title: 256cell_DNMT1_KD_mCG

description:
processed data file: 256cell_DNMT1_KD_mCG.cov.gz
processed data file: 256cell_DNMT1_KD_mCG.bedGraph.gz

growth_protocol: The operated AB females were transferred into fish water containing tricaine (Sigma), penicillin and streptomycin (HyClone, SV30010) after OMIS with dnmt1 MOs. And about 42 hrs later, the females mated with wild type Tu males to produce embryos naturally.

extract_protocol:
STEM-seq was carried out as described in detail previously (Zhang et al., 2018). The deyolked embryos were lysed with 20  µl lysis buffer (10  mM Tris-HCl, pH 7.4, 10  mM NaCl, 3  mM MgCl2, 0.1  mM EDTA, pH 8.0, NP-40 0.5%) and 2  µl protease K (Roche, Cat # 10910000) for at least 3 hrs at 55℃. After heat-inactivation, spike-in λ-DNA (Promega, Cat # D150A) was added at a mass ratio of 1/200. Bisulfite conversion was performed with the EpiTect Fast Bisulfite Conversion Kit (Qiagen, Cat # 59824). The converted DNA was subjected to column purification and desulfonation on MinElute DNA spin columns (Qiagen, Cat # 59824) with carrier RNA (Qiagen, Cat # 59824) according to the manufacturer’s instructions.
The purified DNA was eluted in 30 µl of elution buffer and ready for TELP library preparation (Peng et al., 2015).


title: 256cell_H3K27ac_rep1

status: Public on Oct 25 2018

type: SRA

city: Beijing

first: Bingjie

last: Zhang

state: Beijing

address: 30 Shuangqing Rd

country: China

institute: Tsinghua University

description: processed data file: 256cell_H3K27ac_rep1.bw

library_source: genomic

data_processing:
RNA-seq data were firstly processed using Trim Galore! with default parameters to trim the adapter-containing and low quality reads.The filtered data were then mapped to the zebrafish reference genome (danRer7) by STAR (version: STAR_2.5.3a_modified) with following parameters: --outSAMstrandField intronMotif --outSAMattributes All --outSAMunmapped Within --outSAMattrIHstart 0 --outWigStrand Stranded --outFilterMultimapNmax 20 --twopassMode Basic.
All STAR ChIP-seq reads were aligned to the zebrafish reference genome (danRer7) using Bowtie2 (version 2.2.2) (Langmead and Salzberg, 2012) with the parameters –t –q –N 1 –L 25. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. For downstream analysis, the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM).
All STEM-seq datasets were mapped to the danRer7 reference genome by Bismark (Krueger and Andrews, 2011). Reads were trimmed with cutadaptor (Martin, 2011) using parameters: --minimum-length 20 --pair-filter=any. Alignments were performed with the following parameters: -N 1 -X 600 --score_min L,0,-0.6. Multi-mapped reads and PCR duplicates were removed. bismark_methylation_extractor was used to calculate the DNA methylation level
Genome_build: danRer7
Supplementary_files_format_and_content: Bigwig for ChIP-seq and RNA-seq tracks, gene expression table for RNA-seq data

molecule: genomic DNA

organism: Danio rerio

growth_protocol: The wild type AB females mated with wild type Tu males to produce embryos naturally.

extract_protocol:
The ChIP procedure (STAR ChIP-seq) was based on a previously described method with modifications to adapt it for zebrafish embryos (Gilfillan et al., 2012; Zhang et al., 2016). For oocyte and embryo samples, yolk was firstly removed as described above. After centrifuge, cell pellet was lysed in 40 µl lysis buffer (0.5% NP-40, 0.5% Tween, 0.1% SDS and proteinase inhibitor) with pipetting up and down several times. 0.1 unit of MNase (Sigma, Cat # N3755) was added for chromatin digestion at 37℃ for 5 min. The reaction was then terminated by adding 1 µl 0.5 M EGTA. IP sample was incubated with 1 µg H3K4me3 antibody (Homemade), 2 µg H3K27ac antibody (Active Motif, Cat # 39133), 2 µg H3K27me3 antibody (Active Motif, Cat # 61017), or 2 µg H3K36me3 antibody (Active Motif, Cat # 61021), overnight with rotation at 4℃. In the next day, the sample was incubated with 300 µg protein A or protein G dynabeads (Life technologies, Cat # 10001D or 10003D) for 2 hrs with rotation at 4℃. The beads were washed 5 times in 150 µl RIPA buffer and once in 150 µl LiCl buffer. After washing, spin tubes briefly and remove the supernatant. For each IP sample, resuspend beads with 27 µl ddH2O and 1 µl 10x Ex-Taq buffer (TaKaRa). 1 µl proteinase K (Roche, Cat # 10910000) was then added and the mix was incubated at 55℃ for 90 min to elute DNA from beads. The supernatant was then transferred to a new tube and the proteinase K was inactivated at 72℃ for 40 min. 1 µl rSAP (NEB, Cat # M0371) was then added to dephosphorylate 3’ end of DNA at 37℃ for 1 h. rSAP was inactivated at 65℃ for 10 min. The resulting sample was subjected to TELP library preparation as previously described (Peng et al., 2015).
The resulting sample is ready for TELP library preparation (Peng et al., 2015).

treatment_protocol: In order to obtain a large number of synchronously developing embryos, embryos were acquired via in vitro fertilization using standard procedures. Then these embryos were grown in fresh Holtfreter solution (0.05 g/L KCl, 0.1 g/L CaCl2, 0.025 g/L NaHCO3, 3.5 g/L NaCl, pH 7.0) at 28.5℃ around the 256-cell stage and dechorionated by pronase for 15 min at 28.5℃.  At last the cell pellets of dome stage embryos were collected by spinning down at 5000 rpm for 5 min at 4℃.

tag: strain

value: Tu X AB

tag: cell type

value: embryo

tag: developmental stage

tag: antibody

value: Active Motif, Cat # 39133


title: PB58 38hrs rep1

city: Tampa

first: Rays

last: Jiang

state: FL

address: 4202 E Fowler Ave

department: Department of Global Health

country: USA

institute: University of South Florida College of Public Health

library_source: transcriptomic

data_processing:
Reads were aligned to 3D7 reference release 27 using HISAT2 version 2.0.4
Raw counts were obtained using FeatureCounts Version 1.50.0-p3
Transcripts were assembled using Cufflinks Version 2.2.1
FPKM (Fragments per kilobase per million mapped reads) values calculated using Cuffnorm Version 2.2.1 using the classic-fpkm setting and normalization was performed by strain and time point
Genome_build: Plasmodium falciparum 3D7 Version 28
Supplementary_files_format_and_content: Accession number and either the gene counts or the gene FPKM

molecule: polyA RNA

organism: Plasmodium falciparum

growth_protocol: Standard culture conditions

extract_protocol:
When a culture reached a harvest time point the parasites were separated from the red blood cells with 0.015% saponin at room temperature for 5 minutes. The parasites were then pelleted and washed three times in 10 mL room temperature PBS and the samples were stored at -80 oC in 1 mL TRIzol reagent (Fisher Scientific, Hampton, NH) until extraction. For extraction 200 μl of chloroform was added and the samples vortexed vigorously for 15 seconds and then incubated at room temperature for up to 5 minutes. The samples were then spun down at 12000xg (10800 rpm) at 4oC for 10 minutes and the supernatant discarded. 1 ML of 75% ethanol was added and then the samples spun down at 10000xg (9800 rpm) for 5 minutes. The resulting supernatant was discarded and the pellet briefly allowed to dry and the pellet dissolved in 20-50 μl of DEPC-treated water while being incubated at 55oC for 10-15 minutes.
0.5 μg-1.0 μg of RNA samples were prepped for sequencing using the Illumina TruSeq Stranded mRNA Kit. Library quantification was measured by qPCR and TapeStation (Agilent Technologies).  Sequencing was performed on an Illumina MiSeq using 300-cycle V2 MiSeq reagent kit (Illumina).

treatment_protocol: synchonzied by 3 rounds of sorbitol synchronization. The time points collected were 6, 24, 38, and 48 hours. Time zero was defined as the time when the synchronized culture was half late schizonts and half early rings

tag: genotype/variation

value: Isogenic K13 mutant of NF54

tag: tissue

value: whole organism


title: PB58 26hrs rep3


title: 256cell_DNMT1_control_mCG

description:
processed data file: 256cell_DNMT1_control_mCG.cov.gz
processed data file: 256cell_DNMT1_control_mCG.bedGraph.gz

growth_protocol: The operated AB females were transferred into fish water containing tricaine (Sigma), penicillin and streptomycin (HyClone, SV30010) after OMIS with standard control MOs. And about 44 hrs later, the females mated with wild type Tu males to produce embryos

treatment_protocol: Following OMIS and embryo collection, embryos derived from OMIS with control MO were identified by co-injected rhodamine B dye. Then these embryos were grown in fresh Holtfreter solution (0.05 g/L KCl, 0.1 g/L CaCl2, 0.025 g/L NaHCO3, 3.5 g/L NaCl, pH 7.0) at 28.5℃ around the 256-cell stage and dechorionated by pronase for 15 min at 28.5℃.  At last the cell pellets of 256-cell stage embryos were collected by spinning down at 5000 rpm for 5 min at 4℃.


title: 256cell_H3K27ac_rep2_seq2

description: processed data file: 256cell_H3K27ac_rep2.bw


title: 256cell_H3K36me3_rep1_seq1

description: processed data file: 256cell_H3K36me3_rep1.bw

value: Active Motif, Cat # 61021


title: PB58 12 hrs rep3


title: PB58 12 hrs rep2


title: PB58 24hrs rep1


title: PB58 24hrs rep3


title: PB58 26hrs rep1


title: Hi-C of chicken immature erythocytes rep2

city: Novisibirsk

first: Veniamin

last: Fishman

address: Prospekt Lavrentyeva 10

country: Russia

institute: Institute of Cytology and Genetics The Siberian Branch of the Russian Academy of Sciences

description: To compute erythrocyte spatial map, bioinformatic analysis require to combine the data from the samples CIE_rep1 and CIE_rep2

data_processing:
All unplaced contigs less than 50 KB or containing less than 2 HindIII sites were filtered out, which results in a list of 524 contigs of total lengths 1 022 MB.
Reads were aligned to these contigs as described in Buttulin N. et all Genome Biol. (PMID: 25886366), but using newer version of mirnlib software. This produced a contig-level datasets, used for calculation of dependence of contact probabilities from genomic distance.
For chromosome-level heatmaps, used for domains identification, reads that were aligned to unplaced and unlocalized contigs were discarded. Coordinates of the remaining alignments were converted to coordinate system of assembled chromosomes according to AGP files provided by genome assembly.
Both contig- and chromosome-level datasets were filtered and iteratively corrected as described in Buttulin N. et all Genome Biol. (PMID: 25886366). Heatmaps were generated at different resolutions using mirnlib software. Due to a very high similarity (Pearson R=0.995-0.997 for heatmaps at 1 MB resolution; Supplementary Table 2), corresponding replicas were merged into a single dataset that was used for further analysis.
Genome_build: galGal5
Supplementary_files_format_and_content: Processed data files contain per-chromosome intrachromosomal heatmaps on 40 KB resolution. The data are showed as a matrices. Theirs element i,j represents normalized interactions count between loci i and j within a individual chromosome.

organism: Gallus gallus

source_name: immature erythrocytes

extract_protocol:
Immature erythrocytes was extracted from blood of anemic adult (2-5 months old) female chickens.
Briefly, we injected animals with 1ml of 5% phenylhydrazine (Sigma Aldrich, P26252) solution daily for 4 days. At day 5 after beginning of injections, blood was collected from phenylhydrazinetreated and control animals
According to Brilliant Cresyl Blue staining, proportion of immature erythrocytes at this point was about 95% (189 out of 200 counted cells) in treated animals and 3.5% (9 out of 256 counted cells) in control animals.
Blood was centrifuged at 500 g, 4°C for 10 min. Supernatant containing a layer of white cells was discarded, and red pellet was resuspended in 20 ml of cold PBS. The procedure of centrifugation and PBS-wash was repeated 2 more times.
Finally, cells were counted, and desired amount of erythrocytes was pelleted and resuspended in fixation solution.
For each sample (red blood cells and fibroblasts) two independent fixations (biological replicas) were performed. All Hi-C libraries were prepared using in situ protocol, as described in Rao S.S. at all Cell (PMID: 25497547). DNA libraries were sequenced from both ends on Illumina HiSeq 2500 platform in 3 runs total. The sequencing was conducted in 2x101 and 2x106 mode with TruSeq Rapid SBS chemistry, and in 2x126 mode using HiSeq® SBS Kit v4

value: immature erythrocytes


title: Hi-C of chicken immature erythocytes rep1


title: 256cell_RNA_seq_rep1

description:
processed data file: 256cell_RNA_seq_rep1_str2.bw
processed data file: 256cell_RNA_seq_rep1_str1.bw
processed data file: 256cell_RNA_seq_rep1_genes_fpkm.txt

extract_protocol:
Total RNA were purified using RNeasy Mini kit (QIAGEN, 74104) as recommended protocols
5 μg RNA was DNase I (Fermentas, Cat # EN0521) treated at 37℃ for 1 h. RNA was then purified using AMPure beads. Poly-A tailed mRNA was collected using DynabeadsTM mRNA purification kit (Invitrogen, Cat # 61006). Purified RNA was fragmented with RNA Frag. Buffer (NEB, Cat # E6186A) at 95℃ for 5 min. Reaction was stopped and RNA was purified by AMPure beads. First stand cDNA was synthesized with a commercial kit using both oligo dT and random primers (Invitrogen, Cat # 18080-051). Second strand cDNA was synthesized with second strand synthesis buffer (Invitrogen, Cat # 10812014), MgCl2, DTT, dNTP, dUTP, RNase H (Fermentas, Cat # EN0202), E. coli DNA ligase (NEB, Cat # M0205S) and DNA polymerase I (NEB, Cat # M0209S). DNA was purified after 2 hrs incubation on thermomixer at 16℃. Synthesized cDNA was subjected to library preparation. DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. Libraries were then treated with UDG (AMPErase, Cat # N808-0096) at 37℃ for 1 hour followed by DNA amplification using Phusion HF DNA polymerase (NEB, Cat # M0530L). The amplified DNA was size selected using AMPure Beads for 200-500 bp DNA fragments.


title: 256cell_RNA_seq_rep2

description:
processed data file: 256cell_RNA_seq_rep2_str2.bw
processed data file: 256cell_RNA_seq_rep2_str1.bw
processed data file: 256cell_RNA_seq_rep2_genes_fpkm.txt


title: Med-610FH_ht

type: RNA

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center DKFZ

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing:
MAS5.0 normalized data
For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 = 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: human tumor

label_protocol: Affymetrix protocol

extract_protocol: Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).

treatment_protocol: Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).

tag: tumor subgroup


title: 4cell_H3K27ac_seq2

description: processed data file: 4cell_H3K27ac.bw

treatment_protocol: In order to obtain a large number of synchronously developing embryos, embryos were acquired via in vitro fertilization using standard procedures. Then these embryos were grown in fresh Holtfreter solution (0.05 g/L KCl, 0.1 g/L CaCl2, 0.025 g/L NaHCO3, 3.5 g/L NaCl, pH 7.0) at 28.5℃ around the 4-cell stage and dechorionated by pronase for 15 min at 28.5℃.  At last the cell pellets of dome stage embryos were collected by spinning down at 5000 rpm for 5 min at 4℃.


title: NF54 6hrs rep2

value: Parent


title: NF54 6hrs rep1


title: 4cell_H3K36me3

description: processed data file: 4cell_H3K36me3.bw


title: NF54 48hrs rep3


title: NF54 48hrs rep2


title: GBM-611FH_ht


title: NF54 6hrs rep3


title: PB58 12 hrs rep1


title: 4cell_RNA_seq_rep2

description:
processed data file: 4cell_RNA_seq_rep2_str2.bw
processed data file: 4cell_RNA_seq_rep2_str1.bw
processed data file: 4cell_RNA_seq_rep2_genes_fpkm.txt


title: GBM-311FH_P2

source_name: PDOX


title: dome_amanitin_H3K27ac_rep2

description: processed data file: dome_amanitin_H3K27ac_rep2.bw

source_name: dome

treatment_protocol: The α-amanitin (Sigma, Cat # A2263) was microinjected into naturally fertilized 1-cell stage embryos, according to commonly used zebrafish microinjection protocol. After injection, embryos were grown in fresh Holtfreter solution (0.05 g/L KCl, 0.1 g/L CaCl2, 0.025 g/L NaHCO3, 3.5 g/L NaCl, pH 7.0) at 28.5℃ around the dome stage and dechorionated by pronase for 15 min at 28.5℃.  At last the cell pellets of dome stage embryos were collected by spinning down at 5000 rpm for 5 min at 4℃. The dose of α-amanitin was 0.2 ng per embryo.

value: dome


title: GBM-311FH_ht


title: CRL-1927 CHGA rep1

city: La Jolla

first: Nick

last: Webster

state: CA

address: 9500 Gilman Drive

department: Medicine

institute: UCSD

hyb_protocol: Hybridized using Nimblegen Hybridization System 4 following standard protocols.

scan_protocol: Scanned on GenePix 4000B scanner.

data_processing:
Raw data extracted and normalized by RMA using Arraystar 4.
Raw data analyzed by quantile normalization and baseline transformation to median of all samples in GeneSpring 14.5 or by Bayesian modeling using VAMPIRE on raw data with no prior normalization.

organism: Mus musculus

source_name: CRL-1927 kidney cells

label_protocol: Labeled using Nimblegen's One-color labeling kit.

growth_protocol: Mice maintained on normal chow with a 12 h light/dark cycle.

extract_protocol: Total RNA was extracted with Qiagen RNeasy kits according to manufacturer's. RNA was further cleaned up by NaOAc/EtOH precipitation.

treatment_protocol: Mice received a 5/6ths nephrectomy to create a model for kidney failure. Kidney tissue harvested 10 weeks later. CRL-1927 mesangial kidney cells were treated with recombinant CHGA in vitro.

tag: cell line

value: Kidney cell line

tag: treatment

value: Chromogranin A (CHGA)


title: input DNA_D4_4OHT

city: Bethesda

first: Kai

last: Ge

state: MD

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

data_processing:
Peaks were called using SICER with following configuration: For ChIP-seq of histone modifications: Windows (200), Gaps (200), FDR (1e-3);
For RNA-seq, RPKM (Reads per kilobase per million) values were calculated to measure gene (RefSeq) expression levels using in-house script.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using in-house script and the scores represent RPKM

source_name: Brown preadipocyte cell

growth_protocol: Primary brown preadipocytes were isolated from interscapular BAT of newborn LSL-K4M;CreER or Mll3f/f;Mll4SETf/f;CreER mice) and immortalized with SV40T-expressing retroviruses generated from the pBabeneo-large T plasmid

extract_protocol:
ChIP-Seq: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-Seq: Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA sample prep kit (Cat no. FC-121-2001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, Klenow polymerase and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15-18 cycles and library fragments of 200-400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
RNA-Seq: Total RNA was harvested using Trizol reagent. mRNA wasfurther  purified using Invitrogen Dynabeads® mRNA DIRECT™ Kit  (Cat. 610-11).
RNA-Seq: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For adipogenesis assay, cells were plated in growth medium (DMEM plus 10% FBS) at a density of 1.8x106 cells per 15-cm dish 4 days before induction of adipogenesis. At D0, confluent cells were induced with 0.02 μM insulin, 1 nM T3, 0.5 mM 3-isobutyl-1-methyl-xanthine (IBMX), 2 μg/ml dexamethasone, and 0.125mM indomethacin. At D2, D4, and D6, the cells were replenished with medium containing 10% FBS, 0.02 μM insulin, and 1 nM T3.

value: BAT isolated brown preadipocytes

tag: stage of adipogenesis

value: Immature adipocytes (D4)

tag: chip antibody


title: CRL-1927 CHGA rep3


title: CRL-1927 CHGA rep2


title: input DNA_D4_Mock

value: Mock


title: CRL-1927 CHGA rep4


title: dome_amanitin_H3K27me3_rep2

description: processed data file: dome_amanitin_H3K27me3_rep2.bw

value: Active Motif, Cat # 61017


title: CRL-1927 rep2

value: Control


title: CRL-1927 rep4


title: CRL-1927 rep3


title: KO-Npx rep3

description: RNA from 4 independent mice for 4 replicates.

source_name: kidney

tag: strain/background

value: CHGA knockout

value: Kidney

value: Partial nephrectomy


title: H3K27ac_ChIPSeq_D4_4OHT

value: anti-H3K27ac (Abcam, ab4729)


title: dome_amanitin_H3K36me3_rep1

description: processed data file: dome_amanitin_H3K36me3_rep1.bw

value: Tu X AB

value: embryo


title: KO-Npx rep4


title: KO-Npx rep1


title: NF54 38hrs rep3

value: whole organism


title: NF54 38hrs rep2


title: H3K27ac_ChIPSeq_D4_Mock


title: ESF_1

city: West Haven

first: Kalle

middle: T

last: Rytkönen

state: CT

address: 840 West Campus Drive

department: EEB, Systems Biology institute

institute: Yale University

data_processing:
Basecalls performed using CASAVA version 1.4
mRNA-seq reads were aligned to the human (GRCh37.69) cDNA builds using Tophat2 version 2.0.5
Number of times reads overlapped with known features (gene counts) was counted using HTSeq
Transcripts per million (TPM) values were calculated according to Wagner et al (2012) Theor. Biosci.
Genome_build: GRCh37.69
Supplementary_files_format_and_content: ESF_DSC3days_DSC8days_HTseqcounts_TPMs.txt is a tab limited text file that contains the HTseq read counts and transcripts per million (TPM) values for the samples

source_name: endometrial stromal fibroblasts

extract_protocol:
Cell cultures were treated with trypsin and detached from flasks, and RNA was isolated using the RNeasy Mini or Midi RNA extraction kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: endometrial stromal fibroblast (ATCC:CRL-4003) grown in culture


title: dome_amanitin_H3K36me3_rep2

description: processed data file: dome_amanitin_H3K36me3_rep2.bw

value: Active Motif, Cat # 61021


title: NF54 38hrs rep1

value: Parent


title: NF54 48hrs rep1


title: dome_amanitin_H3K4me3_rep1

description: processed data file: dome_amanitin_H3K4me3_rep1.bw

value: dome

value: Homemade


title: dome_control_MO_RNA_seq_rep1

description:
processed data file: dome_control_MO_RNA_seq_rep1_str2.bw
processed data file: dome_control_MO_RNA_seq_rep1_str1.bw
processed data file: dome_control_MO_rep1_genes_fpkm.txt

growth_protocol: The operated AB females were transferred into fish water containing tricaine (Sigma), penicillin and streptomycin (HyClone, SV30010) after OMIS with standard control MOs. And about 43 hrs later, the females mated with wild type Tu males to produce embryos naturally.

treatment_protocol: Following OMIS and embryo collection, embryos derived from OMIS with control MO were identified by co-injected rhodamine B dye. Then these embryos were grown in fresh Holtfreter solution (0.05 g/L KCl, 0.1 g/L CaCl2, 0.025 g/L NaHCO3, 3.5 g/L NaCl, pH 7.0) at 28.5℃ around the dome stage and dechorionated by pronase for 15 min at 28.5℃.  At last the cell pellets of dome stage embryos were collected by spinning down at 5000 rpm for 5 min at 4℃.


title: CRL-1927 rep1

value: Kidney cell line


title: NF54 26hrs rep2


title: NF54 26hrs rep3


title: dome_control_MO_RNA_seq_rep2_seq2

description: processed data file: dome_control_MO_RNA_seq_rep2_str2.bw

growth_protocol: The operated AB females were transferred into fish water containing tricaine (Sigma), penicillin and streptomycin (HyClone, SV30010) after OMIS with three HATs MOs. And about 42 hrs later, the females mated with wild type Tu males to produce embryos naturally.


title: Mll3/4SET_RNA_D0_4OHT

value: BAT isolated brown preadipocytes

value: Mature adipocytes (D7)


title: H3K4me1_ChIPSeq_D4_Mock

value: Mock

value: Immature adipocytes (D4)

value: anti-H3K4me1 (Abcam, ab8895)


title: dome_H3K27ac_rep1_seq2

description: processed data file: dome_H3K27ac_rep1.bw

treatment_protocol: In order to obtain a large number of synchronously developing embryos, embryos were acquired via in vitro fertilization using standard procedures. Then these embryos were grown in fresh Holtfreter solution (0.05 g/L KCl, 0.1 g/L CaCl2, 0.025 g/L NaHCO3, 3.5 g/L NaCl, pH 7.0) at 28.5℃ around the dome stage and dechorionated by pronase for 15 min at 28.5℃.  At last the cell pellets of dome stage embryos were collected by spinning down at 5000 rpm for 5 min at 4℃.

value: Active Motif, Cat # 39133


title: NF54 26hrs rep1


title: NF54 24hrs rep1


title: KO-Npx rep2

value: CHGA knockout

value: Kidney

value: Partial nephrectomy


title: dome_H3K27me3_rep1_seq2

description: processed data file: dome_H3K27me3_rep1.bw

value: Tu X AB

value: embryo

value: Active Motif, Cat # 61017


title: H3K4me1_ChIPSeq_D4_4OHT


title: LSL-K4M_RNA_D0_4OHT


title: WT-Npx rep3

value: Wild-type


title: NF54 12hrs rep2

value: Parent

value: whole organism


title: dome_H3K36me3_rep1

description: processed data file: dome_H3K36me3_rep1.bw

value: dome

value: Active Motif, Cat # 61021


title: LSL-K4M_RNA_D7_Mock

value: BAT isolated brown preadipocytes


title: NF54 12hrs rep1


title: WT-Npx rep4


title: WT-Npx rep1


title: WT-Npx rep2


title: KO-sham rep4

value: Sham surgery


title: KO-sham rep1


title: OV-3 (small RNA seq)

city: Haikou

first: Feng

last: Pang

address: Renmin Road 58

institute: Hainan University

data_processing:
Single-end sequencing on Illumina HiSeq 2500
ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 21.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Differential expression of miRNAs based on normalized deep-sequencing counts was analyzed by selectively using, Student t test . The significance threshold was set to be 0.01 and 0.05 in each test

organism: Capra hircus

source_name: ORFV infected GSF cells

extract_protocol:
mirVana miRNA isolation kit
TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA)

value: skin on the ear

tag: cell passages

value: Primary goat skin fibroblasts


title: Mll3/4SET_RNA_D7_Mock

value: Mock

value: Mature adipocytes (D7)


title: KO-sham rep3

value: CHGA knockout


title: dome_H3K4me3_rep1_seq3

description: processed data file: dome_H3K4me3_rep1.bw

value: Homemade


title: OV-2 (small RNA seq)


title: WT-sham rep4

value: Kidney


title: dome_H3K4me3_rep2_seq2

description: processed data file: dome_H3K4me3_rep2.bw

value: Tu X AB


title: KO-sham rep2


title: OV-1 (small RNA seq)


title: dome_RNA_seq_rep1

description:
processed data file: dome_RNA_seq_rep1_str2.bw
processed data file: dome_RNA_seq_rep1_str1.bw
processed data file: dome_RNA_seq_rep1_genes_fpkm.txt

value: embryo


title: GSF-3 (small RNA seq)

source_name: GSF cells


title: GSF-2 (small RNA seq)


title: dome_TKD_MO_RNA_seq_rep1

description:
processed data file: dome_TKD_MO_RNA_seq_rep1_str2.bw
processed data file: dome_TKD_MO_RNA_seq_rep1_str1.bw
processed data file: dome_TKD_MO_rep1_genes_fpkm.txt

treatment_protocol: Following OMIS and embryo collection, embryos derived from OMIS with HATs MOs were identified by co-injected rhodamine B dye. Then these embryos were grown in fresh Holtfreter solution (0.05 g/L KCl, 0.1 g/L CaCl2, 0.025 g/L NaHCO3, 3.5 g/L NaCl, pH 7.0) at 28.5℃ around the dome stage and dechorionated by pronase for 15 min at 28.5℃.  At last the cell pellets of dome stage embryos were collected by spinning down at 5000 rpm for 5 min at 4℃.


title: dome_H3K36me3_rep2

description: processed data file: dome_H3K36me3_rep2.bw


title: GSF-1 (small RNA seq)


title: dome_TKD_MO_RNA_seq_rep2_seq2

description: processed data file: dome_TKD_MO_RNA_seq_rep2_str2.bw


title: WT-sham rep3


title: OV-3 (whole transcriptome seq)

data_processing:
paired-end sequencing on an Illumina Hiseq4000
Cutadapt  was utilized to remove reads containing undetermined bases, adaptors, and low quality bases. Then sequence quality was verified using FastQC  (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Bowtie2 and Tophat2 were used to map reads to the Capra hircus (goat) reference genome (RefSeq assembly accession: GCF_001704415.1).The matched reads of each sample were assembled using StringTie.Any unmapped reads were individually mapped to goat reference genome by TopHat-Fusion.reads mapped to goat genome using TopHat-Fusion were analyzed by CIRCexplorer to identify candidate circRNAs
StringTie and Ballgown were utilized to evaluate the expression levels of all transcripts by Fragments per kilobase per million reads (FPKM).
The criteria for identifying circRNA were as follows: 1) GU/AG must occur at both ends of splice sites; 2) less than two mismatches; 3) more than one back-spliced junction read in at least one sample of GSF or OV group; 4) two splice sites are no more than 100 kb apart on the genome.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

extract_protocol:
mirVana miRNA isolation kit
RNA libraries were prepared for sequencing using standard Illumina protocols after ribosome depletion


title: muscle_H3K27ac

description: processed data file: muscle_H3K27ac.bw

source_name: muscle

growth_protocol: The wild type AB female strain were raised as standard protocol.

treatment_protocol: An wild type adult AB fish was euthanized with tricaine, and skeletal muscle was dissected carefully from trunk region after skin elimination by tweezers.

value: AB

value: muscle cell

value: adult

value: Active Motif, Cat # 39133


title: muscle_H3K27me3

description: processed data file: muscle_H3K27me3.bw

value: Active Motif, Cat # 61017


title: OV-1 (whole transcriptome seq)


title: Patient 3 L3

city: Changsha

first: Jinbo

last: Chen

state: Hunan

address: No.87 Xiangya Rd

department: Urology

institute: Xiangya Hospital

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: Bladder cancer metastatic lymph node samples

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: metastatic lymph node

tag: Sex

value: Male

tag: age

value: 62 years


title: WT-sham rep1

value: Wild-type

value: Sham surgery


title: GSF-3 (whole transcriptome seq)

value: skin on the ear

value: Primary goat skin fibroblasts


title: Patient 1 L1

value: Female

value: 55 years


title: GSF-2 (whole transcriptome seq)


title: WT-sham rep2

value: Kidney


title: Patient 2 L2

value: 57 years


title: oocyte_H3K27ac_rep1_seq2

description: processed data file: oocyte_H3K27ac_rep1.bw

source_name: oocyte

treatment_protocol: Unfertilized oocytes were collected with spoon by squeezing sexual maturation female fish gently. Oocytes were placed in ΔHank’s buffer (Hank’s buffer without Ca2+ and Mg2+) with 1% (wt/vol) BSA (Solarbio, Cat # A8020) to avoid activation until enough oocytes were collected. Dechorionation treatment by pronase diluted in ΔHank’s buffer for 15 min at 28.5℃ was conducted to keep oocytes from activation for a longer time. For each batch of about 500 dechorionated oocytes, 1 ml ice-cold 1% BSA ΔHank’s buffer was added. Oocytes were deyolked by repeatedly blowing with a 200 µl pipette and cell pellets were collected by spinning down at 5000 rpm for 5 min at 4℃.

value: metaphase II oocyte

value: stage V


title: muscle_H3K4me3

description: processed data file: muscle_H3K4me3.bw

value: AB

value: muscle cell

value: Homemade


title: Patient 2 C2

source_name: Bladder cancer primary tumor samples

value: primary tumor


title: GSF-1 (whole transcriptome seq)


title: oocyte_H3K4me3_rep1_seq2

description: processed data file: oocyte_H3K4me3_rep1.bw


title: dome_RNA_seq_rep2

description:
processed data file: dome_RNA_seq_rep2_str2.bw
processed data file: dome_RNA_seq_rep2_str1.bw
processed data file: dome_RNA_seq_rep2_genes_fpkm.txt

value: Tu X AB

value: embryo

value: dome


title: oocyte_H3K4me3_rep2

description: processed data file: oocyte_H3K4me3_rep2.bw


title: oocyte_RNA_seq_rep1

description:
processed data file: oocyte_RNA_seq_rep1_str2.bw
processed data file: oocyte_RNA_seq_rep1_str1.bw
processed data file: oocyte_RNA_seq_rep1_genes_fpkm.txt


title: SS1_6b

city: Providence

first: Emily

last: Petruccelli

state: Rhode Island

address: 185 Meeting Street

department: Neuroscience

institute: Brown University

description:
Flies treated 3x 10min/10min isoamyl alcohol / ethyl acetate, space 50min, sacrified 24hr later
transcript_count_matrix.csv

data_processing:
Trimmomatic (v.0.36): java -jar <path to jar file/trimmomatic-0.36.jar> SE <path to input> <path to output> ILLUMINACLIP:<TruSeq3-SE.fa>:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
HISAT2 (v.2.0.5): hisat2 -q -x <reference index/genome_tran> -U <input fastq file> -S <output sam file> -p 50
Samtools (v.1.3.1): samtools sort -@ 4 -o <output bam file> <input sam file>
StringTie (v.1.3.3): stringtie <input.sorted.bam> -b <path to Ballgown tables> -o <output.gtf> -G <reference.gtf>
prepDE.py: python <path to prepDE.py> -i <path to directory that contains all of the sample subdirectories>
Genome_build: BDGP6 + INTACT sequence
Supplementary_files_format_and_content: .csv

organism: Drosophila melanogaster

source_name: MB nuclei

growth_protocol: Flies raised at 25C, 65% humidity, light:dark 14hr:10hr

extract_protocol:
GFP immunoprecipitation, Trizol RNA extraction
Libraries prepared by GeneWiz (South Plainfield, NJ)

treatment_protocol: ~20,000 (for each biological replicate) 2-7 day old male MB010B>unc84-GFP (INTACT) flies collected under light CO2, allowed to recover O/N before treatment

value: Odors

tag: nuclei

value: MB010B > INTACT

tag: gender

value: male


title: sperm_H3K27ac_rep1

description: processed data file: sperm_H3K27ac_rep1.bw

growth_protocol: The wild type Tu male strain were raised as standard protocol.

extract_protocol:
The procedures is adopted from a previous paper (Wu et al., 2011). Sperm were collected by spinning down at 8000 rpm for 5 min at 4℃. The pellet was resuspended and washed with 1 ml PBS/ 1mM PMSF once. The sperm pellet was then treated with 1ml 0.05% lysosphatidylcholine in PBS on ice for 10 min. After washing with 1 ml PBS/1 mM PMSF twice, sperm were collected by spinning down at 8000 rpm for 5 min at 4℃. Sperm were lysed in 91 µl PND buffer (0.1% NP-40, 1 mM DTT in PBS) and 5 µl 20 mM CaCl2. 10 units of MNase were then added to digest chromotin for 5 min at 37℃. 5 µl 0.5 M EGTA was used to stop the reaction. 150 µl release buffer (50 mM Hepes-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.4% Triton X-100, 5 mM EGTA) was then added at 37℃ for 10 min. After spinning down at 12000 rpm for 10 min at 4℃ the supernatant was transferred to a new tube. The rest procedure followed the STAR ChIP-seq protocol.
The resulting sample is ready for TELP library preparation (Peng et al., 2015).

treatment_protocol: Sperm were released by squeezing sexual matured male fish gently under anesthesia and collected with capillary tube. Sperm from several males were pooled in ice-cold, full-strength Hank's buffer (5.4 mM KCl, 136.8 mM NaCl, 4.2 mM NaHCO3, 0.44 mM KH2PO4, 0.25 mM Na2HPO4, 1.3 mM CaCl2 and 1.0 mM MgSO4).

tag: strain

value: Active Motif, Cat # 39133


title: Patient 3 C3

value: Male

value: 62 years


title: SS1_6a


title: sperm_H3K27ac_rep2

description: processed data file: sperm_H3K27ac_rep2.bw

source_name: sperm

value: Tu

tag: cell type

value: mature sperm

value: spermatozoa


title: DSC3days_3

source_name: decidual stromal cells

value: 3 days in vitro decidualized endometrial stromal fibroblast (ATCC:CRL-4003) grown in culture


title: SS1_5b

description:
Flies treated 3x 10min/10min isoamyl alcohol / ethyl acetate + ethanol (90:60), space 50min, sacrified 24hr later
transcript_count_matrix.csv

value: Trained


title: sperm_H3K27me3_rep1_seq2

description: processed data file: sperm_H3K27me3_rep1.bw

extract_protocol: The procedures is adopted from a previous paper (Wu et al., 2011). Sperm were collected by spinning down at 8000 rpm for 5 min at 4℃. The pellet was resuspended and washed with 1 ml PBS/ 1mM PMSF once. The sperm pellet was then treated with 1ml 0.05% lysosphatidylcholine in PBS on ice for 10 min. After washing with 1 ml PBS/1 mM PMSF twice, sperm were collected by spinning down at 8000 rpm for 5 min at 4℃. Sperm were lysed in 91 µl PND buffer (0.1% NP-40, 1 mM DTT in PBS) and 5 µl 20 mM CaCl2. 10 units of MNase were then added to digest chromotin for 5 min at 37℃. 5 µl 0.5 M EGTA was used to stop the reaction. 150 µl release buffer (50 mM Hepes-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.4% Triton X-100, 5 mM EGTA) was then added at 37℃ for 10 min. After spinning down at 12000 rpm for 10 min at 4℃ the supernatant was transferred to a new tube. The rest procedure followed the STAR ChIP-seq protocol.

tag: developmental stage

value: Active Motif, Cat # 61017


title: SS1_5a


title: oocyte_H3K36me3_rep2

description: processed data file: oocyte_H3K36me3_rep2.bw

value: AB

value: metaphase II oocyte

value: stage V

tag: antibody

value: Active Motif, Cat # 61021


title: SS1_4b

description:
Flies treated 3x 10min/10min ethyl acetate / isoamyl alcohol, space 50min, sacrified 24hr later
transcript_count_matrix.csv


title: SS1_4a


title: SS1_3b

description:
Flies treated 3x 10min/10min ethyl acetate / isoamyl alcohol + ethanol (90:60), space 50min, sacrified 24hr later
transcript_count_matrix.csv


title: sperm_H3K4me3_rep1_seq2

description: processed data file: sperm_H3K4me3_rep1.bw

extract_protocol:
The procedures is adopted from a previous paper (Wu et al., 2011). Sperm were collected by spinning down at 8000 rpm for 5 min at 4℃. The pellet was resuspended and washed with 1 ml PBS/ 1mM PMSF once. The sperm pellet was then treated with 1ml 0.05% lysophosphatidylcholine in PBS on ice for 10 min. After washing with 1 ml PBS/1 mM PMSF twice, sperm were collected by spinning down at 8000 rpm for 5 min at 4℃. Sperm were lysed in 91 µl PND buffer (0.1% NP-40, 1 mM DTT in PBS) and 5 µl 20 mM CaCl2. 10 units of MNase were then added to digest chromotin for 5 min at 37℃. 5 µl 0.5 M EGTA was used to stop the reaction. 150 µl release buffer (50 mM Hepes-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.4% Triton X-100, 5 mM EGTA) was then added at 37℃ for 10 min. After spinning down at 12000 rpm for 10 min at 4℃ the supernatant was transferred to a new tube. The rest procedure followed the STAR ChIP-seq protocol.
The resulting sample is ready for TELP library preparation (Peng et al., 2015).

value: Homemade


title: sperm_H3K36me3_rep2

description: processed data file: sperm_H3K36me3_rep2.bw


title: sperm_H3K4me3_rep2

description: processed data file: sperm_H3K4me3_rep2.bw


title: SS1_3a


title: Primary_Unloading_2

city: Boston

first: Gavin

middle: R.

last: Schnitzler

state: MA

address: 800 Washington St. Box 80

department: Molecular Cardiology Research Institute

institute: Tufts Medical Center

hyb_protocol: RNA was processed and hybridized to Affymetrix Porcine Gene 1.0 ST expression microarrays (3 to 4 arrays per condition), using the standard Affymetrix workflow.

data_processing:
Gene level expression values were determined using the Robust Multiarray Average (RMA) method (1) as part of the affy package (version 1.36.1) (2) in the Bioconductor R suite (version 2.12) (3), together with Entrez Gene-specific probeset maping (17.0.0) from the Molecular and Behavioral Neuroscience Institute (Brainarray) at the University of Michigan (4)). Array quality was measured by computing Relative Log Expression (RLE) and Normalized Unscaled Standard Error (NUSE) using the affyPLM package (version 1.34.0) (5). The three best samples from each group, by RLE value, were selected for further analysis. Data was quantile normalized using normalize.quantiles in the R preprocessCore package (version 1.32.0), and differential expression was determined using Limma (6) (version 3.26.9) for three contrasts: Primary Reperfusion vs Sham, Primary Unloading vs. Sham, and Primary Unloading vs. Primary Reperfusion.
Genes showing at least a 2.0 fold change in expression and a raw p.value of less than 0.01.

label: biotin

organism: Sus scrofa

source_name: Infarct zone after 90 min LAD occlusion, 30 min unloading & 120 min reperfusion

growth_protocol: Studies were conducted in adult, male Yorkshire swine. The study protocol was approved by the Institutional Animal Care and Use Committee (IACUC) at Tufts Medical Center. All experiments were performed according to the committee’s guidelines. Animals were pre-medicated with Telazol (0.8ml/kg, intramuscular). General anesthesia was induced and maintained with isoflurane (1-2%). All animals were intubated and mechanically ventilated (Harvard Apparatus Inc) with room air and supplemented oxygen to maintain physiologic pH and oxygen saturation.  Surface electrocardiography leads, an orogastric tube, peripheral 18 G venous catheters, and a rectal thermistor were placed in all animals. Heating pads were used as needed to maintain a core body temperature >99o F. Vascular access sheaths were then deployed into the right internal jugular vein (10Fr), left carotid artery (7Fr), and both femoral arteries (7Fr) and veins (10Fr). Unfractionated heparin boluses with a goal activated clotting time of 300-400 seconds, continuous lidocaine infusion (1mg/kg), and noradrenaline (0.16 mcg/min) were initiated in all animals. A 6Fr Judkins right coronary catheter (Boston Scientific) engaged the left coronary artery via the right femoral artery and baseline angiograms were recorded. A 180 cm guidewire was delivered into the distal left anterior descending artery (LAD) and a 3.0 x 8mm bare-metal stent (Boston Scientific) deployed in the mid-LAD after the first diagonal branch with angiographic confirmation of LAD occlusion. Coronary angiography also performed immediately after reperfusion and again after the end of the study protocol confirmed patency of the LAD. Animals were then euthanized with pentobarbital and phenytoin after 120 minutes of reperfusion.

extract_protocol: RNA was collected from the center of the infarct zone of group 1 (Primary Reperfusion), group 3 (Primary Unloading) animals, or from the same region of the left ventricle in sham operated animals. Total RNA was extracted directly with Trizol (Invitrogen).

treatment_protocol: To explore the optimal duration of mechanical unloading prior to reperfusion, adult, male Yorkshire swine were divided into 4 groups (n=4/group; Figure 1A). All groups underwent 90 minutes of LAD occlusion. In Group 1, LAD occlusion followed by 120 minutes of reperfusion served as the control group (Primary Reperfusion). In Groups 2 and 3, LAD occlusion was followed by insertion and activation of a TV-Pump (Impella CP; Abiomed Inc; Danvers, MA) via a 14Fr sheath in the left femoral artery and maintained at maximal support (44,000 rotations per minute). This was followed by an additional 15 (Group 2) or 30 (Group 3; Primary Unloading) minutes of occlusion respectively, then 120 minutes of reperfusion. In Group 4, LAD occlusion was followed by reperfusion, and after 30 minutes of reperfusion, a TVP was inserted and activated for the remaining 90 minutes of reperfusion (Post Reperfusion Unloading). At the end of each study, animals were euthanized for determination of myocardial infarct size. Three sham-operated animals were intubated, anesthetized, and mechanically ventilated without myocardial infarction or mechanical unloading. LV tissue samples obtained from sham controls were used for tissue analysis.

tag: breed

value: Yorkshire

value: adult

value: LV


title: Ctrl.1

status: Public on Oct 24 2018

city: Saarbrücken

first: Karl

last: Nordström

address: Gebäude A2 4

department: FR 8.3 Biowissenschaften

institute: Universität des Saarlandes

description: Prior Ogran culture of tissue

data_processing:
Adapter and quality trimming (Q>20) with trim_galore
2-pass alignment with STAR
Duplicated reads marked with Picard tools
bigWig files generated with bedtools genomecov and bedGraphToBigWig
Genome_build: hs37
Supplementary_files_format_and_content: For each sample, coverage tracks in bigWig format was generated

source_name: primary limbal epithelial culture

growth_protocol: Biopsies or limbal preparation from donor were cultured in KSFM and expanded to 3x 6 well (13-20 days) and then lysed

extract_protocol:
Cell culture was lysed using Isolate II kit from bioline
1 µg total RNA was subjected to the NEBNext® Ultra™ RNA Library Prep Kit (NEB) following the manufacturer’s instructions to sequence polyA-RNAs

treatment_protocol: Ctrls. Were organ cultured before

value: primary limbal epithelial culture

tag: disease state

value: healthy control

tag: genotype (pax6)

value: WT

value: m

tag: post mortem


title: AN1

description: Tissue obtained from surgery

value: Anirdia associated keratopathy

value: f

value: no


title: Ctrl.2

description: Prior Ogran culture of tissue


title: Primary_Unloading_1

scan_protocol: RNA was processed and hybridized to Affymetrix Porcine Gene 1.0 ST expression microarrays (3 to 4 arrays per condition), using the standard Affymetrix workflow.

value: male

tag: treatment

tag: tissue


title: Sham_1

source_name: Same region of left ventrical in sham operated control

label_protocol: RNA was processed and hybridized to Affymetrix Porcine Gene 1.0 ST expression microarrays (3 to 4 arrays per condition), using the standard Affymetrix workflow.

value: Sham


title: sperm_H3K27me3_rep2_seq2

description: processed data file: sperm_H3K27me3_rep2.bw

value: Tu

value: mature sperm

value: spermatozoa

value: Active Motif, Cat # 61017


title: Primary_Unloading_3


title: Sham_2


title: Primary_Reperfusion_1

source_name: Infarct zone after 90 min LAD occlusion & 120 min reperfusion


title: Primary_Reperfusion_3


title: AN2

description: Tissue obtained from surgery


title: Primary_Reperfusion_2


title: OV-2 (whole transcriptome seq)

value: skin on the ear

value: Primary goat skin fibroblasts


title: genomic DNA from Ewing's Sarcoma Patient 7, bone marrow

type: genomic

city: Seville

first: Ana

middle: Monteiro

last: Amaral

address: avenida manuel siurot s/n

department: Molecular pathology of sarcomas

country: Spain

institute: Institute of Biomedicine of Seville

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Background correction and quantile normalization using the lumi Bioconductor package

label: Cy5 and Cy3

source_name: Patient 7

label_protocol: Standard Illumina Protocol

growth_protocol: Cell lines and Mesenchymal Stem cells were cultured in flasks with medium suplemented with 10%FBS, 1%P/S and glutamine.

extract_protocol: genomic DNA was isolated with QIAamp DNA Mini kit (Qiagen),  according to manufacturer's instructions

tag: subject id

value: Patient 7

value: Ewing Sarcoma

value: Mesenchymal Stem Cells from Bone Marrow


title: genomic DNA from donor 2, bone marrow

source_name: Donor 3

value: Donor 3

value: Healthy Donor


title: genomic DNA from Ewing's Sarcoma Patient 5, bone marrow

source_name: Patient 5

value: Patient 5


title: genomic DNA from EW3 cell line

tag: cell line

value: Tumor


title: genomic DNA from donor 1, bone marrow


title: genomic DNA from Ewing's Sarcoma Patient 6, bone marrow

source_name: Patient 6

value: Patient 6


title: genomic DNA from Ewing's Sarcoma Patient3, bone marrow

source_name: Patient 3

value: Patient 3


title: genomic DNA from SKES-1 cell line


title: genomic DNA from Ewing's sarcoma Patient 2, bone marrow

source_name: Patient 2

value: Patient 2


title: genomic DNA from VH64cell line


title: genomic DNA from Donor 2, bone marrow

source_name: Donor 2

value: Donor 2


title: genomic DNA from TTC466cell line


title: genomic DNA from STAET10 cell line


title: genomic DNA from A4573 cell line


title: genomic DNA from TC71 cell line


title: genomic DNA from Ewing's Sarcoma Patient 1,  bone marrow

source_name: Patient 1

value: Patient 1


title: genomic DNA from STAET1 cell line


title: genomic DNA from RM82 cell line


title: genomic DNA from STAET2.1 cell line


title: genomic DNA from CADO cell line

source_name: CADO

value: CADO


title: genomic DNA from RDES cell line

source_name: RDES

value: RDES


title: genomic DNA from SKNMC cell line

source_name: SKNMC

value: SKNMC


title: genomic DNA from WE68 cell line


title: genomic DNA from A673 cell line


title: hY3 2

city: Manhattan

first: Tenzin

middle: C

last: Lhakhang

state: NY

address: 550 First Avenue

institute: NYU School of Medicine

hyb_protocol: Biotin labeled fragmented complementary RNA (15 μg) was hybridized to GeneChip human genome U133A 2.0 arrays (Affymetrix). Hybridization occurred at 45 °C for 16 h in Hybridization oven 640 (Affymetrix).

scan_protocol: Chips were then washed and stained in a Fluidics station 450 and scanned with a GeneChip Scanner 3000.

data_processing: RMAExpress was used for background adjustment, quintile normalization, summarization and quality analysis

source_name: PBMC derived Macrophages

label_protocol: For each sample, 50 ng total RNA was amplified and labeled with the 2-Cycle cDNA Synthesis and the 2-Cycle Target Labeling (Biotin) and Control Reagent packages (Affymetrix, Santa Clara, CA) following the manufacturers recommendations.

growth_protocol: Monocytes were positively selected using anti-CD14 microbeads (Miltenyi Biotech) and cultured in Teflon beakers (RPMI 1640/10% FBS) for 7 days in the presence of 10 ng/ml GM-CSF to obtain macrophages

extract_protocol: RNA from PBMC-derived macrophages was isolated using an RNeasy kit (Qiagen)

treatment_protocol: Briefly, 2.5 μg ssRNA are mixed with 15 μl DOTAP reagent to a final volume of 75 μl reaction buffer, and incubated at 22°C for 15 min. The mixture is then added to IFN-γ–primed macrophages for an overnight transfection at 37°C.

tag: cells

value: Macrophages

value: hY3 treated


title: hY3 1


title: hY3_Unt 3

value: untreated


title: hY3 4


title: hY3_Unt 4


title: wt_f1_male_mph_rep3

city: Tjele

first: Palle

middle: Duun

last: Rohde

address: Blichers Alle 20

department: Department of Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

description: Gene expression of male offspring from a cross between males exposed to sucrose and females exposed to methylphenidate

hyb_protocol: 15 microgram cDNA were fragmented and loaded onto the Affymetrix probe array cartridge. Incubation, washing and staining procedures were performed in the Affymetrix Fluidics Station 450

scan_protocol: The probe arrays were scanned at 560 nm using a confocal laser-scanning microscope (Affymetrix Scanner 3000 7G; Affymetrix, Santa Clara, CA, USA).

data_processing: The transcriptomic data were normalized using the Robust Multi-array Average (RMA) algorithm (Irizarry et al., 2003) as implemented in the Affy package for R (Gautier et al., 2004). Differentially expressed transcripts were identified using the R package limma (Ritchie et al., 2015), by fitting linear models and empirical Bayesian methods, following a paired t-test and adjustment for multiple testing by Benjamin-Hochberg as implemented in limma.

source_name: Drosophila F1 offspring from cross between males exposed to sucrose and females exposed to methylphenidate

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol (GeneChipTM Expression Analysis Technical Manual)

extract_protocol: Extraction of total RNA was performed according to the manufracturer's instructions.

value: whole flies

tag: Sex

value: male

tag: agent

value: sucrose and methylphenidate


title: wt_f1_male_mph_rep1


title: wt_f1_male_mph_rep2


title: wt_f1_male_sucrose_rep2

description: Gene expression of male offspring from a cross between male and females exposed to sucrose

source_name: Drosophila F1 offspring from cross between males and females exposed to sucrose

value: sucrose


title: wt_male_mph_rep2

description: Gene expression of males exposed to methylphenidate

source_name: Drosophila males exposed to methylphenidate

value: methylphenidate


title: wt_f1_male_sucrose_rep1


title: wt_male_mph_rep3


title: wt_f1_male_sucrose_rep3


title: wt_male_mph_rep1


title: wt_male_sucrose_rep2

description: Gene expression of males exposed to sucrose

source_name: Drosophila males exposed to sucrose


title: SP-3-GACACAC_S3_L001_R1_001: Combo_1 (anti-CTLA-4 + anti-PD-1 DANA)

city: San Francisco

first: Anthony

last: Chang

state: California

address: 513 Parnassus Ave.

institute: University of California, San Francisco

description: Combo vs. Iso.csv

data_processing:
Raw files were analyzed using CLC genomics workbench RNA-Seq analysis tools (Qiagen Bioinformatics)
Fastq files were aligned to ensembl_v86
Reference gene database is refseq_GRCm38.p5.r106
Differential RNA analysis was conducted and normalized with multi-factorail statistics based on a negative binomial GLM
Genome_build: ensembl_v86
Supplementary_files_format_and_content: csv files were generated using the CLC genomics workbench RNA-Seq analysis tools (Qiagen Bioinformatics) and contain the name, chromosome number, Region, fold changes, p-values, and ensembl information

source_name: Spas-1 CD8 cells

extract_protocol:
Live CD45+CD3+CD8+Spas-1+Spas-2- T cells were sorted from draining lymph nodes from TRAMP-C2 bearing mice on day 28 after treatment. Cells from the five mice from each treatment arm were pooled and split into triplicates. RNA was extracted from sorted Live CD45+CD3+CD8+Spas-1+Spas-2- T cells using an Ambion micro RNA isolation kit (AM1931) according to the manufacturer’s protocol. Bulk RNA sequencing was carried out on 0.25ng of RNA in triplicates from each treatment type using the protocol as previously described (Picelli et al., 2014) with the following modifications. The TSO, Oligo-dT30VN, and ISPCR primers were biotinylated on the 5’ end. 21 cycles of pre-amplification were found to be optimal.
Nextera adapters were added and the libraries were pooled and sequenced on an Illumina Hiseq 4000. Approximately 48,710 reads were obtained per library. The Fastq sequences were aligned and quantitated using the CLC genomics workbench RNA-Seq analysis tools (Qiagen Bioinformatics).

treatment_protocol: After tumor injection, mice were treated with their respective checkpoint inhibitor treatments on days 3, 6, and 9

value: Draining lymph node

tag: age

value: post natal day 91

tag: genotype

value: wild type

value: Spas-1 CD8 cells


title: SP-4-ATCCATG_S4_L001_R1_001: Isotype_1 (Iso)

tag: strain


title: SP-4-TCGTCTC_S12_L001_R1_001: Isotype_2 (Iso)

tag: cell type


title: SP-2-TAGGACC_S2_L001_R1_001: anti-PD-1 DANA_2

description: anti-PD-1 DANA vs. Iso.csv


title: SP-4-TTCGCAG_S8_L001_R1_001: Isotype_3 (Iso)


title: SP-3-GTCTACG_S11_L001_R1_001: Combo_2 (anti-CTLA-4 + anti-PD-1 DANA)

description: Combo vs. Iso.csv


title: SP-3-TTGTAGC_S7_L001_R1_001: Combo_3 (anti-CTLA-4 + anti-PD-1 DANA)

description: Combo vs. Iso.csv


title: wt_male_sucrose_rep1


title: SP-2-TCGTTGG_S6_L001_R1_001: anti-PD-1 DANA_3

description: anti-PD-1 DANA vs. Iso.csv


title: hY3_Unt 1


title: hY3_Unt 2


title: SP-1-TGCAGTT_S5_L001_R1_001: anti-CTLA-4_3

description: anti-CTLA-4 vs. Iso.csv


title: SP-2-GTGTCCT_S10_L001_R1_001: anti-PD-1 DANA_1

description: anti-PD-1 DANA vs. Iso.csv


title: PreASKO-GFP (KO)

city: Berkeley

first: Hei Sook

last: Sul

address: Morgan Hall

department: NST

institute: UC Berkeley

description: Dox treated at P1

data_processing:
Qseq
Genome_build: MM10
Supplementary_files_format_and_content: RPKM

source_name: stromal vascular fraction of inguinal white adipose tissue

growth_protocol: SVF from ingWAT was separated by mincing, treatment with collagenase and spinning the samples

extract_protocol:
Total RNA was extracted using TriZol-LS
PrepX on Apollo 324 (TAKARA Bio USA)
Bioanalyzer QC with >RIN8, mRNA selection with magnetic beads, Fragmentation, cDNA synthesis & library pre

treatment_protocol: Cells were stained with PDGFRa-PE antibody for 20 min, washed and resuspended in FACS buffer

value: GFP+ ingWAT SVF cells

tag: gender

value: 3 weeks-old

value: Sox9 PreASKO


title: SP-1-ACTGTGG_S9_L001_R1_001: anti-CTLA-4_1

description: anti-CTLA-4 vs. Iso.csv


title: SP-1-GTACGTC_S1_L001_R1_001: anti-CTLA-4_2

description: anti-CTLA-4 vs. Iso.csv


title: wt_male_sucrose_rep3


title: floxed-GFP (WT)

description: Dox treated at P1

value: Sox9 floxed

value: stromal vascular fraction of inguinal white adipose tissue


title: Input

data_processing:
Basecalls performed using Galaxy 18.05
ChIP-seq reads were aligned to the mm10 genome assembly using Galaxy configurations
In brief, reads were trimed using TrimGalore, QC was perfomed using fast QC2, reads were alligned using Bowtie2.
Peaks were called using MACS2 PeakCalling
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using Galaxy.org

source_name: 3T3-L1 cells

growth_protocol: Wt 3T3-L1 cells were grown to subconfluency and then harvested for ChIP according to Covaris TrueChip kit protocol (cat#520-154)

extract_protocol:
gDNA eas exracted according to kit's recommendations
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

treatment_protocol: Cells were crosslinked for 10 min and sonicated using Covaris sonicator

value: 3T3-L1 cells

tag: confluence

value: subconfluent

tag: antibody

value: input


title: Lexogen iron-loaded diet 3

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
The reads were mapped with STAR 2.5.3a to the mouse genome (mm10 / GRCm38).
Raw counts were generated by specifying --quantMode GeneCounts to STAR during alignment
Genome_build: Mus_musculus.GRCm38.89
Supplementary_files_format_and_content: csv file: each row represents a gene, each column represents a sample; values are raw counts

source_name: Mouse Liver

extract_protocol:
Total RNA was extracted from a 20mg piece of the large lobe of six livers (3 per diet group) using the Qiagen miRNeasy Mini kit (cat# 217004, Qiagen) per the manufacturer’s instructions.
Libraries were prepared from the extracted RNA using two different kits, the QuantSeq 3’mRNA-Seq Library Prep Kit-FWD (cat #15, Lexogen, Vienna, Austria), and the KAPA Stranded mRNA-Seq Kit (cat #KK8421, Kapa Biosystems, Wilmington, MA),  per the manufacturers’ instructions using 1 μg of RNA per library.

treatment_protocol: Eight female SJL/J mice (cat #686, purchased from The Jackson Laboratory, Bar Harbor, ME) housed at 4 mice per cage were placed on an AIN-93G “control” diet containing 50ppm iron (cat #515005, Dyets, Bethlehem, PA) upon arrival at 3 weeks of age. At 6-weeks of age, one cage of these mice was changed to an AIN-93G “high iron” diet containing 2% carbonyl iron (cat #515007, Dyets). At 11 weeks of age, the mice were fasted starting at 6:30am, and tissues were collected between 11:30am and 1pm. Blood was taken from the retroorbital plexus under isoflurane anesthesia using a heparin-coated capillary tube, and then mice were perfused via the heart with ice-cold phosphate buffered saline to flush remaining blood from the tissues. Tissues were collected and frozen in liquid nitrogen and stored at -80°C until analysis.

value: SJL/J

value: liver

tag: diet

value: iron-loaded diet

value: female

value: 11 weeks


title: Sox9 ChIP-Seq


title: Lexogen control diet 1

value: normal diet


title: KAPA iron-loaded diet 3


title: Lexogen control diet 3


title: KAPA iron-loaded diet 2


title: KAPA control diet 1


title: Patient 1 C1

source_name: Bladder cancer primary tumor samples

value: primary tumor

value: Female

value: 55 years


title: Lexogen iron-loaded diet 1


title: Lexogen iron-loaded diet 2


title: KAPA control diet 3


title: ATAC-seq_MEF_Ubc9-WT_rep2

city: Paris

first: Claudia

last: Chica

address: 25-28 Rue du Dr Roux

country: France

institute: Institut Pasteur

data_processing:
For ChIP-seq single-end reads were mapped to the Mus musculus mm9 reference genome using bowtie1; unique matches with no more than 2 mismatches in the best alignment stratum were kept.
Following the ENCODE guidelines, mapped reads were deduplicated with the Picar toolkit v1.94, blacklisted regions removed with bedtools v2.19.1 and the degree of IP fragment clustering determined with phantompeakqualtools v2.0. Peak calling was performed with MACS2  with default parameters for regular peak calling and using the INPUT library for the estimation of the significance of peak enrichment. Consistency of peak calling among biological replicates and the final set of peaks per condition were determined using the Irreproducible Discovery Rate (IDR) approach.
For ATAC-seq paired-end reads were mapped using the end-to-end mode and the very-sensitive parametrization of bowtie2; concordant pairs were kept (including dovetail) with a maximum fragment size of 2 Kbp.
Mapped pairs were deduplicated with the Picar toolkit v1.94 and retained pairs were then classified according to their correspondent fragment; we restricted the analysis to fragment sizes sufficiently sampled in the ATAC-seq library by selecting read pairs coming from fragments between 50 bp and 2 Kbp.
Genome_build: mm9
Supplementary_files_format_and_content: tdf files were generated with igvtools v2.3.25. ChIP-seq and ATAC-seq libraries were merged by pooling the biological replicates. Prior to pooling, quality assurance clustering and principal component analysis were performed to identify and discard outlying replicates. The read coverage of the merged libraries was calculated over non-overlapping windows of 50 bp genome wide and library size normalization was applied to allow comparisons of the read coverage between samples: spike-in normalization for the ChIP-seq and quantile normalization for the ATAC-seq datasets.
Supplementary_files_format_and_content: bed files with selected peaks were generated by MACS2 and then filtered according to the IDR protocol; tab delimited format: chromosome start end MACS_peak_ID -log10(p-value)*10 . foldChange -log10(p-value) -log10(q-value) relativeSummitPosition

source_name: mouse embryonic fibroblast cells E13.5

extract_protocol:
For ChIP-Seq: 10min formaldehyde fixation followed by sonication (histone marks) or Mnase digestion (transcription factors). Immunoprecipitation was performed using ChIP-IT kit (#53040, Active Motif) following manufacturer's protocol. Experiments were done in duplicates.
For ChIP-Seq: Libraries prepared using Microplex library Preparation kit v2 (C05010014, Diagenode) following manufacturer's protocol (V2 02.15). Libraries were size-selected (200-400bp) and clenaed-up using Agencourt AMPure XP beads (#A63881, Beckman).
For ATAC-seq:  according to Buenrostro et al., Nature Methods, 2013. 30min treatment with Tn5 nuclease on isolated nuclei. Experiments were done in triplicates.
For ATAC-seq:  Elute transposed DNA was PCR-amplified using barcode primers and purified using PCR Cleanup kit (QIAGEN)

value: mouse embryonic fibroblast  (MEF) cells

tag: genotype/variation

tag: passages


title: ATAC-seq_MEF_Ubc9-KO_rep1


title: ATAC-seq_MEF_Ubc9-KO_rep2


title: KAPA control diet 2


title: ATAC-seq_MEF_Ubc9-KO_rep3


title: KAPA iron-loaded diet 1


title: Sham_3

source_name: Same region of left ventrical in sham operated control

tag: breed

value: Yorkshire

tag: developmental stage

value: adult

value: male

tag: treatment

value: Sham

value: LV


title: ChIP-seq_INPUT_ES_siUbc9_rep1

source_name: mouse embryonic stem cells

value: mouse embryonic stem (ES) cells

tag: chip antibody


title: ChIP-seq_H3K9me3_ES_siUbc9_rep2

value: H3K9me3 (Abcam, ab8898)


title: ChIP-seq_INPUT_ES_siCtrl_rep1

value: siCtrl


title: ChIP-seq_H3K9me3_ES_siCtrl_rep2


title: ChIP-seq_H3K9me3_ES_siCtrl_rep1


title: ATAC-seq_MEF_Ubc9-WT_rep1


title: Lexogen control diet 2

value: SJL/J

tag: tissue

value: liver


title: C3L

first: Leqian

last: Liu

address: 1700 4th street

department: BTS

institute: UCSF

data_processing:
Demultiplexing of raw reads, trimming of adpater sequences
Alignement to reference genome (mm10) using STAR software
DESeq2 normlizes by size factor as well as by library complexity and then utilizes either a Wald test type statistic or a Generalized Linear Model (GLM)
Genome_build: mm10
Supplementary_files_format_and_content: txt file, abundance measurements for all gene in all samples

source_name: lung cells

extract_protocol:
Lungs were perfused with PBS and dissociated into a single cell solution in 10mM HEPES RPMI containing 0.2% collagenase, 0.1mg/mL Dispase II, and 2000U/mL DNaseI. Cells were passed through a 70um strainer and stained at 4 °C for 30 minutes with following antibodies (1:100), SiglecF-APC, MHCII-APC-Cy7, CD11c-PE. Cells were sorted with BD FACSAria2 or SONY SH800 FACS.
mRNA is isolated from total RNA using Dynabead mRNA purification kit. cDNA was prepared using the NuGen Ovation RNAseq system V2 kit, Sequencing libraries were generated using Nextera XT library preparation kit.

treatment_protocol: Bleomycin (3 U/k) or water was instilled intratracheally to anestherized male 129S1 mice, age 10-12 weeks.

value: lung

value: Control

value: siglecF+,CD11C+, MHCII low


title: C1L


title: 4B3L

value: 4 week post bleomycin


title: 4B1L


title: 4B2L


title: 4B3H

value: siglecF+,CD11C+, MHCII high


title: 4B1H


title: 2B3L

value: 2 week post bleomycin


title: 4B2H


title: hY3 3

tag: cells

value: Macrophages

value: hY3 treated


title: 2B1H


title: 2B2L


title: 2B2H


title: 2B1L


title: ChIP-seq_H3K9me3_ES_siUbc9_rep1


title: Danio_rerio_ChIPseq_intestine_9dpf_input

city: Nijmegen

first: Leonie

middle: M

last: Kamminga

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

description: ChIPseq input in 9 days post fertilization Danio rerio wild type intestines

data_processing:
RNA-seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with --quantMode geneCounts
Normalized counts obtained with DESeq2 version 1.16.1
ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters
Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2
ChIP-seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e-02 relative to respective ChIP input track.
Genome_build: GRCz10
Supplementary_files_format_and_content: Gene counts (.txt); peak files in BED format

source_name: intestine

growth_protocol: Zebrafish (Danio rerio) were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch, reared in E3 medium at 28.5°C and staged following Kimmel et al (1995). Larvae were fed a standard Gemma Micro 75 (Skretting USA) diet, supplemented with rotifer (Brachionus spp.) polyculture and Artemia according to guidelines.

extract_protocol:
Intestines were crosslinked, homogenized for chromatin extraction, and sonicated to get ~300 bp chromatin fragments.
Input DNA was set aside and chromatin fragments were incubated with anti-H3K4me3 (Millipore 04-745, 2 µl) or anti-H3K27me3 (Millipore 07-449, 2 µl) on protein G beads. After elution, standard Illumina (KAPA-HYPERprep) library preparations were made.

value: AB

value: intestine

value: 9 dpf

value: wild type, tg(cldn15la:GFP)

value: none (input)


title: Danio_rerio_ChIPseq_intestine_9dpf_H3K27me3_wt1

description: ChIPseq of H3K27me3 in 9 days post fertilization Danio rerio wild type intestines

value: anti-H3K27me3 (Millipore 07-449)


title: Danio_rerio_ChIPseq_intestine_9dpf_H3K4me3_wt2

description: ChIPseq of H3K4me3 in 9 days post fertilization Danio rerio wild type intestines

value: anti-H3K4me3 (Millipore 04-745)


title: Danio_rerio_ChIPseq_intestine_5dpf_input

description: ChIPseq input in 5 days post fertilization Danio rerio wild type intestines

value: 5 dpf


title: Danio_rerio_ChIPseq_intestine_7dpf_H3K4me3_wt2

description: ChIPseq of H3K4me3 in 7 days post fertilization Danio rerio wild type intestines

value: 7 dpf


title: Danio_rerio_ChIPseq_intestine_9dpf_H3K4me3_wt1


title: Danio_rerio_ChIPseq_intestine_9dpf_H3K27me3_wt2


title: Danio_rerio_ChIPseq_intestine_7dpf_H3K27me3_wt1

description: ChIPseq of H3K27me3 in 7 days post fertilization Danio rerio wild type intestines


title: Danio_rerio_ChIPseq_intestine_5dpf_H3K4me3_wt2

description: ChIPseq of H3K4me3 in 5 days post fertilization Danio rerio wild type intestines


title: Danio_rerio_ChIPseq_intestine_5dpf_H3K4me3_wt1


title: Danio_rerio_ChIPseq_intestine_7dpf_H3K4me3_wt1


title: Danio_rerio_ChIPseq_intestine_5dpf_H3K27me3_wt1

description: ChIPseq of H3K27me3 in 5 days post fertilization Danio rerio wild type intestines


title: Danio_rerio_RNAseq_intestine_9dpf_wt3

description:
Total RNA (rRNA depleted) of 9 days post fertilization Danio rerio wild type embryos
BSwt9dpf3.out.tab

extract_protocol:
Dissected intestines were lyzed in Trizol and total RNA was extracted, followed by in column (ZYMO RNA microprep) Dnase treatment.
Total RNA from dissected intesines was depleted of ribosomal RNA (RiboZero). After RNA fragmentation and cDNA synthesis, standard Illumina (KAPA-HYPERprep) library preparations were made.


title: Danio_rerio_ChIPseq_intestine_5dpf_H3K27me3_wt2


title: Danio_rerio_RNAseq_intestine_9dpf_wt2

description:
Total RNA (rRNA depleted) of 9 days post fertilization Danio rerio wild type embryos
BSwt9dpf2.out.tab


title: Danio_rerio_RNAseq_intestine_9dpf_wt1

description:
Total RNA (rRNA depleted) of 9 days post fertilization Danio rerio wild type embryos
BSwt9dpf1.out.tab


title: 2B3H

value: lung


title: Danio_rerio_RNAseq_intestine_7dpf_wt2

description:
Total RNA (rRNA depleted) of 7 days post fertilization Danio rerio wild type embryos
BSwt7dpf2.out.tab


title: Danio_rerio_ChIPseq_intestine_7dpf_input

description: ChIPseq input in 7 days post fertilization Danio rerio wild type intestines


title: Danio_rerio_ChIPseq_intestine_7dpf_H3K27me3_wt2


title: Danio_rerio_RNAseq_intestine_7dpf_wt1

description:
Total RNA (rRNA depleted) of 7 days post fertilization Danio rerio wild type embryos
BSwt7dpf1.out.tab


title: Danio_rerio_RNAseq_intestine_5dpf_wt1

description:
Total RNA (rRNA depleted) of 5 days post fertilization Danio rerio wild type embryos
BSwt5dpf1.out.tab


title: Danio_rerio_RNAseq_intestine_5dpf_wt2

description:
Total RNA (rRNA depleted) of 5 days post fertilization Danio rerio wild type embryos
BSwt5dpf2.out.tab


title: KDM4B_input_ChIPSeq

city: Wuhan

first: Xiang

last: Ying

address: Donghu road 185

department: medical genetics

institute: Wuhan University

data_processing:
Quality control of the ChIP-seq data was performed using Fastqc, and then, low-quality bases and adaptor contamination were deleted using Trim galore.
The data were mapped to hg38 using the BWA algorithm.
SICER v1.1 was used to identify broad peak distributions, under the setting of false discovery rate (FDR) < 0.01, and the results from this peak calling were stored as bed files.
Genome_build: hg38
Supplementary_files_format_and_content: chipseq peaks files were generated using SICER v1.1;bed files represents the H3K9me3 binding site of ench samples.

source_name: Human breast adenocarcinoma cell-line MCF7

growth_protocol: MCF7 cells were cultured in Eagle’s minimum essential medium (EMEM; Genom, 11700) with 10% FBS, 0.01 mg/mL  human recombinant insulin (Sigma, I9278), and nonessential amino acids (Invitrogen, 11140050)

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

value: female

tag: cell line

value: Human breast adenocarcinoma

tag: passage


title: shKDM4B_input_ChIPSeq


title: Danio_rerio_RNAseq_intestine_5dpf_wt3

description:
Total RNA (rRNA depleted) of 5 days post fertilization Danio rerio wild type embryos
BSwt5dpf3.out.tab

tag: age

tag: genotype


title: WT_H3K9me3_ChIPSeq

value: H3K9me3 (ABclonal, A2360)


title: shKDM4B_H3K9me3_ChIPSeq


title: KDM4B_H3K9me3_ChIPSeq


title: WT_input_ChIPSeq


title: P5 female no 2 percoll

city: Framingham

first: Timothy

middle: R

last: Hammond

address: 49 New York Avenu

institute: Sanofi

data_processing:
Step 1: Demux, Cell Ranger 1.2, 10x Genomics
Step 2: Alignment/Counts, Cell Ranger 1.2, 10x Genomics, Genome build GRCm38 (mm10)
Step 3: Clustering, ICACluster, Saunders et. al Cell 2018
Genome_build: mm10
Supplementary_files_format_and_content: Digital gene expression matrix
Samples 1-16 (All biological replicates): Read 1: 98 bp, Read 2: 14 bp (Barcode), Read 3: 10 bp (UMI)
Samples 17-47 (All biological replicates): Read 1: 26 bp (Barcode:16 bp UMI: 10 bp) Read 2: 98 bp

source_name: brain

extract_protocol:
10x Genomics Single Cell 3' Droplet-based single cell approach
10x Genomics Single Cell 3' library construction

tag: Sex

value: Female

tag: strain

tag: brain region

value: Whole Brain

value: Purified with Percoll


title: P5 female no 3 no percoll

value: Purified without Percoll


title: P5 female no 3 percoll


title: P100 LPC WM male no 3

value: Male

value: Subcortical White Matter

value: Lysolecithin injection


title: P5 female no 1 percoll


title: P5 female no 2 no percoll


title: Control_1_2

data_processing:
Base calls performed with bcl2fastq
Read 2 was aligned with Bowtie
Each aligned read was tagged with its mate-pair UMI and cell barcode.
Each aligned exonic read was tagged with a gene name.
A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes.
Genome_build: mm10 (UCSC)
Supplementary_files_format_and_content: Digital expression matrices. Flat text files with tab delimiters.

growth_protocol: Male 129S1 mice, age 10-12 weeks

extract_protocol:
Lungs were perfused with PBS and dissociated to a single cell solution using 0.13 U of liberase TM (Roche) and gentleMACS (Miltenyi Biotec). Cells were passed through a 70 um and 40um strainer followed by washing.
Libraries were prepared with Drop-seq protocol

treatment_protocol: Intratracheally installed with bleomycin (3 units/kg) (Bleo1-3) or water (Control 1-6) 2 weeks before sacrification.

tag: gender

value: male

value: 2 weeks post water intratracheally installed


title: Danio_rerio_RNAseq_intestine_7dpf_wt3

description:
Total RNA (rRNA depleted) of 7 days post fertilization Danio rerio wild type embryos
BSwt7dpf3.out.tab

value: AB

value: intestine

value: wild type, tg(cldn15la:GFP)


title: P100 saline WM male no 3

value: Saline injection


title: P5 female no 1 no percoll


title: P100 LPC WM male no 2


title: Control_1_1

value: lung


title: P100 saline WM male no 2


title: P100 LPC WM male no 1


title: P100 saline WM male no 1


title: P100 control WB male no 3


title: P100 control WB male no 1


title: P100 control WB male no 2


title: P540 male no 3


title: P540 male no 2


title: P540 male no 4


title: P540 male no 1


title: P100 female no 4


title: P100 female no 3


title: P100 male no 4


title: P100 male no 3


title: P100 male no 1


title: P100 female no 2


title: P100 female no 1


title: P100 male no 2


title: P4 male no 3


title: P30 male no 4


title: P30 male no 3


title: P4 female no 2


title: P4 male no 2


title: P4 female no 3


title: P5 female no 1


title: P5 male no 1


title: P4 female no 1


title: P30 male no 1


title: E14.5 male no 4


title: E14.5 male no 3


title: E14.5 female no 4


title: P30 male no 2


title: E14.5 female no 3


title: E14.5 male no 2


title: P4 male no 1


title: E14.5 female no 1


title: E14.5 male no 1


title: Donor 4 proliferating rep3

city: Leuven

first: Bert

last: Cruys

address: Herestraat 49

country: Belgium

institute: Vesalius Research Center

description:
Replicate 3
9444360049_L

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Background correction was performed in the GenomeStudio software. Using the lumi package in R, the data was normalized by applying variance stabilizing transformation and quantile normalization (followed by probe filtering).

source_name: Umbilical vein

label_protocol: Biotynilated cRNA was prepared with the Ambion Total Prep Kit, according to the manufacturer's protocol.

growth_protocol: Freshly isolated human umbilical vein endothelial cells (ECs) were cultured in standard conditions (37°C, 5% CO2, culture medium (Promocell ECGM2) refreshed at least every other day) for 7 days. At this moment the ECs formed a confluent, contact-inhibited monolayer, in which neighboring cells inhibit each other to proliferate via intercellular contact. On day 7, a portion of the culture dishes of each donor were subcultured to induce cell proliferation. On day 9, the contact-inhibited and proliferating ECs of each donor were harvested on ice using RNA lysis buffer (Invitrogen), snap-frozen and stored at -80°C. The ECs were visually inspected every day to ensure their correct endothelial phenotype.

extract_protocol: Invitrogen standard RLT buffer

treatment_protocol: Human umbilical vein endothelial cells were not specifically treated, and only differentially cultured, as detailed in the Growth protocol.

tag: cell type

value: Umbilical vein endothelial cell


title: Donor 4 proliferating rep1

description:
Replicate 1
9444360049_J


title: PDGFRa+ cells from ingWAT SVF of Sox9 PreASKO mice

description: Dox treated at P1

hyb_protocol: Affymetrix Default

scan_protocol: Affymetrix Default

data_processing: RMA

source_name: female, 6 wk old, PDGFRa+ cells from ingWAT SVF, Sox9 PreASKO

label_protocol: Cells were stained with PDGFRa-PE antibody and sorted for PDGFRa-PE. Gates were properly established based on a negative control (aliquote of the same cells that were not treated with antibody)

extract_protocol: Total RNA was extracted using RNAesy protocol

value: female

value: 6 weeks-old

value: stromal vascular fraction of inguinal white adipose tissue

value: PDGFRa+ cells


title: Donor 4 contact-inhibited rep2

description:
Replicate 2
9444360049_H


title: Donor 3 proliferating rep3

description:
Replicate 3
9444360049_F


title: E14.5 female no 2

value: Female

value: Whole Brain


title: Donor 2 proliferating rep3

description:
Replicate 3
9444360021_L


title: Wild type intestinal spheroid cells

city: Kyoto

first: Yukiko

last: Hiramatsu

state: Kyoto

address: 54 Shogoin-Kawahara-cho, Sakyo-ku

department: Department of Gastroenterology and Hepatology

country: Japan

institute: Kyoto University Graduate School of Medicine

data_processing:
FASTQ conversion and Demultiplex performed using bcl2fastq v2.17.1.
ChIP-seq reads were mapped to the mouse reference genome (mm10) by Bowtie v1.1.1.
Enriched-regions (peaks) were determined using MACS2 peak caller (version 2.9.10) with a q-value cutoff of 0.05.
Peaks were annotated by in-house scripts. MEME software (version 1.10.1) was used to identify the binding motif.
Genome_build: mm10
Supplementary_files_format_and_content: bed files were generated usingMACS2; Columns represent chromosome number, peak start potision, peak end position, peak name, score for UCSC, fold enrichment, p value, ane q value

source_name: intestinal spheroid cells of wild type mice

growth_protocol: Isolated crypts of the proximal small intestine were embedded in Matrigel (BD Biosciences).For spheroid culture of normal epithelium, 50% conditioned medium of L-cell line secreting Wnt3a, R-spondin3, and Noggin (L-WRN CM) supplemented with 5 µmol/L Y-27632 (Tocris Bioscience) was added to each well.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Sequencing libraries were prepared using the TruSeq ChIP Sample Prep Kit (Illumina) following the manufacturer's instructions. The libraries were sequenced on the HiSeq 2500 sequencing platform using HiSeq SBS Kit v4 reagents with 2 x 101 cycles.

value: Arid1a (Cell Signaling Technology, #12354)


title: PreASKO (KO)

description: Dox treated at P1

extract_protocol:
Total RNA was extracted using TriZol-LS
PrepX on Apollo 324 (TAKARA Bio USA)
Bioanalyzer QC with >RIN8, mRNA selection with magnetic beads, Fragmentation, cDNA synthesis & library prep

value: 3 weeks-old

value: Sox9 PreASKO


title: Donor 3 contact-inhibited rep2

description:
Replicate 2
9444360049_B


title: floxed (WT)

description: Dox treated at P1

value: male

value: Sox9 floxed


title: PDGFRa+ cells from ingWAT SVF of floxed mice

description: Dox treated at P1

source_name: female, 6 wk old, PDGFRa+ cells from ingWAT SVF, Sox9 floxed


title: Donor 4 proliferating rep2

description:
Replicate 2
9444360049_K


title: Donor 4 contact-inhibited rep1

description:
Replicate 1
9444360049_G


title: Donor 2 proliferating rep2

description:
Replicate 2
9444360021_K


title: Donor 3 proliferating rep1

description:
Replicate 1
9444360049_D


title: ChIP-seq_INPUT_MEF_Ubc9-KO_rep1

data_processing:
For ChIP-seq single-end reads were mapped to the Mus musculus mm9 reference genome using bowtie1; unique matches with no more than 2 mismatches in the best alignment stratum were kept.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated with WigMaker3 by merging read counts every 25 bp

extract_protocol:
For ChIP-Seq: 10min formaldehyde fixation followed by sonication. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with SUMO antibody.
Libraries prepared using Microplex library Preparation kit v2 (C05010014, Diagenode) following manufacturer's protocol (V2 02.15). Libraries were size-selected (200-400bp) and clenaed-up using Agencourt AMPure XP beads (#A63881, Beckman).

value: mouse embryonic fibroblast (MEF) cells


title: Donor 4 contact-inhibited rep3

description:
Replicate 3
9444360049_I


title: ChIP-seq_INPUT_MEF_Ubc9-WT_rep1


title: ChIP-seq_SUMO-2_MEF_Ubc9-KO_rep1

value: SUMO-2 (gift from Dr. M. Dasso)


title: Donor 2 contact-inhibited rep1

description:
Replicate 1
9444360021_G


title: Donor 2 contact-inhibited rep2

description:
Replicate 2
9444360021_H


title: Donor 3 contact-inhibited rep3

description:
Replicate 3
9444360049_C


title: Donor 2 proliferating rep1

description:
Replicate 1
9444360021_J


title: Donor 3 contact-inhibited rep1

description:
Replicate 1
9444360049_A


title: ChIP-seq_SUMO-2_MEF_Ubc9-WT_rep1


title: ChIP-seq_SUMO-1_MEF_Ubc9-WT_rep1

value: SUMO-1 (Abcam, ab32058)


title: Bleomycin_2

value: 2 weeks post bleomycin intratracheally installed


title: Bleomycin_3

value: lung


title: ChIP-seq_SUMO-1_MEF_Ubc9-KO_rep1


title: Control_6

value: 2 weeks post water intratracheally installed


title: Donor 3 proliferating rep2

description:
Replicate 2
9444360049_E

value: Umbilical vein endothelial cell


title: Donor 1 proliferating rep3

description:
Replicate 3
9444360021_F


title: Donor 2 contact-inhibited rep3

description:
Replicate 3
9444360021_I


title: Bleomycin_1


title: Donor 1 proliferating rep2

description:
Replicate 2
9444360021_E


title: R-A7

data_processing:
Quality control metrics were measured on the FASTQ files using the FASTQC 0.11.4 tool.
Read mapping was then performed using Tophat 2.0.9 against the hg19 human reference genome.
The resulting binary alignment map files were processed using the HTSeq 0.6.1 python framework and respective hg19 gene transfer format annotation, obtained from the UCSC database.
The Bioconductor package DESeq2 (3.2) was then used to identify differentially expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: csv

source_name: human Leukocytes

growth_protocol: The hearts were cannulated through the aorta, and the coronary arteries were continuously perfused with proteolytic enzymes to yield a single cell suspension of primary human fetal cardiac cells for the culturing experiments or flow cytometry.

extract_protocol:
leukocytes were lysed in QIAzol solution (Qiagen) for RNA extraction using the Direct-zol RNA Miniprep kit (ZymoResearch) in accordance with the manufacturer’s instructions.
RNA sequencing (RNA-seq) libraries were made using the SMARTer Ultra Low RNA kit by Illumina employing 10 ng of total RNA to prepare cDNA libraries.

value: human Leukocytes

tag: cell

value: Primary cells isolated from cell types of human fetal heart

tag: disease state

value: healthy


title: CHB_Luekocytes

value: CHB


title: CHB-4


title: R2-FITC


title: Donor 1 proliferating rep1

description:
Replicate 1
9444360021_D


title: Donor 1 contact-inhibited rep2

description:
Replicate 2
9444360021_B


title: Donor 1 contact-inhibited rep3

description:
Replicate 3
9444360021_C


title: Donor 1 contact-inhibited rep1

description:
Replicate 1
9444360021_A


title: Control_4


title: Healthy-8


title: Control_2


title: Control_3


title: CHB-F


title: Control_5


title: CTL_48_73422

city: Ann Arbor

first: William

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

description: RNA extracted from SH-SY5Y neuroblastoma cells

data_processing:
Cutadapt was used to remove Illumina adaptor sequence (AGATCGGAAGAGC) with maximum error rate (-e) of 5% and minimum read length (-m) of 20 base pairs .
To remove sequences mapping to rRNA, an initial tophat2 run was carried out using an edited gtf file specifying only rRNA sequence coordinates for the UCSC GRCh38/hg38 genome sequence, with 1 transcriptome alignment reported per read (-g 1 --transcriptome-only) and disabling of coverage-based junction search (--no-coverage-search). Further analyses were then performed using only the unmapped reads from this preliminary tophat2 run.
Cutadapt was used to trim reads from the 3’ end using a quality score threshold of 30 (-q) and minimum read length of 20. Reads were then filtered using the Fastx toolkit function fastq_quality_filter to retain only those reads with quality scores above 30 for at least 50% of base pairs (settings: -q 30 -p 50).
tophat2 was used to map remaining reads to the UCSC GRCh38/hg38 transcriptome (--transcriptome-only) with disabling of read multi-mapping (-g 1) and coverage-based junction search (--no-coverage-search)
Read counts for each GRCh38/hg38 human gene were tabulated using htseq-count, with reads assigned to a gene only when the alignment quality was greater than 10 (-a 10) and when the read completely and unambiguously overlapped a gene’s sequence (-m intersection-strict). FPKM values and 95% confidence intervals were calculated using Cufflinks with default settings.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Processed data includes raw read counts and FPKM values for all human genes (GRCh38/hg38) and each sample (.txt files).

source_name: SH-SY5Y cells

growth_protocol: Subconfluent SH-SY5Y cells (Sigma, St. Louis, MO) were grown using supplemented Eagle's Minimum Essential / F12 (1:1) Medium.

extract_protocol:
RNA extractions were performed using the NucleoSpin RNA II kit (Machery-Nagel; Bethlehem, PA) with the DNA digestion step and robotic Qiacube (Qiagen, Valencia, CA) workstation. Purified total RNA was assessed at 260nm and 280nm with a NanoDrop Lite (Thermo Fisher Scientific, Waltham, MA) spectrophotometer.
Polyadenylated RNA was purified and used to prepare complementary DNA libraries for high throughput sequencing using the Illumina mRNA-Seq kit according to the manufacturer’s protocol (Illumina, San Diego, CA). Sequencing of fragmented complementary cDNA was performed using the Illumina Genome Analyzer Iix

treatment_protocol: The experiments were performed at Sunny BioDiscovery laboratories (Santa Paula, CA). The test material (GM6 peptide) was dissolved in cell culture medium and tested at a final concentration of 1mg/ml for incubation times of 6, 24 or 48 hours. Subconfluent SH-SY5Y cells (Sigma, St. Louis, MO) were incubated with GM6 in the supplemented Eagle's Minimum Essential / F12 (1:1) Medium. Experiments were terminated after microscopic observation of cells through Nikon (Tokyo, Japan) Eclipse TS100 inverted microscope.

value: SH-SY5Y cells

value: CTL

tag: time point

value: 48 hours


title: GM6_48_73421


title: GM6_48_73417


title: GM6_48_73419


title: GM6_48_73420


title: GM6_48_73418


title: CTL_48_73424


title: CTL_48_73425


title: CTL_48_73426


title: EGF_IWR1_S01

city: York

first: Katherine

last: Newling

address: Wentworth Way

department: Biology

country: United Kingdom

institute: University of York

data_processing:
Illumina HiSeq 3000 sequencing
Reads were trimmed using Cutadapt v.1.8.3
Reads were aligned to version GRCh38 of the human genome using HISAT2 v 2.0.5
Transcriptomes were assembled and gene expression quantified using the Tuxedo pipeline (version 2.2.1). Transcriptome assembly, merging, quantification and normalisation to fragments per kilobase per million mapped reads (FPKM) were performed using Cufflinks, Cuffmerge, Cuffquant and Cuffnorm, respectively.
An analysis of variance model with experimental condition (Control, EGF, EGF+IWR-1) as factor was fit to the FPKM values in the R stats package, followed by Tukey HSD test to calculate adjusted p-values to estimate which groups differed.
Genome_build: Human genome GRCh38 GCA_000001405.15
Supplementary_files_format_and_content: Cufflinks_FPKMs_and_TukeyHSD_results.txt: tab-delimited text file containing Cuffnorm output, including FPKM values for each gene in all 9 samples, as well as Tukey HSD results in the form of p-values.

source_name: femoral heads/knee bone explants

growth_protocol: Primary human MSCs at p4 were plated into two wells of three 6 well plates in triplicate.

extract_protocol:
After 24hrs, media was aspirated and total cellular RNA was extracted following the manufacturer’s guidelines using a Nucleospin RNA II kit from Macherey-Nagel having pooled cells from two wells for each RNA column to increase yield.
RNA yield was quantified and checked for quality using a Nanodrop spectrophotometer before quality control and further quantification using an Agilent bioanalyser prior to RNAseq

treatment_protocol: Cells were allowed to adhere overnight in MSC basal medium before stimulation for 24hrs with 10 nM epidermal growth factor (EGF) alone, EGF in the presence of 10 µM IWR-1 or left untreated in 2 ml MSC basal medium.

value: Mesenchymal stromal cells

value: EGF + IWR-1


title: EGF_S03

description: Cufflinks_FPKMs_and_TukeyHSD_results.txt

value: EGF


title: CTL_24_73416

value: 24 hours


title: EGF_S02


title: GM6_24_73411


title: CTL_24_73414


title: untreated_S01

value: untreated


title: EGF_S01


title: untreated_S02


title: untreated_S03


title: CTL_24_73412


title: CTL_24_73415


title: CTL_48_73423


title: EGF_IWR1_S03


title: GM6_24_73410


title: C3-rep3.input

city: Research Triangle Park

first: Paul

middle: A

last: Wade

state: NC

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

institute: NIEHS

data_processing:
For ChIP-seq data, cutadapt v1.2.1 was used to remove adapter from raw reads (parameters -a GATCGGAAGAG -O 5 -q 0), then read pairs were filtered out if average base quality was <20 or if shorter than 30nt after removing adapter.
Reads were mapped against mm9 reference genome with Bowtie v1.2 (parameters: -m 1 -X 1000 --chunkmbs 1024).
Duplicate read pairs were removed via Picard v1.110 MarkDuplicates.jar.
Replicates were combined via Picard v1.110 MergeSamFiles.jar, then downsampled to match lowest read total among the 4 sample conditions (N=33055298).
For visualization of ChIP-seq data, each read pair was converted to a single fragment by filling in the gap between ends, converted to bedGraph format via Bedtools v2.24.0 genomeCoverageBed, then converted to bigWig via UCSC utility bedGraphToBigWig.
Genome_build: mm9
Supplementary_files_format_and_content: Genomic depth after merging replicates and downsampling; format=bigWig.

source_name: liver

growth_protocol: Animals were housed in a pathogen-free environment, and no pathogens were identified in sentinel testing of serum and feces. At 20 weeks, all animals were euthanized by carbon dioxide asphyxiation. All animal studies were approved by the Alion Animal Care and Use Committee.

extract_protocol:
Chromatin was  fragmented by sonication with Covaris S220. Immunoprecipitation  was performed with FOXA1 antibody (abcam, ab5089)
NEXTflex Rapid DNA-Seq Library Prep Kit

treatment_protocol: Frozen livers were fixed with 1% formaldehyde at room temperature for 10 min. The fixed tissues were treated with a hypotonic buffer. Nuclei were resuspended with a lysis buffer containing 20 mM Tris-  HCl pH 8.0, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM PMSF,  5 mM sodium butyrate, 0.1 % SDS and protease inhibitor  cocktail).

value: male

tag: replicate animal


title: EGF_IWR1_S02

tag: treatment


title: GM6_24_73409


title: 274L_S7

city: Seattle

first: Raghav

last: Chawla

state: WA

address: 3720 15th Ave NE

department: Department of Genome Sciences

institute: University of Washington

data_processing:
Paired-end sequencing reads were aligned to the human genome version GRCh38 and quantified with RSEM using the STAR alignment algorithm with default settings.
Genome_build: GRCh38
Supplementary_files_format_and_content: Expected counts per gene from the RSEM output

source_name: Bulks from HUES8 Differentiation flask #274

extract_protocol:
Buds were detached and separated from the spheroids at stage 5 of the differentiation protocol by mechanical agitation and filtering. RNA-sequencing of buds versus bulks was performed on samples from 5 separate differentiation flasks, whereby bulks could be collected from all and buds from 3 of the differentiation flasks.
Polyadenylated RNA was selected from total RNA using the PrepX PolyA mRNA Isolation Kit (Takara Bio USA) and sequencing libraries were prepared using the PrepX RNA-Seq for Illumina Library Kit (Takara Bio USA). After additional enrichment, indexing and cleanup steps, libraries were sequenced on an Illumina NextSeq 500.

tag: differentiation flask number

tag: bulks (large) vs. buds (small)

value: Bulks (L)