title: CP31


title: C2: hsf1-mC

status: Public on Apr 16 2019

type: SRA

city: Houston

first: Kevin

middle: A

last: Morano

state: TX

address: 6431 Fannin St, MSB 1.300

department: Microbiology and Molecular Genetics

country: USA

institute: UT Medical School at Houston

library_source: transcriptomic

data_processing:
The original raw data from Illumina are transformed to Sequenced Reads by base calling. Raw data are recorded in a FASTQ file, which contains sequence information (reads) and corresponding sequencing quality information.
Raw reads are filtered to remove reads containing adapters or reads of low quality, so that downstream analyses are based on clean reads.
Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v.2.0.12.
HTSeq  v0.6.1 was used to count the read numbers mapped to each gene, and FPKM calculated based on gene length and mapped reads using the union mode.
Genome_build: Saccharomyces_cerevisiae.Ensembl_release81.exon.gtf
Supplementary_files_format_and_content: Tab-delimited spreadsheet with FPKM for each sample

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: yeast, mutated carboxyl-terminal Hsp70 site

growth_protocol: Cell cultures grown to mid-log phase in rich YPD medium at 30˚C, harvested by centrifugation and cell pellet defanted and frozen immediately -80˚C.

extract_protocol:
Hot phenol total RNA isolation
Novogene Corp library service: After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. The mRNA is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment. Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies), and then diluted to 1 ng/µl before checking insert size on an Agilent 2100 and quantifying to greater accuracy by quantitative PCR (Q-PCR) (library activity >2 nM).

treatment_protocol: As control, but shifted to 37˚ C for 15 min prior to harvest.

tag: genotype

tag: treatment

value: untreated


title: N2: hsf1-mN

source_name: yeast, mutated amino-terminal Hsp70 site


title: irCLIP in HUH751-DENV of Vigilin bioRep 1

city: Stanford

first: Ryan

middle: Alexander

last: Flynn

state: CA

address: 380 Roth Way, Room 265

institute: Stanford University

description:
Protein enriched RNA
irCLIP_HUH751_DENV_Vigilin_norm_minusStrand.bw, irCLIP_HUH751_DENV_Vigilin_norm_plusStrand.bw

data_processing:
Library strategy: irCLIP
Sequencing reads were trimmed of 3' adaptors, collapsed for PCR duplicates, stripped of the 5' barcode, and mapped to the human (hg38) genome using bowtie2
RT stop identificaiton, gene assignment, and peak calling was performed as in FAST-iCLIP (PMID: 25411354)
Genome_build: hg38
Supplementary_files_format_and_content: bigWig file containing unique RT stops from the high confidence intersection of biological replicates of RRBP1 and vigilin irCLIP

organism: Homo sapiens

source_name: Dengue virus infection

growth_protocol: Huh7.5.1 cells were grown in DMEM with 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
Lysates were sonicated RRBP1-RNA complexes or vigilin-RNA complexes were isolated with anti-RRBP1 (Bethyl A303-996A) or anti-vigilin (Bethyl A303-971A) antibody.
Libraries were prepared according to the irCLIP protocol (PMID: 27111506)

treatment_protocol: Cells were UV crosslinked at 254nm for 0.3J/cm^2 to in vivo fix RNA-RBP interactions

tag: cell line

tag: cell type

value: Hepatocarcinoma cell line

tag: gender

value: male


title: uninj_exp1_st9p_polyA-RNA_rep2

city: London

first: George

middle: E.

last: Gentsch

state: Greater London

address: 1 Midland Road

department: Developmental Biology Laboratory

country: United Kingdom

institute: The Francis Crick Institute

description: uninjected, stage 9+ (late blastula), experiment 1, poly(A)+ RNA, biological replicate 2

data_processing:
Bases were called using Casava version 1.8.2
ChIP-Seq: Single reads of maximal 50 bases were processed using trim_galore v0.4.2 to trim off low-quality bases and adapter contamination from the 3’ end. Processed reads were aligned to the X. tropicalis genome assembly v7.1 (and v9.1 for some ChIP-Seq) running Bowtie2 v2.2.9 with default settings. Alignments were converted to HOMER’s tag density format with redundant reads being removed (makeTagDirectory -single -tbp 1 -unique -mapq 10 -fragLength 175 -totalReads all). For all genomic regions except for the mir427 gene cluster, only uniquely aligned reads (i.e. MAPQ ≥10) were processed. The highly repetitive mir427 locus was profiled with all reads only best aligning up to 80 times (-k 80) to this region. In this case the mass of each read was normalised to the number of alignments. We pooled all input alignments from various developmental stages. This created a comprehensive mappability profile that covered ~400 million unique base pair positions. All chromatin profiles were position-adjusted and normalised to the effective total of 1 million aligned reads including multimappers (counts per million aligned reads, CPM). Transcription factor binding sites were identified using the following or otherwise default parameters of HOMER’s calling of ChIP-mediated read enrichments (hereafter called peaks): findpeaks -style factor -minDist 175 -fragLength 175 -inputFragLength 175 -fdr 0.001 -gsize 1.435e9 -F 3 -L 1 -C 0.97. This means that both ChIP and input alignments were extended 3’ to 175 bp for the detection of significant (0.1% FDR) peaks being separated by ≥175 bp. The effective size of the X. tropicalis genome assembly v7.1 was set to 1.435 billion bp, an estimate obtained from the mappability profile. These peaks showed equal or higher tag density than the surrounding 10 kb, ≥3-fold more tags than the input and ≥0.97 unique tag positions relative to the expected number of tags. To detect focal RNAPII recruitment to putative cis-regulatory elements and avoid calling peaks within broad regions of RNAPII elongation, the threshold of focal ratio and local enrichment within 10 kb was elevated to 0.6 and 3 (-L 3), respectively. To further eliminate any false positive peaks, we removed any peaks with <0.5 (transcription factors including signal mediators) or <1 (RNAPII) CPM and those falling into blacklisted regions showing equivocal mappability due to genome assembly errors, gaps or simple/tandem repeats. Regions of equivocal mappability were identified by a 2-fold lower (poor) or 3-fold higher (excessive) read coverage than the average detected in 400-bp windows sliding at 200-bp intervals through normalised ChIP input and DNase-digested naked genomic DNA. All identified regions ≤800 bp apart were subsequently merged. Gap coordinates were obtained from the Francis Crick UCSC genome browser (http://genomes.crick.ac.uk). Simple repeats were masked with RepeatMasker v4.0.6 using the crossmatch search engine v1.090518 and the following settings: RepeatMasker -species "xenopus silurana tropicalis" -s -xsmall. Tandem repeats were masked with Kent’s trfBig wrapper script of the Tandem Repeat Finder v4.09 using the following settings: weight for match, 2; weight for mismatch, 7; delta, 7; matching probability, 80; indel probability, 10; minimal alignment score, 50; maximum period size, 2,000; and longest tandem repeat array (-l), 2 [million bp].
DNase-Seq: Single and paired-end reads of maximal 50 bases were processed using trim_galore v0.4.2 to trim off low-quality bases and adapter contamination from the 3’ end. Processed reads were aligned to the X. tropicalis genome v7.1 and v9.1 using Bowtie2 v2.2.9 with default settings apart from -X (fragment length), which was reduced to 250 bp for paired-end reads. Alignments were sorted by genomic coordinates and only those with a quality score of ≥10 were retained using samtools v1.3.1. Duplicates were removed using Picard (MarkDuplicates). Paired-end alignments were dissociated using hex flags (-f 0x40 or 0x80) of samtools view. Single alignments were converted to HOMER’s tag density format (makeTagDirectory -single -unique -fragLength 100 -totalReads all). DNase hypersensitive sites (DHSs) were identified using the following or otherwise default parameters of HOMER’s peak calling: findpeaks -style factor -minDist 100 -fragLength 100 -inputFragLength 100 -fdr 0.001 -gsize 1.435e9 -F 3 -L 1 -C 0.97. This means that alignments of DNase-digested chromatin fragments (or naked genomic DNA fragments considered here as ‘input’) were extended 3’ by 100 bp from the DNase cleavage site to detect significant (0.1% FDR) DNase-mediated read enrichments (hereafter called peaks) being separated by ≥100 bp. The effective size of the X. tropicalis genome assembly v7.1 was set to 1.435 billion bp, an estimate obtained from the mappability profile (see ‘ChIP-Seq’ section). These peaks showed equal or higher tag density than the surrounding 10 kb, ≥3-fold more tags than the input and ≥0.97 unique tag positions relative to the expected number of tags. Peaks falling into blacklisted regions (see ‘ChIP-Seq’ section) were removed. DNase-probed chromatin accessibility profiles were position-adjusted and normalised to the effective total of 1 million aligned reads including multimappers.
Next-generation capture-C: Paired-end reads were processed using trim_galore v0.4.2 to trim off low-quality bases and adapter contamination from the 3’ end. Only complete mate pairs were processed further to reconstruct single reads from overlapping paired-end sequences using FLASH v1.2.11 with interleaved output settings for non-extended reads (flash --interleaved-output --max-overlap 150). FLASH reads were split in silico at DpnII restriction sites using a designated perl script (dpnII2E.pl, https://github.com/Hughes-Genome-Group/captureC/releases) before aligning them to the X. tropicalis genome assembly 7.1 using Bowtie2 v2.2.9. The alignment was run with default settings and one thread only to maintain the order of reads. The view function of samtools v1.3.1 was used to retain alignments with a quality score of ≥10. The alignments were analysed further using a suite of perl scripts (https://github.com/Hughes-Genome-Group/captureC/releases) modified to process both chromosome and scaffold coordinates. Viewpoint coordinates included a 1-kb proximity exclusion range. Restriction fragments were classified as capture, proximity-exclusion or reporter. PCR duplicates were removed. The interaction map was based on the number of unique paired-end reads per restriction fragment. Windows of 2 kb incrementing by 200 bp were used to consolidate interactions, which were normalised to 10,000 interactions per viewpoint. Significant chromatin conformation changes were identified using the R package DESeq2 v1.14.1.
RNase-Seq: Paired-end reads were aligned to the X. tropicalis genome assembly v7.1 using STAR v2.5.3a with default settings and a revised version of gene models v7.2 to improve mapping accuracy across splice junctions. The alignments were sorted by read name using the sort function of samtools v1.3.1. Exon and intron counts (-t 'exon;intron') were extracted from unstranded (-s 0) alignment files using VERSE v0.1.5 in featureCounts (default) mode (-z 0). Intron coordinates were adjusted to exclude any overlap with exon annotation. Differential expression analysis was performed with both raw exon and intron counts excluding those belonging to ribosomal and mitochondrial RNA using the R package DESeq2 v1.14.1. In an effort to find genes with consistent fold changes over time, p-values were generated according to a likelihood ratio test reflecting the probability of rejecting the reduced (~ developmental stage) over the full (~ developmental stage + condition) model. Resulting p-values were adjusted to obtain false discovery rates (FDR) according to the Benjamini-H

molecule: polyA RNA

organism: Xenopus tropicalis

source_name: whole embryo

growth_protocol: Embryos were grown to the indicated developmental stage in 5% MMR at 25ºC.

extract_protocol:
Chromatin immunoprecipitation (ChIP): Briefly, dejellied X. tropicalis embryos were treated with 1% formaldehyde (in 1% Marc’s Modified Ringer’s, MMR) for 15-45 min at room temperature to cross-link chromatin proteins to nearby genomic DNA. Duration of fixation was determined empirically and depended mainly on the developmental stage and antibody epitopes as described in Gentsch and Smith (2017). Efficient Preparation of High-Complexity ChIP-Seq Profiles from Early Xenopus Embryos. Methods in Molecular Biology, 1507, 23-42. Fixation was terminated by rinsing embryos three times with ice-cold 1% MMR. If required, post-fixation embryos were dissected to select specific anatomical regions in ice-cold 1% MMR. Fixed embryos were homogenized in CEWB1 (10 mM Tris pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% Igepal CA-630, 0.25% sodium deoxycholate and 0.1% SDS) supplemented with 0.5 mM DTT, protease inhibitors and, if using phospho-specific antibodies, phosphatase blockers (0.5 mM orthovanadate and 2.5 mM NaF). To solubilise yolk platelets and separate them from the nuclei, the homogenate was left on ice for 5 min and then centrifuged (1000 g) for 5 min at 4ºC. Homogenization and centrifugation was repeated once before resuspending the nuclei containing pellet in 1-3 ml CEWB1. Nuclear chromatin was solubilized and fragmented by isothermal focused or microtip-mediated sonication. The solution of fragmented chromatin was cleared by centrifuging (15,000 g) for 5 min at 4ºC. If required, ~1% of the cleared chromatin extract was set aside for the input sample (negative control for ChIP). ChIP-grade antibodies were used to recognize specific chromatin features and to enrich these by coupling the antibody-chromatin complex to protein G magnetic beads and extensive washing. These steps were carried out at 4ºC. The beads were washed twice in CEWB1, twice in WB2 (10 mM Tris pH 8.0, 500 mM NaCl, 1 mM EDTA, 1% Igepal CA-630, 0.25% sodium deoxycholate and 0.1% SDS), twice in WB3 (10 mM Tris pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% Igepal CA-630 and 1% sodium deoxycholate) and once in TEN (10 mM Tris pH 8.0, 150 mM NaCl and 1 mM EDTA). ChIP was eluted off the beads twice with 100 µl SDS elution buffer (50 mM Tris pH 8.0, 1 mM EDTA and 1% SDS) at 65ºC. ChIP eluates were pooled before reversing DNA-protein cross-links. Input (filled up to 200 µl with SDS elution buffer) and ChIP samples were supplemented with 10 µl 5 M NaCl and incubated for 6-16 h at 65ºC in a hybridization oven. Samples were treated with proteinase K and RNase to remove any proteins and RNA from the co-immunoprecipitated DNA fragments. The DNA was purified with phenol:chloroform:isoamyl alcohol (25:24:1, pH 7.9) using phase-lock gel heavy microcentrifuge tubes for phase separation and precipitated with 1/70 volume of 5 M NaCl, 2 volumes of absolute ethanol and 15 µg blue glycogen (GlycoBlue). After centrifugation, the DNA pellet was air-dried and dissolved in 11 µl elution buffer (10 mM Tris-HCl, pH 8.5). The DNA concentration was determined on a fluorometer using high-sensitivity reagents for double-stranded DNA (10 pg/µl to 100 ng/µl).
DNase-probed chromatin accessibility: The assay to probe chromatin accessibility with DNase was adapted to early X. tropicalis embryos using a novel approach. Ultracentrifugation- or gel electrophoresis-mediated size selection was replaced by two rounds of solid phase reverse immobilization (SPRI) to remove high molecular weight (HMW) DNA from the informative, short DNA fragments. Wide-bore pipette tips were used for the resuspensions and the transfers of biological samples from the second homogenization step until after SPRI to avoid the shearing of HMW DNA. About 250 dejellied mid-blastula embryos (stage 8+) were collected in 2-ml round-bottom microcentrifuge tubes and homogenized in 2 ml ice-cold LB-DNase buffer (15 mM Tris-HCl pH 8.0, 15 mM NaCl, 60 mM KCl, 1 mM EDTA, 0.5 mM EGTA, 0.5 mM and 0.5 mM spermidine) supplemented with 0.05% Igepal CA-630. The homogenate was left on ice for 3 min before centrifuging (1,000 g) for 2 min at 4ºC. The pellet was gently resuspended in 2 ml ice-cold LB-DNase buffer (without Igepal CA-630) before centrifuging (1,000 g) again for 2 min at 4ºC. The pellet was resuspended in 600 µl of room temperature LB-DNase buffer supplemented with 6 mM CaCl2. The sample was distributed equally to two 1.5-ml microcentrifuge tubes. Approximately 0.1 U DNase I was added to one aliquot while leaving the other aliquot untreated (internal control). Both samples were incubated for 8 min at 37ºC before adding 300 µl STOP buffer (50 mM Tris pH8.0, 100 mM NaCl, 100 mM EDTA, 0.1% SDS, 80 µg RNase A, 333 nM spermine and 1 µM spermidine). The samples were incubated for 15 min at 55ºC. Next, they were digested with 200 µg proteinase K for 2 h at 55ºC. The digests were transferred to phase-lock gel heavy microcentrifuge tubes for phenol:chloroform:isoamylalcohol (25:24:1) purification. The DNA was precipitated with 1/20 volume of 3 M sodium acetate (pH 5.2) and 2 volumes of absolute ethanol. The DNA pellets were dissolved in 27 µl elution buffer (10 mM Tris pH8.5). To remove any remaining RNA (i.e. not digested in a first round of RNase treatment), 10 µg RNase A were added to the DNA samples. 5 µl (an equivalent of 20 mid-blastula embryos) from the internal control was digested with 0.3 U DNase I for 5 min at 37ºC to generate a negative control profile (i.e. DNase-treated naked genomic DNA) for chromatin accessibility. The purification and precipitation of negative control DNA was carried out along with the chromatin digest after SPRI-mediated size selection. The DNA sample from the chromatin digest was further processed by two rounds of SPRI. 22.5 µl SPRI beads were added to 25 µl DNA sample without pipetting up and down. After 3 min, by which time HMW DNA caused beads to coalesce, the tubes were clipped into a magnetic stand for microcentrifuge tubes. After 3 min, the supernatant was transferred to a 96-well microplate. 47.5 µl elution buffer and 43 µl SPRI beads were added sequentially and mixed gently by slowly pipetting up and down. After 3 min, the plate was transferred to a magnetic stand for 96-well plates. Once the beads have settled to bottom of the well, the supernatant and the digest of naked genomic DNA (see above) were transferred to separate 1.5-ml phase-lock gel heavy microcentrifuge tubes and purified with phenol:chloroform:isoamylalcohol (25:24:1, pH7.9). The DNA fragments were precipitated with 1/20 volume of 3 M sodium acetate (pH 5.2) and 3 volumes of absolute ethanol. After centrifugation, the DNA pellets were dissolved in 12 µl elution buffer. The DNA concentrations were determined on a fluorometer using high-sensitivity reagents for double-stranded DNA (10 pg/µl to 100 ng/µl).
Chromatin conformation capture (3C): About 500 dejellied mid-blastula embryos (stage 8+) were fixed with 1% formaldehyde (in 1% Marc’s Modified Ringer’s, MMR) for 40 min at room temperature. The fixation reaction was terminated by rinsing the embryos three times with ice-cold 1% MMR. The embryos were aliquoted equally into two 2-ml round-bottom microcentrifuge tubes and homogenized in 2 ml ice-cold CEB-3C (10 mM Tris pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% Igepal CA-630, 0.25% sodium deoxycholate and 0.2% SDS) supplemented with protease inhibitors and 0.05 mM DTT (=CEB-3C*). The homogenates were kept on ice for 5 min before centrifuging (1,000 g) for 2 min at 4ºC. The pellet was resuspended in 0.5 ml ice-cold CEB-3C*. The resuspensions were pooled and then equally divided to two 50-ml conical tubes and each filled up with CEB-3C to 50 ml. The embryonic extracts were incubated at 37ºC for 1 h in a hybridization oven with the tubes rotating inside a hybridization bottle. The tubes were then centrifuged (1,000 g) for 5 min at room temperature. The pellets were resuspended in 50 ml double distilled water. The tubes were centrifuged (1,000 g) agai

treatment_protocol: Injections were carried out into the zygote's animal pole: MyoD-HA mRNA (80 pg); mPouV MO (5 ng Pou5f3.2 MO, 5 ng Pou5f3.3 MO and 5 ng standard control MO); mPouV/Sox3 MOs (5 ng Pou5f3.2 MO, 5 ng Pou5f3.3 MO and 5 ng Sox3 MO); β-catenin MO (5 ng); mVegT MO (10 ng); standard control MO (5-10 ng according to the dose used for the β-catenin or mVegT loss-of-function experiment); and α-amanitin (30 pg). Embryos were treated with 100 µM SB431542 or 10 µM LDN19318 from the 8-cell stage onwards to block Nodal or BMP signaling. Control embryos were treated accordingly with DMSO, the solvent of these antagonists.

tag: strain

value: wild-type (out-bred Nigerian)

tag: developmental stage

value: 9+ (late blastula)

tag: chip antibody


title: N1: hsf1-mN


title: NC1: hsf1-mNmC

source_name: yeast, mutated amino- and carboxyl-terminal sites


title: CP30

city: Torun

first: CHANDRA

middle: SHEKHAR

last: PAREEK

state: Kuj. Pom.

address: ul. Wilenska 4

department: Centre for Modern Interdisciplinary Technologies

country: Poland

institute: Nicolaus Copernicus University

description:
young bull
fpkm calculated using cufflinks

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to UMD cattle genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
fpkm calculated using cufflinks
Genome_build: UMD Bos Taurus plus y-chromosome
Supplementary_files_format_and_content: tab-delimited text files with option of excel file format, include RPKM values for each Sample ...

organism: Bos taurus

source_name: liver

extract_protocol:
Total RNA isolation from bovine liver tissues of three cattle breeds were harvested using Trizol reagent. Illumina TruSeq mRNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Polish-HF

tag: age

tag: tissue

value: liver


title: CP29


title: CP28


title: irCLIP in HUH751-NI of Vigilin bioRep 2

description:
Protein enriched RNA
irCLIP_HUH751_NI_Vigilin_norm_minusStrand.bw, irCLIP_HUH751_NI_Vigilin_norm_plusStrand.bw

source_name: non-infected


title: uninj_exp1_st9p_polyA-RNA_rep1

description: uninjected, stage 9+ (late blastula), experiment 1, poly(A)+ RNA, biological replicate 1


title: irCLIP in HUH751-NI of Vigilin bioRep 1


title: CP27


title: H3: wild type HSF1

source_name: yeast, wild type HSF1 allele

value: wild type HSF1


title: uninj_exp1_st10p_polyA-RNA_rep2

description: uninjected, stage 10+ (early gastrula), experiment 1, poly(A)+ RNA, biological replicate 2

value: 10+ (early gastrula)


title: H2: wild type HSF1


title: uninj_exp1_st8p_polyA-RNA_rep3

description: uninjected, stage 8+ (mid-blastula transition), experiment 1, poly(A)+ RNA, biological replicate 3

value: 8+ (mid-blastula transition)


title: irCLIP in HUH751-ZIKV of RRBP1 bioRep 2

description:
Protein enriched RNA
irCLIP_HUH751_ZIKV_RRBP1_norm_minusStrand.bw, irCLIP_HUH751_ZIKV_RRBP1_norm_plusStrand.bw

source_name: Zika virus infection


title: CP24

value: Polish-Red


title: irCLIP in HUH751-DENV of Vigilin bioRep 2


title: CP23


title: input_st20_ChIP

description:
ChIP input, stage 20 (early tailbud)
input_xt7_unique.bw

library_source: genomic

molecule: genomic DNA

value: 20 (early tailbud stage)


title: H1: wild type HSF1


title: irCLIP in HUH751-DENV of RRBP1 bioRep 2

description:
Protein enriched RNA
irCLIP_HUH751_DENV_RRBP1_norm_minusStrand.bw, irCLIP_HUH751_DENV_RRBP1_norm_plusStrand.bw


title: uninj_exp1_st8p_polyA-RNA_rep1

description: uninjected, stage 8+ (mid-blastula transition), experiment 1, poly(A)+ RNA, biological replicate 1


title: uninj_exp1_st9p_polyA-RNA_rep3

description: uninjected, stage 9+ (late blastula), experiment 1, poly(A)+ RNA, biological replicate 3


title: CP22


title: input_st12_ChIP_rep2

description:
ChIP input, stage 12+ (late gastrula), biological replicate 2
input_xt7_unique.bw

value: 12+ (late gastrula)


title: irCLIP in HUH751-DENV of RRBP1 bioRep 1


title: amanitin_exp1_st10p_polyA-RNA_rep3

description: α-amanitin injected, stage 10+ (early gastrula), experiment 1, poly(A)+ RNA, biological replicate 3

value: injection of α-amanitin (inhibition of transcription)


title: CP21


title: input_st8_ChIP_rep1

description:
ChIP input, stage 8 (1,000-cell), biological replicate 1
input_xt7_unique.bw

value: 8 (1,000-cell stage)


title: irCLIP in HUH751-NI of RRBP1 bioRep 2

description:
Protein enriched RNA
irCLIP_HUH751_NI_RRBP1_norm_minusStrand.bw, irCLIP_HUH751_NI_RRBP1_norm_plusStrand.bw


title: CP20


title: amanitin_exp1_st10p_polyA-RNA_rep1

description: α-amanitin injected, stage 10+ (early gastrula), experiment 1, poly(A)+ RNA, biological replicate 1


title: amanitin_exp1_st10p_polyA-RNA_rep2

description: α-amanitin injected, stage 10+ (early gastrula), experiment 1, poly(A)+ RNA, biological replicate 2


title: irCLIP in HUH751-NI of RRBP1 bioRep 1


title: Tbx6_st20_ChIP

description: Tbx6 ChIP, stage 20 (early tailbud)

value: rabbit polyclonal anti-Tbx6 (#4596; Smith Lab)


title: CP19


title: uninj_exp1_st8p_polyA-RNA_rep2

description: uninjected, stage 8+ (mid-blastula transition), experiment 1, poly(A)+ RNA, biological replicate 2


title: irCLIP in HUH751-ZIKV of RRBP1 bioRep 1


title: RNA-seq in HUH751-ZIKV bioRep 2

description:
Ribosome depleted RNA
ZIKV_Rep2_CPM

data_processing:
Sequencing reads were trimmed of 3' adaptors, collapsed for PCR duplicates, stripped of the 5' barcode, and mapped to the human (hg38) genome using bowtie2.
The featureCount tool of the Subread package (version 1.6.0) was used to count aligned reads supporting transcripts annotated from Gencode Release 26 (GRCh38 https://www.gencodegenes.org/releases/26.html).
Genes supported by at least 10 reads in a sample were considered expressed and counts were normalized by the total counts for all expressed genes in each sample to produce counts per million reads.
Genome_build: hg38
Supplementary_files_format_and_content: excel file containing counts per million of each gene identified across all 6 samples.

extract_protocol:
Lysates were sonicated, proteinase K treated, and RNA extracted with TRIzol.
Libraries were prepared according to the icSHAPE protocol (PMID: 26766114)


title: amanitin_exp1_st9p_polyA-RNA_rep3

description: α-amanitin injected, stage 9+ (late blastula), experiment 1, poly(A)+ RNA, biological replicate 3


title: Sox3_st8_ChIP

description: Sox3 ChIP, stage 8 (1,000-cell)

value: rabbit polyclonal anti-Sox3 (Klymkowsky Lab)


title: ND_liver_2

city: Guangzhou

first: Wen

last: Luo

state: Guangdong

address: Wushan

country: China

institute: South China Agricultural University

description: liver RNA_repeat 2

data_processing:
BGI SOAPnuke software used for trimming and filtering.
Sequenced reads were mapped to gga5 whole genome using HISAT2 v2.0.4 with parameters --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000
Gene expression analysis step 1: sequenced reads were then mapped to gga5 whole genome using Bowtie2 v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression analysis step 2: Expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were calculated using RSEM v1.2.12.
Genome_build: gga5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Gallus gallus

source_name: liver of broiler fed with normal diet

extract_protocol:
Livers and abdominal fats were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard BGI protocols

tag: diet

value: normal diet

value: Xinghua with dw gene


title: ND_liver_3

description: liver RNA_repeat 3


title: amanitin_exp1_st9p_polyA-RNA_rep2

description: α-amanitin injected, stage 9+ (late blastula), experiment 1, poly(A)+ RNA, biological replicate 2


title: amanitin_exp1_st9p_polyA-RNA_rep1

description: α-amanitin injected, stage 9+ (late blastula), experiment 1, poly(A)+ RNA, biological replicate 1


title: NG capC_mPS-LOF_rep3

description:
Next-generation capture-C, stage 8+ (mid-blastula transition), mPouV/Sox3 loss-of-function, biological replicate 3
capC_mPSkd_exp123_xt7.bdg

data_processing:
Library strategy: Next-generation capture-C
Bases were called using Casava version 1.8.2
ChIP-Seq: Single reads of maximal 50 bases were processed using trim_galore v0.4.2 to trim off low-quality bases and adapter contamination from the 3’ end. Processed reads were aligned to the X. tropicalis genome assembly v7.1 (and v9.1 for some ChIP-Seq) running Bowtie2 v2.2.9 with default settings. Alignments were converted to HOMER’s tag density format with redundant reads being removed (makeTagDirectory -single -tbp 1 -unique -mapq 10 -fragLength 175 -totalReads all). For all genomic regions except for the mir427 gene cluster, only uniquely aligned reads (i.e. MAPQ ≥10) were processed. The highly repetitive mir427 locus was profiled with all reads only best aligning up to 80 times (-k 80) to this region. In this case the mass of each read was normalised to the number of alignments. We pooled all input alignments from various developmental stages. This created a comprehensive mappability profile that covered ~400 million unique base pair positions. All chromatin profiles were position-adjusted and normalised to the effective total of 1 million aligned reads including multimappers (counts per million aligned reads, CPM). Transcription factor binding sites were identified using the following or otherwise default parameters of HOMER’s calling of ChIP-mediated read enrichments (hereafter called peaks): findpeaks -style factor -minDist 175 -fragLength 175 -inputFragLength 175 -fdr 0.001 -gsize 1.435e9 -F 3 -L 1 -C 0.97. This means that both ChIP and input alignments were extended 3’ to 175 bp for the detection of significant (0.1% FDR) peaks being separated by ≥175 bp. The effective size of the X. tropicalis genome assembly v7.1 was set to 1.435 billion bp, an estimate obtained from the mappability profile. These peaks showed equal or higher tag density than the surrounding 10 kb, ≥3-fold more tags than the input and ≥0.97 unique tag positions relative to the expected number of tags. To detect focal RNAPII recruitment to putative cis-regulatory elements and avoid calling peaks within broad regions of RNAPII elongation, the threshold of focal ratio and local enrichment within 10 kb was elevated to 0.6 and 3 (-L 3), respectively. To further eliminate any false positive peaks, we removed any peaks with <0.5 (transcription factors including signal mediators) or <1 (RNAPII) CPM and those falling into blacklisted regions showing equivocal mappability due to genome assembly errors, gaps or simple/tandem repeats. Regions of equivocal mappability were identified by a 2-fold lower (poor) or 3-fold higher (excessive) read coverage than the average detected in 400-bp windows sliding at 200-bp intervals through normalised ChIP input and DNase-digested naked genomic DNA. All identified regions ≤800 bp apart were subsequently merged. Gap coordinates were obtained from the Francis Crick UCSC genome browser (http://genomes.crick.ac.uk). Simple repeats were masked with RepeatMasker v4.0.6 using the crossmatch search engine v1.090518 and the following settings: RepeatMasker -species "xenopus silurana tropicalis" -s -xsmall. Tandem repeats were masked with Kent’s trfBig wrapper script of the Tandem Repeat Finder v4.09 using the following settings: weight for match, 2; weight for mismatch, 7; delta, 7; matching probability, 80; indel probability, 10; minimal alignment score, 50; maximum period size, 2,000; and longest tandem repeat array (-l), 2 [million bp].
DNase-Seq: Single and paired-end reads of maximal 50 bases were processed using trim_galore v0.4.2 to trim off low-quality bases and adapter contamination from the 3’ end. Processed reads were aligned to the X. tropicalis genome v7.1 and v9.1 using Bowtie2 v2.2.9 with default settings apart from -X (fragment length), which was reduced to 250 bp for paired-end reads. Alignments were sorted by genomic coordinates and only those with a quality score of ≥10 were retained using samtools v1.3.1. Duplicates were removed using Picard (MarkDuplicates). Paired-end alignments were dissociated using hex flags (-f 0x40 or 0x80) of samtools view. Single alignments were converted to HOMER’s tag density format (makeTagDirectory -single -unique -fragLength 100 -totalReads all). DNase hypersensitive sites (DHSs) were identified using the following or otherwise default parameters of HOMER’s peak calling: findpeaks -style factor -minDist 100 -fragLength 100 -inputFragLength 100 -fdr 0.001 -gsize 1.435e9 -F 3 -L 1 -C 0.97. This means that alignments of DNase-digested chromatin fragments (or naked genomic DNA fragments considered here as ‘input’) were extended 3’ by 100 bp from the DNase cleavage site to detect significant (0.1% FDR) DNase-mediated read enrichments (hereafter called peaks) being separated by ≥100 bp. The effective size of the X. tropicalis genome assembly v7.1 was set to 1.435 billion bp, an estimate obtained from the mappability profile (see ‘ChIP-Seq’ section). These peaks showed equal or higher tag density than the surrounding 10 kb, ≥3-fold more tags than the input and ≥0.97 unique tag positions relative to the expected number of tags. Peaks falling into blacklisted regions (see ‘ChIP-Seq’ section) were removed. DNase-probed chromatin accessibility profiles were position-adjusted and normalised to the effective total of 1 million aligned reads including multimappers.
Next-generation capture-C: Paired-end reads were processed using trim_galore v0.4.2 to trim off low-quality bases and adapter contamination from the 3’ end. Only complete mate pairs were processed further to reconstruct single reads from overlapping paired-end sequences using FLASH v1.2.11 with interleaved output settings for non-extended reads (flash --interleaved-output --max-overlap 150). FLASH reads were split in silico at DpnII restriction sites using a designated perl script (dpnII2E.pl, https://github.com/Hughes-Genome-Group/captureC/releases) before aligning them to the X. tropicalis genome assembly 7.1 using Bowtie2 v2.2.9. The alignment was run with default settings and one thread only to maintain the order of reads. The view function of samtools v1.3.1 was used to retain alignments with a quality score of ≥10. The alignments were analysed further using a suite of perl scripts (https://github.com/Hughes-Genome-Group/captureC/releases) modified to process both chromosome and scaffold coordinates. Viewpoint coordinates included a 1-kb proximity exclusion range. Restriction fragments were classified as capture, proximity-exclusion or reporter. PCR duplicates were removed. The interaction map was based on the number of unique paired-end reads per restriction fragment. Windows of 2 kb incrementing by 200 bp were used to consolidate interactions, which were normalised to 10,000 interactions per viewpoint. Significant chromatin conformation changes were identified using the R package DESeq2 v1.14.1.
RNase-Seq: Paired-end reads were aligned to the X. tropicalis genome assembly v7.1 using STAR v2.5.3a with default settings and a revised version of gene models v7.2 to improve mapping accuracy across splice junctions. The alignments were sorted by read name using the sort function of samtools v1.3.1. Exon and intron counts (-t 'exon;intron') were extracted from unstranded (-s 0) alignment files using VERSE v0.1.5 in featureCounts (default) mode (-z 0). Intron coordinates were adjusted to exclude any overlap with exon annotation. Differential expression analysis was performed with both raw exon and intron counts excluding those belonging to ribosomal and mitochondrial RNA using the R package DESeq2 v1.14.1. In an effort to find genes with consistent fold changes over time, p-values were generated according to a likelihood ratio test reflecting the probability of rejecting the reduced (~ developmental stage) over the full (~ developmental stage + condition) model. Resulting p-values were adjusted to obtain false discov

value: injection of mPouV/Sox3 MOs


title: ND_liver_1

description: liver RNA_repeat 1


title: amanitin_exp1_st8p_polyA-RNA_rep3

description: α-amanitin injected, stage 8+ (mid-blastula transition), experiment 1, poly(A)+ RNA, biological replicate 3

value: wild-type (out-bred Nigerian)


title: RNA-seq in HUH751-DENV bioRep 2

description:
Ribosome depleted RNA
DENV_Rep2_CPM

value: Hepatocarcinoma cell line

value: male


title: NG capC_mPS-LOF_rep2

description:
Next-generation capture-C, stage 8+ (mid-blastula transition), mPouV/Sox3 loss-of-function, biological replicate 2
capC_mPSkd_exp123_xt7.bdg


title: HD_liver_3

description: liver RNA_repeat 3

source_name: liver of broiler fed with high-fat diet

value: high-fat diet

value: liver


title: RNA-seq in HUH751-DENV bioRep 1

description:
Ribosome depleted RNA
DENV_Rep1_CPM


title: amanitin_exp1_st8p_polyA-RNA_rep2

description: α-amanitin injected, stage 8+ (mid-blastula transition), experiment 1, poly(A)+ RNA, biological replicate 2


title: HD_liver_2

description: liver RNA_repeat 2


title: NG capC_mPS-LOF_rep1

description:
Next-generation capture-C, stage 8+ (mid-blastula transition), mPouV/Sox3 loss-of-function, biological replicate 1
capC_mPSkd_exp123_xt7.bdg


title: amanitin_exp1_st8p_polyA-RNA_rep1

description: α-amanitin injected, stage 8+ (mid-blastula transition), experiment 1, poly(A)+ RNA, biological replicate 1


title: RNA-seq in HUH751-NI bioRep 1

description:
Ribosome depleted RNA
Noninfected_Rep1_CPM


title: NG_capC_ctrl_rep3

description:
Next-generation capture-C, stage 8+ (mid-blastula transition), control, biological replicate 3
capC_ctrl_exp123_xt7.bdg


title: RNA-seq in HUH751-NI bioRep 2

description:
Ribosome depleted RNA
Noninfected_Rep2_CPM


title: DNase_st8_mPS-LOF_rep2

description:
DNase, stage 8+ (mid-blastula transition), mPouV/Sox3 loss-of-function, biological replicate 2;  made two libraries from same DNA, sequenced independently, reads trimmed for adapter contamination
dnase_mPSkd_st8p_exp12_xt7_unique.bw


title: NG_capC_ctrl_rep2

description:
Next-generation capture-C, stage 8+ (mid-blastula transition), control, biological replicate 2
capC_ctrl_exp123_xt7.bdg


title: HD_liver_1

description: liver RNA_repeat 1


title: Sox3_st12p_ChIP

description: Sox3 ChIP, stage 12+ (late gastrula)


title: RNA-seq in HUH751-ZIKV bioRep 1

description:
Ribosome depleted RNA
ZIKV_Rep1_CPM


title: NBL_RNA-seq

city: Shenzhen

first: Desheng

last: Gong

address: No.7 PengFei road

institute: Agricultural Genomes Institute at Shenzhen

data_processing:
Raw sequencing data were processed using the Illumina base-calling pipeline (Illumina Pipeline v1.3.1). The cDNA library products were sequenced using the Illumina HiSeq 2500;
We used SOAPnuke Version: 1.0.0 filtered adaptor and low quality data (Low-quality reads that contained more than 30% ‘N’s or more than 10% of the sequence with low quality value (quality value <20) per read were omitted from the data analysis.)
For methylated data, the cleaned data were mapped to genome reference and we detected the methyleted level for each cytosine by BSMAP pipline(BSMAP v2.73).
For transcriptome data, we mapped the cleaned reads to genome reference by HISAT2 version 2.0.4. The calculation of Unigene expression used RPKM method (Reads Per kb per Million reads) (Mortazavi, Williams et al. 2008)
Genome_build: Trichinella.pseudospiralis.fa
Supplementary_files_format_and_content: Cout files include chromosome ID,C sites' coordinate, the number of methylated reads and non-methylated reads,RPKM files include GeneID, unique mapped reads to gene, Gene length, Coverage and RPKM value.

organism: Trichinella pseudospiralis

source_name: body

growth_protocol: Infective T.p muscle  larvae  were  obtained  from  infected  mice  at  35  days  post  infection  (dpi)  by digestion of minced skeletal muscle in 1% pepsin and 1% HCl for 45 min at 42°C with agitation.Seventy  male  6-week-old  Wistar  rats  were  then  orally  inoculated with a dose of 8000 infective muscle larvae. Adult worms (Ad1) were obtained from the intestine of ten rats at 30 h post infection. The remaining sixty rats were sacrificed at 6 dpi, and the adult worms  (Ad6)  were  recovered  and  incubated  in  IMDM  in  75-cm2 cell  culture  plates  at  37°C.Newborn larvae were harvested every 6 h.

extract_protocol: Prior to library construction, 5 µg of genomic DNA spiked with 25 ng unmethylated  cl857  Sam7 Lambda DNA (Promega, Madison, WI) was fragmented using a Covarias sonication system to a mean size of approximately 200 bp. After fragmentation, libraries were constructed according to the Illumina Pair-End protocol with some modifications. cDNA libraries were prepared  according  to  the  manufacturer’s  instructions  (Illumina).  The poly(A)-containing mRNA molecules were purified using Oligo(dT) Beads (Illumina)from 20  g of total RNA from each sample. Tris-HCl (10 mM) was used to elute the mRNA from the magnetic beads. To avoid priming bias when synthesizing cDNA, mRNA was fragmented before the cDNA synthesis. Fragmentation was performedusing divalent cations at an elevated temperature. The cleaved mRNA fragments were converted into double-stranded cDNA using SuperScript II, RNaseH and DNA Pol I, primed by random primers. The resulting cDNA was purified using the QIAquick PCR  Purification  Kit  (Qiagen).

value: newborn larvae


title: β-catenin_st9p_mPS-LOF_ChIP_rep2

description:
β-catenin ChIP, stage 9+ (late blastula), mPouV/Sox3 loss-of-function, biological replicate 2
bcat_mPSkd_st9p_xt7_exp12_unique.bw

value: 9+ (late blastula)

value: rabbit polyclonal anti-β-catenin (H-102, Santa-Cruz)


title: NG_capC_ctrl_rep1

description:
Next-generation capture-C, stage 8+ (mid-blastula transition), control, biological replicate 1
capC_ctrl_exp123_xt7.bdg

value: 8+ (mid-blastula transition)


title: ML_RNA-seq

value: muscle larvae


title: ND_fat_3

description: abdominal fat RNA_repeat 3

source_name: abdominal fat of broiler fed with normal diet

value: abdominal fat


title: DNase_st8_ctrl_rep2

description:
DNase, stage 8+ (mid-blastula transition), control, biological replicate 2; made four libraries from same DNA, sequenced independently, reads trimmed for adapter contamination
dhs_st8p_xt7.bed
dnase_ctrl_st8p_exp12_xt7_unique.bw


title: Ad_RNA-seq

value: adults


title: β-catenin_st9p_mPS-LOF_ChIP_rep1

description:
β-catenin ChIP, stage 9+ (late blastula), mPouV/Sox3 loss-of-function, biological replicate 1
bcat_mPSkd_st9p_xt7_exp12_unique.bw


title: ML_WGBS


title: NBL_WGBS


title: HD_fat_2

description: abdominal fat RNA_repeat 2

source_name: abdominal fat of broiler fed with high-fat diet


title: ND_fat_1

description: abdominal fat RNA_repeat 1


title: Ad_WGBS


title: HD_fat_1

description: abdominal fat RNA_repeat 1


title: fOS B

city: Dallas

last: Yan

address: 6000 Harry Hines Blvd

institute: UT Southwestern Medical Center

data_processing:
Genes expression level is quantified by a software package called RSEM
Supplementary_files_format_and_content: The file all.gene. FPKM .xlsis a expression table for all samples

organism: Mus musculus

source_name: RAW 264.7 murine macrophages

growth_protocol: Cells were grown in DMEM 25mM Glc 10% FBS

extract_protocol: Total RNA was isolated with using the Trizol reagent. Quality was examined using a bioanalizer.

treatment_protocol: Cells were permeabilized with digitonin and incubated with a final concentration of 10uM of the corresponding ligand for 24 hours.

value: Murine macrophages

tag: passage

value: 10uM of Trex1-/- fOS in H2O


title: ManGn A

value: 10uM ManGn in H2O


title: Ctrl A

value: Ultrapure H2O


title: ND_fat_2

description: abdominal fat RNA_repeat 2

value: normal diet

value: Xinghua with dw gene


title: PF228.TGFbeta.2

status: Public on Apr 15 2019

city: Austin

first: Ningling

last: Kang

state: MN

address: 801 16th AVE NE

department: Hormel Institute

institute: University of Minnesota

data_processing:
Illumina Real time Analysis and CASAVA software 1.8.2 were used for basecalling.
Raw reads were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30.  Quality control checks on raw sequence data for each sample were performed with FastQC.  Read mapping was performed via Bowtie (v2.2.4.0) using the Human genome (hg19) as reference
Raw reads for each gene generated from the HiSeq2500 sequencer were subjected to statistical analysis using the edgeR package and cuffdiff2 package based on two selection criteria (fold change ≥ 2 & FDR < 0.05, and fold change ≥ 1.5 & FDR < 0.01).  The overlap of these four criteria was used to identify genes.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited excel files include FPKM values for all samples

source_name: Liver hepatic stellate cells

growth_protocol: HSCs obtained from ScienCell were cultured with DMEM supplemented with 10%FBS, streptomycin and penicillin.

extract_protocol:
RNA samples were isolated from HSCs using a RNeasy Plus Mini kit (Qiagen, 74134) and gDNA Eliminator columns were used to eliminate genomic DNA contamination.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were first subjected to serum-starvation for overnight and they were incubated with TGFbeta1 (5 ng/ml) in the presence or absence of PF228 (5 µM)

value: PF228 +TGFbeta

value: hepatic stellate cells


title: PF228.3


title: PF228.TGFbeta.3


title: PF228.TGFbeta.1


title: PF228.2


title: DMSO.TGFbeta.3

value: DMSO + TGFbeta


title: DMSO.TGFbeta.2


title: DMSO.TGFbeta.1


title: Ctrl B

value: Mock fOS extraction H2O


title: β-catenin_st9p_ctrl_ChIP_rep1

description:
β-catenin ChIP, stage 9+ (late blastula), control, biological replicate 1
bcat_ctrl_st9p_xt7_exp12_unique.bw

value: wild-type (out-bred Nigerian)


title: β-catenin_st9p_ctrl_ChIP_rep2

description:
β-catenin ChIP, stage 9+ (late blastula), control, biological replicate 2
bcat_ctrl_st9p_xt7_exp12_unique.bw

value: 9+ (late blastula)


title: HD_fat_3

description: abdominal fat RNA_repeat 3

value: high-fat diet


title: DMSO.2

value: DMSO


title: DMSO.3


title: DMSO.1


title: Pa_CTRL_16h_rep2

type: RNA

city: Hanover

first: Deborah

middle: Ann

last: Hogan

state: NH

department: Microbiology and Immunology

institute: Geisel School of Medicine

description: P. aeruginosa PA14 wild type tryptone agar 16h colony biofilm control

hyb_protocol: Labeled cDNAs were hybridized to Pseudomonas GeneChips using the GeneChip fluidics station 450 (Affymetrix) according to manufacturer’s instructions

scan_protocol: GeneChips were scanned in the Dartmouth Genomics and Microarray Laboratory using the GeneChip Scanner 3000 7G (Affymetrix) and the BioConductor Affy library was used to read CEL file data.

data_processing:
Data were normalized with RMA in BioConductor
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
affymetrix-array-type = Pae_G1a
program-name = Expression Console
program-version = 1.3.1.187

label: Biotin

organism: Pseudomonas aeruginosa

source_name: Whole cell extracts_CTRL_16h

label_protocol: cDNAs labeled with biotin-ddUTP (Enzo Bio-Array terminal labeling kit, Affymetrix)

growth_protocol: Cultures of P. aeruginosa PA14 wild type were grown overnight in LB at 37C on a roller drum. 5 μL of overnight culture were spotted onto T-broth plates (1.5% agar) ± 1% ethanol. Plates were incubated at 37° for 16 h.

extract_protocol: Colonies were scraped up from the plates for RNA isolation using the Qiagen RNeasy Mini kit. The samples were DNase treated using the Invitrogen Turbo DNA-Free kit.

tag: genotype/variation

value: wild type

value: Control


title: Pa_EtOH_16h_rep1

description: P. aeruginosa PA14 wild type tryptone agar 16h colony biofilm with 1% ethanol

source_name: Whole cell extracts_EtOH_16h

value: 1% EtOH


title: Pa_EtOH_16h_rep2


title: ompcre_rad21ko_RNASeq_rep2

city: San Francisco

first: Daniele

last: Canzio

address: 555 Mission Bay Boulevard South

department: Neurology

institute: University of California San Francisco

description: RNA-Seq, Paired End

data_processing:
Adapter Sequences were trimmed with cutadapt (v1.9.1) (--minimum-length 18)
Alignment: All mouse samples were aligned to mm10, human samples aligned to hg19. For paired-end data sets, only read 1 was used for alignment and downstream analysis. Crosslinked ChIP-Seq samples were aligned with Bowtie2 (2.3.2) with default parameters. RNA-seq samples were aligned with STAR (v2.5.3a) with the following parameters:  --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20
Filtering: Unmapped reads and reads with a mapping quality below 30 were removed with Samtools (1.3.1). For ChIP-seq, duplicate reads were marked with Picard and removed with samtools.
For ChIP-Seq, bigWig files  were generated using HOMER (4.7) (-fsize 1e20 -fragLength given). For RNA-Seq, bigWig files were generated with RSeQC (2.6.4).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files at base pair resolution normalized to a library size of 10,000,000 reads

source_name: mOSNs with Rad21 KO

growth_protocol: HEK293T cells were purchased from ATCC and cultured in DMEM supplemented with 10% (vol/vol) FBS, 1X GlutaMax, 1mM sodium pyruvate, 1X non-essential amino acids, 1% penicillin-streptomycin. Cells were maintained at 37°C in a 5% (vol/vol) CO2 incubator.

extract_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The main olfactory epithelium (MOE) was dissected and transferred to ice-cold PBS. The MOE was cut in to small pieces with a razor blade, and then dissociated with a papain dissociation system (Worthington Biochemical). For RNA-seq, dissociated cells were washed once with sort media (PBS + 2% Fetal Bovine Serum) and then resuspended in sort media supplemented with 100 U/mL DNase I (Worthington Biochemical), 4mM MgCl2, and 500ng/mL DAPI (Invitrogen). For Crosslinked-ChIP samples, cells were fixed prior to sorting. For fixation, dissociated cells were resuspended in PBS + 1% methanol-free formaldehyde (Pierce). Cells were fixed at room temperature for 5 minutes, and then fixation was quenched by adding 1/10th volume of 1.25M glycine. Fixed cells were pelleted (500 rcf, 5 minutes, room temperature), washed once with PBS + 2% FBS, and then resuspended in sort media. All cells were passed through a 40uM cell strainer prior to sorting.

value: mOSNs


title: Pa_CTRL_16h_rep1


title: PF228.1


title: tetotet3iresgfp_omptta_CTCF_ChIPSeq_rep1

description: ChIP-Seq, Single End

source_name: mOSNs overexpressing Tet3

value: anti-CTCF


title: tetogfp_omptta_CTCF_ChIPSeq_rep1

description: ChIP-Seq, Single End

source_name: mOSNs

value: tetogfp;omptta


title: tetogfp_omptta_input_ChIPSeq_rep1

description: ChIP-Seq, Single End

value: none (input)


title: tetotet3iresgfp_omptta_RNASeq_rep2

description: RNA-Seq, Paired End


title: tetogfp_omptta_CTCF_ChIPSeq_rep2

description: ChIP-Seq, Single End


title: ngn1_totRNASeq_rep2

description: RNA-Seq, Paired End

data_processing:
For RNA-Seq experiments, raw FASTQ files were aligned with either Tophat or STAR using hg19 or mm10 reference genomes. When libraries were made following the SMARTer Stranded Total RNA-Seq, the initial 4 base pairs of both paired reads were trimmed prior to alignment.
For ChiP-Seq experiments, raw FASTQ files were aligned using Bowtie2 using hg19 reference genome upon adapter sequences removal using CutAdapt. Uniquely aligning reads were selected using Samtools and reads with alignment quality below 30 (-q 30) were removed. The HOMER software package was used to generate signal tracks.
For in situ Hi-C experiments, raw FASTQ files were processed through use of the Juicer Tools Version 1.76 pipeline (Durand et al., 2016)  with one modification. Reads were aligned to hg38 using BWA 0.7.17 mem algorithm and specifying the -5 option implemented specifically for in situ Hi-C data.
Adapter Sequences were trimmed with cutadapt (v1.9.1) (--minimum-length 18)
Alignment: All samples were aligned to mm10. For paired-end data sets, only read 1 was used for alignment and downstream analysis. Crosslinked ChIP-Seq samples were aligned with Bowtie2 (2.3.2) with default parameters. RNA-seq samples were aligned with STAR (v2.5.3a) with the following parameters:  --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20
Filtering: Unmapped reads and reads with a mapping quality below 30 were removed with Samtools (1.3.1). For ChIP-seq, duplicate reads were marked with Picard and removed with samtools.
For ChIP-Seq, bigWig files  were generated using HOMER (4.7) (-fsize 1e20 -fragLength given). For RNA-Seq, bigWig files were generated with RSeQC (2.6.4).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files at base pair resolution normalized to a library size of 10,000,000 reads

source_name: ngn1 positive cells from mouse olfactory epithelium

growth_protocol: SK-N-SH cells were purchased from ATCC and cultured in RPMI-1640 supplemented with 10% (vol/vol) FBS, 1X GlutaMax, 1mM sodium pyruvate, 1X non-essential amino acids, 1% penicillin-streptomycin. HEK293T cells were purchased from ATCC and cultured in DMEM supplemented with 10% (vol/vol) FBS, 1X GlutaMax, 1mM sodium pyruvate, 1X non-essential amino acids, 1% penicillin-streptomycin. Cells were maintained at 37°C in a 5% (vol/vol) CO2 incubator.

value: total RNA


title: tetotet3iresgfp_omptta_input_ChIPSeq_rep1

description: ChIP-Seq, Single End


title: Omp_PolyARNASeq

description: RNA-Seq, Paired End

source_name: Omp positive cells from mouse olfactory epithelium


title: icam1_totRNASeq_rep1

description: RNA-Seq, Paired End

source_name: icam1 positive cells from mouse olfactory epithelium


title: omp_totRNASeq_rep1

description: RNA-Seq, Paired End

source_name: omp positive cells from mouse olfactory epithelium


title: tetogfp_omptta_RNASeq_rep1

description: RNA-Seq, Paired End


title: ompcre_rad21ko_RNASeq_rep1

description: RNA-Seq, Paired End


title: tetotet3iresgfp_omptta_HiC_rep2

description:
HiC-Seq, Paired End
Processed data file includes data for both rep1 and 2. File is available on GSM3514556


title: ompcre_rad21ko_RNASeq_rep3

description: RNA-Seq, Paired End


title: tetotet3iresgfp_omptta_RNASeq_rep1

description: RNA-Seq, Paired End


title: ngn1_totRNASeq_rep1

description: RNA-Seq, Paired End

value: ngn1 positive cells from mouse olfactory epithelium


title: omp_totRNASeq_rep2

description: RNA-Seq, Paired End

value: omp positive cells from mouse olfactory epithelium


title: tetotet3iresgfp_omptta_CTCF_ChIPSeq_rep2

description: ChIP-Seq, Single End


title: tetogfp_omptta_RNASeq_rep2

description: RNA-Seq, Paired End


title: icam1_totRNASeq_rep2

description: RNA-Seq, Paired End

value: icam1 positive cells from mouse olfactory epithelium


title: INFG_ID_241

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

country: Germany

institute: University Münster

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software10.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using Qiagen RNAeasy Kit. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Whole blood was collected into PAXgene Blood RNA tubes (BD systems, NJ, USA), stored at -20oC, and RNA was extracted  using (PAXgene Blood RNA kit, Qiagen).

tag: diagnosis

value: influenza

value: blood

tag: Sex

value: m

tag: severity


title: INFG_ID_245


title: INFG_ID_244


title: INFG_ID_240


title: INFG_ID_246


title: INFG_ID_242


title: INFG_ID_239


title: INFG_ID_238


title: INFG_ID_243


title: INFG_ID_224

value: f


title: INFG_ID_212


title: INFG_ID_204


title: INFG_ID_216


title: INFG_ID_225


title: INFG_ID_214


title: INFG_ID_235


title: INFG_ID_228


title: INFG_ID_211


title: INFG_ID_236


title: INFG_ID_197


title: INFG_ID_198


title: INFG_ID_206


title: INFG_ID_209


title: INFG_ID_201


title: INFG_ID_199


title: INFG_ID_219


title: INFG_ID_210


title: INFG_ID_195


title: INFG_ID_178


title: INFG_ID_190


title: INFG_ID_193


title: INFG_ID_176


title: INFG_ID_183


title: INFG_ID_170


title: INFG_ID_175


title: INFG_ID_173


title: INFG_ID_177


title: INFG_ID_169

value: healthy


title: INFG_ID_164


title: INFG_ID_160


title: INFG_ID_166


title: INFG_ID_153


title: INFG_ID_156


title: INFG_ID_163


title: INFG_ID_157


title: INFG_ID_167


title: INFG_ID_159


title: INFG_ID_161


title: INFG_ID_152


title: INFG_ID_208


title: INFG_ID_168


title: INFG_ID_158


title: INFG_ID_162


title: INFG_ID_155


title: INFG_ID_151


title: INFG_ID_165


title: INFG_ID_144


title: INFG_ID_141


title: INFG_ID_149


title: INFG_ID_147


title: INFG_ID_145


title: INFG_ID_148


title: INFG_ID_140


title: INFG_ID_142


title: INFG_ID_150


title: INFG_ID_146


title: INFG_ID_154


title: INFG_ID_143


title: INFG_ID_137


title: INFG_ID_124


title: INFG_ID_128


title: INFG_ID_139


title: INFG_ID_130


title: INFG_ID_119


title: INFG_ID_132


title: INFG_ID_138


title: INFG_ID_129


title: INFG_ID_131


title: INFG_ID_126


title: INFG_ID_127


title: INFG_ID_125


title: INFG_ID_122


title: INFG_ID_118


title: INFG_ID_121


title: INFG_ID_120


title: INFG_ID_117


title: INFG_ID_123


title: INFG_ID_116


title: INFG_ID_115


title: INFG_ID_109


title: INFG_ID_108


title: INFG_ID_113


title: INFG_ID_114


title: INFG_ID_107


title: INFG_ID_110


title: INFG_ID_103


title: INFG_ID_106


title: INFG_ID_099


title: INFG_ID_098


title: INFG_ID_100


title: INFG_ID_104


title: INFG_ID_101


title: INFG_ID_102


title: INFG_ID_095


title: INFG_ID_094


title: INFG_ID_090


title: INFG_ID_092


title: INFG_ID_080


title: INFG_ID_079


title: INFG_ID_111


title: INFG_ID_066


title: INFG_ID_065


title: INFG_ID_077


title: INFG_ID_093


title: INFG_ID_097


title: jejunal Peyer's patches_0ppm_FB1_Ctrl_rep4

city: Toulouse

first: Yannick

last: Lippi

address: 180 chemin de tournefeuille

department: GeT-TRiX facility

country: France

institute: INRAE

description: 4 weeks diet

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to GPL19893 microarray (Agilent 8X60K, Design 037880)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_20120213). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 10 out of 12 microarrays or with a minimal weight of 5 per group from at least one experimental group. At this step, 38638 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 38637 rows each corresponding to a unique ProbeName (provided as data Matrix).

organism: Sus scrofa

source_name: jejunal Peyer's patches

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: 12 crossbred weanling piglets housed in floored indoor pens were used in this study. The piglets were weaned at the age of 28 days and transported to the animal facility of the INRA Research Center in Food Toxicology (Toxalim, Toulouse, France).

extract_protocol: Total RNA was extracted in lysing matrix D tubes (MP Biomedicals, Illkirch, France) containing guanidine thiocyanate-acid phenol (Eurobio, Courtaboeuf, France). Quality of these samples was assessed on Bioanalyzer 2100 (Agilent RNA 6000 Nano Kit, Agilent Technologies, Santa Clara, CA). All samples had a RIN over 7.5.

treatment_protocol: Animals were 6 weeks old at the begining of the study. Animals had ad libitum access to water and feed for the duration of the trial. The first group of pigs was fed with the control diet while the second group was fed with control diet artificially contaminated with 10 ppm Fumonisin B1. They were fed during 4 weeks prior to sacrifice. They were cared for in accordance with the National Institute of Health Guide and the French Ministry of Agriculture for the Care and Use of Laboratory Animals. At the conclusion of the experiment, immediately after electrical stunning, the piglets were sacrificed by exsanguination. A portion of the jejunum with Jejunal Peyers' patches were collected from euthanatized animals, flash-frozen in liquid nitrogen, and stored at -80°C until processed for total RNA extraction.

tag: condition

value: Ctrl


title: INFG_ID_062


title: INFG_ID_063


title: INFG_ID_056


title: INFG_ID_078


title: INFG_ID_064


title: INFG_ID_055


title: INFG_ID_052


title: INFG_ID_060


title: INFG_ID_057


title: INFG_ID_059


title: 1205Lu high HDAC8

city: TAMPA

first: Marco

last: Davila

state: Florida

address: 12902 USF MAGNOLIA DRIVE, MRC2

institute: Moffitt Cancer Center

description:
05_43748036_1205Lu HDAC8 OE
processed data file: rnaseq_processed.txt

data_processing:
Log2 transformation was applied to RNA-Seq after examining histograms and boxplots of gene expression across samples. Gene/probesets with undetected gene expression across all samples were excluded from the analyses.
Moderated t-statistics were used to compare the RNA expression between baseline (EV) and HDAC8 overexpression (HDAC8) samples in RNA-seq data for each of 18,452 genes using the limma package in R. After fitting a linear model, this package uses a simple empirical Bayes procedure to moderate the standard errors across genes.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: rnaseq_processed.txt: Tab-delimited text file containing gene symbols (first column) and log2 expression for the four samples (columns two through five).

source_name: melanoma cell line

growth_protocol: Cells were grown in RPMI media containing 5% FBS. Cells were seeded at 500,000 cells per 100 cm plate for 48 hours (60-70% confluency).

extract_protocol:
Cells were lysed with Trizol and RNA was isolated with chloroform. RNA was cleaned up using a Qiagen RNeasy kit.
One hundred nanograms of RNA were then processed for RNA-sequencing using the NuGen Ovation Universal RNA-Seq (San Carlos, CA) following manufacturer’s instructions. Libraries’ qPCR-based quantitation was performed with the Kapa Library Quantification Kit, the libraries were sequenced on the Illumina NextSeq 500 sequencer with a 75-base paired-end run which generated 30-40 million read pairs per sample.

treatment_protocol: No treatment was applied.

value: Melanoma cell line

value: BRAF V600E mutation

tag: hdac8 expression

value: High


title: INFG_ID_054


title: INFG_ID_048


title: INFG_ID_040


title: INFG_ID_046


title: INFG_ID_053


title: INFG_ID_051


title: INFG_ID_058


title: INFG_ID_043


title: 1205Lu low HDAC8

description:
04_43749027_1205Lu
processed data file: rnaseq_processed.txt

tag: cell line

value: Low


title: INFG_ID_042


title: INFG_ID_049


title: WM164 low HDAC8

description:
01_43749028_WM164
processed data file: rnaseq_processed.txt

tag: cell type


title: Input_Lmnb1_KD_MLE12_rep2

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

institute: Medical Faculty Mannheim/University of Heidelberg

data_processing:
ChIP-seq reads were mapped to the mouse reference genome mm10 (UCSC assembly) using the default settings of Bowtie2 (Langmead and Salzberg, 2012). The PCR duplicates were removed with MarkDuplicates.jar from picard-tools-1.119. Peaks in H3K27me3-ChIP-seq were called using findPeaks from homer (-region -size 1000 -minDist 10000 -style histone) using the Input as control sample. The common peaks between replicates (n = 2) were obtained by the use of bedtools intersect (-wa). Distribution of the H3K27me3-ChIP mapped reads from control and lamin B1 KD MLE12 cells at all peaks in MLE12 was performed using ngs.plot (Shen et al., 2014) with mm10. The BAM files were normalized to reads per genome coverage by the use of BamCoverage from deepTools2 (Ramírez et al., 2014); -b 20 -smooth 40 -e 150 --normalizeTo1x 2652783500).
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files

source_name: Input from Lmnb1 KD MLE12 cells

growth_protocol: Control and Lmnb1 KD MLE12 cells were cultured in DMEM/F12 medium supplemented with 10% fetal calf serum (FCS), penicillin/streptomycin/glutamine (PSG) and 2 µg/ml puromycin.

extract_protocol: 5 × 106 control and lamin B1 KD MLE12 cells were fixed with 1% formaldehyde for 10 min at room temperature. Fixation was quenched with 125 mM glycine followed by washes with cold PBS for 3 × 10min. Cells were further lysed in 600 µl of ice-cold L1 lysis buffer (Tris pH 8.0, 50 mM; EDTA pH 8, 2 mM; NP-40 0.1%; and glycerol 10%) for 5 min and nuclei were spun down. Next, nuclei were resuspended in 600 µl L2 lysis buffer (SDS 1%; EDTA pH 8, 5 mM; and Tris pH 8, 50 mM) and DNA was sheared by sonication. Extracts were precleared with 80 µl protein G beads for 1 h followed by incubation with 10 µg primary antibody overnight at 4°C and binding to 30 µl BSA-coated protein G beads. Immunoprecipitates were washed two times with NaCl-washing buffer (0.1% SDS, NP-40 1%, 2 mM EDTA, 500 mM NaCl, and 20 mM Tris pH8), followed by two washes with LiCl-washing buffer (0.1% SDS, 1% NP-40, 2 mM EDTA, 500 mM LiCl, and 20 mM Tris pH 8) and eluted with extraction buffer (Tris pH 8.0, 20 mM, EDTA pH 8, 2 mM, 2% SDS). Cross-linking was reverted by incubation overnight at 65°C. DNA was purified using Qiagen mini-elute PCR purification kit (catalog no. 28004). Immunoprecipitated DNA was either used for qPCR analysis or sequenced on NextSeq500 instrument (Illumina).

value: Lung epithelial cells

tag: sample description

value: input from Lmnb1 KD MLE12 cells


title: Input_Lmnb1_KD_MLE12_rep1


title: Input_Lmnb1_ctrl_MLE12_rep2

source_name: Input from control MLE12 cells

value: input from control MLE12 cells


title: Input_Lmnb1_ctrl_MLE12_rep1


title: H3K27me3_Lmnb1_KD_MLE12_ChIP_seq_rep2

description: processed data file: H3K27me3_Lmnb1_KD_MLE12_ChIP_seq.bw

source_name: H3K27me3 ChIP-Seq of Lmnb1 KD MLE12 cells

value: H3K27me3 (Millipore, 07-449)


title: H3K27me3_Lmnb1_ctrl_MLE12_ChIP_seq_rep2

description: processed data file: H3K27me3_Lmnb1_ctrl_MLE12_ChIP_seq.bw

source_name: H3K27me3 ChIP-Seq of control MLE12 cells

value: H3K27me3 ChIP-Seq of Control MLE12 cells


title: H3K27me3_Lmnb1_ctrl_MLE12_ChIP_seq_rep1

data_processing:
ChIP-sequencing reads were mapped to the mouse reference genome mm10 (UCSC assembly) using the default settings of Bowtie2 (Langmead and Salzberg, 2012) the PCR duplicates were removed with MarkDuplicates.jar from picard-tools-1.119. Peaks in H3K27me3-ChIP-seq were called using findPeaks from homer (-region -size 1000 -minDist 10000 -style histone) using the Input as control sample. The common peaks between replicates (n=2) were obtained by the use of bedtools intersect (-wa). Distribution of the H3K27me3-ChIP mapped reads from control and lamin B1 KD MLE12 cells at all peaks in MLE12 was performed using ngs.plot (Shen et al., 2014) with mm10. The BAM files were normalized to reads per genome coverage (RPGC), by the use of BamCoverage from deepTools2 (PMID: 24799436) (-b 20 -smooth 40 -e 150 --normalizeTo1x 2652783500).
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files

value: H3K27me3 ChIP-Seq of control MLE12 cells


title: INFG_ID_035


title: MEFs D2_Input_Tbx5

first: Eric

middle: N

last: Olson

address: 6000 Harry Hines Blvd.

department: Molecular Biology

institute: University of Texas Southwestern Medical Center at Dallas

data_processing:
The raw reads were aligned to the mouse reference genome (GRCh38/mm10) using default parameters in BWA v0.7.12 (Li and Durbin, 2009).
The aligned reads were subsequently filtered for quality and uniquely mappable reads were retained for further analysis using Samtools version 1.3 (Li et al., 2009) and Sambamba version 0.6.6 (Tarasov et al., 2015).
Library complexity was measured using BEDTools version 2.26.0 (Quinlan and Hall, 2010) and meets ENCODE data quality standards (Landt et al., 2012).
Relaxed peaks were called using MACS version 2.1.0 (Feng et al., 2012) with a p-value of 1x10-2 for H2K27ac and SPP version 1.4 (Kharchenko et al., 2008) with an IDR = 0.01 for each replicate and pseudoreplicates. For H3K27ac peak calls that are either observed in both pseudoreplicates were used for subsequent analysis.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: ChIP-seq BigWig files were generated using MACS version 2.1.0; Scores represent the ChIP-seq fold change over control

source_name: MEFs D2_Input_Tbx5

extract_protocol:
MEFs from E13.5-14.5 C57BL/6 mice were prepared as preciously described (Nam et al., 2014) and cultured in fibroblast growth medium (DMEM containing 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin) until experiments were performed. MEFs infected were induced using DMEM/199 (4:1), 10% FBS, 5% horse serum, 1% penicillin/streptomycin, 1% nonessential amino acids, 1% essential amino acids, 1% B-27, 1% insulin-selenium-transferrin, 1% vitamin mixture, and 1% sodium pyruvate (Invitrogen). The induction medium was replaced every other two or three days until experiments were performed.
MEFs two or seven days after retroviral transduction were crosslinked with 1% formaldehyde in PBS for 30 min and neutralized by the addition of glycine to a final concentration of 0.125M for 5min. MEFs were then harvested and washed with cold PBS for ChIP. For mouse heart sample preparation, ChIP was performed as previously described (Huang et al., 2016; Xu et al., 2012), or by using ChIP-IT Express ChIP kits (Active Motif) following the vender’s protocol.
ChIP-seq libraries were generated using KAPA Hyper Prep Kit following the manufacturer’s protocol (Kapa Biosystems).

treatment_protocol: MEFs were transduced with indicated retroviruses cocktail twice for 24 hours period followed by induction media. Cells were then harvested for at indicated timepoints post-induction for experiments.

value: Mouse embryonic fibroblast (MEF)

tag: background strain

tag: treatment

value: Single Factor

tag: induction time

value: 2 days

tag: development stage

tag: antibody

value: Input (IgG control)


title: MEFs D2_Input_Mef2c

source_name: MEFs D2_Input_Mef2c


title: MEFs D2_Input_Gata4

source_name: MEFs D2_Input_Gata4


title: MEFs D2_Input_Hand2

source_name: MEFs D2_Input_Hand2


title: INFG_ID_038

value: influenza

tag: tissue

value: blood

value: m

tag: age


title: INFG_ID_041


title: MEFs D2_Input_Akt

source_name: MEFs D2_Input_Akt


title: INFG_ID_036

value: f


title: MEFs D2_Tbx5_H3K27ac

source_name: MEFs D2_Tbx5_H3K27ac

value: H3K27ac (Diagenode, C15410196)


title: INFG_ID_033


title: INFG_ID_039


title: INFG_ID_034


title: INFG_ID_031


title: INFG_ID_028


title: MEFs D2_Mef2c_H3K27ac

source_name: MEFs D2_Mef2c_H3K27ac


title: INFG_ID_022


title: INFG_ID_020


title: INFG_ID_007


title: INFG_ID_030


title: INFG_ID_011


title: INFG_ID_021


title: INFG_ID_009


title: 4sURDB-Seq slow/slow ESCs, treated with DRB, 15' post DRB wash, replicate 3

city: Edinburgh

first: Magdalena

middle: Maria

last: Maslon

address: Crewe Road

institute: University of Edinburgh

description: Sample 14.3

data_processing:
Reads were aligned to GRCm38 (mm10) using Bowtie2 (2.2.9) resulting in one sam file per replicate.
Read profiles per chromosome were derived from sam files using the reads2chr C utility, and boundary values (distances from transcript start sites at 5min and 15min) were found using matlab code, code from Fuchs et al., (2015) Nature Protoc doi:10.1038/nprot.2015.035. These steps used a genePred transcript database built from the ensembl GRCm38 87 gtf file. Transcript profiles per replicate were compared to the averaged profile at time 0.
Elongation rates were found by linear regression from inferred boundary values at 5min and 15min from the processed data files. Linear model were not constrained to pass through 0. Only transcripts greater than 20kb in length  were considered. Multiple occurrences of the default boundary (2500) were filtered.
Genome_build: mm10
Supplementary_files_format_and_content: tab separated text file with ensembl transcript ids and boundary values (bp from start)

source_name: Embryonic stem cells (ESCs)

growth_protocol: ESCs were cultured in 2i medium on gelating coated-plates

extract_protocol:
Total RNA was extracted with Trizol following manufacturer instructions
Total RNA (100–200 μg) was used for biotinylation and purification of 4sU-labeled nascent RNAs. cDNA libraries were prepared using NEB Next Ultra Directional RNA Library Prep Kit according to the manufacturer’s instructions. Libraries were pooled and sequenced on an Illumina HiSeq 4000 system.

tag: genotype

value: treated with DRB for 4 hours, following by realease from DRB treatment for 15'


title: INFG_ID_006


title: INFG_ID_008


title: MEFs D2_Gata4_H3K27ac

source_name: MEFs D2_Gata4_H3K27ac


title: MEFs D2_Akt1_H3K27ac

source_name: MEFs D2_Akt1_H3K27ac


title: 4sURDB-Seq slow/slow ESCs, treated with DRB, 30' post DRB wash, replicate 3

description: Sample 15.3

value: treated with DRB for 4 hours, following by realease from DRB treatment for 30'


title: INFG_ID_005

source_name: blood


title: MEFs D0_Tbx5_Tbx5

source_name: MEFs D0_Tbx5_Tbx5

value: Tbx5 (Santa Cruz Biotechnology, sc-17866)


title: INFG_ID_004


title: INFG_ID_002


title: INFG_ID_023


title: 4sURDB-Seq slow/slow ESCs, treated with DRB, 0' post DRB wash, replicate 3

description: Sample 12.3

value: treated with DRB for 4 hours, following by realease from DRB treatment for 0'


title: 4sURDB-Seq slow/slow ESCs, not treated with DRB, replicate 3

description: Sample 11.3

value: not treated


title: MEFs D0_Mef2c_Mef2C

source_name: MEFs D0_Mef2c_Mef2C

value: Mef2C (Diagenode, C15200054)


title: 4sURDB-Seq wt/slow ESCs, treated with DRB, 30' post DRB wash, replicate 3

description: Sample 10.3


title: MEFs D0_Gata4_Gata4

source_name: MEFs D0_Gata4_Gata4

value: Gata4 (Santa Cruz Biothechnology, sc1237)


title: MEFs D0_Hand2_Hand2

source_name: MEFs D0_Hand2_Hand2

value: Hand2 (Diagenode, C15200054)


title: MEFs D2_Hand2_H3K27ac

source_name: MEFs D2_Hand2_H3K27ac

value: Mouse embryonic fibroblast (MEF)


title: 4sURDB-Seq slow/slow ESCs, treated with DRB, 5' post DRB wash, replicate 3

description: Sample 13.3

value: treated with DRB for 4 hours, following by realease from DRB treatment for 5'


title: 4sURDB-Seq wt/slow ESCs, treated with DRB, 15' post DRB wash, replicate 3

description: Sample 9.3


title: P4 Atrium_H3K27ac

source_name: P4 Atrium_H3K27ac

value: atrium


title: 4sURDB-Seq wt/slow ESCs, treated with DRB, 5' post DRB wash, replicate 3

description: Sample 8.3


title: GMT_2d_rep3

data_processing:
Reads with phred quality scores less than 20 and less than 35 bp after trimming were removed from further analysis using trimgalore version 0.4.1.
Quality-filtered reads were then aligned to the mouse reference genome GRCm38 (mm10) using the HiSAT2 (v 2.0.1) (Pertea et al., 2016) aligner using default settings and marked duplicates using Sambamba version 0.6.6 (Tarasov et al., 2015).
Aligned reads were quantified using featurecount (v1.4.6) (Liao et al., 2014) per gene ID against Gencode version 10 (Mudge and Harrow, 2015).
Differential gene expression analysis was done using the R package DEseq2 (v 1.6.3).
Read counts were normalized by taking the median of each gene count across samples and dividing each sample gene count by the relative ratio of library sizes between the calculated median and sample size. The averaged normalized expressions values of the samples were used to calculate fold change and p-values.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text files include raw counts and logCPM values for all samples.

source_name: MEFs D2_GMT_3

growth_protocol: MEFs from E13.5-14.5 C57BL/6 mice were prepared as preciously described (Nam et al., 2014) and cultured in fibroblast growth medium (DMEM containing 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin) until experiments were performed. MEFs infected were induced using DMEM/199 (4:1), 10% FBS, 5% horse serum, 1% penicillin/streptomycin, 1% nonessential amino acids, 1% essential amino acids, 1% B-27, 1% insulin-selenium-transferrin, 1% vitamin mixture, and 1% sodium pyruvate (Invitrogen). The induction medium was replaced every other two or three days until experiments were performed.

extract_protocol:
Total RNA was extracted from MEFs two or seven days after retroviral transduction, using TRIzol (Invitrogen) according to the vender’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: GMT

value: 2 days


title: 4sURDB-Seq wt/slow ESCs, treated with DRB, 0' post DRB wash, replicate 3

description: Sample 7.3


title: GMT_2d_rep1

source_name: MEFs D2_GMT_1


title: 4sURDB-Seq wt/slow ESCs, not treated with DRB, replicate 3

description: Sample 6.3


title: GMT_2d_rep2

source_name: MEFs D2_GMT_2


title: 4sURDB-Seq wt ESCs, treated with DRB, 30' post DRB wash, replicate 3

description: Sample 5.3

value: wt/wt


title: 4sURDB-Seq wt ESCs, treated with DRB, 5' post DRB wash, replicate 3

description: Sample 3.3


title: 4sURDB-Seq wt ESCs, treated with DRB, 15' post DRB wash, replicate 3

description: Sample 4.3


title: Fib_2d_rep2

source_name: MEFs D2_Mock_2

value: Mock


title: Fib_2d_rep3

source_name: MEFs D2_Mock_3


title: Fib_2d_rep1

source_name: MEFs D2_Mock_1


title: GHMT_2d_rep2

source_name: MEFs D2_GHMT_2

value: GHMT


title: 4sURDB-Seq slow/slow ESCs, treated with DRB, 30' post DRB wash, replicate 2

description: Sample 15.2

source_name: Embryonic stem cells (ESCs)


title: 4sURDB-Seq wt ESCs, not treated with DRB, replicate 3

description: Sample 1.3


title: GHMT_2d_rep1

source_name: MEFs D2_GHMT_1


title: 4sURDB-Seq wt ESCs, treated with DRB, 0' post DRB wash, replicate 3

description: Sample 2.3


title: 4sURDB-Seq slow/slow ESCs, treated with DRB, 15' post DRB wash, replicate 2

description: Sample 14.2


title: 4sURDB-Seq slow/slow ESCs, treated with DRB, 5' post DRB wash, replicate 2

description: Sample 13.2


title: 4sURDB-Seq slow/slow ESCs, treated with DRB, 0' post DRB wash, replicate 2

description: Sample 12.2


title: AGHMT_2d_rep3

source_name: MEFs D2_AGHMT_3

value: AGHMT


title: H3K27me3_Lmnb1_KD_MLE12_ChIP_seq_rep1

source_name: H3K27me3 ChIP-Seq of Lmnb1 KD MLE12 cells

value: Lung epithelial cells

tag: chip antibody

value: H3K27me3 (Millipore, 07-449)


title: AGHMT_2d_rep2

source_name: MEFs D2_AGHMT_2


title: AGHMT_2d_rep1

source_name: MEFs D2_AGHMT_1


title: 4sURDB-Seq slow/slow ESCs, not treated with DRB, replicate 2

description: Sample 11.2


title: Fib_7d_rep3

source_name: MEFs D7_Mock_3

value: 7 days


title: GHMT_2d_rep3

source_name: MEFs D2_GHMT_3


title: Fib_7d_rep2

source_name: MEFs D7_Mock_2


title: Fib_7d_rep1

source_name: MEFs D7_Mock_1


title: 4sURDB-Seq wt/slow ESCs, treated with DRB, 30' post DRB wash, replicate 2

description: Sample 10.2

value: treated with DRB for 4 hours, following by realease from DRB treatment for 30'


title: 4sURDB-Seq wt/slow ESCs, treated with DRB, 0' post DRB wash, replicate 2

description: Sample 7.2

value: treated with DRB for 4 hours, following by realease from DRB treatment for 0'


title: 4sURDB-Seq wt/slow ESCs, treated with DRB, 5' post DRB wash, replicate 2

description: Sample 8.2


title: AGHMT_7d_rep3

source_name: MEFs D7_AGHMT_3


title: 4sURDB-Seq wt ESCs, treated with DRB, 0' post DRB wash, replicate 2

description: Sample 2.2


title: GHMT_7d_rep1

source_name: MEFs D7_GHMT_1


title: GHMT_7d_rep2

source_name: MEFs D7_GHMT_2


title: 4sURDB-Seq wt ESCs, treated with DRB, 30' post DRB wash, replicate 2

description: Sample 5.2


title: GHMT_7d_rep3

source_name: MEFs D7_GHMT_3


title: 4sURDB-Seq wt ESCs, treated with DRB, 5' post DRB wash, replicate 2

description: Sample 3.2


title: INFG_ID_091

source_name: blood

tag: diagnosis

value: influenza

value: blood

value: m


title: AGHMT_7d_rep2

source_name: MEFs D7_AGHMT_2

value: Mouse embryonic fibroblast (MEF)


title: GMT_7d_rep3

source_name: MEFs D7_GMT_3


title: 4sURDB-Seq wt ESCs, not treated with DRB, replicate 2

description: Sample 1.2

source_name: Embryonic stem cells (ESCs)

value: not treated


title: GMT_7d_rep2

source_name: MEFs D7_GMT_2


title: 4sURDB-Seq slow/slow ESCs, treated with DRB, 15' post DRB wash, replicate 1

description: Sample 14.1

value: treated with DRB for 4 hours, following by realease from DRB treatment for 15'


title: P4 Ventricle_Tbx5

source_name: P4 Ventricle Tbx5

extract_protocol:
MEFs two or seven days after retroviral transduction were crosslinked with 1% formaldehyde in PBS for 30 min and neutralized by the addition of glycine to a final concentration of 0.125M for 5min. MEFs were then harvested and washed with cold PBS for ChIP. For mouse heart sample preparation, ChIP was performed as previously described (Huang et al., 2016; Xu et al., 2012), or by using ChIP-IT Express ChIP kits (Active Motif) following the vender’s protocol.
ChIP-seq libraries were generated using KAPA Hyper Prep Kit following the manufacturer’s protocol (Kapa Biosystems).

value: ventricle

value: Tbx5 (Santa Cruz Biotechnology, sc-17866)


title: 4sURDB-Seq slow/slow ESCs, treated with DRB, 30' post DRB wash, replicate 1

description: Sample 15.1


title: 4sURDB-Seq slow/slow ESCs, treated with DRB, 5' post DRB wash, replicate 1

description: Sample 13.1

value: treated with DRB for 4 hours, following by realease from DRB treatment for 5'


title: GMT_7d_rep1

source_name: MEFs D7_GMT_1

value: GMT


title: 4sURDB-Seq wt/slow ESCs, treated with DRB, 15' post DRB wash, replicate 2

description: Sample 9.2


title: 4sURDB-Seq slow/slow ESCs, treated with DRB, 0' post DRB wash, replicate 1

description: Sample 12.1


title: P4 Ventricle_H3K27ac

source_name: P4 Ventricle H3K27ac

value: H3K27ac (Diagenode, C15410196)


title: 4sURDB-Seq wt/slow ESCs, not treated with DRB, replicate 2

description: Sample 6.2


title: 4sURDB-Seq wt/slow ESCs, treated with DRB, 30' post DRB wash, replicate 1

description: Sample 10.1


title: P1 Heart_Input

source_name: P1 Heart Input

value: whole heart

value: Input (IgG control)


title: MEFs  D0_Input

source_name: MEFs  D0_Input

value: Input

value: 0 days


title: 4sURDB-Seq wt ESCs, treated with DRB, 15' post DRB wash, replicate 2

description: Sample 4.2

value: wt/wt


title: 4sURDB-Seq wt/slow ESCs, treated with DRB, 15' post DRB wash, replicate 1

description: Sample 9.1


title: AGHMT_7d_rep1

source_name: MEFs D7_AGHMT_1

value: AGHMT

value: 7 days


title: 4sURDB-Seq wt/slow ESCs, treated with DRB, 5' post DRB wash, replicate 1

description: Sample 8.1


title: 4sURDB-Seq wt/slow ESCs, not treated with DRB, replicate 1

description: Sample 6.1


title: MEFs  D2_Mock_H3K27ac

source_name: MEFs  D2_Mock_H3K27ac

value: Mock

value: 2 days


title: INFG_ID_017

value: influenza

value: blood

tag: Sex

value: f


title: 4sURDB-Seq wt/slow ESCs, treated with DRB, 0' post DRB wash, replicate 1

description: Sample 7.1

value: treated with DRB for 4 hours, following by realease from DRB treatment for 0'


title: 4sURDB-Seq wt ESCs, treated with DRB, 30' post DRB wash, replicate 1

description: Sample 5.1

value: treated with DRB for 4 hours, following by realease from DRB treatment for 30'


title: MEFs  D2_GMT_H3K27ac

source_name: MEFs  D2_GMT_H3K27ac

value: Mouse embryonic fibroblast (MEF)


title: MEFs  D2_GMT_Mef2C

source_name: MEFs  D2_GMT_Mef2C

value: GMT

value: Mef2C (Diagenode, C15200054)


title: 4sURDB-Seq wt ESCs, treated with DRB, 0' post DRB wash, replicate 1

description: Sample 2.1


title: MEFs  D7_GMT_H3K27ac

source_name: MEFs  D7_GMT_H3K27ac

value: H3K27ac (Diagenode, C15410196)


title: 4sURDB-Seq wt ESCs, treated with DRB, 5' post DRB wash, replicate 1

description: Sample 3.1

value: treated with DRB for 4 hours, following by realease from DRB treatment for 5'


title: MEF  D2_GMT_Gata4

source_name: MEF  D2_GMT_Gata4

value: Gata4 (Santa Cruz Biothechnology, sc1237)


title: 4sURDB-Seq slow/slow ESCs, not treated with DRB, replicate 1

description: Sample 11.1

value: not treated


title: 4sURDB-Seq wt ESCs, not treated with DRB, replicate 1

description: Sample 1.1

value: wt/wt


title: P4 Ventricle_Gata4

source_name: P4 Ventricle Gata4

value: ventricle


title: MEFs  D2_GHMT_H3K27ac

source_name: MEFs  D2_GHMT_H3K27ac

value: GHMT


title: Neo-Skin-ILC2

first: Jinwoo

last: Lee

address: 513 Parnassus Ave

institute: UCSF

data_processing:
Illumina software used for base-calling.
cellranger mkfastq (10X Genomics) used for demultiplexing the base call files into FASTQ files.
cellranger count (10X Genomics) used for alignment, filtering, barcode counting, and UMI counting.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data files are matrix files.

source_name: Skin ILC2s

growth_protocol: Mice were born and housed in the UCSF SPF animal facility in accordance with the guidelines estabilshed by the IACUC and LARC.

extract_protocol:
Cells were sorted using a MoFlo XDP (Beckman Coulter) into ice-cold 0.5% BSA in PBS.
Sorted cells were processed on the same day through the Chromium Single Cell 3’ v2 Library Kit (10X Genomics) per the manufacturer’s protocol.

treatment_protocol: Arg1(Yarg), Il5(Red5), and Il13(Smart13) reporter alleles on wild-type C57BL/6 background were used to prepare single cell suspensions from lung and skin as previously described (von Moltke J et al, Nature 2016; Van Dyken SJ et al, Immunity 2014; Molofsky AB et al, J. Exp Med 2013; Ricardo-Gonzalez RR et al, Nat Immunol 2018). Cells were sorted as Lin-CD45+Red5+.

tag: strain

value: skin

value: post-natal day 14


title: MEFs  D7_GHMT_H3K27ac

source_name: MEFs  D7_GHMT_H3K27ac

value: 7 days


title: Neo-Lung-ILC2

source_name: Lung ILC2s

value: lung


title: MEFs  D2_GHMT_Hand2

source_name: MEFs  D2_GHMT_Hand2

value: 2 days

value: Hand2 (Diagenode, C15200054)


title: RNA-seq of slow/slow mature neurons, replicate 3

data_processing:
Base calling was performed with Illumina cassava and bcl2fastq2-v2.17.1.14
RNA-seq reads were processed for alternative splicing and expression analysis using vast-tools, version 1.0 (Tapial et al., Genome Res. 2017), which is available on github (https://github.com/vastgroup/vast-tools).
Alternative splicing analysis: From primary vast-tools output, events with poor coverage or junction balance were filtered out (vast-tools quality column score 3 other than SOK/OK/LOW for cassette exon [CE], microexon [MIC] and alternative 5'/3'-ss events or coverage less than 15 reads for intron retention [IR] events; score 4 other than OK/B1 for CE and MIC events or less than 0.05 for IR events). Significantly differential AS was assessed with the diff module of vast-tools under development and were additionally required to have a PSI difference >10.
Expression analysis: Expression differences were calculated based on vast-tools raw read counts per gene using the GLM stream in the R package edgeR (McCarthy JD et al., NAR 2012) with a one-column design matrix describing genotype and time point.
Genome_build: mm9
Supplementary_files_format_and_content: vast-tools.altSplicing.tab.gz: Primary vast-tools output for alternative splicing
Supplementary_files_format_and_content: AltSplicing.tab.gz: Filtered PSI values and differential alternative splicing annotation
Supplementary_files_format_and_content: Expression.tab.gz: Raw read counts per gene, normalized expression and fold-change (edgeR analysis)

source_name: Post-mitotic neurons

growth_protocol: At day 7 of neuronal precursor differentiation, cultures of  were detached using accutase, replated onto poly-l-ornithine/laminin (100 μg/ml and 10 μg/ml, respectively, Sigma–Aldrich) coated surfaces at 1.5-2x10e4 cells/cm2 in N2B27 medium containing 0.2 mM ascorbic acid and 0.25 mM cAMP. Cells were grown for the additional 14 days, with 80% media exchange every second day.

extract_protocol:
Total RNA was extracted with the Qiagen RNeasy kit
1ug of total RNA was used for poly-A selection, TruSeq stranded mRNA-seq library kit was used to prepare libraries

value: Post-mitotic neurons


title: RNA-seq of slow/slow mature neurons, replicate 2


title: MEFs  D2_GHMT_Mef2C

source_name: MEFs  D2_GHMT_Mef2C

value: Mouse embryonic fibroblast (MEF)


title: MEFs  D7_Mock_H3K27ac

source_name: MEFs  D7_Mock_H3K27ac

value: Mock


title: WM164 high HDAC8

description:
02_3743040_WM164 HDAC8 OE
processed data file: rnaseq_processed.txt

source_name: melanoma cell line

value: Melanoma cell line

tag: genotype/variation

value: BRAF V600E mutation

value: High


title: MEFs  D2_GMT_Tbx5

source_name: MEFs  D2_GMT_Tbx5

value: GMT

value: Tbx5 (Santa Cruz Biotechnology, sc-17866)


title: RNA-seq of slow/slow mature neurons, replicate 1


title: 4sURDB-Seq wt ESCs, treated with DRB, 15' post DRB wash, replicate 1

description: Sample 4.1

source_name: Embryonic stem cells (ESCs)

value: wt/wt

value: treated with DRB for 4 hours, following by realease from DRB treatment for 15'


title: MEF  D2_GHMT_Gata4

source_name: MEF  D2_GHMT_Gata4

value: GHMT

value: Gata4 (Santa Cruz Biothechnology, sc1237)


title: RNA-seq of wt mature neurons, replicate 3


title: MEFs  D2_AGHMT_Tbx5

source_name: MEFs  D2_AGHMT_Tbx5

value: AGHMT


title: MEFs  D7_AGHMT_H3K27ac

source_name: MEFs  D7_AGHMT_H3K27ac

value: 7 days

value: H3K27ac (Diagenode, C15410196)


title: MEFs  D2_GHMT_Tbx5

source_name: MEFs  D2_GHMT_Tbx5

value: 2 days


title: MEFs  D2_AGHMT_Input

source_name: MEFs  D2_AGHMT_Input

value: Input (IgG control)


title: RNA-seq of wt mature neurons, replicate 2

value: Post-mitotic neurons


title: RNA-seq of slow/slow PSA-NCAM+ cells, replicate 3

source_name: PSA-NCAM+ cells

growth_protocol: One day prior to induction of differentiation, ESCs were seeded at high density in 2i medium. The following day, cells were detached using accutase, resuspended in N2B27 media (1:1 Neurobasal and DMEM/F12, supplemented with 0.5X N2, 0.5x B27, 0.1 mM β-mercaptoethanol, 0.2 mM L-glutamine), counted and plated at the appropriated density onto either 15 cm plates or 6-well plates that have been coated with a 0.1% gelatin solution. The initial plating density varied between WT and slow/slow ESCs, and was established to be 1x10e4 and 3x10e4 per cm2, respectively. Culture medium was changed every second day. After 10 days of culture, cells were detached using accutase and PSA-NCAM+ cells were purified using PSA-NCAM beads (Miltenyi).

value: PSA-NCAM+ cells


title: RNA-seq of wt mature neurons, replicate 1


title: RNA-seq of slow/slow PSA-NCAM+ cells, replicate 2


title: MEFs  D2_AGHMT_Gata4

source_name: MEFs  D2_AGHMT_Gata4

value: Mouse embryonic fibroblast (MEF)


title: RNA-seq of wt PSA-NCAM+ cells, replicate 2


title: MEFs  D2_AGHMT_Hand2

source_name: MEFs  D2_AGHMT_Hand2

value: Hand2 (Diagenode, C15200054)


title: RNA-seq of slow/slow PSA-NCAM+ cells, replicate 1


title: Zikv-hNPC-2 (small RNA)

city: Wuhan

first: xi

last: zhou

state: Hubei

address: Luojia Hill

department: State Key Laboratory of Virology, College of Life Sciences

institute: Wuhan University

data_processing:
The sequencing reads were mapped to the human genome (release hg19) or mosquito genome (AaeGL5.0) by using Bowite 2.2.5 and the cellular miRNA expression level was determined on the
basis of the number of reads that was identical to the annotated miRNA sequences in miRBase version 18, only allowing −2 or +2 nt to be templated by the corresponding genomic sequence at the 3′ end. Viral small RNA (vsRNA) reads which cannot be mapped to human genome were then mapped to ZIKV genome with 100% identity. The subsequent analysis of length and location of these vsRNAs were calculated using in-house Perl scripts. Pairs of complementary
22-nt vsRNAs in each library in different distance categories were computed using principles as previously described(Li et al., 2016; Li et al., 2013).
Genome_build: hg19, AaeGL5.0
Supplementary_files_format_and_content: txt files generated by bowtie2

source_name: Human neural progenitor cells

extract_protocol: TruSeq Small RNA Library Preparation Kits (Illumina)

value: hNPC

tag: infection

value: Zika virus


title: Zikv-RD (small RNA)

source_name: Human Rhabdomyosarcoma Cell Lines

value: RD


title: RNA-seq of wt PSA-NCAM+ cells, replicate 3


title: Zikv-hNPC-1 (small RNA)


title: RNA-seq of wt PSA-NCAM+ cells, replicate 1


title: RNA-seq of slow/slow NPCs, replicate 2

source_name: Neuronal progenitor cells (NPCs)

growth_protocol: One day prior to induction of differentiation, ESCs were seeded at high density in 2i medium. The following day, cells were detached using accutase, resuspended in N2B27 media (1:1 Neurobasal and DMEM/F12, supplemented with 0.5X N2, 0.5x B27, 0.1 mM β-mercaptoethanol, 0.2 mM L-glutamine), counted and plated at the appropriated density onto either 15 cm plates or 6-well plates that have been coated with a 0.1% gelatin solution. The initial plating density varied between WT and slow/slow ESCs, and was established to be 1x10e4 and 3x10e4 per cm2, respectively. Culture medium was changed every second day. Cells were considered NPCs at day 7 of this culture

value: Neuronal progenitor cells (NPCs)


title: RNA-seq of slow/slow NPCs, replicate 3


title: RNA-seq of wt NPCs, replicate 3

value: wt/wt


title: Zikv-hNeurn (small RNA)

source_name: Human  neuron cells

value: hNeurn


title: HEK_a12eCBS_dCas9-VPR_sorted_HiC_rep3

description:
captureHiC-Seq, Paired End
Processed data file includes data for rep1, 2 and 3. File is available on GSM3514561

source_name: HEK293T cells

value: HEK293T cells

value: HEK293T cells positively transfected with dCas9-VPR targeting the eCBS of Pcdha12


title: HEK_a12eCBS_dCas9-VPR_sorted_HiC_rep2


title: HEK_a12pCBS_dCas9-VPR_sorted_HiC_rep3

description:
captureHiC-Seq, Paired End
Processed data file includes data for rep1, 2 and 3. File is available on GSM3514558

value: HEK293T cells positively transfected with dCas9-VPR targeting the pCBS of Pcdha12


title: MEFs  D2_AGHMT_Mef2C

source_name: MEFs  D2_AGHMT_Mef2C

value: AGHMT

value: Mef2C (Diagenode, C15200054)


title: RNA-seq of wt NPCs, replicate 1


title: RNA-seq of slow/slow embryonic stem cells, replicate 3

growth_protocol: ESCs were cultured in 2i medium (1:1 Neurobasal and DMEM/F12, supplemented with 0.5X N2, 0.5x B27, 0.05% BSA, 1uM 0325901, 3uM CHIR99021, 2mM L-glutamine, 0.15mM monothioglycerol, 100U/ml LIF) on gelatin coated-plates

value: Embryonic stem cells (ESCs)


title: RNA-seq of wt NPCs, replicate 2


title: RNA-seq of slow/slow embryonic stem cells, replicate 1


title: RNA-seq of wt embryonic stem cells, replicate 2