title: Spt5V1008D_2i_Gro_2

city: Dallas

first: Xiaoying

last: Bai

state: Texas

address: 5323 Harry Hines Blvd., J7.130

department: Department of Obstetrics and Gynecology

institute: UT Southwestern Medical Center

description: run-on nascent transcripts

data_processing:
Library strategy: GRO-seq
The GRO-seq reads were aligned to the mm10 mouse reference genome using the BWA aligner (Li and Durbin, 2010) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome by using the writeWiggle function in the GRO-seq package  for presentation as genome browser tracks  (Quinlan et al, 2010).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: mouse E14 embryonic stem cells

growth_protocol: Embryonic stem cells were cultured without feeders in the presence of leukaemia inhibitory factor (LIF) either in medium containing 15% fetal bovine serum or in serum-free medium containing the MEK inhibitor PD0325901 (1uM) and the Gsk3 inhibitor CH99021 (3uM), together known as 2i. E14Tg2a cells are male ES cells of 129 background, established and grown in serum without feeders according to standard protocols.

extract_protocol:
Cells were pelleted, washed twice with ice-cold PBS and kept on ice. Lysis buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 3 mM CaCl2, 2 mM MgCl2, 0.5 % NP40, 0.5 mM DTT, 300 mM sucrose, 1X protease inhibitor cocktail and SUPERase-In) was added and cells were pipetted up and down through 1 ml tips to release nuclei. The nuclei were washed twice with lysis buffer and resuspended in 100ul freezing buffer (50 mM Tris-HCl, pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1mM EDTA, and 4 units of SUPERase-In per mL). 5 x 106 nuclei were used for each library. Nuclear run-on performed as previously described (Williams et al 2015)
library construction were performed as previously described  (Franco et al., 2015)

tag: cell type

value: Spt5 mutant ES-cells

tag: culture

value: serum-free medium of MEK and Gsk3 inhibitors


title: E16.5_Ctrl_rep1 (RNA-seq)

status: Public on Dec 08 2017

type: SRA

city: Freiburg

first: Holger

last: Greschik

address: Breisacher Strasse 66

department: ZKF

country: Germany

institute: University Medical Center Freiburg

library_source: transcriptomic

data_processing:
Reads were aligned to the mm10 build of the mouse genome using TopHat version 2.
Aligned reads were counted with the Homer software (analyzeRepeats) and differentially expressed genes identified using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: Excel tables containing normalized read counts obtained from edgeR

molecule: total RNA

organism: Mus musculus

source_name: skeletal muscle

extract_protocol:
Trizol extraction of total RNA (according to the manufacturer's instructions) from skeletal muscle of front and hind limb of fetuses at E15.5 and E16.5, and from tibialis anterior of mice at three weeks of age (P21).
RNA samples were sequenced by the standard Illumina protocol to create raw sequence files (.fastq).

tag: strain

tag: tissue

value: skeletal muscle

tag: age


title: E16.5_KO_rep1 (RNA-seq)


title: WT_2i_Gro_3

country: USA

description: run-on nascent transcripts

value: wild type ES-cells


title: BisPCR2_F2_control_2

city: Olso

first: Jorke

last: Kamstra

address: Ullevålsveien 72

department: Basic Sciences and Aquatic Medicine

country: Norway

institute: Norwegian University of Life Sciences

description:
BisPCR2
processed data file:
Results_BisPCR2.xlsx

library_source: genomic

data_processing:
Trimming was performed with trim_galore (v0.4.1) with the following parameters: BisPCR2:  trim_galore –fastqc --paired --clip_R1 20 --clip_R2 20
Bismark (0.15) mapping was performed with the following parameters:   bismark –bowtie2 -N 0 -L 30 --score_min L,0,-0,4
BisPCR2: Data from Bismark methylation extractor loaded into Seqmonk (v0.33) genome browser. Used the logistic regression filter in R to assess differential methylation
genome build: GRCz10
processed data files format and content: Processed data files are in excel format. They represent differential methylated sites or regions, as analyzed by Seqmonk or MethylKit.

molecule: genomic DNA

organism: Danio rerio

source_name: 5.5 hpf zebrafish embryos

extract_protocol:
DNA was purified with the Gentra puregene tissue DNA extraction kit (Qiagen, Germany), with modifications. Embryos were lysed in 300 µL lysis buffer and disrupted with the use of a 20G needle. To remove RNA, 5 µL of 20 mg/mL RNAse A (Qiagen, Germany) was added, followed by an overnight proteinase K incubation (20 µL of 20 mg/mL) (Qiagen, Germany) at 65 °C, under continuous shaking at 300 rpm. Following incubation, an extra 5 µL RNAse A was added and incubated at room temperature for 1 hr to ensure complete removal of RNAs. Protein precipitation buffer (supplied by kit) was added (100 µL) and after vigorously shaking, the precipitate was centrifuged at 13000 rpm for 3 min. Supernatant was added to a 1.5 mL reaction tube containing 300 µL isopropanol, supplemented with 90 µL of 3M sodium acetate (pH 5.3). The mixture was mixed by inverting 50 times and centrifuged for 1 min at 13000 rpm. Supernatant was discarded and the pellet was rinsed twice with 70 % freshly prepared ethanol (300 µL) by gentle shaking and centrifugation at 13000 rpm for 1 min. The pellet was air dried for 5 minutes and resuspended in hydration buffer, supplied with the kit. DNA was assessed for RNA contamination and length with gel electrophoreses and measured for concentration and quality by Nanodrop (ND-1000; Thermo Scientific). DNA was stored at -20 °C until further analysis.
We used the BisPCR2 method (Bernstein et al. 2015), which was adapted at our lab and is extensively described (Kamstra et al. 2017). In short, the method uses specific developed primers for bisulfite converted DNA (Epitect kit, Qiagen, Germany), with an Illumina adapter overhang (Supplemental material, Table 1). Primers were developed using the online Bisearch tool (http://bisearch.enzim.hu/), and validated for specificity and amplicon size by gel electrophoresis, as described previously (Kamstra et al. 2017). From every bisulfite converted DNA sample, PCRs for each of the 20 targets were performed, these were pooled in equal volumes, purified (PCR purification kit, Qiagen, Germany) and subjected to a second PCR with Illumina specific barcoded primers (sequences described previously (Bernstein et al. 2015)). Following the second PCR, products were purified with AMPure XP beads (Beckman Coulter, USA), and measured using Qubit. Random samples were analyzed on the Agilent 2100 bioanalyzer for library quality, which showed high quality libraries (data not shown). Concentrations were converted to nM with c (nM) = (Qubit conc (ng/µL) * 1000000) / (660 * average length). All second PCR products were pooled in equimolar portions to a final concentration of 2 nM, followed by 150 base paired end sequencing analysis on Miseq (Illumina, US) as described previously (Bernstein et al. 2015).
DNA was purified with the Gentra puregene tissue DNA extraction kit (Qiagen, Germany), with modifications. Embryos were lysed in 300 µL lysis buffer and disrupted with the use of a 20G needle. To remove RNA, 5 µL of 20 mg/mL RNAse A (Qiagen, Germany) was added, followed by an overnight proteinase K incubation (20 µL of 20 mg/mL) (Qiagen, Germany) at 65 °C, under continuous shaking at 300 rpm. Following incubation, an extra 5 µL RNAse A was added and incubated at room temperature for 1 hr to ensure complete removal of RNAs. Protein precipitation buffer (supplied by kit) was added (100 µL) and after vigorously shaking, the precipitate was centrifuged at 13000 rpm for 3 min. Supernatant was added to a 1.5 mL reaction tube containing 300 µL isopropanol, supplemented with 90 µL of 3M sodium acetate (pH 5.3). The mixture was mixed by inverting 50 times and centrifuged for 1 min at 13000 rpm. Supernatant was discarded and the pellet was rinsed twice with 70 % freshly prepared ethanol (300 µL) by gentle shaking and centrifugation at 13000 rpm for 1 min. The pellet was air dried for 5 minutes and resuspended in hydration buffer, supplied with the kit. DNA was assessed for RNA contamination and length with gel electrophoreses and measured for concentration and quality by Nanodrop (ND-1000; Thermo Scientific). DNA was stored at -20 °C until further analysis.

value: whole embryos

value: AB

value: 5.5 hpf

tag: parental treatment

value: control

tag: generation


title: E15.5_Ctrl_rep4 (RNA-seq)


title: Spt5V1008D_2i_Gro_1

description: run-on nascent transcripts


title: WT_2i_Gro_2

description: run-on nascent transcripts


title: WT_2i_Gro_1

description: run-on nascent transcripts


title: E15.5_Ctrl_rep2 (RNA-seq)


title: WT_serum_Gro_2

description: run-on nascent transcripts

value: serum


title: E15.5_Ctrl_rep3 (RNA-seq)


title: BisPCR2_F2_control_1


title: BisPCR2_F1_exposed_5

value: 8.7 mGy/h


title: P4D7C5(FLXist)_24hDox_R2

city: Oxford

first: Guifeng

last: Wei

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

data_processing:
The libraries were sequenced by Illumina HiSeq 2000 or NextSeq 500.
The raw reads were filtered by removing the reads mapping to rRNA bulid.
Filtered and adptor-removed reads were aligned to N-masked mm10 genome by STAR
Unique alignment were split by SNPsplit.
Allelic expression value and repression score were calculated by custom scripts.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig
Not all the samples have processed data. The bigwig files are generated for the samples which has been performed deep analysis on our studies.

source_name: mouse embryonic stem cells

growth_protocol: ES cells were grown in ES cell medium, which consisted of Dulbecco’s Modified Eagle Medium (DMEM, from Life Technologies) supplemented with 9% foetal calf serum (FCS, from Seralab), 2mM L-glutamine, 1x non-essential amino acids, 50 μM β-mercaptoethanol, 50g/mL penicillin/streptomycin (all from Invitrogen) and LIF- conditioned medium, made in house, at a concentration equivalent to 1000U/mL. Non-differentiating ES cells were grown on tissue culture dishes coated with PBS+1% gelatine. EC10 medium consisted of DMEM, supplemented with 9% FCS, 2mM L-glutamine, 1x non-essential amino acids, 50 μM β-mercaptoethanol and 50 g/mL penicillin/streptomycin. Cells were grown at 37ºC in a humid atmosphere with 5% CO2. Cells were passaged using 0.05% trypsin-EDTA (Life Technologies) with 2% Chicken Serum (Life Technologies) and frozen in FCS + 10% DMSO.

extract_protocol:
Total RNAs were extracted according to TRIzol manuals, followed by DNaseI treatment.For each μg of total RNA, 2μL of Biotin-HPDP (Pierce, 50mg EZ-Link Biotin-HPDP), previously dissolved in DMF at a concentration of 1mg/mL, and 1μL of 10xBiotinylation buffer (100mM Tris HCl pH 7.4, 10mM EDTA), were added. The reaction was incubated with rotation for 15 min at 25ºC. Biotinylated 4sU-RNA was recovered using the μMacs Streptavidin Kit.
Illumina TruSeq Stranded Total RNA Library Prep Kit

treatment_protocol: Xist expression driven by TetO promoter was induced by adding doxycycline (1.5μg/mL) to the culture medium for 24 hours to 3 days. To achieve differentiation, ES cells were plated at a low density (0.6·10^6 cells) in 14cm non-gelatineised tissue culture dishes in EC10 medium, and grown in LIF-depleted conditions for 72 hours. 4sU was thawed just before use and added to the cells in the growing media at a concentration of 500μM. Cells were incubated with the 4sU-implemented medium for 12 minutes.

tag: strain background

value: 129S1 x Cast

tag: gender

value: male

tag: cell line

value: Cell line integrating with FLXist randomly

tag: agent

value: Dox

tag: time point


title: BisPCR2_F1_exposed_4


title: E15.5_KO_rep3 (RNA-seq)


title: WGBS_exposed_3

description:
WGBS
processed data file:
Results_methylKit_WGBS.xlsx

data_processing:
Trimming was performed with trim_galore (v0.4.1) with the following parameters: WGBS: trim_galore --quality 20 --phred64 --paired --three_prime_clip_R1 2 --clip_R2 5 --three_prime_clip_R2 2 --fastqc
Bismark (0.15) mapping was performed with the following parameters:   bismark –bowtie2 -N 0 -L 30 --score_min L,0,-0,4
WGBS: Differential methylation was assessed with methylKit (v1.0.0) in R (v3.3.1). Differentially methylated regions were found using logistic regression with a sliding linear model (SLIM) (Akalin et al. 2012). Following import of the Bismark CpG calls in methylKit, we used a 99.9% percentile cut-off in read depth, in order to exclude areas with extremely high read depths due to either PCR bias or mapping to repeat regions. We generated 250 bp tiles with a sliding window of 125 bp and ran methylKit analysis on tiles with at least 5 mutually analyzed Cs with at least 5 reads per C.
Data from Bismark methylation extractor loaded into Seqmonk (v1.36) genome browser. (used to feature enrichment)
For visualization we used the Bsseq package (v 1.10.0) in R. Bsseq uses local likelihood smoothing and is specifically designed for WGBS data, with generally low coverage of CpG sites
genome build: GRCz10
processed data files format and content: Processed data files are in excel format. They represent differential methylated sites or regions, as analyzed by Seqmonk or MethylKit.

extract_protocol:
DNA was purified with the Gentra puregene tissue DNA extraction kit (Qiagen, Germany), with modifications. Embryos were lysed in 300 µL lysis buffer and disrupted with the use of a 20G needle. To remove RNA, 5 µL of 20 mg/mL RNAse A (Qiagen, Germany) was added, followed by an overnight proteinase K incubation (20 µL of 20 mg/mL) (Qiagen, Germany) at 65 °C, under continuous shaking at 300 rpm. Following incubation, an extra 5 µL RNAse A was added and incubated at room temperature for 1 hr to ensure complete removal of RNAs. Protein precipitation buffer (supplied by kit) was added (100 µL) and after vigorously shaking, the precipitate was centrifuged at 13000 rpm for 3 min. Supernatant was added to a 1.5 mL reaction tube containing 300 µL isopropanol, supplemented with 90 µL of 3M sodium acetate (pH 5.3). The mixture was mixed by inverting 50 times and centrifuged for 1 min at 13000 rpm. Supernatant was discarded and the pellet was rinsed twice with 70 % freshly prepared ethanol (300 µL) by gentle shaking and centrifugation at 13000 rpm for 1 min. The pellet was air dried for 5 minutes and resuspended in hydration buffer, supplied with the kit. DNA was assessed for RNA contamination and length with gel electrophoreses and measured for concentration and quality by Nanodrop (ND-1000; Thermo Scientific). DNA was stored at -20 °C until further analysis.
We analyzed 3 control and 3 exposed F1 DNA samples for WGBS. From each sample, DNA concentration was analyzed by the Qubit system (Life technologies, Norway). To each sample 0.1% lambda DNA was added to measure bisulfite conversion efficiency. DNA was disrupted into 200-300 bp fragments using the Covaris system (S220, Covaris, US). Library was prepared by the Illumina tru-seq DNA methylation kit (Illumina, US). DNA was terminal repaired, A-ligated, followed by ligation of methylated adapters according to the Illumina tru-seq protocol. Each library was bisulfite converted using the EZ DNA methylation gold kit (Zymo Research, US). Subsequently, the library was size selected and PCR amplified. Library was checked for quality by Qubit measurements and for size by Agilent bioanalyzer 2100, and finally by QPCR. Each library was analyzed on a separate lane on the Hiseq 4000 (Illumina, US) in paired end mode using 150 bp sequence length.
DNA was purified with the Gentra puregene tissue DNA extraction kit (Qiagen, Germany), with modifications. Embryos were lysed in 300 µL lysis buffer and disrupted with the use of a 20G needle. To remove RNA, 5 µL of 20 mg/mL RNAse A (Qiagen, Germany) was added, followed by an overnight proteinase K incubation (20 µL of 20 mg/mL) (Qiagen, Germany) at 65 °C, under continuous shaking at 300 rpm. Following incubation, an extra 5 µL RNAse A was added and incubated at room temperature for 1 hr to ensure complete removal of RNAs. Protein precipitation buffer (supplied by kit) was added (100 µL) and after vigorously shaking, the precipitate was centrifuged at 13000 rpm for 3 min. Supernatant was added to a 1.5 mL reaction tube containing 300 µL isopropanol, supplemented with 90 µL of 3M sodium acetate (pH 5.3). The mixture was mixed by inverting 50 times and centrifuged for 1 min at 13000 rpm. Supernatant was discarded and the pellet was rinsed twice with 70 % freshly prepared ethanol (300 µL) by gentle shaking and centrifugation at 13000 rpm for 1 min. The pellet was air dried for 5 minutes and resuspended in hydration buffer, supplied with the kit. DNA was assessed for RNA contamination and length with gel electrophoreses and measured for concentration and quality by Nanodrop (ND-1000; Thermo Scientific). DNA was stored at -20 °C until further analysis.


title: E15.5_Ctrl_rep1 (RNA-seq)


title: E15.5_KO_rep2 (RNA-seq)


title: BisPCR2_F1_exposed_3


title: WGBS_exposed_2


title: E16.5_Ctrl_rep2 (RNA-seq)


title: E15.5_KO_rep1 (RNA-seq)


title: WT_2i_ATAC_2

data_processing:
The ATAC-seq reads were aligned to the mm10 mouse reference genome using the BWA aligner (Li and Durbin, 2010) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks  (Quinlan et al, 2010).
The seqeunce length was 33 for R1 and 33 for R2 for paired-end data.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

extract_protocol:
Cells were harvested with 0.25% trypsin for 5 minutes, collected, and counted. 50,000 cells were spun down at 500xg for 5 minutes at 4°C and washed once with 50µL of cold PBS. After a second wash at 500xg for 5 minutes at 4°C, cells were lyzed in 100 ul cold lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Cells were spun for 500xg for 10 minutes at 4°C and nuclei pellets were subjected to 50 ul Transposase reaction (1X Tagmentation buffer, 2.5 ul Tn5 transposase enzyme (Illumina)) and incubated for 30min at 37°C. Subsequent steps of the protocol were performed as described in PMID: 24097267.
library construction were performed as previously described  (Buenrostro et al., 2013)

value: ES-cells


title: BisPCR2_F1_exposed_2


title: WGBS_control_3


title: ΔbaaR [SC-215-3m_S12]

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
The obtained RNA-seq reads were aligned to the genome sequence of B. abortus 2308 (RefSeq AM040265) using the readmapper tool in CLC Genomics Workbench (Qiagen) (mismatch cost=2; insertion cost=3, deletion cost=3, length fraction=0.8, similarity fraction=0.8)
Differential expression analysis of normalized data and false-discovery rate (FDR) p-values were calculated in CLC Genomic Workbench.

Supplementary_files_format_and_content: normalized counts for each gene on each chromosome across all samples. Please note that B. abortus has two chromosomes. Thus there are two speadsheets for each sample;  one for chromosome 1 (I) and one for chromosome 2 (II); in the 'normalized_expression_table.xlsx' (with total 12 spreadsheets).

organism: Brucella abortus

source_name: ΔbaaR_cell culture

growth_protocol: B. abortus strains (WT and ΔbaaR) were incubated overnight in 5 ml Brucella broth at 37°C with shaking at 220 rpm

extract_protocol:
Hot-phenol RNA extraction
Libraries were prepared with Illumina TruSeq RNA kit according to manufacturer’s instructions and were then quantified using a 2100 Bioanalyser (Agilent) and sequenced on a HiSeq2500 (Illumina).

treatment_protocol: The next morning, the OD600 of the cultures was adjusted to 0.1 in 3 ml BB and grown for another 6 hours at 37°C with shaking at 220 rpm. Cultures (final OD600 ~0.3–0.4) were then pelleted, and the cells were immediately frozen at -80°C until RNA extraction

tag: genotype/variation

value: bab2_0215 (baaR) deleted


title: BisPCR2_F1_exposed_1


title: ΔbaaR [SC-215-2m_S11]


title: BisPCR2_F1_control_4


title: ΔbaaR [SC-215-1m_S10]


title: The CK group that was grown at 25/15°C under 300 μmol m-2 s-1.

city: Zhengzhou

first: Wang

middle: jia

last: wan

state: Henan

address: Wenhua Road

department: academy of forestry

country: China

institute: Henan Agricultural University

description: CK

data_processing:
The raw data (raw reads) in fastq format were first processed using in-house Perl scripts. In this step, clean data (clean reads) were obtained by removing reads that contained adapters or poly-Ns and low-quality reads from the raw data. The Q20 and Q30 values, GC content and sequence duplication levels of the clean data were calculated. All downstream analyses were based on high-quality, clean data.
The left files (read1 files) from all libraries/samples were pooled into one large left.fq file, and the right files (read2 files) were pooled into one large right.fq file. The transcriptome assembly was accomplished based on the left.fq and right.fq files using Trinity with min_kmer_cov set to 2 by default and all other parameters set to default.

organism: Begonia x semperflorens-cultorum

source_name: leaf

extract_protocol:
A total of 3 μg of RNA per sample was used as the input material for RNA sample preparation. Sequencing libraries were generated using a NEBNext®Ultra™ RNA Library Prep Kit from Illumina® (New England Biolabs, Ipswich, Massachusetts, USA) following the manufacturer’s recommendations. Index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T-oligo-conjugated magnetic beads.
RNA library were prepared for sequencing using Illumina protocol

tag: ecotype

value: Super Olympia

value: leaf

tag: growth


title: The High Light group that was grown at 25/15°C under 500 μmol m-2 s-1.

description: HL


title: The Low Temperature group that was grown at 15/5°C under 300 μmol m-2 s-1

description: LT

value: grown at 15/5°C under 300 μmol m-2 s-1


title: wild type [SC-WT-2m_S8]

source_name: wild-type_cell culture

value: wild type


title: WT_serum_Gro_1

description: run-on nascent transcripts

value: wild type ES-cells


title: BisPCR2_F1_control_2

value: whole embryos


title: wild type [SC-WT-3m_S9]


title: BisPCR2_F1_control_1

value: AB


title: BisPCR2_F1_control_3

value: 5.5 hpf


title: WGBS_exposed_1


title: wild type [SC-WT-1m_S7]


title: nuclei-ctx-PTZ2

status: Public on Dec 07 2017

city: Philadelphia

first: Hao

last: Wu

state: PA

address: 415 Curie Boulevard

department: Genetics

institute: University of Pennsylvania

data_processing:
Paired-end sequencing reads of Single-cell/nucleus RNA-seq were processed using publicly available the Drop-Seq Tools v1.12 software. Briefly, each mRNA read (read2) was tagged with the cell barcode (bases 1 to 12 of read 1) and unique molecular identifier (UMI, bases 13 to 20 of read 1), trimmed of sequencing adaptors and poly-A sequences, and aligned using STAR v 2.5.2a to the mouse (mm10, Gencode release vM13) or a concatenation of the mouse and human (for the species-mixing experiment) reference genome assembly. Because a substantial proportion (~50%) of reads derived from nuclear transcriptomes of mouse cortices were mapped to the intronic regions, the intronic reads were retained for downstream analysis. A custom Perl script was implemented in the Drop-Seq Tools pipeline to retrieve both exonic and intronic reads mapped to predicted strands of annotated genes. Uniquely mapped reads were grouped by cell barcodes. Cell barcodes were corrected for possible bead synthesis errors, using the DetectBeadSynthesisErrors program from the Drop-Seq Tools v1.12 software. To generate digital expression matrix, a list of UMIs in each gene (as rows), within each cell (as columns), was assembled, and UMIs within ED = 1 were merged together. The total number of unique UMI sequences was counted, and this number was reported as the number of transcripts of that gene for a given cell.
Genome_build: mm10
Supplementary_files_format_and_content: gene expression matrix containing read counts for each gene (rows) in each cell/nucleus (columns)

source_name: Animal #17

growth_protocol: Mouse NIH3T3 cells were purchased from ATCC and were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) (Life Technologies) supplemented with 10% fetal bovine serum (FBS) (Life Technologies) and 2 mM L-glutamine (Life Technologies) at 37°C in 5% CO2. The culture was passaged every 2-3 days using 0.05% Trypsin (Life Technologies). Mice were group-housed in cages of three to five in a 12-h light/dark cycle with food and water provided ad libitum. All mice used for experiments were naive to behavioral assays and other procedures.

extract_protocol:
Mouse brains (postnatal 6-10 weeks) were rapidly resected on ice. Cortices were freshly processed or flash frozen in liquid nitrogen for 2 minutes and subsequently kept at -80°C before nuclear isolation. Briefly, 14 mL of sucrose cushion was added to the bottom of centrifuge tubes (Beckman Coulter). Using a glass homogenizer (Wheaton), a freshly isolated or frozen mouse cortex sample was subjected to dounce homogenization (21 times with loose pestle followed by 7 times with tight pestle) in 12 mL of homogenization buffer. For in vitro cultured cells, cell pellets (~5 million cells) were resuspended in homogenization buffer and dounced 20 times with a loose pestle. Homogenates (~12 mL) were layered onto the sucrose cushion in the centrifuge tubes, and 10 mL of homogenization buffer was added atop of the homogenates. The tubes were then centrifuged in a Beckman Coulter L7-65 Ultracentrifuge at 25,000 rpm at 4°C for 2 hours using a Beckman Coulter SW28 swinging bucket rotor (Beckman Coulter). The supernatant was carefully removed via aspiration. 1 mL of chilled DPBS with protease and RNase inhibitor (Lucigen) was added to resuspend the nuclear pellet, and nuclei were subsequently transferred to a 1.5-mL tube. Nuclei were pelleted at 5,000 rpm for 10 min at 4°C, and then resuspended in 0.01% BSA (Sigma-Aldrich) in DPBS. After resuspension, nuclei were filtered through a 40-μm cell strainer (Fisher Scientific), visually inspected for morphology and quality assurance, and counted using a Fuchs-Rosenthal counting chamber before droplet microfluidic encapsulation.
Single cell or nucleus RNA sequencing was performed using the Drop-Seq method. Briefly, single cells, polyA-containing barcoded beads (ChemGenes), and droplet generation oil (Bio-Rad) were each flowed into individual input ports on a microfluidic device (uFluidix). Cells in droplets were lysed and hybridized to beads. Beads were isolated and subjected to reverse transcription (Thermo Fisher) and exonuclease I (NEB) treatment, followed by PCR of full length transcripts (Kapa). Final libraries were created by tagmentation of cDNA (Illumina), and amplified by PCR and purified by SPRI beads.

treatment_protocol: For pentylenetetrazole (PTZ)-induced seizures, 10-week old, wild type, male F1 mice from a C56BL/6J to FVB/NJ breeding were used. Mice were injected intrapertitoneally with PTZ at 50 mg/kg body weight (n=2) or received an injection with saline as a control (n=2). One hour after injection, the mice were sacrificed and nuclei were immediately isolated from the cortex for sNucDrop-Seq analysis.

value: whole cortex + striatum

tag: age (approx)

value: 8 weeks

tag: treatment

value: PTZ

tag: Sex

value: Male

tag: datatype

value: sNucDrop-Seq

tag: molecule

value: Nuclear RNA


title: WT_2i_ATAC_1

tag: strain

tag: cell type

tag: culture

value: serum-free medium of MEK and Gsk3 inhibitors


title: WGBS_control_2

tag: tissue

tag: age

tag: parental treatment

value: control

tag: generation


title: S427F DMSO 2

city: St. Louis

first: Vivek

middle: K

last: Arora

state: MO

address: 660 S Euclid Ave

institute: Washington University School of Medicine

data_processing:
Basecalling with Illumina RTA 1.18.64 for the HiSeq 2500 samples and Illumina RTA 2.7.3 for the HiSeq 3000 samples
Demultiplexing with custom demultipler written in python
Technical replicate fastq files were combined and aligned with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and annotated with Ensembl Biomart
Genome_build: Ensembl GRCh38.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text table

organism: Homo sapiens

source_name: urinary bladder carcinoma cells

growth_protocol: Cells were seeded in biological triplicate in 6-well tissue culture plates at 300,000 cells (JMSU-1) or 125,000 (575A) cells per well.  48 hours later, 0.1% DMSO or 1 µM pioglitazone was added to cells.  RNA was isolated 16-17 hours after addition of drugs.  Cells were cultured in recommended medium supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin, and 1x GlutaMAX Supplement.  Cells were grown at 37°C in 5% CO2

extract_protocol:
RNeasy Mini Kit (Qiagen) was used to isolate RNA from cell pellets
Ribosomal RNA was removed by poly-A selection using Oligo-dT beads. mRNA was then fragmented and reverse transcribed to yield double stranded cDNA using random hexamers. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 cycles using primers incorporating unique index tags.

treatment_protocol: Cells were cultured in 0.1% DMSO or 1 uM pioglitazone for 16-17 hours prior to RNA extraction

value: bladder

tag: cell line

tag: passages

tag: drug treatment

value: 0.1% DMSO


title: BisPCR2_F1_control_5


title: S427F DMSO 3


title: nuclei-ctx-PTZ1

source_name: Animal #15


title: WGBS_control_1


title: WT Pio 3

value: 1 uM pioglitazone


title: nuclei-ctx-saline1

source_name: Animal #14

value: Saline


title: nuclei-ctx-11

source_name: Animal #11

value: whole cortex

value: 6-10 weeks


title: WT Pio 2


title: nuclei-ctx-12

source_name: Animal #12


title: WT Pio 1


title: S427F DMSO 1


title: nuclei-ctx-7

source_name: Animal #7


title: nuclei-ctx-saline2

source_name: Animal #16


title: WT DMSO 2


title: nuclei-ctx-8

source_name: Animal #8


title: WT DMSO 1


title: nuclei-ctx-6

source_name: Animal #6


title: WT DMSO 3


title: nuclei-ctx-13

source_name: Animal #13


title: nuclei-ctx-5

source_name: Animal #5


title: nuclei-ctx-4

source_name: Animal #4


title: nuclei-ctx-3

source_name: Animal #3


title: DMSO repeat 1

city: Shanghai

first: Cheng

last: Luo

state: Shanghai

address: No. 555 Zuchongzhi Road

institute: Shanghai Institute of Materia Medica

description:
MDA-MB-231 cells treated with DMSO repeat 1, R1
cpd1-con-1-ATCACG_L006

data_processing:
tophat2 with default parameters
samtools to sort and convert the file format
cufflinks with default parameters
cuffmerge with default parameters
cuffdiff with default parameters
Genome_build: mm9
Supplementary_files_format_and_content: gene_exp.diff, generated by Cuffdiff, normalized expression values for each sample type

source_name: breast cancer

growth_protocol: density 1x10e7 MDA-MB-231 cells in 15cm dish, 24 hours, to 70% confluentence

extract_protocol:
2100 Bioanalyzer for quality check, DNaseI (Takara, Japan) for digestion at 37 C and 30 mins
100ng purified RNA, NEBNext® UltraTM RNA Library Prep Kit for Illumina (NEB, USA)

treatment_protocol: treatment with compounds or DMSO, after 24 hours

value: MDA-MB-231 cells

tag: agent

value: DMSO


title: inhibitor 100uM repeat 1

description:
MDA-MB-231 cells treated with inhibitor 100uM repeat 1, R1
cpd1-100-1-GCCAAT_L006

value: inhibitor


title: nuclei-ctx-2

source_name: Animal #2


title: inhibitor 100uM repeat 2

description:
MDA-MB-231 cells treated with inhibitor 100uM repeat 2, R1
cpd1-100-2-GATCAG_L006


title: DMSO repeat 2

description:
MDA-MB-231 cells treated with DMSO repeat 2, R1
cpd1-con-2-ACAGTG_L006


title: healthy donor bone marrow- sorted NK-cells

city: New Haven

first: Kavita

last: Dhodapkar

address: 333 Cedar Street

institute: Yale

data_processing:
Reads were aligned, filtered, de-duplicated, and converted into a digital count matrix using Cell Ranger 1.2 (10X Genomics)
Additional quality control (QC) was performed by visual inspection of QC plots using Seurat [Satija et al. Nat Biotech 33, 495-502 (2015)]. Outlier cells were identified and filtered based on (1) anomalously high mitochondrial gene expression (cells with >10% mitochondrial content were removed) and (2) potential doublets/multiplets, as identified by comparing the number of expressed genes detected by per cell versus the number of unique molecular identifiers (UMIs) detected per cell (cells with greater than 3000 expressed genes were removed). In addition, we clusters of B-cells (cells expressing CD79A, IGLC3, MS4A1, IGHM, and IGLC2), and myeloid cells (cells expressing CD14, S100A9, S100A8, and CSF3R).
To co-analyse both data-sets, an aggregate digital expression matrix was produced using Seurat, and then the above steps were carried out.
The processed files are combined digital expression matrix divided in three files for each of the sample.  The matrix.mtx file contains the values, barcodes.tsv contains the cell barcodes detected, and genes.tsv contains the list of genes detected.  The three files for each sample are copied in one folder, and this folder was read-in using the Seurat package.
For Seurat to work correctly the suffix for each file has to be removed.
Genome_build: hg38
Supplementary_files_format_and_content: The processed files are combined digital expression matrix divided in three files for each of the sample.  The matrix.mtx file contains the values, barcodes.tsv contains the cell barcodes detected, and genes.tsv contains the list of genes detected.  The three files for each sample are copied in one folder, and this folder was read-in using the Seurat package.

source_name: NK cells

growth_protocol: Bone marrow sample from a healthy donor was thawed and sorted for desired cell popualtion using flow associated cell sorter.

extract_protocol: To prepare the libraries for sequencing, the Chromium Gel Bead and Library Kit (10X Genomics) and Chromium instrument (10X Genomics) were used following manufacturer’s protocol. Further, the barcoded libraries were sequenced using HiSeq2500.

value: Bone marrow

value: Sorted live NK-cells


title: nuclei-ctx-10

source_name: Animal #10


title: nuclei-3T3

source_name: NIH3T3 (nuclei)

value: cultured NIH3T3 cells


title: healthy donor bone marrow- sorted ILC1s

source_name: ILC1 cells

value: Sorted live ILC1s


title: cell-3T3

source_name: NIH3T3 (cell)

value: Drop-Seq

value: Total RNA


title: Col-Wt rep 3 [RNA-Seq]

city: Amsterdam

first: Maike

last: Stam

address: Science Park 904

department: Swammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

description:
ColWt_3
(cDNA library)

data_processing:
Basecalls performed using Illumina’s real-time analysis software (RTA).
Quality filtering of RNA-seq reads were done using Trimmomatic (Q20).
RNA-seq reads were aligned to the TAIR10 genome assembly using Tophat.
RNA-seq reads were assembled using Cufflink.
Gene expression level calculation and differential expression analysis was done using Cuffquant, Cuffnorm and Cuffdiff.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited file containing gene expression level (RPKM) and differential expression data from Cuffdiff per line and per replicates.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Aerial rosette tissue

growth_protocol: Arabidopsis lines (epiRILs 92, 150, 193, 232 and epiHybrids 92H, 150H, 193H, 232H and Col-wt) were grown in a climate-controlled growth chamber in long day (16h light, 8h dark) conditions.

extract_protocol:
Plant tissues were ground in liquid nitrogen and RNA was extracted using a combination of trizol and the RNeasy Plant Mini Kit (Qiagen, Cat No./ID: 74903.
1-2μg RNA per sample were submitted for library preparation and sequencing on an Illumina HiSeq2500 instrument to Wageningen University (WUR)

treatment_protocol: Aerial rosette tissue 21/22 days after sowing (DAS) was harvested.

value: Aerial rosette tissue at 21/22 DAS (days after sowing)

tag: line

value: Col-Wt


title: D96M

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description: fovea/macula at D96M

data_processing:
FASTQ files were evaluated for quality control using FastQC (v0.11.5).
Raw reads were trimmed for Illumina adapter (SLIDINGWINDOW:4:5; LEADING:5; TRAILING:5; MINLEN:25) in Trimmomatic (v0.36)
Sequence alignment was performed using STAR (v2.5.2a) with reference assembly GRCh38.p3 and Ensembl annotation 82 with ENCODE options. Per sample, 2-pass transcriptome guided mapping was used.
RSEM (v1.2.31) was used to estimate gene and transcript expression levels.
Gene expected counts from RSEM output were TMM normalized using edgeR (v3.16.5)
Genome_build: GRCh38.p3 and Ensembl annotation 82
Supplementary_files_format_and_content: Text files containing raw transcript and gene counts and normalized gene CPM values

source_name: Retina

extract_protocol:
Tissues were dissected and homogenized in Trizol (Invitrogen, Carlsbad, CA) and stored at -80°C. Total RNA was extracted following manufacturer’s instructions. RNA integrity number (RIN) and quantity of RNA was assessed using Bioanalyzer RNA 6000 Pico Assay (Agilent Technologies, Santa Clara, CA). Average RIN for all samples was 8.6 and ranged from 6.8–10.
Strand-specific libraries were constructed with 100 ng of total RNA using TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, CA).

tag: age (days post conception)

tag: region

value: fovea/macula


title: nuclei-ctx-9

source_name: Animal #9

tag: age (approx)

tag: treatment

tag: Sex

value: Male

value: sNucDrop-Seq

value: Nuclear RNA


title: Col-Wt rep 2 [RNA-Seq]

description:
ColWt_2
(cDNA library)


title: D96NC

description: nasal central at D96NC

value: nasal central


title: D132NC

description: nasal central at D132NC


title: 232 rep 2 [RNA-Seq]

description:
232_2
(cDNA library)

value: epiRIL 232


title: 232 rep 1 [RNA-Seq]

description:
232_1
(cDNA library)


title: D73M

description: fovea/macula at D73M


title: 193 rep 3 [RNA-Seq]

description:
193_3
(cDNA library)

value: epiRIL 193


title: D59C

description: central retina at D59C

value: central retina


title: D96P

description: peripheral retina at D96P

value: peripheral retina


title: 150 rep 3 [RNA-Seq]

description:
150_3
(cDNA library)

value: epiRIL 150


title: D73P

description: peripheral retina at D73P


title: 150 rep 2 [RNA-Seq]

description:
150_2
(cDNA library)


title: 193 rep 2 [RNA-Seq]

description:
193_2
(cDNA library)


title: 193 rep 1 [RNA-Seq]

description:
193_1
(cDNA library)


title: 150 rep 1 [RNA-Seq]

description:
150_1
(cDNA library)


title: D59P-2

description: peripheral retina at D59P


title: D132P

description: peripheral retina at D132P


title: 92 rep 1 [RNA-Seq]

description:
92_1
(cDNA library)

value: epiRIL 92


title: D132

description: whole retina at D132

value: whole retina


title: D59P

description: peripheral retina at D59P


title: nuclei-ctx-1

source_name: Animal #1

value: whole cortex

value: 6-10 weeks

tag: datatype

tag: molecule


title: D125

description: whole retina at D125


title: D136

description: whole retina at D136


title: 92 rep 2 [RNA-Seq]

description:
92_2
(cDNA library)


title: 232H rep 2 [RNA-Seq]

description:
232H_2
(cDNA library)

value: epiHybrid 232


title: 193H rep 3 [RNA-Seq]

description:
193H_3
(cDNA library)

value: Aerial rosette tissue at 21/22 DAS (days after sowing)

value: epiHybrid 193


title: D115

description: whole retina at D115


title: 232H rep 1 [RNA-Seq]

description:
232H_1
(cDNA library)


title: D105

description: whole retina at D105


title: 193H rep 2 [RNA-Seq]

description:
193H_2
(cDNA library)


title: D94-2

description: whole retina at D94


title: D132M

description: fovea/macula at D132M

value: fovea/macula


title: 193H rep 1 [RNA-Seq]

description:
193H_1
(cDNA library)


title: D94

description: whole retina at D94


title: 150H rep 3 [RNA-Seq]

description:
150H_3
(cDNA library)

value: epiHybrid 150


title: D80

description: whole retina at D80


title: 150H rep 2 [RNA-Seq]

description:
150H_2
(cDNA library)


title: D67

description: whole retina at D67


title: Col-Wt rep 1 [RNA-Seq]

description:
ColWt_1
(cDNA library)

value: Col-Wt


title: 150H rep 1 [RNA-Seq]

description:
150H_1
(cDNA library)


title: D57

description: whole retina at D57


title: 92H rep 1 [RNA-Seq]

description:
92H_1
(cDNA library)

value: epiHybrid 92


title: D52/54

description: whole retina at D52/54


title: P4D7D1(DelXN)_NoDox

source_name: mouse embryonic stem cells

tag: strain background

value: 129S1 x Cast

tag: gender

value: male

value: Cell line integrating with XistDelXN randomly

value: Dox

tag: time point


title: RNA-seq IVC+2d rep2

city: Beijing

first: Wei

last: Xie

address: Zhongguancun north street

institute: Tsinghua University

description:
FPKM_IVC_D1-2.txt
Processed data file: FPKM_replicates.txt.gz

data_processing:
RNA-Seq reads were aligned to the mm9 genome assembly using Tophat2 version 2.0.11. The replicates were merged together, and transcript abundance (FPKM) was calculated based on Refseq annotation using Cufflinks version 2.0.2.
Genome_build: mm9
Supplementary_files_format_and_content: A tab-delimited text file includes RPKM values for each sample, available on the series record.

source_name: In vitro culture embryo

extract_protocol:
After removing the zona pellucida, ICM was isolated by immunosurgery and then directly lysed in hypotonic lysis buffer. RNA-Seq libraries were prepared using Smart-Seq2 protocol with slight modification.
RNA-Seq libraries were prepared using Smart-Seq2 protocol with slight modification.

treatment_protocol: C57BL/6N female mice were induced for superovulation by injections of 5 IU of pregnant mare’s serum gonadotrophin and 5 IU of human chorionic gonadotrophin (44-48 hours apart) and mated to DBA/2N males. Embryos were flushed out from uterus at E4.5 and cultured 1, 2 or 4 days in CMRL 1066 supplemented with 1mM glutamine, 1mM sodium pyruvate and 20% fetal bovine serum.

tag: strain

value: C57BL/6N x DBA/2N

tag: developmental stage

value: Embryo

tag: tissue

value: whole embryo


title: D53

description: whole retina at D53

value: whole retina


title: unc-8f-s3

city: Kansas City

first: Alejandro

last: Sanchez Alvarado

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

description: UNC RNAi 8 feedings replicate s3

data_processing:
Alignment with bowtie2 (-k 100)
Genome_build: Combined transcriptome of GDAG01, GCZZ01 and genbank S. mediterranea transcripts

organism: Schmidtea mediterranea

source_name: Whole Animal

extract_protocol: PolyA selection

tag: biotype

value: Sexual S2F2


title: RNA-seq IVC+2d rep1


title: unc-8f-s2

description: UNC RNAi 8 feedings replicate s2


title: unc-8f-s1

description: UNC RNAi 8 feedings replicate s1


title: RNA-seq IVC+1d rep2


title: D107

description: whole retina at D107


title: RNA-seq IVC+1d rep1


title: unc-8f-1

description: UNC RNAi 8 feedings replicate 1


title: unc-7f-s1

description: UNC RNAi 7 feedings replicate s1


title: unc-6f-s2

description: UNC RNAi 6 feedings replicate s2


title: dgKlotho rep3

city: La Jolla

first: Hsin-Kai

last: Liao

address: 10010 N. Torrey Pines Rd.

institute: Salk Institute

description:
mRNA (oligo-dT selected)
K_3_S46_R1_001

data_processing:
Reads were aligned by STAR. Only the reads aligned uniquely to one genomic location were retained.
Reads Per Kilobase of transcript per Million mapped reads (RPKM) were calculated using Cufflink
Genome_build: mm9
Supplementary_files_format_and_content: XLSX files contain gene expression information (RPKM) in each samples

growth_protocol: 8 - 12 weeks old Cas9 transgenic mice

extract_protocol:
Total RNA was extracted from injected mouse liver using the Trizol reagents
Libraries were prepared according to Illumina's instructions accompanying TruSeq Stranded mRNA Library Prep Kit. Briefly, total RNA (0.5µg) from each sample was used to isolate poly(A) mRNA. Steps involved in library preparation were mRNA fragmentation, first strand cDNA synthesis followed by second strand cDNA synthesis and adaptor ligation, cDNA fragments isolation and amplification.

treatment_protocol: AAV-dgRNAs injected through tail vein for 8 days, followed by 4 days cisplatin treatments

value: liver

tag: genotype

value: Cas9 homozygous

tag: age

value: 8-12 weeks old


title: unc-6f-s1

description: UNC RNAi 6 feedings replicate s1


title: dgKlotho rep1

description:
mRNA (oligo-dT selected)
K_1_S22_R1_001


title: unc-6f-1

description: UNC RNAi 6 feedings replicate 1


title: dgIL-10 rep2

description:
mRNA (oligo-dT selected)
I_3_S45_R1_001


title: dgIL-10 rep3

description:
mRNA (oligo-dT selected)
I_4_S71_R1_001


title: dgMock rep3

description:
mRNA (oligo-dT selected)
C_3_S23_R1_001


title: unc-4f-s1

description: UNC RNAi 4 feedings replicate s1


title: unc-4f-s2

description: UNC RNAi 4 feedings replicate s2


title: dgIL-10 rep1

description:
mRNA (oligo-dT selected)
I_2_S24_R1_001


title: unc-4f-s3

description: UNC RNAi 4 feedings replicate s3


title: dgMock rep1

description:
mRNA (oligo-dT selected)
C_1_S19_R1_001


title: unc-11f-s3

description: UNC RNAi 11 feedings replicate s3


title: dgMock rep2

description:
mRNA (oligo-dT selected)
C_2_S21_R1_001


title: unc-4f-1

description: UNC RNAi 4 feedings replicate 1


title: unc-11f-s2

description: UNC RNAi 11 feedings replicate s3


title: unc-11f-1

description: UNC RNAi 11 feedings replicate 1


title: D32.2

data_processing:
Fastq files were generated from reads passing chastity filter and used for further analysis. Illumina adapter, polyA, and polyT sequence trimming was performed with Trimmomatic v0.36.
Transcript level quantitation was performed using Kallisto v0.42.4 employing a merged transcript cDNA and ncRNA FASTA file downloaded from the Ensembl ftp site. Gene level quantification was generated by summarization of the transcript level quantitation using tximport v0.99.9 with the option “countFromAbundance=lengthScaledTPM”. The gene level count values were TMM normalized and converted to count per million (CPM) via edgeR.
Genome_build: GRCm38.p4 using Ensembl v84 annotation

source_name: iPSC-derived Retina organoids_D32

growth_protocol: The mouse Nrl-GFP wild-type (WT) induced pluripotent stem cells (iPSC) clone was generated, characterized and maintained as previously described (PMID: 27667917). Briefly, the iPSC clone was reprogrammed from fibroblasts of embryonic day 14.5 WT Nrl-GFP mice, by infection of individual Doxycyclin-inducible lentiviral vectors carrying Oct3/4, Sox2, Klf4, and c-Myc genes. Embryonic stem cell-like colonies were picked and evaluated by morphology, proliferation rate and Nanog expression. The selected Nrl-GFP iPSCs were maintained on feeder cells (Millipore) at 37℃, 5% CO2. Maintenance medium was comprised of Knockout DMEM (Life Technologies), 1x MEM non-essential amino acids (NEAA)(Sigma), 1x GlutaMAX (Life Technologies), 1x Penicillin-Streptomycin (PS) (Life Technologies), 2000 U/ml LIF (Millipore), and 15% ES cell-qualified fetal bovine serum (FBS) (Life Technologies). Media were full changed performed every day, with 1x 2-Mercaptoethanol (2-ME) (Life Technologies) freshly added. Cells were passaged using TrypLE Express (Life Technologies) every two days.

extract_protocol:
For RNA extraction, 1-2 million induced pluripotent stem cells or 36 D4 organoids were directly homogenized in 0.5 ml TriPure isolation reagent (Roche). Later time points, from D7 and onward, neural retina were dissected from intact retinal organoids (30 organoids at D7, 20 at D10, 12 from D12 to D32) using a moria nickel-plated pin holder (Fine Science Tools) with 0.25 mm-diameter tungsten needles (Fine Science Tools), before being lysed in 0.5 ml TriPure isolation reagent. RNA was extracted following manufacturer’s instructions and the quality was assessed using Agilent 4200 TapeStation system (Agilent).
Directional RNA-seq library construction was performed from 100 ng of high quality RNA (RIN > 8.0) using the Illumina Stranded mRNA Library Prep Kit (Illumina). Library construction from three biological replicates for all time points was performed.

treatment_protocol: Nrl-GFP iPSCs were differentiated into retinal organoids using the modified HIPRO protocol (PMID: 27667917). At differentiation day (D) 0, iPSCs were plated in PrimeSurface low adhesion U-shaped 96-well plate (Wako) at a density of 3000 cells per well in 100 ml retinal differentiation medium constituted by GMEM (Life Technologies), 1x NEAA (Sigma), 1x sodium pyruvate (Sigma) and 1.5%(v/v) knockout serum replacement (Life Technologies). 20 ml diluted Matrigel (120 ml >9.5 mg/ml Matrigel diluted in 900 ml retinal differentiation medium) (Corning) was added to each well at D1. At D7, Retinal organoids were transferred a 100 mm Poly(2-hydroxyethyl methacrylate) (Sigma)-coated petri dish with 10 ml DMEM/F12 with GlutaMAX (Life Technologies) supplemented with 1x N2 supplement (Life Technologies) and 1x PS (Life Technologies). From D10 to D26, retinal organoids were maintained in DMEM/F12 with GlutaMAX (Life Technologies), 1x PS (Life Technologies), 1x N2 supplement (Life Technologies), 1 mM taurine (Sigma), 500 nM 9-cis retinal (Sigma) and 100 ng/ml insulin-like growth factor 1 (Life Technologies). From D26 and onward, 1x NEAA acid (Sigma), 1x B27 supplement without Vitamin A (Life Technologies) and 2%(v/v) FBS (Atlanta Biologicals) were added to the culture. Half-media exchanges were performed every two days. 1x 2-ME was freshly added to media. The cultures were incubated in 5% O2 from D0 to D10 and in 20% O2 from D10 onwards.

tag: cell type source

tag: tissue/cell type

value: iPSC-derived Retina organoids


title: dgKlotho rep2

description:
mRNA (oligo-dT selected)
K_2_S25_R1_001


title: unc-11f-s1

description: UNC RNAi 11 feedings replicate s2


title: 84-8f-s3

description: NHR-1 RNAi 8 feedings replicate s3


title: D32.1

value: Nrl-GFP wild-type (WT) induced pluripotent stem cells (iPSC)


title: D25.2

source_name: iPSC-derived Retina organoids_D25


title: D25.3


title: D25.1


title: 84-8f-s2

description: NHR-1 RNAi 8 feedings replicate s2


title: 84-8f-s1

description: NHR-1 RNAi 8 feedings replicate s1


title: 84-8f-1

description: NHR-1 RNAi 8 feedings replicate 1


title: D22.3

source_name: iPSC-derived Retina organoids_D22


title: 84-6f-s3

description: NHR-1 RNAi 6 feedings replicate s3


title: D22.2


title: D32.3


title: 84-6f-1

description: NHR-1 RNAi 6 feedings replicate 1


title: D18.2

source_name: iPSC-derived Retina organoids_D18


title: 84-6f-s2

description: NHR-1 RNAi 6 feedings replicate s2


title: D18.3


title: 84-6f-s1

description: NHR-1 RNAi 6 feedings replicate s1


title: 84-4f-s3

description: NHR-1 RNAi 4 feedings replicate s3


title: D18.1


title: D15.3

source_name: iPSC-derived Retina organoids_D15


title: 92H rep 2 [RNA-Seq]

description:
92H_2
(cDNA library)

value: Aerial rosette tissue at 21/22 DAS (days after sowing)

tag: line


title: 84-4f-s1

description: NHR-1 RNAi 4 feedings replicate s1


title: D15.2


title: D15.1


title: 84-11f-s4

description: NHR-1 RNAi 11 feedings replicate s4


title: 84-4f-1

description: NHR-1 RNAi 4 feedings replicate 1


title: 84-11f-s3

description: NHR-1 RNAi 11 feedings replicate s3


title: D12.2

source_name: iPSC-derived Retina organoids_D12


title: 84-11f-s2

description: NHR-1 RNAi 11 feedings replicate s2


title: D12.3


title: D12.1


title: D10.3

source_name: iPSC-derived Retina organoids_D10


title: D22.1


title: 84-11f-1

description: NHR-1 RNAi 11 feedings replicate 1


title: D10.2


title: D10.1


title: 3C-seq of E. coli wt cells in exponential phase 30°C -Replicate 2

city: Paris

first: Axel

last: Cournac

address: 25 rue Dr. Roux

country: France

institute: Institut Pasteur

description: 3 % Formaldehyde

data_processing:
Library strategy: 3C-seq
3C-seq libraries were proccessed using the 3C-seq pipeline available at (https://github.com/koszullab/).
Removal of PCR duplicates based on the 20 first bp of the read containing a 6 nt random tag (home made script).
Iterative alignment, Min-leght=20, step=5, bowtie2 --very-sensitive
Filtering, Mapping quality=30, no ambiguous reads
Assignment to restriction fragment
Removal of un-informative events (uncuts, loops etc) as described in Cournac et al. BMC 2012.
Binning at 5kb.
Genome_build: E. coli MG1655 GenBank: U00096.2,total length : 4639675 bp
Supplementary_files_format_and_content: rna-seq: genomic position (middle of the 5kb-bin) to each count. 3C seq: contact maps (2D array of 928 5kb-bins x 928 5kb-bins).

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E coli cells

growth_protocol: E. coli cells were grown at 22°C, 30°C and 37°C in either Lennox Broth (LB) or liquid minimal medium A supplemented with 0.12% casamino acids and 0.4% glucose. The cultures were grown to OD600 = 0.2 (early exponential) or 2 (stationary phase).

extract_protocol:
For 3C-seq: ≈ 1-2 x 109 crosslinked cells (7% formaldehyde, unless otherwise stated ) are suspended in 600 μl Tris 10 mM EDTA 0.5 mM (TE) (pH 8) with 4 μl of lysozyme (35 U/μl; Tebu Bio), and incubated at RT for 20 minutes. SDS is added to the mix (final concentration 0.5%) and the cells are incubated for 10 minutes at RT. 50μl of lysed cells are then transferred in 8 tubes containing 450μL of digestion mix (1X NEB 1 buffer, 1% triton X-100, and 100U HpaII enzyme). DNA is digested for 3 hours at 37°C, split in 4 aliquots, and diluted in 8 ml ligation buffer (1X ligation buffer NEB without ATP, 1 mM ATP, 0.1 mg/ml BSA, 125 Units of T4 DNA ligase 5 U/μl). Ligation is then performed at 16°C for 4 hours, followed by incubation overnight (ON) at 65°C in presence of 250 μg/ml proteinase K and 5 mM EDTA. Precipitation of DNA is performed using an equal volume of 3 M Na-Acetate (pH 5.2) and two volumes of iso-propanol. After one hour at -80°C, DNA is pelleted, suspended in 500μl 1X TE buffer, and incubated for 30 minutes at 37°C in presence of RNAse A (0.03 mg/ml). DNA is then transferred into 2 ml centrifuge tubes, extracted twice with 500 μl phenol-chloroform pH 8.0, precipitated, washed with 1 ml cold ethanol 70% and diluted in 30 μl 1X TE buffer. All tubes are pooled and the resulting 3C library is quantified on gel using Quantity One software (BioRad).
3C-seq: 5 µg of a 3C library was suspended in water (final volume 130 µL) and sheared using a Covaris S220 instrument (Duty cycle 5, Intensity 5, cycles/burst 200, time 60 sec for 4 cycles). The DNA was purified and processed according to manufacturer instructions (Paired-End DNA sample Prep Kit – Illumina – PE-930-1001), except that DNA was ligated to custom-made adapters (see Marbouty M. et al, 2015, Mol Cell) for 4 hours at room temperature. Tubes were then incubated at 65°C for 20 minutes. DNA fragments ranging in size from 400 to 900 pb were purified using a PippinPrep apparatus (SAGE Science). For each library, four test PCR reactions were performed to determine the optimal number of PCR cycles (1 or 2 µL of the collected DNA, Illumina primers PE1.0 and PE2.0 using Taq Phusion [Finnzymes]). A large-scale PCR (8 reactions) was then set-up with the number of PCR cycles determined previously. The PCR product was finally purified on Qiagen MinElute columns and subject to paired-end sequenced on an Illumina sequencer.

tag: growth condition

value: MM + 0.12% casaminoacids +0.4% glucose at 30°C

value: F- lambda- ilvG- rfb-50 rph-1


title: 3C-seq of E. coli wt cells in exponential phase 30°C -Replicate 1


title: D7.3

source_name: iPSC-derived Retina organoids_D7


title: D7.1


title: 84-4f-s2

description: NHR-1 RNAi 4 feedings replicate s2


title: D4.2

source_name: iPSC-derived Retina organoids_D4


title: D7.2


title: D4.3


title: D0.3

source_name: iPSC-derived Retina organoids_D0


title: D4.1


title: D0.1


title: D0.2


title: E14_ZFP57-/-  SMAD1/5 rep2 ChIP-seq

city: Naples

first: Marco

last: Cammisa

state: Naples

address: Via Castellino Pietro, 111

country: Italy

institute: Institute of Genetics and Biophysics "A. Buzzati Traverso" (IGB-ABT)

data_processing:
Basecalls and adaptor trimming was performed using Illumina Pipeline Casava (v1.8.2).
Reads were aligned to the NCBI37/mm9 genome assembly using Bowtie (v1.1.1) with uniquely mapping options.
Duplicate mapped reads were removed. A bedGraph file format was built by normalizing total reads to reads per million (RPM) using BEDtools v2.14.3-1 and SAMtools v0.1.18 and subtracting input with DeepTools v2.2.3.0
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph file reports scores of genomic coverage

growth_protocol: WT and Zfp57 -/- E14 mESCs were cultured under standard feeder-free conditions on gelatinized tissue culture dishes with media containing DMEM (EuroClone ECM0101L) supplemented with 100 mM 2-beta-mercaptoethanol (Sigma), 1 mM sodium pyruvate, 2 mM L-glutamine, 1x penicillin–streptomycin, 15% fetal calf serum (HyClone) and 10^3 U/ml leukemia inhibitory factor (LIF, Millipore) at 37 °C under an atmosphere of 5% CO2.

extract_protocol:
ChIPs were performed on formaldehyde cross-linked chromatin isolated from cells grown on 10 cm dishes to ∼80% confluency. Briefly, formaldehyde was added to the attached cells suspended in Phosphate Buffered Saline (PBS) at a final concentration of 1% and the cells were incubated at room temperature for 10 min with shaking. The reaction was stopped by addition of glycine to a final concentration of 0.125 M. Approximately 2 × 107 cells were washed twice in ice-cold PBS, centrifuged and resuspended in lysis buffer 1 (50 mM HEPES pH 8, 10 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40 and 0.25% Triton X-100) for 90 min at 4 °C. Cells were lysed in lysis buffer 2 (10 mM Tris–HCl pH 8.0, 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA) for 60 min at 4 °C. The chromatin was sheared in sonication buffer (10 mM Tris–HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate and 0.5% N-lauroylsarcosine) to an average size of 200–600 bp using the Bioruptor™. For each immunoprecipitation, 100 μg of sonicated chromatin were diluted in a final volume of 1 ml with dilution buffer and pre-cleared with 30 μl protein A/G agarose beads (SantaCruz) for 4 h at 4 °C on a rotating wheel.  Anti-SMAD1 antibody or rabbit IgG were added to the pre-cleared chromatin and incubated overnight at 4 °C on a rotating wheel. Chromatin was precipitated with 30 μl protein A/G agarose beads for 4 h at 4 °C with rotation. The beads were then washed five times with 500 μl RIPA buffer (10 mM Tris–HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 1% Triton X-100 and 0.1% SDS) and once with each of the following buffers: WASH buffer (50 mM HEPES, 0.5% sodium deoxycholate, 1% Triton X-100, 1 mM EDTA, 500 mM NaCl and 0.2% NaN3), LiCl buffer (0.25 M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA and 10 mM Tris pH 8) and TE buffer (10 mM Tris pH 8, 1 mM EDTA). The bound chromatin was eluted in 100 μl TE buffer. Crosslinks were reversed by incubation O.N. at 65 °C after addition of 1 μl RNAse cocktail (Ambion) and 2 h at 50 °C after addition of 2.5 μl SDS 20% + 2.5 μl 20 mg/ml proteinase K (Sigma). The DNA was extracted by using the QIAquick PCR Purification Kit (Qiagen).
2 ng DNA of immunoprecipitated and input chromatin were used for Illumina library preparation. Libraries were generated by using the NuGen Ovation Ultralow Library System v2 Kit.

tag: cell type

value: Embryonic stem cells

tag: chip antibody

value: SMAD1/5 (Abcam, ab53745)


title: E14_ZFP57-/-  SMAD1/5 rep1 ChIP-seq


title: E14_ZFP57-/- Input ChIP-seq


title: E14 wildtype SMAD1/5 rep2 ChIP-seq

value: wild type


title: E14 wildtype Input ChIP-seq


title: E14 wildtype SMAD1/5 rep1 ChIP-seq


title: 3C-seq of E. coli matP cells in exponential phase 30°C -Replicate 1

value: F- lambda- ilvG- rfb-50 rph-1 [delta]matP::frt-cam-frt


title: SLX-15090_Input_2_none

city: York

first: Andrew

middle: Nicholas

last: Holding

address: Wentwork Way

department: Biology

institute: University of York

data_processing:
alignement, bowtie2 (v2.3.2)
blacklist filtering, bedtools (v2.25.0)
peakcalling, macs2 (2.1.1.2016030)
normalisation, Brundle (1.0.6)
differintial bnding analysis, Diffbind (2.5.6)
Genome_build: hg19
Supplementary_files_format_and_content: csv; Fold-chage in ER binding normalised to control

growth_protocol: MCF7 cells were grown in T175 flast in DEM + 10% FBS + Pen/Strep + Glutamine

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to the Thruplex DNA-seq Kit Manual

treatment_protocol: Treated samples were exposed to 100 nM E2 for 45 minutes or 2 hours

tag: cell line

tag: experiment number

value: mammary epithelial cells

value: H4K12ac (07-595,Millipore)

tag: control antibody

value: CTCF (3418 XP, Cell Signaling)

tag: treatment

tag: replicate

value: Input


title: SLX-15090_CTCF_none

value: CTCF


title: SLX-15090_1b_H4K12ac_2h

value: Estrogen


title: SLX-15090_2b_H4K12ac_2h


title: SLX-15090_CTCF_2h


title: SLX-15090_3a_H4K12ac_none


title: SLX-15090_Input_1_none


title: SLX-15090_3b_H4K12ac_2h


title: SLX-15090_2a_H4K12ac_none


title: P21.2

description:
PolyA RNA
Processed data file: Transcript_Counts.txt
Processed data file: Gene_Counts.txt
Processed data file: Gene_Normalized-CPM.txt
Processed data file: DifferentialExpression.txt

data_processing:
Fastq files were generated from reads passing chastity filter.
Transcript level quantitation was performed using Kallisto v0.42.4 employing a merged transcript cDNA and ncRNA FASTA file downloaded from the Ensembl v84 ftp site.
Gene level quantification was generated by summarization of the transcript level quantitation using tximport v0.99.9 with the option “countFromAbundance=lengthScaledTPM”. The gene level count values were TMM normalized and converted to count per million (CPM) via edgeR v3.13.9.
Genome_build: Assembly GRCm38.p5, Annotation Ensembl v84
Supplementary_files_format_and_content: *txt: Tab-delimited text files containing transcript level counts, gene level counts, normalized gene level counts-per-million, or differential expression results.

source_name: Retina at age P21

growth_protocol: Retinas for embryonic day E11, E12, E14, and E16 and postnatal day P0, P2, P4, P6, P10, P14, P21, and P28 were excised rapidly, frozen on dry ice, and stored at -80°C until use.

extract_protocol:
Fresh frozen mouse retinas were lysed with a mortar and pestle in Trizol Reagent, and total RNA was isolated per manufacturer’s protocol (Invitrogen, Carlsbad, CA). RNA quality and quantity were assessed with RNA 6000 Nano Kit (Agilent, Santa Clara, CA).
Directional RNA-seq library construction was performed as previously described (Brooks et al., 2012). Briefly, 100ng (embryonic days 11 and 12) or 1ug of total RNA was used for library construction using Illumina mRNA Library Prep Kit with modifications for directionality.

tag: strain/background

value: Retina


title: SLX-15090_1a_H4K12ac_none


title: SLX-15091_2b_ER_45min

value: ER  (sc-543, Santa Cruz)


title: SLX-15091_Input_45min


title: P14.1

source_name: Retina at age P14


title: P14.2


title: P21.1


title: SLX-15091_CTCF_none


title: SLX-15091_CTCF_45min


title: P10.2

source_name: Retina at age P10


title: P10.1


title: SLX-15091_3b_ER_45min


title: SLX-15091_3a_ER_none


title: P4.2

source_name: Retina at age P4


title: P28.2

source_name: Retina at age P28


title: SLX-15091_1a_ER_none


title: SLX-15091_Input_none


title: P28.1


title: RNA-seq of E. coli wt cells in stationary phase 30°C (30h) -Replicate 1

data_processing:
3C-seq libraries were proccessed using the 3C-seq pipeline available at (https://github.com/koszullab/).
Removal of PCR duplicates based on the 20 first bp of the read containing a 6 nt random tag (home made script).
Iterative alignment, Min-leght=20, step=5, bowtie2 --very-sensitive
Filtering, Mapping quality=30, no ambiguous reads
Assignment to restriction fragment
Removal of un-informative events (uncuts, loops etc) as described in Cournac et al. BMC 2012.
Binning at 5kb.
Genome_build: E. coli MG1655 GenBank: U00096.2,total length : 4639675 bp
Supplementary_files_format_and_content: rna-seq: genomic position (middle of the 5kb-bin) to each count. 3C seq: contact maps (2D array of 928 5kb-bins x 928 5kb-bins).


title: P2.1

source_name: Retina at age P2


title: P0.2

source_name: Retina at age P0


title: RNA-seq of E. coli wt cells in stationary phase 30°C (30h)

extract_protocol:
For RNA-seq: total RNA was extracted using RNeasy Protect Bacteria according to manufacturer instructions (QIAGEN - # 74524)
For 3C-seq: ≈ 1-2 x 109 crosslinked cells (7% formaldehyde, unless otherwise stated ) are suspended in 600 μl Tris 10 mM EDTA 0.5 mM (TE) (pH 8) with 4 μl of lysozyme (35 U/μl; Tebu Bio), and incubated at RT for 20 minutes. SDS is added to the mix (final concentration 0.5%) and the cells are incubated for 10 minutes at RT. 50μl of lysed cells are then transferred in 8 tubes containing 450μL of digestion mix (1X NEB 1 buffer, 1% triton X-100, and 100U HpaII enzyme). DNA is digested for 3 hours at 37°C, split in 4 aliquots, and diluted in 8 ml ligation buffer (1X ligation buffer NEB without ATP, 1 mM ATP, 0.1 mg/ml BSA, 125 Units of T4 DNA ligase 5 U/μl). Ligation is then performed at 16°C for 4 hours, followed by incubation overnight (ON) at 65°C in presence of 250 μg/ml proteinase K and 5 mM EDTA. Precipitation of DNA is performed using an equal volume of 3 M Na-Acetate (pH 5.2) and two volumes of iso-propanol. After one hour at -80°C, DNA is pelleted, suspended in 500μl 1X TE buffer, and incubated for 30 minutes at 37°C in presence of RNAse A (0.03 mg/ml). DNA is then transferred into 2 ml centrifuge tubes, extracted twice with 500 μl phenol-chloroform pH 8.0, precipitated, washed with 1 ml cold ethanol 70% and diluted in 30 μl 1X TE buffer. All tubes are pooled and the resulting 3C library is quantified on gel using Quantity One software (BioRad).
3C-seq: 5 µg of a 3C library was suspended in water (final volume 130 µL) and sheared using a Covaris S220 instrument (Duty cycle 5, Intensity 5, cycles/burst 200, time 60 sec for 4 cycles). The DNA was purified and processed according to manufacturer instructions (Paired-End DNA sample Prep Kit – Illumina – PE-930-1001), except that DNA was ligated to custom-made adapters (see Marbouty M. et al, 2015, Mol Cell) for 4 hours at room temperature. Tubes were then incubated at 65°C for 20 minutes. DNA fragments ranging in size from 400 to 900 pb were purified using a PippinPrep apparatus (SAGE Science). For each library, four test PCR reactions were performed to determine the optimal number of PCR cycles (1 or 2 µL of the collected DNA, Illumina primers PE1.0 and PE2.0 using Taq Phusion [Finnzymes]). A large-scale PCR (8 reactions) was then set-up with the number of PCR cycles determined previously. The PCR product was finally purified on Qiagen MinElute columns and subject to paired-end sequenced on an Illumina sequencer.


title: SLX-15091_1b_ER_45min


title: P2.2


title: E16.2

source_name: Retina at age E16


title: P0.1


title: 3C-seq of E. coli wt cells in stationary phase 30°C (30h) -Replicate 1


title: 3C-seq of E. coli wt cells in stationary phase 30°C (30h)


title: E16.1


title: P6.2

source_name: Retina at age P6


title: P6.1


title: E14.2

source_name: Retina at age E14


title: E12.2

source_name: Retina at age E12


title: 3C-seq of E. coli zapB cells harbouring plasmid pGBM2-5xmatS in exponential phase 30°C

value: F- lambda- ilvG- rfb-50 rph-1 [delta]zapB::frt-kan-frt


title: E14.1


title: 3C-seq of E. coli zapB cells harbouring plasmid pGBM2 in exponential phase 30°C


title: 3C-seq of E. coli matPDC20 cells harbouring plasmid pGBM2-5xmatS in exponential phase 30°C

description: A DNA fragment of  750 bp containing 5 matS sites (HindII- blunt end) was cloned into pGBM2 previously digested with HindIII-SmaI

value: F- lambda- ilvG- rfb-50 rph-1 matP[delta]C20::frt-cam-frt


title: E12.1


title: E11.1

source_name: Retina at age E11


title: E11.2


title: P4.1


title: 3C-seq of E. coli wt cells harbouring plasmid pGBM2-5xmatS in exponential phase 30°C


title: 3C-seq of E. coli wt cells harbouring plasmid pGBM2-5xmatS in exponential phase 30°C -Replicate 1


title: 3C-seq of E. coli hupAB cells in exponential phase 37°C -Replicate 1

value: LB at 37°C

value: F- lambda- ilvG- rfb-50 rph-1 phi80+ [delta]hupA::frt- kan -frt [delta]hupB::frt-cam-frt


title: 3C-seq of E. coli wt cells harbouring plasmid pGBM2 in exponential phase 30°C

value: MM + 0.12% casaminoacids +0.4% glucose at 30°C

value: F- lambda- ilvG- rfb-50 rph-1


title: St K27me3

city: San Antonio

first: Zhenqing

last: Ye

state: TX

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio

data_processing:
Basecalls performed using CASAVA version 1.4
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (hg19) using Mayo HiChIP pipeline with defautl parameters
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated from bedGraph files that generated from Mayo HiChIP pipeline, Scores represent reads coverage siganl

source_name: Hela cells

growth_protocol: HeLa cells were purchased from ATCC. Cells were grown in Advanced DMEM (Dulbecco’s Modified Eagle Medium) containing 10% calf bovine serum at 37°C and 5% CO2..

extract_protocol:
Chromatin input was prepeared by the combination of MNase treatment and sonication, and the chromatin associated with histone modification was isolated using indicated antibody.
Libraries were prepared using ThruPLEX® DNA-seq Kit V2 (Rubicon Genomics, Ann Arbor, MI) according to the manufacturer’s instructions. The adapter-ligated DNA was PCR amplified for 12 cycles.

value: HeLa


title: Ne K27me3


title: 3C-seq of E. coli matPDC20 cells harbouring plasmid pGBM2 in exponential phase 30°C

source_name: E coli cells


title: Zy K27me3


title: 3C-seq of E. coli wt cells harbouring plasmid pGBM2 in exponential phase 30°C -Replicate 1


title: 3C-seq of E. coli wt cells in exponential phase 37°C


title: Qm K27me3


title: 3C-seq of E. coli wt cells in exponential phase 37°C -Replicate 1


title: 3C-seq of E. coli hns cells in exponential phase 30°C -Replicate 1

value: LB at 30°C

value: F- lambda- ilvG- rfb-50 rph-1 [delta]hns::frt- kan -frt


title: SLX-15091_2a_ER_none

value: mammary epithelial cells


title: 3C-seq of E. coli hns cells in exponential phase 30°C


title: Zy K4me3

value: H3K4me3  (in-house EDL Lot 1)


title: Ne K4me3


title: 3C-seq of E. coli wt cells in exponential phase LB 30°C -Replicate 1


title: St K4me3


title: 3C-seq of E. coli wt cells in exponential phase LB 30°C


title: Qm K4me3


title: 3C-seq of E. coli hupAB cells in exponential phase 37°C


title: EDL Input

value: none (input)


title: 3C-seq of E. coli matP cells in exponential phase 22°C

value: MM + 0.12% casaminoacids +0.4% glucose at 22°C

value: F- lambda- ilvG- rfb-50 rph-1 [delta]matP::frt-cam-frt


title: 3C-seq of E. coli mukBmatP cells in exponential phase 22°C

value: F- lambda- ilvG- rfb-50 rph-1phi80+ [delta]mukB::frt- apra [delta]matP::frt-cam-frt


title: Ba K27me3


title: 232H rep 3 [RNA-Seq]

description:
232H_3
(cDNA library)

source_name: Aerial rosette tissue

value: Aerial rosette tissue at 21/22 DAS (days after sowing)

value: epiHybrid 232


title: 3C-seq of E. coli mukB cells in exponential phase 22°C -Replicate 1

value: F- lambda- ilvG- rfb-50 rph-1 [delta]mukB::frt- kan


title: ChIP-Seq: CTCF WAPL-+PDS%-depleted

city: Vienna

first: Roman

middle: R

last: Stocsits

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

description: p-val. threshold 1e-5

data_processing:
Basecalling software: Illumina RTA
Hi-C preprocessing of PE fastq files using hicup_v0.5.8
bowtie-align version 1.2.1.1
truncating, mapping, filtering and deduplicating of Hi-C raw data with hicup.
ChIP-seq: Bowtie 0.12.5 and 1.0.0 for ChIP-Seq readmapping, reads are trimmed and mapped uniquely to genome with 0 to 2 errors
ChIP-Seq MACS peak calling version 1.4.2
Genome_build: hg19
Supplementary_files_format_and_content: juicer tools derived .hic files (Aiden Lab) containing Hi-C matrices for usage with juicebox and juicer tools for Hi-C, and wiggle resp. bed files for ChIP-Seq data
Supplementary_files_format_and_content: wig files were generated using MACS 1.4.2 with output switches [-w -S] and represent genomic distribution of the factors as described in the paper.

source_name: cervical carcinoma

growth_protocol: HeLa Kyoto cells were synchronized at G1, S, G2, or in ProMeta-Phase.

extract_protocol:
ChIP-Seq: Cells were cross-linked and scrapped of the plate. The DNA was fragmented and the protein of interest was immunoprecipitated with indicated antibodies; Adaptors were ligated to the 5' and 3' ends and the library was prepared for Illumina sequencing by a qPCR amplification step.
ChIP as well as Hi-C libraries were prepared for sequencing using standard Illumina protocols.

value: HeLa Kyoto

tag: RNAi

value: Wapl/Pds5A/B RNAi

value: Wapl/Pds5A/B depletion

value: CTCF


title: D59C-2

description: central retina at D59C

source_name: Retina

tag: age (days post conception)

tag: region

value: central retina


title: ChIP-Seq: CTCF PDS5-depleted

description: p-val. threshold 1e-5

value: Pds5SA/B RNAi

tag: genotype

value: Pds5SA/B depletion


title: ChIP-Seq: SMC3 PDS5-depleted rep2

description: union of 2 replicates, p-val. threshold 1e-10 each


title: 3C-seq of E. coli fis cells in exponential phase 30°C -Replicate 1

value: MM + 0.12% casaminoacids +0.4% glucose at 30°C

value: F- lambda- ilvG- rfb-50 rph-1 [delta]fis::frt-kan-frt


title: Ba K4me3

value: HeLa

value: H3K4me3  (in-house EDL Lot 1)


title: 3C-seq of E. coli wt cells in exponential phase 22°C

value: MM + 0.12% casaminoacids +0.4% glucose at 22°C

value: F- lambda- ilvG- rfb-50 rph-1


title: ChIP-Seq: CTCF WAPL-depleted

description: p-val. threshold 1e-5

value: Wapl RNAi

value: Wapl-depleted


title: ChIP-Seq: CTCF control

description: p-val. threshold 1e-5


title: ChIP-Seq: SMC3 WAPL+PDS5-depleted rep2


title: 3C-seq of E. coli zapB cells in exponential phase 30°C

value: F- lambda- ilvG- rfb-50 rph-1 [delta]zapB::frt-kan-frt


title: 3C-seq of E. coli mukB cells in exponential phase 22°C

value: F- lambda- ilvG- rfb-50 rph-1 [delta]mukB::frt- kan


title: ChIP-Seq: SMC3 WAPL-depleted rep2

value: HeLa Kyoto


title: 3C-seq of E. coli matPDC20 cells in exponential phase 30°C

value: F- lambda- ilvG- rfb-50 rph-1 matP[delta]C20::frt-cam-frt


title: 3C-seq of E. coli matP cells in exponential phase 30°C


title: 3C-seq of E. coli wt cells in exponential phase 22°C -Replicate 1


title: ChIP-Seq: SMC3 PDS5-depleted rep1


title: ChIP-Seq: SMC3 WAPL-depleted rep1


title: 3C-seq of E. coli wt cells in exponential phase 30°C


title: ChIP-Seq: SMC3 control rep2


title: Col-Wt rep 2 [WGS]

data_processing:
Basecalls performed using Illumina’s real-time analysis software (RTA).
Quality filtering and adapter trimming of BS-seq reads were done using Cutadapt (Q20).  Reads with less than 40 bps were discarded.
WGS reads were aligned to the TAIR10 genome assembly using BWA.
SNPs, TE insertions and deletions were identified
Genome_build: TAIR10
Supplementary_files_format_and_content: None

extract_protocol:
Plant tissues were ground in liquid nitrogen and DNA was extracted using a CTAB-based extraction protocol.
Approximately 5000 ng of total DNA was submitted to the Beijing Genome Institute (BGI) for library construction and sequencing on an Illumina HiSeq4000 instrument.

tag: tissue

value: Aerial rosette tissue at 21/22 DAS (days after sowing)

value: Wt


title: ChIP-Seq: SMC3 control rep1


title: Col-Wt rep 1 [WGS]


title: Hi-C: Scc1-AID WAB + auxin, 180 min

description: HindIII digestion

value: Wapl/Pds5A/B RNAi

value: Wapl/Pds5A/B depletion


title: 232 rep 2 [WGS]

value: epiRIL 150


title: Hi-C: Scc1-AID WAB + auxin, 0 min

description: HindIII digestion


title: Hi-C: Scc1-AID WAB + auxin, 15 min

description: HindIII digestion


title: 193 rep 2 [WGS]


title: ChIP-Seq: SMC3 WAPL+PDS5-depleted rep1


title: 3C-seq of E. coli fis cells in exponential phase 30°C

value: MM + 0.12% casaminoacids +0.4% glucose at 30°C


title: Hi-C: CTCF-AID control + auxin, 120 min

description: HindIII digestion


title: 193 rep 1 [WGS]

value: epiRIL 92


title: Hi-C: CTCF-AID control + auxin, 0 min

description: HindIII digestion


title: 150 rep 1 [WGS]

value: epiHybrid 232


title: Hi-C: control

description: HindIII digestion


title: 92 rep 2 [WGS]


title: 150 rep 2 [WGS]


title: Hi-C: Scc1-AID control + auxin, 120 min

description: HindIII digestion


title: 92 rep 1 [WGS]


title: Hi-C: Scc1-AID control + auxin, 15 min

description: HindIII digestion


title: 575A S427F DMSO 3

data_processing:
Basecalling with Illumina RTA 1.18.64 for the HiSeq 2500 samples and Illumina RTA 2.7.3 for the HiSeq 3000 samples
Demultiplexing with custom demultipler written in python
Technical replicate fastq files were combined and aligned with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and annotated with Ensembl Biomart
Genome_build: Ensembl GRCh38.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text table

source_name: urinary bladder carcinoma cells

extract_protocol:
RNeasy Mini Kit (Qiagen) was used to isolate RNA from cell pellets
Ribosomal RNA was removed by poly-A selection using Oligo-dT beads. mRNA was then fragmented and reverse transcribed to yield double stranded cDNA using random hexamers. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 cycles using primers incorporating unique index tags.

value: bladder

tag: passages

tag: drug treatment

value: 0.1% DMSO


title: Hi-C: Scc1-AID control + auxin, 0 min 1

description: HindIII digestion


title: 575A S427F DMSO 2


title: 575A S427F DMSO 1


title: 232 rep 1 [WGS]

tag: line


title: 575A RXRA WT Pio 3

value: 1 uM pioglitazone


title: Hi-C: Pro-M control sync.

description: HindIII digestion

value: w.t. Pro-M control


title: 575A RXRA WT Pio 2


title: 193H rep 1 [WGS]

value: epiHybrid 150


title: 575A RXRA WT Pio 1


title: 232H rep 2 [WGS]

value: epiHybrid 193


title: 193H rep 2 [WGS]


title: 150H rep 1 [WGS]


title: 92H rep 2 [WGS]

value: epiHybrid 92


title: Hi-C: S control sync.

description: HindIII digestion

value: HeLa Kyoto

value: w.t. S control


title: 150H rep 2 [WGS]

value: Aerial rosette tissue at 21/22 DAS (days after sowing)


title: 575A RXRA WT DMSO 3


title: Hi-C: Scc1-AID control + auxin, 180 min

description: HindIII digestion


title: 232H rep 1 [WGS]


title: Hi-C: Pds5SA/B RNAi

description: HindIII digestion

value: Pds5SA/B RNAi

value: Pds5SA/B depletion


title: Hi-C: Wapl/Pds5A/B RNAi

description: HindIII digestion

value: Wapl/Pds5A/B RNAi

value: Wapl/Pds5A/B depletion


title: Col-Wt rep 2 [Bisulfite-Seq]

description: meth_levels_windows_qtl_intervals_w_100_s_50_c_3.txt

data_processing:
Basecalls performed using Illumina’s real-time analysis software (RTA).
Quality filtering and adapter trimming of BS-seq reads were done using Cutadapt (Q20).  Reads with less than 40 bps were discarded.
Read alignment and methylation calling were performed using BS-Seeker2 and Bowtie2.
Average methylation were calculated for 100 bp windows with 50 bp step size.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited file containing methylation levels (absolute, mid-parents value, absolute difference and fold change) for each genomic window

extract_protocol:
Plant tissues were ground in liquid nitrogen and DNA was extracted using a CTAB-based extraction protocol.
Approximately 5000 ng of total DNA was submitted to the Beijing Genome Institute (BGI) for BS-treatment, library construction and sequencing on an Illumina HiSeq4000 instrument.

value: Col-Wt


title: Hi-C: G1 control sync.

description: HindIII digestion

value: w.t. G1


title: Hi-C: Wapl RNAi

description: HindIII digestion

value: Wapl RNAi

value: Wapl-depleted


title: 575A RXRA WT DMSO 2

value: bladder

value: 0.1% DMSO


title: 575A RXRA WT DMSO 1


title: Hi-C: G2 control sync.

description: HindIII digestion

value: w.t. G2 control


title: RXRA_S427F_Rep3

description: RXRA_S427F_Rep1_pooled_peaks-sorted-optimum.narrowPeak

data_processing:
Base calls performed on the HiSeq 3000 run with RTA 2.7.3 and the HiSeq 2500 run was processed with RTA 1.18.66.3
ChIP-seq reads were aligned to hg19 using NovoAlign version 3.04.06 with the command: novoalign -r None -l 30 -e 100 -i 230 140 –H
ChIP peaks for each condition were called using the IDR methodology with MACS version 2.1.1 as the peakcaller: macs2 callpeak --pvalue 1e-2 --to-large.  The output of this
For each genotype the IDR peaks of RXRA were intersected with the IDR peaks of H3K27Ac using bedtools intersect.  These intersected regions were used as the peak lists to run DiffBind on the H3K27Ac alignments.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files contain peaks called by the IDR pipeline as being reproducible between biological replicates for each genotype and factor combination
Supplementary_files_format_and_content: broadPeak file contains regions called by DiffBind to be differentially bound between H3K27Ac mutant versus H3k27Ac wild type at a FDR cutoff of 0.1.  The signalValue column is the log2 fold change of mutant over wild type

source_name: bladder cancer cells

growth_protocol: JMSU-1 cells stably expressing RXRAwt or RXRAS427F were seeded in biological triplicate in 150 mm TC-treated culture dish and collected when 70-90% confluency was reached.

extract_protocol:
Crosslinking and ChIP were performed as described for adherent cells in the ENCODE experiment summary for ENCSR000BJW (https://www.encodeproject.org/experiments/ENCSR000BJW/) .
Chromatin was sonicated using the Diagenode Pico Bioruptor.  DNA-protein complexes were precipitated with antibodies against RXRA (PP-K8508-00 R&D Systems) and H3K27Ac (ab4729 Abcam).

value: RXRA (Perseus Proteomics, K8508, lot A2)

value: RXRA S427F


title: RXRA_S427F_Rep2


title: Col-Wt rep 1 [Bisulfite-Seq]


title: 232 rep 1 [Bisulfite-Seq]

value: epiRIL 232


title: 92H rep 1 [WGS]

value: epiHybrid 92


title: 193 rep 2 [Bisulfite-Seq]

value: epiRIL 193


title: MCF7_DAC+455_Input

city: Baltimore

first: Benjamin

last: Leadem

address: 1650 Orleans St. Suite 541

institute: Johns Hopkins University

data_processing:
All reads were mapped to hg19 in Bowtie2.  Next, given that KDM5i increases H3K4me3 levels genome wide, we determined that conventional ChIP-seq normalization techniques were incompatible with our analysis.  Accordingly, we performed quantile normalization to control for sequencing variation between samples.  First, we measured sequencing depth in adjacent 25bp bins using the “bamCoverage” tool in deepTools2 (Ramirez et al. 2014).  Read counts for each bin were then quantile normalized using the normalizeQuantiles function in the Limma R package.  Finally, ChIP samples were normalized to respective inputs using the “bigwigCompare” tool in deepTools2.  Peaks were called using the “MACS2 bdgcallpeak” function in the Galaxy platform (cutoff= 2.0, min size= 1500, max gap=300) (Afgan et al. 2016; Zhang et al. 2008)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, quantile and input normalized ChIP samples

source_name: MCF-7, DAC+455 treatment

growth_protocol: standard as recommended by ATCC

extract_protocol:
ChIP DNA was prepared as described previously by our group (O’Hagan et al. 2011).  Briefly, following drug treatment, cells were crosslinked with 37% formaldehyde and nuclei were subsequently extracted.  Nuclear lysate was sonicated on Diagenode Bioruptor until majority of chromatin fragments were in the 100-300 bp range.  Antibodies were incubated with sonicated chromatin overnight at 4°C, followed by capturing primary antibodies by adding ProteinA/G magnetic beads (DynaBeads) and incubating at room temperature for 3 hrs.  Captured antibody complexes were then washed with low and hi-salt buffers.  Chromatin was eluted off of the beads in elution buffer and cross-linking was reversed with an overnight incubation at 65°C.  Chromatin fragments were then incubated with Rnase A for 1 hr at 37°C, and then Proteinase-K for 2 hrs at 55°C.
Libraries were constructed according to the protocol provided by Illumina’s TruSeq DNA Sample Preparation v2 Kit

treatment_protocol: MCF-7 cells were treated with either 62.5 nM DAC or treament mock for 3 days, followed by 3 days of  9.375 uM KDM5i or treatment mock.  Cells were fixed and chromatin was isolated immediately following this treatment.  H3K4me3 and H3K27ac localization was determined by ChIP-seq

value: MCF-7 Breast adenocarcinoma cell line

value: Input


title: NCM356_Vector-3

city: Galveston

first: Celia

last: Chao

address: 301 University Boulevard

department: Surgery

institute: Univ TX Medical Branch

data_processing:
Illumina bcl2fastq-1.8.4 was used for base calling.
Human hg19 reference genome and the hg19.gtf annotation file were downloaded from iGenome. http://support.illumina.com/sequencing/sequencing_software/igenome.html
Reads were mapped to the human hg19 genome using STAR v2.4.2a with default parameters.
Differential gene expression was determined with Cufflinks v2.2.1 using default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text file output from cuffdiff containing FPKM values, log2 fold-change and FDR adjusted p-values.

source_name: Normal colon mucosa cell line NCM356D, Incell LLC, San Antonio, Texas

extract_protocol:
Total cellular RNA was extracted using  RNAqueous™ phenol-free total RNA isolation kits (Life Technologies, CA) according to the manufacturer’s recommendations
RNA sequencing libraries were generated from ~1 ug total RNA using the illumina TruSeq RNA kit v2, according to the manufacturers' directions

tag: phenotype

value: Vector control


title: RXRA_WT_Rep3

description: RXRA_WT_Rep1_pooled_peaks-sorted-optimum.narrowPeak

tag: cell type

value: RXRA WT


title: NCM356_Vector-2


title: MCF7_DAC_ChIP_H3K27ac

source_name: MCF-7, DAC treatment

tag: chip antibody

value: anti-acetyl H3K27 (abcam #ab4729).


title: 193 rep 1 [Bisulfite-Seq]

value: Aerial rosette tissue at 21/22 DAS (days after sowing)


title: Hi-C: Scc1-AID control + auxin, 0 min 2

description: HindIII digestion

value: HeLa Kyoto


title: RXRA_S427F_Rep1


title: MCF7_DAC_ChIP_H3K4me3

tag: cell line

value: anti-trimethyl Histone H3K4 (Millipore #07-473)


title: 150 rep 2 [Bisulfite-Seq]

value: epiRIL 150


title: 150 rep 1 [Bisulfite-Seq]


title: NCM356_Vector-1


title: NCM356_CBS15-3

value: CBS overexpression


title: 232 rep 2 [Bisulfite-Seq]


title: RXRA_WT_Rep2


title: MCF7_DAC_Input


title: RXRA_WT_Rep1


title: MCF7_DAC+455_ChIP_H3K27ac


title: MCF7_CPI-455_ChIP_H3K4me3

source_name: MCF-7, CPI-455 treatment


title: MCF7_CPI-455_ChIP_H3K27ac


title: H3K27Ac_S427F_Rep3

description: H3K27Ac_S427F_Rep1_pooled_peaks-sorted-optimum.narrowPeak


title: 92 rep 1 [Bisulfite-Seq]

value: epiRIL 92


title: 92 rep 2 [Bisulfite-Seq]


title: MCF7_DAC+455_ChIP_H3K4me3


title: NCM356_CBS15-1


title: H3K27Ac_S427F_Rep2


title: Bdf1-AA_60min_TBP

city: Boston

first: Yoo Jin

last: Joo

state: MA

address: 240 Longwwod Ave.

department: BCMP

institute: HMS/Harvard University

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads mapped to sacCer3 whole genome using bowtie v1.1.1 with parameters -S -p 4 -m 1
peaks were called using Macs2 (v2.1.0) with parameters –c  -f BAM -g 12100000 -B -q 0.01 --nomodel --extsize 150 --SPMR
Genome_build: sacCer3
Supplementary_files_format_and_content: Bedgraph file generated by macs2 possessing SPMR value.

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown in rich media (YPD) and harversted at early exponetial growing stage (OD600 was not over 0.5) after crosslinking with 1% formaldehyde.

extract_protocol:
Sheared chromatin (100 bp ~ 300 bp) was prepared using a Misonix sonicator 300 with cup horns. Crosslinked chromatin was precipitated by standard methods with specific antibodies.
Libraries were prepared according to previous methods (Wong, K.H., Jin, Y., and Moqtaderi, Z. (2013). Multiplex Illumina sequencing using DNA barcoding. Curr Protoc Mol Biol Chapter 7,  unit7.11.–7.11.11.).

treatment_protocol: Rapamycin (1 µg/ml; LC Laboratories) were treated for 1 hour at 30 ℃ to anchor away a target protein from nuclear.

tag: strain

tag: Stage

value: early exponential growing

value: MATalpha, ura3-, leu2-3,112, trp1-1, his3-11,15, fpr1::NAT, RPL13A-2xFKBP12::TRP1, tor1-1, ade2-1, can1-100, BDF1-FRB::HIS3MX

value: anti-TBP rabbit polyclonal (custom made)


title: MCF7_CPI-455_Input


title: H3K27Ac_S427F_Rep1

value: RXRA S427F


title: H3K27Ac_WT_Rep3

description: H3K27Ac_WT_Rep1_pooled_peaks-sorted-optimum.narrowPeak


title: Bdf1-AA_60min_Taf1

value: anti-taf1 rabbit polyclonal (custom made)


title: NCM356_CBS15-2


title: MCF7_Mock_ChIP_H3K27ac

source_name: MCF-7 mock treatment


title: Bdf1-AA_0min_TBP


title: MCF7_Mock_ChIP_H3K4me3


title: H3K27Ac_WT_Rep2


title: Bdf1-AA_0min_Taf1


title: H3K27Ac_WT_Rep1


title: 193H rep 1 [Bisulfite-Seq]

value: epiHybrid 193


title: 193H rep 2 [Bisulfite-Seq]


title: MCF7_Mock_Input

value: MCF-7 Breast adenocarcinoma cell line


title: 13hpf PGC - dead end MO, 2

city: Muenster

first: Theresa

last: Gross-Thebing

department: Institute of Cell Biology

institute: University Clinic Muenster

data_processing:
After trimming of remaining adapter sequences and primers with Cutadapt v1.10 (Martin, 2011),
reads were aligned against GRCz10 using STAR v2.5.2b (Dobin et al., 2013).
Gene-level differential expression between the Dnd knockdown sample and the control was assessed using Cufflinks v2.2.1 (Trapnell et al., 2012).
Results not passing Cuffdiff’s default test criteria were filtered out and a cutoff for the FDR-adjusted p-value of 0.05 (Student's t-test) was chosen.
Data were subsequently divided into separate lists containing either up- or downregulated transcripts. For gene ontology (GO) analysis, a cutoff of 10 FPKM/transcript was applied in the list of upregulated transcripts (in this case at least 10 FPKM/transcript in Dnd knockdown condition) and downregulated transcripts (in this case at least 10 FPKM/transcript in control condition).
GO analysis was performed using the PANTHER Overrepresentation test (Mi et al., 2013) and the “GO biological process complete” annotation dataset based on the Gene ontology database (released 2017-02-28).
Subsequently, terms with a minimum of 5-fold enrichment were visualized using REVIGO (Supek et al., 2011) (Reduce and visualize GO, 0.9 similarity large and SimRel as a semantic similarity measure).
Genome_build: Zv9
Supplementary_files_format_and_content: Excel files with Gene Ids and FPKM values for differentially expressed genes between the two conditions, GO terms and REVIGO analysis for each up- or downregulated group of genes

source_name: germ cells

extract_protocol:
PGCs were FACSed based on germline specific EGFP fluorescence and total RNA extraction was performed using the Arcturus PicoPure RNA isolation kit. DNA was removed using DNAfree Kit of Ambion and mRNA was extracted from total RNA using NEXTflex Bead preparation of BIOO Scientific
A cDNA library was prepared using the NEXTflex Rapid Directional RNA-Seq kit of BIOO Scientific

tag: agent

value: dead end MO

value: AB

value: germ cell

tag: developmental stage

value: 13 hpf


title: Rpb1-AA_60min_TBP

value: MATalpha, ura3-, leu2-3,112, trp1-1, his3-11,15, fpr1::NAT, RPL13A-2xFKBP12::TRP1, tor1-1, ade2-1, can1-100, RPB1-FRB::HIS3MX


title: Rpb1-AA_0min_TBP


title: Input_S427F_B

city: St. Louis

first: Vivek

last: Arora

institute: Washington University School of Medicine

description:
H3K27Ac_S427F_Rep1_pooled_peaks-sorted-optimum.narrowPeak
RXRA_S427F_Rep1_pooled_peaks-sorted-optimum.narrowPeak


title: 232H rep 2 [Bisulfite-Seq]

value: Aerial rosette tissue at 21/22 DAS (days after sowing)

value: epiHybrid 232


title: 150H rep 1 [Bisulfite-Seq]

value: epiHybrid 150


title: Input_S427F_A


title: 13hpf PGC - control MO, 2

value: control MO


title: 150H rep 2 [Bisulfite-Seq]


title: 13hpf PGC - dead end MO, 1


title: Input_WT_B

description:
H3K27Ac_WT_Rep1_pooled_peaks-sorted-optimum.narrowPeak
RXRA_WT_Rep1_pooled_peaks-sorted-optimum.narrowPeak

value: RXRA WT


title: Rpb1-AA_60min_Taf1

value: early exponential growing


title: Rpb1-AA_0min_Taf1


title: 232H rep 1 [Bisulfite-Seq]


title: 92H rep 2 [Bisulfite-Seq]

value: epiHybrid 92


title: 13hpf PGC - control MO, 1


title: Input_WT_A


title: 92H rep 1 [Bisulfite-Seq]


title: i12J-EC_rep2_RNA-seq

status: Public on Dec 06 2017

city: Stanford

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

data_processing:
hisat2 -x hg38.idx -U ESO7-CM_rep1.fastq.gz -S ESO7-CM_rep1.sam -p 2
featureCounts -T 2 -t exon -g gene_name -s 1 -a hg38_P2_ERCC.gtf -o MingTao_NT_mRNA.txt 12C-CM_rep1_sorted.bam 12C-CM_rep2_sorted.bam 12C-EC_rep1_sorted.bam
trim_galore --paired ESO7-CM_R1.fq.gz ESO7-CM_R2.fq.gz
bismark bt2_hg38 --bowtie2 -1 ESO7-CM_R1_val_1.fq.gz -2 ESO7-CM_R2_val_2.fq.gz
MethylKit
Genome_build: hg38

source_name: iPSC-ECs

growth_protocol: Pluripotent stem cells (iPSC, nt-ESCs, and IVF-ESCs) were maintained in chemically defined E8 medium on Matrigel-coated plates. PSC-derived cardiomyocytes (PSC-CMs) were cultured in RPMI-1640 medium plus B27 supplement on Matrigel-coated plates. PSC-derived endothelial cells (PSC-ECs) were maintained in EGM2 medium on 0.2% gelatin-coated plates.

extract_protocol:
Total RNAs were extracted by RNeasy Plus Mini kit (Qiagen, cat no. 74134) according to the manufacturer’s protocol. Genomic DNA was isolated using a DNeasy Blood and Tissue kit (Qiagen, cat no. 69506).
For RNA-seq library preparation, mRNAs were isolated from total RNAs using the Dynabeads Oligo (dT)25 in a Dynabeads mRNA DIRECT Micro Kit (Thermo Fisher Scientific, cat no. 61021). ERCC Spike-In Control Mix (Thermo Fisher Scientific, cat no. 4456740) was added to total RNA input before mRNA isolation. RNA-seq libraries were constructed using an Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific, cat no. 4479789). For RRBS-seq library construction, 300 ng of genomic DNA was digested with MspI (NEB, cat no. R0106S) at 37°C for 1 hr. Unmethylated lambda DNA (Promega, cat no. D1521) was spiked in as the quality control for sodium bisulfite conversion. The DNA fragments were then purified and selected using Agencourt AMPure XP beads (Beckman Coulter, cat no. A63880). DNA fragments were repaired to blunt ends by Klenow fragments (NEB, cat no. M0212S). DNA fragments were then ligated to the methylated Illumina adapters (NEB, cat no. E7535L) using a NEBNext Ultra Ligation Module (NEB, cat no. E7445S). The ligation product was purified using Agencourt AMPure XP beads and subsequently subjected to sodium bisulfite conversion using an EZ DNA Methylation-Gold Kit (Zymo Research, cat no. D5005). The purified bisulfite-converted DNA was amplified using the EpiMark Hot Start Taq DNA Polymerase (NEB, cat no. M0490). NEBNext Index Primers were used to barcode different samples during PCR amplification.
RNA-seq and RRBS-seq

treatment_protocol: Different reprogramming mechanisms: iPSCs, somatic cell nuclear transfer, and IVF.

value: Endothelial cells

tag: passage


title: i12C-iPSC_rep2_RNA-seq

source_name: iPSCs

value: Pluripotent stem cells


title: NT1-CM_rep2-RNA-seq

source_name: nt-ESC-CMs

value: Cadiomyocytes

value: Day 30


title: NT2-EC_rep2-RNA-seq

source_name: nt-ESC-ECs


title: NT1-EC_rep1-RNA-seq


title: i12J-EC_rep1_RNA-seq


title: NT1-NT_rep1-RNA-seq

source_name: nt-ESCs


title: i12C-iPSC_rep1_RNA-seq


title: NT2-NT_rep2-RNA-seq


title: i12J-iPSC_rep1_RNA-seq


title: i12J-CM_rep1_RNA-seq

source_name: iPSC-CMs


title: NT2-CM_rep1-RNA-seq


title: NT2-NT_rep1-RNA-seq


title: NT2-CM_rep2-RNA-seq


title: i12J-iPSC_rep2_RNA-seq


title: i12C-CM_rep2_RNA-seq


title: i12J-CM_rep2_RNA-seq


title: NT1-NT_rep2-RNA-seq


title: i12C-EC_rep2_RNA-seq


title: NT1-CM_rep1-RNA-seq


title: NT2-EC_rep1-RNA-seq


title: i12C-CM_rep1_RNA-seq


title: ESO8-ESC_rep1_RNA-seq

source_name: IVF-ESCs


title: i12C-EC_rep1_RNA-seq


title: ESO8-EC_rep2_RNA-seq

source_name: IVF-ESC-ECs


title: ESO8-ESC_rep2_RNA-seq


title: NT1-EC_rep2-RNA-seq


title: ESO8-CM_rep2_RNA-seq

source_name: IVF-ESC-CMs


title: ESO8-CM_rep1_RNA-seq


title: ESO7-ESC_rep1_RNA-seq


title: ESO7-ESC_rep2_RNA-seq


title: ESO7-EC_rep1_RNA-seq


title: T2(small yellow follicle with higher expression level of FSHR)

city: Tai'an

first: Wang

last: Yiya

state: Shandong

address: Daizong Street no.61

institute: Shandong Agricultural University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Cufflinks are used for assemble transcripts and remap and quanlity gene-expression level, which is estimate by FPKM value.
Genome_build: Gallus_gallus-5.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Gallus gallus

source_name: Chicken follicle

extract_protocol:
RNA was extracted from follicle samples (stored at liquid nitrogen) according to the EZNA Tissue RNA Kit instruction manual. RNA sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina (Cat# E7420L).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: follicle

tag: age

value: 30 weeks

value: wild type


title: T4(small yellow follicle with lower expression level of FSHR)