name: lung tissue_hypoxia_tolerant_female

value: first gasp observed in more than 1 hour

value: Tolerant female (designated as Tol(F))

value: female


title: Normal_RNASeq

description: Each spreadsheet of processed file contains genes differentially expressed in samples as compared to Normal male (as reference).

source_name: lung tissue_hypoxia_normal

value: first gasp observed between 15-20 minutes

value: Normal or Moderate male (designated as Nor(M))


title: Young rep2


title: EBV+6-3p

city: Changsha

first: Jian

last: Ma

state: Hunan

address: 110  Xiangya  Road

department: Cancer  Research Institute

institute: Central South University

description: cells were transfected with BART6-3p mimics (6-3p) for 48 h and then infected with EBV virions for 2h

data_processing:
Raw data (raw reads) were processed using NGS QC Toolkit. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference human genome using Tophat.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count. DEGs were identified using the DESeq functions estimate Size Factors and nbinomTest. P value < 0.05 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
Genome_build: human genome build 38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each samples

source_name: B lymphoma cells (EBV negative)

growth_protocol: BJAB cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum. Cultures were incubated at 37°C in a humidified incubator at 5% CO2.

extract_protocol:
mirVana miRNA ISOlation Kit (Ambion#1561) extraction of RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Solexa protocols.

treatment_protocol: BJAB cells were transfected with negative control mimics or BART6-3p mimics for 48 h and then infected with EBV virons for 2h.

value: BJAB cells


title: EBV+NC

description: cells were transfected with negative control mimics (NC) for 48 h and then infected with EBV virions for 2h


title: Mock

description: cells with no infection and treatment


title: Normoxia_RNASeq

description: Each spreadsheet of processed file contains genes differentially expressed in samples as compared to control male (as reference).

source_name: lung tissue_normoxia

value: not screened for gasping

value: Control or normoxic male  (designated as Con(M))


title: EBV

description: cells were infected with EBV virions for 2h


title: Nr5a2(fl/fl);Ptf1a(CreER/+) 2LPFCb-12-6

city: Dallas

first: Galvin

last: Swift

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: U TX Southwestern Medical Center

description: RNA-seq library reads

data_processing:
Illumina HiSeq Control Software used for basecalling
Sequences were mapped to mm10 mouse genome using TopHat v2.0.11(by use of Bowtie v2.2.2.0) with allowed segment-mismatches 3
Sequences per gene were counted using Samtools ( v0.1.19.0) /HTSeq (v0.6.0)
Genome_build: mm10
Supplementary_files_format_and_content: Normalized counts-per-million (CPM) for each gene in tab-delimited text file
Supplementary_files_format_and_content: Pancreas_TF-ko_RNAseq_Summary.xlsx: Excel file with all Htseq results in single table.  2nd sheet identifies libraries. Available on series record.

source_name: pancreas

growth_protocol: Weanlings of the desired genotypes were identified.  Strain backgrounds were predominantly C57BL6.

extract_protocol:
RNA preparation:  pancreas was homogenized in 4 M Guanidine Thiocyanate, 0.1 M Tris HCl pH 7.5, 1% 2-mercaptoethanol with a Tekmar Tissuemizer.  RNA was isolated from an aliquot of the homogenate by addition of N-Lauroylsarcosine sodium salt to 0.5%, Potassium Acetate pH 5.5 to 0.1 M, and Acetic Acid to 0.08 M, followed by addition of 0.75 volume ethanol while vortexing.  RNA was allowed to precipitate from the solution at -20 C for at least 1 hour, collected by centrifugation at 12,000 g for 5 minutes, and the RNA pellet resuspended in Trizol (equal volume to starting homogenate).  Subsequent steps were as per manufacturer's protocol (Life Technologies) or with Zymo Research Direct-Zol RNA mini-prep.
RNA libraries were prepared for sequencing using standard Illumina True-seq protocols

treatment_protocol: Tamoxifen treatment: Most mice were approximately 8-9 weeks at initiation of treatment.  At approximately 4 PM on day 0, 1, 2, mice received 0.25 mg tamoxifen/g mouse at 50 mg/ml in corn oil by gavage.  Mice were sacrificed on day 6 at approximately 4 PM.

value: pancreas

value: M

tag: age at sacrifice (days)


title: Nr5a2(fl/fl);Ptf1a(CreER/+) 2LPFCb-12-9

description: RNA-seq library reads

tag: genotype

value: F


title: Nr5a2(fl/fl);Ptf1a(CreER/+) 2LPFCb-13-7

description: RNA-seq library reads

tag: rin


title: Nr5a2(fl/fl);Ptf1a(CreER/+) 2LPFCb-13-11

description: RNA-seq library reads


title: Foxa2(fl/fl); Gata4(fl/fl);Ptf1a(CreER/+) FGPC-11-6

description: RNA-seq library reads


title: Nr5a2(fl/fl);Ptf1a(CreER/+) FGPC-11-12

description: RNA-seq library reads


title: Foxa2(fl/fl); Gata4(fl/fl);Ptf1a(CreER/+) FGPC-11-12

description: RNA-seq library reads


title: Nr5a2(fl/fl);Ptf1a(CreER/+) 2LPFCb-12-2

description: RNA-seq library reads


title: Foxa2(fl/fl); Gata4(fl/fl);Ptf1a(CreER/+) FGPC-11-11

description: RNA-seq library reads


title: Foxa2(fl/fl);Ptf1a(CreER/+) FPFC-30-2

description: RNA-seq library reads


title: Foxa2(fl/fl); Gata4(fl/fl);Ptf1a(CreER/+) FGPC-11-9

description: RNA-seq library reads


title: PTPN2_KO1

city: New York

first: Shuibing

last: Chen

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Illumina CASAVA v1.8.4 software used for basecalling.
Sequenced reads were trimmed for low-quality sequences by using fastq_quality_trimmer in the FASTX toolkit with parameters "-t 10 -l 45" and were trimmed for adapter sequences using cutadapt with parameters "-O 5 -m 45"; then mapped to the UCSC hg19 human reference genome using tophat v2.0.11.
Gene abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.1.1 package.
Genome_build: hg19
Supplementary_files_format_and_content: excel file including gene name, RefSeq id, locus, RPKM values of each sample, for each gene

source_name: hESCs derived beta cells

growth_protocol: hESC stepwise differnetiation protocol, The full protocol has been submitted as a manuscript for peer review.

extract_protocol:
Qiagen RNeasy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: GFP+ cells sorted by FACS

tag: cell type

value: human beta cells

tag: cell marker

value: GFP+


title: Foxa2(fl/fl);Ptf1a(CreER/+) FPFC-30-1

description: RNA-seq library reads


title: Foxa2(fl/fl); Gata4(fl/fl);Ptf1a(CreER/+) FGPC-11-8

description: RNA-seq library reads


title: Foxa2(fl/fl);Ptf1a(CreER/+) FPFC-30-3

description: RNA-seq library reads


title: Foxa2(fl/fl);Ptf1a(CreER/+) FPFC-30-6

description: RNA-seq library reads


title: PTPN2_KO2


title: PTPN2_WT2

value: wildtype


title: Foxa2(fl/fl);Ptf1a(CreER/+) FPFC-29-3

description: RNA-seq library reads


title: Gata4(fl/fl);Ptf1a(CreEr/+) GPFC-28b-7

description: RNA-seq library reads


title: PTPN2_WT1


title: Gata4(fl/fl);Ptf1a(CreEr/+) GPFC-28b-8

description: RNA-seq library reads


title: Propargite_with_GSH

source_name: hESCs derieved beta cells


title: Foxa2(fl/fl); Gata4(fl/fl);Ptf1a(CreER/+) FGPC-11-4

description: RNA-seq library reads


title: Gata4(fl/fl);Ptf1a(CreEr/+) GPFC-28b-6

description: RNA-seq library reads


title: Propargite


title: DMSO_with_GSH


title: Gata4(fl/fl);Ptf1a(CreEr/+) GPFC-28b-4

description: RNA-seq library reads


title: Gata4(fl/fl);Ptf1a(CreEr/+) GPFC-28b-3

description: RNA-seq library reads


title: DMSO


title: Gata4(fl/fl);Ptf1a(CreEr/+) GPFC-28b-2

description: RNA-seq library reads


title: Gata4(fl/fl); Nr5a2(fl/fl);Ptf1a(CreEr/+) LGPT-8-3

description: RNA-seq library reads


title: Gata4(fl/fl); Nr5a2(fl/fl);Ptf1a(CreEr/+) LGPT-9-1

description: RNA-seq library reads


title: Gata4(fl/fl); Nr5a2(fl/fl);Ptf1a(CreEr/+) LGPT-8-2

description: RNA-seq library reads


title: Gata4(fl/fl); Nr5a2(fl/fl);Ptf1a(CreEr/+) LGPT-9-2

description: RNA-seq library reads


title: Hepatoblastoma liver 19

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

description: Hepatoblastoma tissue from a Hepatoblastoma Pediatric liver

data_processing:
Following removal of barcodes and primers, raw reads were aligned to the human genome (hg38) and quantified using Kallisto.
TPM were log2 transformed and normalized using quantile normalization, and baselined to the median of all samples.
Genome_build: Hg38
Supplementary_files_format_and_content: RNAseq

source_name: Pediatric liver

growth_protocol: Normal, background, and hepatoblastoma liver samples were obtained from Cincinnati Children's Hospital Medical Center BioBank repository, in addition to fresh live tissue collected from the Division of Pediatric Surgery at CCHMC. All samples were pathological confirmed through histological analysis.

extract_protocol:
Total RNA was isolated using RNEasy Plus mini kit (Qiagen) according to manufacturer's instructions.
Standard Illumina protocols

tag: hbl status

value: Hepatoblastoma

tag: tissue type

tag: age in years

tag: Sex

value: Male


title: Hepatoblastoma liver 18

institute: Cincinnati Children's Hospital Medical Center


title: Hepatoblastoma liver 21


title: Hepatoblastoma liver 23

value: Missing


title: Hepatoblastoma liver 20


title: Hepatoblastoma liver 22


title: Hepatoblastoma liver 11

value: Female


title: Hepatoblastoma liver 12


title: Ptf1a(CreEr/fl);Foxa2(fl/fl) FPFC-9-1

description: RNA-seq library reads


title: Hepatoblastoma liver 16


title: Hepatoblastoma liver 15


title: Hepatoblastoma liver 14


title: Foxa2(fl/fl);Gata4(fl/fl);Nr5a2(fl/fl);Ptf1a(CreEr/fl) FLGPt-19-2

description: RNA-seq library reads


title: Foxa2(fl/fl);Gata4(fl/fl);Nr5a2(fl/fl);Ptf1a(CreEr/fl) FLGPt-19-8

description: RNA-seq library reads


title: Hepatoblastoma liver 17


title: Hepatoblastoma liver 13


title: Hepatoblastoma liver 10


title: Ptf1a(CreEr/fl);Foxa2(fl/fl) FPFC-12-7

description: RNA-seq library reads


title: Foxa2(fl/fl);Gata4(fl/fl);Nr5a2(fl/fl);Ptf1a(CreEr/fl) FLGPt-19-1

description: RNA-seq library reads


title: Ptf1a(CreEr/fl);Foxa2(fl/fl) FPFC-10-8

description: RNA-seq library reads


title: Ptf1a(CreEr/fl);Foxa2(fl/fl) FPFC-9-5

description: RNA-seq library reads


title: Hepatoblastoma liver 9


title: Ptf1a(CreEr/fl);Foxa2(fl/fl) FPFC-9-3

description: RNA-seq library reads


title: Ptf1a(CreEr/fl);Gata4(fl/fl) GPFC-11-7

description: RNA-seq library reads


title: Hepatoblastoma liver 8


title: Hepatoblastoma liver 7


title: Ptf1a(CreEr/fl);Gata4(fl/fl) GPFC-11-6

description: RNA-seq library reads


title: Hepatoblastoma liver 4


title: Hepatoblastoma liver 5


title: Ptf1a(CreEr/fl);Gata4(fl/fl) GPFC-11-1

description: RNA-seq library reads


title: Ptf1a(CreEr/fl);Gata4(fl/fl)  GPFC-11-2

description: RNA-seq library reads


title: Gata4(fl/fl); Nr5a2(fl/fl);Ptf1a(CreEr/+) LGPT-8-4

description: RNA-seq library reads


title: Foxa2(fl/fl);Gata4(fl/fl);Nr5a2(fl/fl);Ptf1a(CreEr/fl) FLGPt-19-7

description: RNA-seq library reads


title: Foxa2(fl/fl);Gata4(fl/fl);Nr5a2(fl/fl);Ptf1a(CreEr/fl) FLGPt-19-10

description: RNA-seq library reads


title: Ptf1a(CreEr/fl);Gata4(fl/fl) GPFC-11-4

description: RNA-seq library reads


title: Hepatoblastoma liver 3


title: Ptf1a(CreER/fl);Nr5a2(fl/fl) LPFC-7-9

description: RNA-seq library reads


title: Hepatoblastoma liver 6


title: Hepatoblastoma liver 1


title: Ptf1a(CreER/fl);Nr5a2(fl/fl) LPFC-7-6

description: RNA-seq library reads


title: Background liver 4

description: Background tissue from a Hepatoblastoma Pediatric liver

value: Background


title: Hepatoblastoma liver 2


title: Background liver 3


title: Background liver 5


title: Ptf1a(CreER/fl);Nr5a2(fl/fl)  LPFC-9-2

description: RNA-seq library reads


title: Ptf1a(CreER/fl) 3Ptf1aFC-7-3_re-analyzed

description:
RNA-seq library reads
GSM2299181


title: Ptf1a(CreER/fl) 3Ptf1aFC-37-1

description: RNA-seq library reads


title: Background liver 1


title: Ptf1a(CreER/fl) 3Ptf1aFC-41-12

description: RNA-seq library reads


title: Ptf1a(CreER/fl) 3Ptf1aFC-41-13

description: RNA-seq library reads


title: Background liver 2


title: Ptf1a(CreER/fl) 3Ptf1aFC-37-4

description: RNA-seq library reads


title: Ptf1a(CreER/+) 3Ptf1aFC-44-7

description: RNA-seq library reads


title: Normal liver 1

description: Normal tissue from a Normal Pediatric liver

value: Normal


title: Normal liver 3


title: Normal liver 2


title: Ptf1a(CreER/+) Ptf1aC-10-6_re-analyzed

description:
RNA-seq library reads
GSM2299175


title: Ptf1a(CreER/+) 3Ptf1aFC-45-2

description: RNA-seq library reads


title: Ptf1a(CreER/+) 3Ptf1aFC-45-1

description: RNA-seq library reads


title: Background liver 6


title: Ptf1a(CreER/+) 3Ptf1aFC-41-11

description: RNA-seq library reads


title: Ptf1a(CreER/fl);Nr5a2(fl/fl) LPFC-7-1

description: RNA-seq library reads


title: Cx

city: Nanning

first: Yan

middle: mei

last: zhu

address: XiXiangTang District University Road No. 100

institute: Guangxi University

data_processing:
Clean reads were gained after raw reads were filtered to remove reads with adaptor, and the sequences of low-quality and containing unknown bases.
Reads were mapped to different position of referent sequences were counted with annotations from the referent sequences using TopHat v2.0.12.
Cufflinks-2.2.1was used to complete the quanlity analysis of gene expression, and FPKM was used to estimate the transcript abundance.
Genome_build: https://www.ncbi.nlm.nih.gov/genome/?term=Manihot+esculenta+Crantz
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Manihot esculenta

source_name: Cx, leaf

extract_protocol:
four total RNA-Seq liibraries,including KU50 under normal and drought conditions,and Xinxuan048 under normal and drought conditions.
RNA libraries were prepared for sequencing using Illumina HiSeqTM2000

tag: cultivar

tag: stress

value: control

value: leaf


title: Ptf1a(CreER/+) Ptf1aC-10-3_re-analyzed

description:
RNA-seq library reads
GSM2299174


title: Ck

source_name: Ck, leaf


title: Ptf1a(CreER/+) 3Ptf1aFC-41-9

description: RNA-seq library reads

value: nc


title: Sx

source_name: Sx, leaf

value: drought


title: Zebrafish 24hpf_4C_view12_TG

city: Utrecht

first: Robin H.

last: van der Weide

address: Uppsalalaan 8

institute: Hubrecht Institute

description: Libraries prepared from 3C template

data_processing:
Library strategy: 4C
Reads for every sample were demultiplexed and trimmed based on the reading primer adding GATC to the start of the sequence. Trimmed reads were mapped to the genome using bwa bwasw (Li and Durbin, 2010). Reads that did not start at a DpnII restriction site were filtered out as they probably do not represent ligation events. Non-unique fragments and fragments created by the digestion of two DpnII sites (“blind” fragments) were also filtered out.
Genome_build: danRer10
Supplementary_files_format_and_content: Wiggle files of each experiment

source_name: Zebrafish 24hpf

extract_protocol:
Carefully staged embryo’s were dechorionated, deyolked and made single cell in three consecutive steps. First embryos were dounched and spun down at 500 rcf at 4 degrees. The precipitant was thereafter incubated in 2 ml of TRIPLE (life, Cat# 12605-010) for 5 min at RT after which 10% end concentration FBS was added. This solution was filtered using a 100uM cell strainer (Sigma, Cat# CLS431752-50EA and cells was spun down at 500 rcf at 4 degrees to collect the single cells.
In brief after obtaining a single cell suspension, crosslinking, primary digestion with DPNII and ligation the DNA was reverse crosslinked o/n at 65C. DNA was isolated by phenol/chloroform extraction and subsequently digested with a 2nd restriction enzyme (CSP6I). Digested DNA was again ligated, but this time under diluted conditions (10ml). DNA was precipitated with 1/10 volume 3M sodium acetate and 1 volume isopropanol. DNA was quantified using QUBIT (thermo fisher). 4C pcr was done using NEB-Next High-Fidelity (NEB,M0541) in 4 separate PCR reactions using ~1-200ng per PCR

value: embryo

tag: developmental stage


title: Zebrafish 24hpf_4C_view11_TG

description: Libraries prepared from 3C template


title: Zebrafish 4hpf_4C_view12_AC

description: Libraries prepared from 3C template

source_name: Zebrafish 4hpf

value: Dome


title: Zebrafish 4hpf_4C_view11_AC

description: Libraries prepared from 3C template


title: Zebrafish 24hpf_4C_view10_TG

description: Libraries prepared from 3C template


title: Ptf1a(CreER/+) 3Ptf1aFC-45-4

description: RNA-seq library reads

value: pancreas

tag: gender


title: Zebrafish 4hpf_4C_view10_AC

description: Libraries prepared from 3C template


title: Zebrafish 24hpf_4C_view9_TG

description: Libraries prepared from 3C template


title: Zebrafish 24hpf_4C_view8_TG

description: Libraries prepared from 3C template


title: Zebrafish 4hpf_4C_view9_AC

description: Libraries prepared from 3C template


title: Zebrafish 4hpf_4C_view7_AC

description: Libraries prepared from 3C template


title: Zebrafish 24hpf_4C_view7_TG

description: Libraries prepared from 3C template


title: Zebrafish 4hpf_4C_view5_AC

description: Libraries prepared from 3C template


title: Zebrafish 4hpf_4C_view4_AC

description: Libraries prepared from 3C template


title: Sk

source_name: Sk, leaf


title: Zebrafish 4hpf_4C_view3_AC

description: Libraries prepared from 3C template


title: Zebrafish 24hpf_4C_view4_TG

description: Libraries prepared from 3C template


title: Zebrafish 24hpf_4C_view3_TG

description: Libraries prepared from 3C template


title: Zebrafish 24hpf_4C_view2_TG

description: Libraries prepared from 3C template


title: 24hpf Hi-C rep1 (HiSeq 2500)

data_processing:
Raw sequence data was mapped and processed using HiC-Pro v2.9 (Servant et al., 2015).
Genome_build: danRer10
Supplementary_files_format_and_content: Hi-C summary files contain the genomic position and strand of the two pairs of a Hi-C ligation

extract_protocol:
Carefully staged embryo’s were dechorionated, deyolked and made single cell in three consecutive steps. First embryos were dounched and spun down at 500 rcf at 4 degrees. The precipitant was thereafter incubated in 2 ml of TRIPLE (life, Cat# 12605-010) for 5 min at RT after which 10% end concentration FBS was added. This solution was filtered using a 100uM cell strainer (Sigma, Cat# CLS431752-50EA and cells was spun down at 500 rcf at 4 degrees to collect the single cells.
These cells were subsequently processed following the standard 4C protocol using DPNII as the restriction enzyme (and CSP6I as the second restion enzyme in the case of 4C-Seq). Successful digestion and ligation was confirmed using the agilent TAPEStation.We omitted the usual biotin incorporation and enrichment step due to the low amounts of DNA obtained from the early developmental stages. Instead we generated paired-end deep-sequencing libraries suitable for illumina sequencing after shearing the 3C template to 500-900bp and computationally filtered for ligation events.


title: Zebrafish 4hpf_4C_view2_AC

description: Libraries prepared from 3C template


title: Zebrafish 24hpf_4C_view1_TG

description: Libraries prepared from 3C template


title: 8hpf Hi-C rep2 (HiSeq 2500)

source_name: Zebrafish 8hpf

value: 80% epiboly


title: 24hpf Hi-C rep2 (HiSeq 2500)


title: Zebrafish 4hpf_4C_view1_AC

description: Libraries prepared from 3C template


title: 8hpf Hi-C rep1 (HiSeq 2500)


title: 4hpf Hi-C (HiSeq 2500)


title: 2.3hpf Hi-C (HiSeq 2500)

source_name: Zebrafish 2.3hpf


title: Zebrafish 4hpf_4C_view8_AC

description: Libraries prepared from 3C template


title: Zebrafish 24hpf_4C_view5_TG

description: Libraries prepared from 3C template


title: TGF-beta1-treated Smad3-knockout bone marrow-derived macrophage [S3KO-MMT3]

city: Hong Kong

first: Hui-Yao

last: Lan

address: Prince of Wales Hospital, Shatin, N.T.

department: Li Ka Shing Institute of Health Sciences, Department of Medicine & Therapeutics, CUHK-Shenzhen Research Institute

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Processed data file: Expression.matrix.RSEM.TPM.txt

data_processing:
The raw reads were quality-checked with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Low quality reads and adapters were removed using Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
TPM were calculated for genes defined by the Ensembl (release 67) annotation using RSEM.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Expression.matrix.RSEM.TPM.txt: Tab-separated text file; expression matrix (TPM) for each sample.

growth_protocol: The macrophages were differentiated from bone marrow cells by 50ng/ml M-CSF in DMEM/F12 medium with 10% FBS for 7 days.

extract_protocol:
Total RNA from a single-cell suspension was extracted by RNeasy Plus mini kit (Qiagen), and then prepared the cDNA following the SMART-seq2 protocol according to manufacturer’s instruction.
A total of 2 ng amplified cDNA products purified by 1 x Agencourt AMPure XP beads (Beckman Coulter) were subjected for library construction by TruePrepTM Mini DNA Sample Prep Kit (Vazyme Biotech).

treatment_protocol: The bone marrow-derived macrophages were further stimulated with 5ng/ml of TGF-beta1 in the above medium to undergo MMT process for additional 5 days.

tag: strain/background

tag: genotype/variation

value: bone marrow-derived macrophages

tag: treatment


title: TGF-beta1-treated Smad3-knockout bone marrow-derived macrophage [S3KO-MMT2]


title: TGF-beta1-treated Smad3-knockout bone marrow-derived macrophage [S3KO-MMT1]


title: J1_Flag_ZNHIT1 ChIP-seq

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to the mm9 genome using Bowtie v1.1.0; RNA-seq reads were aligned to mm9 genome using tophat v2.0.10
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq wig files were generated using MACS-1.4.2; Scores represent the ChIP-seq tag numbers; RNA-seq htseq file include differential significance across treatment and control and the tag numbers in all samples. The ChIP-seq profiles were normalized to 20,000,000 total tag numbers, and peaks were called at P ≤ 1 × 10−8.

source_name: J1 cells

growth_protocol: J1 mouse ES cells were maintained in cell cultured dishes coated with 0.1 % (w/v) gelatin (Sigma) without feeders in ESC media [Dulbecco’s modified Eagle’s medium (DMEM, Cellgro) supplemented with 15 % Stasis™ Stem Cell Qualified Fetal Bovine Serum (Gemini), 100 U/ml penicillin, 100 µg/ml streptomycin, 292 µg/ml L-glutamine, 0.1 mM β-mercaptoethanol and 1000 U/mL leukemia inhibitory factor (LIF, ESGRO, Millipore, USA)]. mESCs were plated on 96 well ultra-low attachment round bottom plate (Corning) at 1,000 cells /well in ES cell medium without LIF. Media was changed every other day and every day before and after day 9, respectively. Undifferentiated mESCs cultured in with LIF on gelatin-coated dish, are considered as EB day 0.

extract_protocol:
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20.
ChIP analysis was performed as described previously (Li et al., 2014) with minor modification. In brief, cells were cross-linked with 1% formaldehyde for 10 min and stopped with 125 mM glycine for 5 min. Fixed cells were scraped from dishes and washed with PBS for 2 times. Cell pellets were resuspended with cell lysis buffer (5 mM PIEPES pH 8.0, 85 mM KCl, 1% NP-40) with protease inhibitor cocktail (Roche) and 10 mM phenylmethanesulfonyl fluoride (PMSF). After 20 min rotation in 4 °C, cell nuclei were pelleted by centrifugation. The nuclei were resuspended with nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) containing protease inhibitors and sonicated using Bioruptor Sonicator (Diagenode). Length of most sheared DNA fragments were between 100-400 base pairs. Sonicated chromatin contains approximately 20-30 μg of DNA were diluted 4 fold with dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.01% SDS) and were subjected to immunoprecipitation with 2–3 μg of antibodies overnight at 4 °C. Protein A/G beads (Millipore) were then added and incubated for 2 hr. The immunoprecipitates were washed twice with low-salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and high-salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and then once with LiCl buffer (20 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP40, 1% Na-Deoxycholate). DNA was eluted with vigorously shaking in elution buffer (50 mM NaHCO3, 1% SDS) for 15 min and then reverse crosslink in the presence of 0.3M NaCl at 67 °C for 12 hr. DNA was purified using PCR purification kit (Qiagen) and analyzed by quantitative real-time PCR on the ABI 7500-FAST System using the Power SYBR Green PCR Master Mix (Applied Biosystems).
ChIP–seq samples were sequenced using the Illumina Solexa Hiseq 2000 or NextSeq 500.

treatment_protocol: For infections, J1 cells were incubated with viral supernatants in the presence of 8 µg/ml polybrene for 14 hr. After 48 hr, the infected cells were selected with puromycin (1 µg/ml) or blasticidin (5 µg/ml) for knockdown or overexpression experiments, respectively. All knockdown samples were harvested 8 days after infected with shRNA viruses.

tag: cell line

value: J1 mouse ES cells

value: No treatment

tag: antibody

value: Flag, Sigma, F1804


title: J1_shZNHIT1-6_H2AZ ChIP-seq

extract_protocol:
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_25.
ChIP analysis was performed as described previously (Li et al., 2014) with minor modification. In brief, cells were cross-linked with 1% formaldehyde for 10 min and stopped with 125 mM glycine for 5 min. Fixed cells were scraped from dishes and washed with PBS for 2 times. Cell pellets were resuspended with cell lysis buffer (5 mM PIEPES pH 8.0, 85 mM KCl, 1% NP-40) with protease inhibitor cocktail (Roche) and 10 mM phenylmethanesulfonyl fluoride (PMSF). After 20 min rotation in 4 °C, cell nuclei were pelleted by centrifugation. The nuclei were resuspended with nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) containing protease inhibitors and sonicated using Bioruptor Sonicator (Diagenode). Length of most sheared DNA fragments were between 100-400 base pairs. Sonicated chromatin contains approximately 20-30 μg of DNA were diluted 4 fold with dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.01% SDS) and were subjected to immunoprecipitation with 2–3 μg of antibodies overnight at 4 °C. Protein A/G beads (Millipore) were then added and incubated for 2 hr. The immunoprecipitates were washed twice with low-salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and high-salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and then once with LiCl buffer (20 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP40, 1% Na-Deoxycholate). DNA was eluted with vigorously shaking in elution buffer (50 mM NaHCO3, 1% SDS) for 15 min and then reverse crosslink in the presence of 0.3M NaCl at 67 °C for 12 hr. DNA was purified using PCR purification kit (Qiagen) and analyzed by quantitative real-time PCR on the ABI 7500-FAST System using the Power SYBR Green PCR Master Mix (Applied Biosystems).
ChIP–seq samples were sequenced using the Illumina Solexa Hiseq 2000 or NextSeq 500.

value: Znhit1 Knock Down

value: H2AZ, Abcam, ab4174


title: J1_Flag_Gas41_WT ChIP-seq

description: side-by-side control of Flag_Gas41_W93A ChIP

extract_protocol:
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_22.
ChIP analysis was performed as described previously (Li et al., 2014) with minor modification. In brief, cells were cross-linked with 1% formaldehyde for 10 min and stopped with 125 mM glycine for 5 min. Fixed cells were scraped from dishes and washed with PBS for 2 times. Cell pellets were resuspended with cell lysis buffer (5 mM PIEPES pH 8.0, 85 mM KCl, 1% NP-40) with protease inhibitor cocktail (Roche) and 10 mM phenylmethanesulfonyl fluoride (PMSF). After 20 min rotation in 4 °C, cell nuclei were pelleted by centrifugation. The nuclei were resuspended with nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) containing protease inhibitors and sonicated using Bioruptor Sonicator (Diagenode). Length of most sheared DNA fragments were between 100-400 base pairs. Sonicated chromatin contains approximately 20-30 μg of DNA were diluted 4 fold with dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.01% SDS) and were subjected to immunoprecipitation with 2–3 μg of antibodies overnight at 4 °C. Protein A/G beads (Millipore) were then added and incubated for 2 hr. The immunoprecipitates were washed twice with low-salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and high-salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and then once with LiCl buffer (20 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP40, 1% Na-Deoxycholate). DNA was eluted with vigorously shaking in elution buffer (50 mM NaHCO3, 1% SDS) for 15 min and then reverse crosslink in the presence of 0.3M NaCl at 67 °C for 12 hr. DNA was purified using PCR purification kit (Qiagen) and analyzed by quantitative real-time PCR on the ABI 7500-FAST System using the Power SYBR Green PCR Master Mix (Applied Biosystems).
ChIP–seq samples were sequenced using the Illumina Solexa Hiseq 2000 or NextSeq 500.