title: ES_2i_shSetdb1-2

description:
2i_shSetdb1-2
Processed data file: gene_expression_vsd.txt
Processed data file: repeat_expression_vsd.txt

data_processing:
Adaptors and low-quality base calls were trimmed using trim_galore! v0.3.3 with default parameters.
Trimmed reads were mapped to mm9 using tophat v2.0.9 with -g 1.
Raw read counts for each gene or repeat (from RepeatMasker annotation) were generated in Seqmonk with the RNA-seq quantitation pipeline. Reads from repeats belonging to the same class were pooled. Normalised gene and repeat expression values were calculated with the variance stabilizing transformation in DESeq2.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: gene_expression_vsd.txt: Tab-delimited text file containing normalised gene expression values (log2) for each sample.
Supplementary_files_format_and_content: repeat_expression_vsd.txt: Tab-delimited text file containing normalised repeat expression values (log2) for each sample.

source_name: embryonic stem cells, naive, shSetdb1

extract_protocol:
RNA was extracted using either the AllPrep DNA/RNA mini kit (QIAGEN) and DNase treated with the TURBO DNA-free kit (Ambion).
Directional rRNA-depleted RNA-Seq libraries were generated from 200-500 ng of total RNA using the ScriptSeq Complete Gold kit (Epicentre).

tag: strain/background


title: ES_2i_shSetdb1-1

status: Public on Sep 25 2017

type: SRA

city: London

first: Miguel

middle: R

last: Branco

address: 4 Newark Street

country: United Kingdom

institute: Blizard Institute

description:
2i_shSetdb1-1
Processed data file: gene_expression_vsd.txt
Processed data file: repeat_expression_vsd.txt

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

growth_protocol: ESCs were cultured on gelatin-coated plates without feeders, in either: 1) serum media (DMEM supplemented with 15% fetal bovine serum and 1,000 U/ml LIF), or 2) 2i media (DMEM F-12 and neurobasal media supplemented with N2, B27, LIF, PD0325901 and CHIR99021).

treatment_protocol: Lentiviral particles containing pLKO.1 shRNA vectors were produced by standard methods in 293T cells. Transduced ES cells were selected with 1 µg/ml puromycin 48 hours post-infection and collected after 3 days of selection.

tag: cell line

tag: medium

tag: shRNA


title: ES_2i_shScr-2

description:
2i_shScr-2
Processed data file: gene_expression_vsd.txt
Processed data file: repeat_expression_vsd.txt

source_name: embryonic stem cells, naive, shScr

value: shScr


title: ES_2i_shScr-3

description:
2i_shScr-3
Processed data file: gene_expression_vsd.txt
Processed data file: repeat_expression_vsd.txt


title: ES_2i_shSetdb1-3

description:
2i_shSetdb1-3
Processed data file: gene_expression_vsd.txt
Processed data file: repeat_expression_vsd.txt


title: ES_serum_shSetdb1-3

description:
Serum_shSetdb1-3
Processed data file: gene_expression_vsd.txt
Processed data file: repeat_expression_vsd.txt

source_name: embryonic stem cells, primed, shSetdb1

value: serum


title: ES_2i_shScr-1

description:
2i_shScr-1
Processed data file: gene_expression_vsd.txt
Processed data file: repeat_expression_vsd.txt


title: ES_serum_shSetdb1-1

description:
Serum_shSetdb1-1
Processed data file: gene_expression_vsd.txt
Processed data file: repeat_expression_vsd.txt


title: ES_serum_shSetdb1-2

description:
Serum_shSetdb1-2
Processed data file: gene_expression_vsd.txt
Processed data file: repeat_expression_vsd.txt


title: MEF+Ascl1_5d_negative_B2_rep1

city: Singapore

first: Qian Yi

last: Lee

address: Biopolis Drive

department: R&D

country: Singapore

institute: Nuevocor

description: merged_macspeaks_all_wo.new.rtta_RPKM.quantile.filtered.stepminer.annotated.txt

library_source: genomic

data_processing:
Trimmed adaptors
Mapped with bowtie to mm9
Removed mitochondria reads and duplicate fragments
Called peaks with MACS2 (-q 0.01 --nomodel  --shift 0) based on reads aggregated from all replicates for that time point.
Merged peaks for relevant timepoints and compute RPKM of paired end read endpoints that fell within the region for all the biological replicates
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample at all peaks present at 1) early timepoints (12-48 hours) and 2) all samples

molecule: genomic DNA

source_name: MEF+Ascl1 5d, Tau::EGFP-

growth_protocol: Homozygous TauEGFP knock-in mice (Tucker et al., 2001) were bred with C57B/6 mice (Taconic) to generate heterozygous embryos. MEFs were isolated from E13.5 embryos and cultured in MEF media (5% cosmic calf serum + sodium pyruvate + pen/strep + MEM NEAA + 0.8% 2-Mercaptoethanol in DMEM). Cortical neurons were isolated by dissecting cortical tissue from E15.5 embryos and sorting for TauEGFP+ cells.

extract_protocol: Cells were trypsinzed in 0.05% trypsin and processed at different time points post-dox. From day 5, cells were FAC sorted by TauEGFP. ATAC-seq protocol outlined by Buenrostro, et al (Nat. Methods, 2013)

treatment_protocol: MEFs were infected with rtTA alone or with Ascl1+rtTA. Doxycycline (dox) was added one day post infection. For cells harvested after 48 hours, MEF media was replaced neuronal media (DMEM-F12 + N2 supplement + B27 supplement + insulin + dox), and media was refreshed every 2-3 days.

tag: genotype

tag: cell type

value: E13.5 fibroblast

tag: time post dox

value: 5 days


title: ES_serum_shScr-3

description:
Serum_shScr-3
Processed data file: gene_expression_vsd.txt
Processed data file: repeat_expression_vsd.txt

source_name: embryonic stem cells, primed, shScr


title: TET2rescue-WT-2i-3

data_processing:
Adaptors and low-quality base calls were trimmed using trim_galore! v0.3.3 with default parameters.
Trimmed reads were mapped to mm9 using tophat v2.0.9 with -g 1.
Raw read counts for each gene or repeat (from RepeatMasker annotation) were generated in Seqmonk with the RNA-seq quantitation pipeline. Reads from repeats belonging to the same class were pooled. Normalised gene and repeat expression values were calculated with the variance stabilizing transformation in DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files containing normalised gene expression values (log2) for each sample.

molecule: polyA RNA

source_name: embryonic stem cells

extract_protocol:
RNA was extracted using either the AllPrep DNA/RNA mini kit (QIAGEN) and DNAse treated with the TURBO DNA-free kit (Ambion).
Non-directional mRNA-Seq libraries were generated using the Dynabeads mRNA purification kit (Life Technologies) and the NEBnext Ultra RNA library prep kit (NEB).

value: Tet2 KO

tag: rescue

value: TET2 WT


title: ES_serum_shScr-2

description:
Serum_shScr-2
Processed data file: gene_expression_vsd.txt
Processed data file: repeat_expression_vsd.txt


title: ES_serum_shScr-1

description:
Serum_shScr-1
Processed data file: gene_expression_vsd.txt
Processed data file: repeat_expression_vsd.txt


title: Vector_control_K562_20161128

city: Guangzhou

first: Alexander

middle: V.

last: Strunnikov

state: Guangdong

address: 190 Kai Yuan Avenue

country: China

institute: GIBH

description:
EV_7
PLKO_161128
Infected with pLKO-Tet-On-neo lentivirus.
18-30nt RNA
Processed data file: all_RNA_expression_TPM.xlsx

data_processing:
The image file obtained by sequencing was converted into raw FASTQ file.
Removed low quality reads.
Removed reads with 5' primer contaminants.
Removed reads without 3' primer.
Removed reads without the insert.
Removed reads with polyA.
Clean FASTQ files generated.
Aligned to reference genome GRCh38. Bowtie2 : -q -L 16 --phred64 -p 6
Align to sRNA databases. cmsearch: --cpu 6 --noali
Classify sRNAs. miRNA > piRNA > snoRNA > Rfam > other sRNA.
Differential expression analysis by DEGseq.
Genome_build: hg38, hsa_mirbase_v21_hg38
Supplementary_files_format_and_content: all_RNA_expression_TPM.xlsx: Excel matrix includes fields: sRNA id, Type, Description, D_161115_TPM, D_161213_TPM, L_161128_TPM, N_161213_TPM, PLKO_161115_TPM, PLKO_161128_TPM.

organism: Homo sapiens

source_name: bone marrow, chronic myelogenous leukemia (CML)

growth_protocol: K562 cells and stably infected derivatives were grown in IMDM with 10% or 20% Tet-On certified FBS. BORIS knockdown (KD) vectors were constructed to express either the shRNA template GGTGTGAAATGCTCCTCAACA cloned into the pLKO-Tet-On-neo vector. K562 infected with lentivirus stock were selected for 4 weeks or more in media supplemented with 600µg/ml G418, followed by the selection of individual clones.

extract_protocol:
Trizol, small RNA standard, followed by 18-30nt PAGE size selection.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For BORIS knockdown and/or empty vector control, the stably infected cells were induced with 200ng/ml doxycycline for 96 hours.

value: immortalized tumor cells

tag: transgene

value: pLKO-Tet-On-neo lentivirus


title: Vector_control_K562_20161115

description:
EV_3
PLKO_161115
Infected with pLKO-Tet-On-neo lentivirus.
18-30nt RNA
Processed data file: all_RNA_expression_TPM.xlsx


title: acc1-5 acla-1i-1 mock input

first: Chen

last: Chen

address: 723 Xinke Rd.

institute: South China Botanical Garden, Chinese Academy of Science

data_processing:
ChIP-seq reads were aligned to the TAIR10 genome assembly using Bowtie for Illumina (Galaxy Version 1.1.2) with default settings.
Mapped reads were filtered by removing PCR duplications and randomly selected certain amount of reads.
Peaks were called by using MACS model-based analysis of ChIP-seq (Galaxy Version 1.0.1).
Genome_build: TAIR10
Supplementary_files_format_and_content: Wig files were generated by using MACS (Galaxy Version 1.0.1).

organism: Arabidopsis thaliana

source_name: seedlings, acc1-5 acla-1i-1, mock, input

growth_protocol: Arabidopsis seedlings were grown on 1/2 MS plates for 12 days under 16h light/ 8h dark condition.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
10 ng of ChIP DNA immunoprecipitated by corresponding antibodies was used for ChIP-seq library construction. Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol. Illumina HiSeq 2500 was used for high-throughput sequencing of the ChIP-seq library.

treatment_protocol: DMSO or 20 μM β-estradiol was sprayed onto 11-day-old seedlings for 24h induction.

tag: ecotype

tag: genotype/variation

value: acc1-5 acla-1i-1

tag: tissue

value: seedlings

tag: developmental stage

value: 12 days after germination

tag: treatment

value: mock

tag: chip antibody


title: acc1-5 H4K8ac rep1

source_name: seedlings, acc1-5, H4K8ac ChIP

value: H4K8ac (Millipore 07-328)


title: BORIS_shRNA2_K562_20161213_new

description:
KD_13
N_161213
Infected with Tet-On-neo-anti-BORIS-shRNA lentivirus.
18-30nt RNA
Processed data file: all_RNA_expression_TPM.xlsx

value: Tet-On-neo-anti-BORIS-shRNA lentivirus


title: acc1-5 H4K12ac rep1

source_name: seedlings, acc1-5, H4K12ac ChIP

value: H4K12ac (Millipore 07-595)


title: acc1-5 acla-1i-1 induced input

source_name: seedlings, acc1-5 acla-1i-1, beta-estrodial induced, input

value: beta-estrodial


title: acc1-5 H4K16ac rep1

source_name: seedlings, acc1-5, H4K16ac ChIP

value: H4K16ac (Millipore 07-329)


title: acc1-5 H4K5ac rep1

source_name: seedlings, acc1-5, H4K5ac ChIP

value: H4K5ac (Millipore 07-327)


title: BORIS_shRNA2_K562_20161213

description:
KD_9
D_161213
Infected with Tet-On-neo-anti-BORIS-shRNA lentivirus.
18-30nt RNA
Processed data file: all_RNA_expression_TPM.xlsx


title: P20 32F rRSeT methylC-seq

city: Crawley

first: Ethan

middle: Edward

last: Ford

state: WA

address: 35 Stirling Highway

department: Plant Energy Biology

country: Australia

institute: University of Western Australia

description: Agilent SureSelect Methyl-Seq

data_processing:
Reads were quality and adapter trimmed with Cutadapt using the following parameters: -q 20,20 -m 30 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC. Trimmed reads were mapped to the in silico bisulfite converted human genome build hg19 using the bs-seeker2 software package (Guo et al, BMC Genomics, 2013, 14:774) with the following parameters: —aligner=bowtie —am=1. Methylation calling was also performed with bs-seeker2 using the default options. The heatmap of methylation levels in imprinted regions was made by calculating fraction of methyl-cytosine basecalls in the CpG context in each imprinted region and plotting the data with the pheatmap function in R.
Genome_build: hg19
Supplementary_files_format_and_content: allC - tab deliminted text files (chromosome, position, strand, context, methyl cytosine base calls, all base calls)

source_name: human induced pluripotent stem cells

growth_protocol: to generate human primed and naïve iPSCs used for this study, somatic cell reprogramming with the Cytotune 2.0 kit, experiments were performed according to the manufacturer’s instructions (Invitrogen). Briefly, HDFa were seeded at ~5x10^4 cells per well of a 6-well plate in mouse embryonic fibroblasts (MEF) medium containing DMEM (Gibco), 10% FBS (Hyclone), 1% nonessential amino acids (Gibco), 1mM GlutaMAX (Gibco), Pen-strep (Gibco), 0.1mM 2-mercaptoethanol (Gibco) and 1mM sodium pyruvate (Gibco) . After 2 days, cells were transduced with Sendai viruses in MEF medium with multiplicity of infections (MOIs) as follows, KOS MOI=5, c-MYC MOI=5, KLF4 MOI=6. After 24 hours, the medium was replaced with fresh MEF medium and media were changed every other day thereafter. On day 7, cells were trypsinized and seeded onto a layer of iMEF feeders or alternatively onto VTN-N (Gibco) coated T25 flasks at ~0.5x10^5~1x10^5 per flask in MEF medium. The next day, the cells were switched to different culture media. 21 days after transduction, cells were passaged and expanded using methods and media described below. Essential 8 medium: Add 10ml of Essential 8 supplement (Gibco) to 500ml medium basal (Gibco), supplement with 1% Pen-strep (Gibco); NHSM medium:DMEM/F12 medium (Gibco) (For 500ml) supplemented with 10mg/ml AlbuMAXI (Gibco), 1% Pen-strep (Gibco), 1mM GlutaMAX (Gibco), 1% nonessential amino acids (Gibco), 10% KnockOut Serum Replacement (Gibco), 5ml N2 supplement (Gibco), 12.5µg/ml recombinant human insulin (Sigma), 50µg/ml L-ascorbic acid (Sigma), 20ng/ml of recombinant human LIF (made in house), 8ng/ml FGF2 (Peprotech), 2ng/ml recombinant TGF-β1 (Peprotech), 20ng/ml human LR3-IGF1 (Prospec), and small molecule inhibitors: 1µM PD0325901 (Miltenyi Biotec), 3µM CHIR99021 (Miltenyi Biotec), 5µM SP600125 (Tocris), 2µM BIRB796 (Axon), 0.4µM LDN193189 (Axon), 10µM Y-27632 (supplemented daily to media from freshly thawed stock aliquot; abcam) and 1µM Gö6983 (supplemented daily to media from freshly thawed stock aliquot; Tocris); RSeT medium: Add 100ml of RSeT 5X Supplement, 1ml of RSeT 500X Supplement and 0.5ml of RSeT 1000X Supplement into 398.5ml of RSeT Basal Medium; (Stem cell technologies) supplement with 1% Pen-strep (Gibco); 5iLAF medium: A 50:50 mixture of DMEM/F-12 (Gibco) and Neurobasal medium (Gibco) supplemented with 1% N2 supplement (Gibco), 2% B27 supplement (Gibco), 1% nonessential amino acids (Gibco), 1mM GlutaMAX (Gibco), 1% Pen-strep (Gibco), 0.1mM 2-mercaptoethanol (Gibco), 50μg/ml BSA (Gibco), 1μM PD0325901 (Miltenyi Biotec), 1μM IM-12 (Millipore), 0.5μM SB590885 (Tocris), 1μM WH-4-023 (A Chemtek), 10μM Y-27632 (abcam), 20ng/ml Activin A (Peprotech), 8ng/ml FGF2 (Miltenyi Biotec), 20ng/ml human LIF (made in house) and 0.5% KSR (Gibco); t2iLGöY medium: A 50:50 mixture of DMEM/F-12 (Gibco) and Neurobasal medium (Gibco), supplemented with 2mM L-glutamine (Gibco), 0.1mM 2-mercaptoethanol (Gibco), 0.5% N2 supplement (Gibco), 1% B27 supplement (Gibco), 1% Pen-strep (Gibco), 10ng/ml human LIF (made in house), 250μM L-ascorbic acid (Sigma), 10µg/ml recombinant human insulin (Sigma), 1μM PD0325901 (Miltenyi Biotec), 1μM CHIR99021 (Miltenyi Biotec), 2.5μM Gö6983 (Tocris), 10μM Y-27632 (abcam).  For conversion of established naive t2iLGöY cells to primed state, naive cells are trypsinized, counted and seeded onto VTN-N (Gibco) coated 6-well plates (in a range of density) in t2iLGöY media for 24 hours.The next day cells are transitioned to E8 medium (Gibco). Cells are then cultured and passaged as E8 primed cells.

extract_protocol:
DNeasy Blood & Tissue Kit (Qiagen)
Following DNA extraction, 700ng-1µg of DNA for each sample was sheared to 200-bp using the Covaris DNA Shearing System. Methylated adapters (BIOO Scientific) were ligated to fragmented genomic DNA using the NxSeq AmpFREE Low DNA Library Kit (Lucigen). To capture regions of interest, we used baits provided in the SureSelectXT Human Methyl-Seq kit (Agilent) for enriching 84Mb covering 3.7 million CpGs. Sodium bisulfite conversion using the EZ-DNA Methylation Gold kit (Zymo Research) was performed on the enriched DNA followed by 11-14 cycles of polymerase chain reaction (PCR) amplification with KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems). We performed sequencing of 101-bp single-end reads using the Illumina HiSeq 1500 sequencer as per the manufacturer’s instructions.

value: naive-like hiPS cells derived from adult human dermal fibroblasts

tag: age

tag: Sex

value: Female

tag: identifier

tag: media

value: RSeT

tag: reprogramming strategy

value: Sendai virus

tag: passage number

value: 20 passages


title: P17 32F rNHSM methylC-seq

description: Agilent SureSelect Methyl-Seq

tag: cell line

value: NHSM

value: 17 passages


title: P12 32F E8 Primed methylC-seq

description: Agilent SureSelect Methyl-Seq

value: 12 passages


title: WT H4K16ac rep1

source_name: seedlings, WT, H4K16ac ChIP

value: WT

value: seedlings


title: acc1-5 H3K14ac rep1

source_name: seedlings, acc1-5, H3K14ac ChIP

value: 12 days after germination

value: H3K14ac (Millipore 07-353)


title: myotube_dicr_2

city: Bethesda

first: Apratim

last: Mitra

state: MD

address: 6 Center Dr Building 6B Room 2B206

department: Division of Developmental Biology

country: USA

institute: NICHD

description: Processed data file: raw_counts_genes.txt

data_processing:
Raw data from the Illumina HiSeq 2000 was aligned to mouse genome version mm9 using Tophat2. Colorspace XSQ data was aligned to mouse genome version mm9 using Lifescope software (Thermo Fisher Scientific).
Reads within exons of genes (n=23366, Downloaded from UCSC genome browser on March 6, 2013) were calculated using htseq-count (Anders, 2014).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: raw_counts_genes.txt: Tab-delimited matrix table of raw sequencing counts for each gene per sample (23366 genes x 13 samples).

source_name: skeletal muscle from dICR/dICR

growth_protocol: Hind limb skeletal muscle was isolated from p2 to p3 pups and myoblasts isolated as described (Bois, 2003) and grown at 37C in 10% CO2 in F10 supplemented with 10% calf serum and 2.5 µg/ml fibroblast growth factor.

extract_protocol:
RNA was isolated from primary myoblast and 24-hour-differentiated myotube cells using Tripure (Roche) followed by the RNeasy Micro kit (Qiagen). Samples with RNA Integrity numbers >9 were used for sequencing. Ribosomal RNA was depleted from 1-5 μg total RNA using the RiboZero Gold kit (Illumina).
Library preparation for the Illumina HiSeq 2000 was performed using the TruSeq RNA Sample Prep V2 kit (Illumina). Pooled barcoded libraries were sequenced to generate paired-end 101 bp reads. For the ABI SOLiD sequencing, libraries were prepared using the SOLiD Whole Transcriptome Analysis kit (Thermo Fisher Scientific). Pooled barcoded libraries were sequenced to generate paired-end 35 x 75 bp reads.

treatment_protocol: Primary myoblasts were transferred from growth medium to DMEM supplemented with 1% horse serum and differentiated for 24 hours.

tag: strain/background

value: mixed

tag: cell type

value: 24-hour differentiated myotube

value: dICR/dICR


title: P11 plus 10 32F rt2iLGöY to E8 Primed methylC-seq

description: Agilent SureSelect Methyl-Seq

value: 11 passages in t2iLGöY and then 10 passages in E8


title: acc1-5 H3K9ac rep1

source_name: seedlings, acc1-5, H3K9ac ChIP

value: H3K9ac (Millipore 07-352)


title: BORIS_shRNA2_K562_20161115

description:
KD_2
D_161115
Infected with Tet-On-neo-anti-BORIS-shRNA lentivirus.
18-30nt RNA
Processed data file: all_RNA_expression_TPM.xlsx

value: immortalized tumor cells

value: Tet-On-neo-anti-BORIS-shRNA lentivirus


title: myotube_dicr_1


title: WT H4K8ac rep1

source_name: seedlings, WT, H4K8ac ChIP

value: H4K8ac (Millipore 07-328)


title: P10 32F r5iLAF methylC-seq

description: Agilent SureSelect Methyl-Seq

value: naive-like hiPS cells derived from adult human dermal fibroblasts

value: Female

value: Sendai virus

value: 10 passages


title: myotube_wt_5

source_name: skeletal muscle from wild type

value: wild type


title: WT H4K12ac rep1

source_name: seedlings, WT, H4K12ac ChIP

value: WT

value: H4K12ac (Millipore 07-595)


title: WT H4K5ac rep1

source_name: seedlings, WT, H4K5ac ChIP

value: seedlings

value: 12 days after germination

value: H4K5ac (Millipore 07-327)


title: myotube_wt_4

value: mixed

value: 24-hour differentiated myotube


title: WT H3K18ac rep1

source_name: seedlings, WT, H3K18ac ChIP

value: H3K18ac (Millipore 07-354)


title: acc1-5 H3K18ac rep1

source_name: seedlings, acc1-5, H3K18ac ChIP


title: myoblast_wt_4

value: primary myoblast


title: myoblast_wt_3


title: BORIS_shRNA2_K562_20161128

description:
KD_4
L_161128
Infected with Tet-On-neo-anti-BORIS-shRNA lentivirus.
18-30nt RNA
Processed data file: all_RNA_expression_TPM.xlsx

source_name: bone marrow, chronic myelogenous leukemia (CML)

value: immortalized tumor cells


title: acc1-5 H3K27ac rep1

source_name: seedlings, acc1-5, H3K27ac ChIP

value: H3K27ac (Millipore 07-360)


title: WT H3K27ac rep1

source_name: seedlings, WT, H3K27ac ChIP


title: WT H3K9ac rep1

source_name: seedlings, WT, H3K9ac ChIP

value: H3K9ac (Millipore 07-352)


title: acc1-5 acla-1i-1 mock H3K27ac rep2

source_name: seedlings, acc1-5 acla-1i-1, mock, H3K27ac ChIP

value: acc1-5 acla-1i-1

value: mock


title: Wild type 4h Starvation Biological Replicate 2

city: Ithaca

first: Lori

middle: B

last: Huberman

state: NY

address: 236 Tower Rd.

department: Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science

institute: Cornell University

data_processing:
Illumina Casava1.8 software used for base calling
Sequence reads were trimmed for adaptor sequence and aligned to the predicted transcripts from the N. crassa OR74A genome (v12) with HiSat2 v2.0.5 with the parameters --max-intronlen 5000 --rna-strandness R --dta-cufflinks
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using Cufflinks v2.2.1 with the parameters --library-type fr-firststrand -u -b -G --compatible-hits-norm --max-bundle-frags=10000000
Genome_build: Neurospora crassa OR74A genome v12
Supplementary_files_format_and_content: tab-deliminated text files include FPKM values for each sample

organism: Neurospora crassa

source_name: Neurospora crassa mycelia

growth_protocol: N. crassa conidia were inoculated into 100ml of Vogel's minimal media + 2% sucrose and incubated at 25C in constant light with constant shaking at 200rpm for 16h

extract_protocol:
Mycelia were filtered using Whatman paper #1 and flash frozen using liquid nitrogen. RNA was isolated by bead beating in Trizol reagent and then cleaned up using the Qiagen RNeasy kit.
RNA were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mycelia were washed in media lacking a carbon source and then transferred to 100ml of Vogel's minimal media without a carbon source or Vogel's minimal media+2%Avicel and incubated at 25C in constant light with constant shaking at 200rpm for the indicated amount of time

tag: genotype

value: FGSC 2489

value: Vogel's minimal media lacking a carbon source

tag: time


title: P11 32F rt2iLGöY methylC-seq

description: Agilent SureSelect Methyl-Seq

source_name: human induced pluripotent stem cells

value: naive-like hiPS cells derived from adult human dermal fibroblasts

value: Female

value: Sendai virus

value: 11 passages


title: acc1-5 acla-1i-1 induced H3K27ac rep2

source_name: seedlings, acc1-5 acla-1i-1, beta-estrodial induced, H3K27ac ChIP

tag: ecotype

value: seedlings

value: 12 days after germination

value: beta-estrodial


title: Wild type 4h Avicel Biological Replicate 3

value: Vogel's minimal media + 2% Avicel


title: VAESBJ_Empty_H3K4me3

city: Boston

first: Cigall

last: Kadoch

state: MA

address: 450 Brookline Avenue

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: VA-ES-BJ empty anti-H3K4me3 ChIP-seq

data_processing:
ChIP-seq reads were mapped to the human reference genome (hg19) using Bowtie2(Langmead and Salzberg, 2012) version 2.1.0 with parameters –k 1.
Peaks were called against input reads using MACS2(Zhang et al., 2008) version 2.1.0 at q=1e-3.
Peaks were filtered to remove peaks that overlap with ENCODE blacklisted regions, as well as peaks mapped to unmappable chromosomes (only chr1-22,X,Y included). Duplicate reads were removed using samtools rmdup for all downstream analyses.
ChIP-seq track densities were generated per million mapped reads with MACS2 2.1.0 using parameters –B –SPMR.
Genome_build: hg19

source_name: VA-ES-BJ (EpS)

growth_protocol: Cell lines were cultured either in DMEM/F12, RPMI1640, or DMEM medium (Gibco, Grand Island, NY, USA), supplemented with 10% fetal bovine serum, 1% Glutamax (Gibco) and 1% Penicillin-Streptomycin (Gibco).

extract_protocol:
Chromatin immunoprecipitation (ChIP) experiments were performed per standard protocols (Millipore, Billerica, MA) with minor modifications. Briefly, 10M cells were crosslinked with 1% formaldehyde for 10 min at 37 °C. This reaction was subsequently quenched with 0.125M glycine.
All library prep and sequencing were 75bp single end on Illuminia Nextseq 500

treatment_protocol: Lentiviral particles were prepared in 293T packaging cells via polyethylenimine-mediated transfection as previously described (Bell et al 2012). The cells were harvested following 48-hour exposure to the lenti-virus and 5-day selection with 10 μg/ml of Blasticidin.

tag: antibody

tag: antibody vendor/catalog

value: Millipore 05-745R


title: VAESBJ_BAF47_H3K4me3

description: VA-ES-BJ BAF47 anti-H3K4me3 ChIP-seq


title: Wild type 4h Avicel Biological Replicate 2


title: Wild type 4h Avicel Biological Replicate 1


title: Pccg1-clr-2 4h Starvation Biological Replicate 3

value: Pccg1-clr-2 [delta]clr-2


title: HSES2M_Empty_H3K4me3

description: HS-ES-2M empty anti-H3K4me3 ChIP-seq

source_name: HS-ES-2M (EpS)


title: HSES2M_BAF47_H3K4me3

description: HS-ES-2M BAF47 anti-H3K4me3 ChIP-seq


title: Pccg1-clr-2 4h Starvation Biological Replicate 2


title: TTC1240_Empty_H3K4me3

description: TTC1240 empty anti-H3K4me3 ChIP-seq

source_name: TTC1240 (MRT)


title: TTC1240_BAF47_H3K4me3

description: TTC1240 BAF47 anti-H3K4me3 ChIP-seq


title: [delta]clr-2 4h Avicel Biological Replicate 3


title: [delta]clr-2 4h Avicel Biological Replicate 2


title: G401_BAF47_H3K4me3

description: G401 BAF47 anti-H3K4me3 ChIP-seq


title: WT H3K14ac rep1

source_name: seedlings, WT, H3K14ac ChIP

tag: genotype/variation

value: WT

tag: tissue

tag: developmental stage

value: H3K14ac (Millipore 07-353)


title: Pccg1-clr-2 4h Starvation Biological Replicate 1


title: Wild type 4h Starvation Biological Replicate 3


title: G401_Empty_H3K4me3

description: G401 empty anti-H3K4me3 ChIP-seq


title: [delta]clr-2 4h Avicel Biological Replicate 1


title: Wild type 4h Starvation Biological Replicate 1


title: [delta]clr-1 4h Avicel Biological Replicate 3


title: [delta]clr-1 4h Avicel Biological Replicate 2


title: TTC1240_BAF47_BAF200

description:
antibody: BAF200 PP12 P62240 Cell Signaling
TTC1240 BAF47 anti-BAF200 ChIP-seq

value: Malignant rhabdoid tumor


title: [delta]clr-1 4h Avicel Biological Replicate 1


title: TTC1240_empty_BAF200

description:
antibody: BAF200 PP12 P62240 Cell Signaling
TTC1240 empty anti-BAF200 ChIP-seq


title: TTC1240_empty_H3K4me1

description:
antibody: K3K4me1 GR149018-1 ab8895 Abcam
TTC1240 empty anti-H3K4me1 ChIP-seq


title: [delta]clr-3 4h Starvation Biological Replicate 3


title: [delta]clr-3 4h Starvation Biological Replicate 2


title: [delta]clr-3 4h Starvation Biological Replicate 1


title: TTC1240_Empty_Day3_B

description: TTC1240 Empty vector RNA-seq Day 3 B

data_processing:
RNA-seq reads were mapped to the human reference genome (hg19) using STAR(Dobin et al., 2013) version 2.3.1 with default parameters.
RPKM values for biological duplicate RNA-seq samples were generated using GFold(Feng et al., 2012) version 1.1.0.
Genome_build: hg19
Supplementary_files_format_and_content: the column headers for the read_cnt file format is: GeneSymbol, GeneName, Read Count, Gene Exon, Length, RPKM

extract_protocol:
All RNA was produced using the RNeasy Mini Kit (Qiagen).
All library prep and sequencing were 75bp single end on Illuminia Nextseq 500

treatment_protocol: Lentiviral particles were prepared in 293T packaging cells via polyethylenimine-mediated transfection as previously described (Bell et al 2012). The cells were harvested following 48-hour exposure to the lenti-virus and 1-day selection with 10 μg/ml of Blasticidin.


title: TTC1240_BAF47_Day3_B

description: TTC1240 BAF47 vector RNA-seq Day 3 B


title: TTC1240_BAF47_Day3_A

description: TTC1240 BAF47 vector RNA-seq Day 3 A


title: acc1-5 rep1

data_processing:
ChIP-seq reads were aligned to the TAIR10 genome assembly using Bowtie for Illumina (Galaxy Version 1.1.2).
Mapped reads were filtered by removing PCR duplications and randomly selected certain amount of reads.
Bed files were generated by using BAM to BED conversion (Galaxy Version 2.22.0).
Peaks were called by using MACS model-based analysis of ChIP-seq (Galaxy Version 1.0.1).
RNA-seq reads were aligned to the TAIR10 genome assembly using Tophat version 1.4.0 with the minimum and maximum intron length setting being 20 bp and 2000bp, respectively.
Mapped reads were assembled according to TAIR10 version of genome annotation using cufflinks version 2.1.1
Assembled transcripts from three independent biological replicates in Col and acc1-5 were included and compared by using cuffdiff version 2.1.1
Genome_build: TAIR10
Supplementary_files_format_and_content: wig files: Shifted Merged MACS tag counts for every 10 bp

source_name: acc1-5 rep1

extract_protocol:
RNA were extracted from 12 days old seedlings following the instructions of RNeasy Plant Total RNA Isolation kit(Qiagen). Genomic DNA was removed by treating with DNase TURBO (Ambion).
Libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the manufacture’s protocol

tag: chip antibody


title: G401_empty_BRG1

description: G401 empty anti-BRG1 ChIP-seq


title: acc1-5 rep3

source_name: acc1-5 rep3


title: acc1-5 rep2

source_name: acc1-5 rep2


title: TTC1240_Empty_Day3_A

description: TTC1240 Empty vector RNA-seq Day 3 A


title: G401_BAF47_Day3_B

description: G401 BAF47 vector RNA-seq Day 3 B


title: WT rep3

source_name: WT rep3


title: G401_BAF47_Day3_A

description: G401 BAF47 vector RNA-seq Day 3  A


title: WT rep2

source_name: WT rep2


title: TTC1240_BAF47_H3K4me1

description:
antibody: K3K4me1 GR149018-1 ab8895 Abcam
TTC1240 BAF47 anti-H3K4me1 ChIP-seq


title: WT rep1

source_name: WT rep1


title: G401_Empty_Day3_B

description: G401 Empty vector RNA-seq Day 3 B


title: G401_Empty_Day3_A

description: G401 Empty vector RNA-seq Day 3 A


title: TTC1240_BAF47_Day 7

description:
TTC1240 BAF47 vector RNA-seq Day 7 A
TTC1240 BAF47 vector RNA-seq Day 7 B

data_processing:
RNA-seq reads were mapped to the human reference genome (hg19) using STAR(Dobin et al., 2013) version 2.3.1 with default parameters.
RPKM values for biological duplicate RNA-seq samples were generated using GFold(Feng et al., 2012) version 1.1.0.
Genome_build: hg19


title: acc1-5 input

source_name: acc1-5 input

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
10 ng of ChIP DNA immunoprecipitated by anti-GFP antibody was used for ChIP-seq library construction. Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol. Illumina Hiseq 2000 was used for high-throughput sequencing of the ChIP-seq library.


title: TTC1240_Empty_Day 7

description:
TTC1240 Empty vector RNA-seq Day 7 A
TTC1240 Empty vector RNA-seq Day 7 B


title: G401_BAF47_Day 7

description:
G401 BAF47 vector RNA-seq Day 7 A
G401 BAF47 vector RNA-seq Day 7 B


title: acc1-5 H4K12ac rep2

source_name: acc1-5 H4K12ac rep2

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
10 ng of ChIP DNA immunoprecipitated by anti-H4K12ac antibody was used for ChIP-seq library construction. Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol. Illumina Hiseq 2500 was used for high-throughput sequencing of the ChIP-seq library.

value: H4K12ac (Millipore 07-595)


title: acc1-5 H4K8ac rep2

source_name: acc1-5 H4K8ac rep2

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
10 ng of ChIP DNA immunoprecipitated by anti-H4K8ac antibody was used for ChIP-seq library construction. Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol. Illumina Hiseq 2500 was used for high-throughput sequencing of the ChIP-seq library.

value: H4K8ac (Millipore 07-328)


title: G401_Empty_Day 7

description:
G401 Empty vector RNA-seq Day 7 A
G401 Empty vector RNA-seq Day 7 B


title: acc1-5 H4K5ac rep2

source_name: acc1-5 H4K5ac rep2

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
10 ng of ChIP DNA immunoprecipitated by anti-H4K5ac antibody was used for ChIP-seq library construction. Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol. Illumina Hiseq 2500 was used for high-throughput sequencing of the ChIP-seq library.

value: H4K5ac (Millipore 07-327)


title: Ca_2

city: beltsville

first: Tianbao

last: Yang

address: 10300 BALTIMORE AVENUE

department: BARC

institute: USDA-ARS

description: sample spray with calcium chloride

data_processing:
The paired-end raw reads were filtered with Illumina Pipeline (CASAVA) v1.8.2 with the default parameter.
The raw reads after filtered were separately aligned to the Brassica oleracea (v2.1) genome and CDS with RNA-Seq analysis algorithm included in the CLC Genomics Workbench 7.0.4 (CLC bio, Boston, MA, USA) using the default parameters
Genome_build: Brassica_oleracea v2.1
Supplementary_files_format_and_content: xls, rpkm value

organism: Brassica oleracea

growth_protocol: Seeds were sown in 0.54 m × 0.28 m × 0.06 m culture trays (Vacuum-Formed Standard 1020 Open Flats without holes, Growers Supply, Dyersville, IA, USA). The media was hydroponic ‘Sure to grow’ pads (0.208 m × 0.254 m, Growers Supply, USA).  Seeds were spread evenly over the damp pad and grown in a temperature controlled (25 °C) growth chamber. The trays were kept in the dark in a growth chamber at 25 °C for 4 days after seed sowing before exposing to light at an intensity of 42 µmol/ (s•m2) for 12h/12h (light/dark).

extract_protocol:
Ten days harvested broccoli RNAs (10 m mol/L CaCl2 and H2O sprayed samples) were extracted using the RNeasy Plant Mini kit (Qiagen, Valencia, CA, USA).
Illumina TruSeq RNA sample preparation kit

treatment_protocol: The seedlings were sprayed once a day with H2O (pH 5.5-6.0) only, or 1, 10, or 20 m mol/ L CaCl2 (Sigma-Aldrich, Inc., St. Louis, MO, USA).

value: hypocotyls

tag: age

value: 10 days


title: Water_2

description: sample spray with water


title: Water_1

description: sample spray with water


title: VA-ES-BJ_BAF47_SUZ12

description: VA-ES-BJ BAF47 anti-SUZ12 ChIP-seq

value: VA-ES-BJ

value: epithelioid sarcoma


title: TTC1240_empty_SS18

description: TTC1240 empty anti-SS18 ChIP-seq


title: VA-ES-BJ_BAF47_Input

description: VA-ES-BJ BAF47 Input ChIP-seq


title: TTC1240_BAF47_SS18

description: TTC1240 BAF47 anti-SS18 ChIP-seq


title: VA-ES-BJ_BAF47_H3K27ac

description: VA-ES-BJ BAF47 anti-H3K27ac ChIP-seq


title: WT input

source_name: WT input


title: VA-ES-BJ_BAF47_H3K27me3

description: VA-ES-BJ BAF47 anti-H3K27me3 ChIP-seq


title: VA-ES-BJ_BAF47_BAF155

description: VA-ES-BJ BAF47 anti-BAF155 ChIP-seq


title: E15.5_Neurons_B2_rep2

description: merged_macspeaks_all_wo.new.rtta_RPKM.quantile.filtered.stepminer.annotated.txt

source_name: E15.5 neurons, Tau::EGFP+

value: E15.5 cortex

tag: time post dox


title: WT H4K5ac rep2

source_name: WT H4K5ac rep2

value: seedlings


title: VA-ES-BJ_BAF47_BRG1

description: VA-ES-BJ BAF47 anti-BRG1 ChIP-seq

source_name: VA-ES-BJ (EpS)


title: E15.5_Neurons_B2_rep1


title: VA-ES-BJ_empty_Input

description: VA-ES-BJ empty Input ChIP-seq


title: Ca_1

description: sample spray with calcium chloride


title: WT H3K18ac rep2

source_name: WT H3K18ac rep2

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
10 ng of ChIP DNA immunoprecipitated by anti-H3K18ac antibody was used for ChIP-seq library construction. Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol. Illumina Hiseq 2500 was used for high-throughput sequencing of the ChIP-seq library.

value: 12 days after germination

value: H3K18ac (Millipore 07-354)


title: WT H4K12ac rep2

source_name: WT H4K12ac rep2

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
10 ng of ChIP DNA immunoprecipitated by anti-H4K12ac antibody was used for ChIP-seq library construction. Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol. Illumina Hiseq 2000 was used for high-throughput sequencing of the ChIP-seq library.


title: VA-ES-BJ_empty_SUZ12

description: VA-ES-BJ empty anti-SUZ12 ChIP-seq


title: WT H4K16ac rep2

source_name: WT H4K16ac rep2

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
10 ng of ChIP DNA immunoprecipitated by anti-H4K16ac antibody was used for ChIP-seq library construction. Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol. Illumina Hiseq 2500 was used for high-throughput sequencing of the ChIP-seq library.

value: H4K16ac (Millipore 07-329)


title: acc1-5 H3K14ac rep2

source_name: acc1-5 H3K14ac rep2

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
10 ng of ChIP DNA immunoprecipitated by anti-H3K14ac antibody was used for ChIP-seq library construction. Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol. Illumina Hiseq 2500 was used for high-throughput sequencing of the ChIP-seq library.


title: WT H4K8ac rep2

source_name: WT H4K8ac rep2


title: WT H3K14ac rep2

source_name: WT H3K14ac rep2


title: E15.5_Neurons_B1_rep2

extract_protocol: Cells were trypsinzed in 0.05% trypsin and processed at different time points post-dox. From day 5, cells were FAC sorted by TauEGFP. ATAC-seq protocol outlined by Buenrostro, et al (Nat. Methods, 2013)


title: E15.5_Neurons_B1_rep1


title: acc1-5 H3K9ac rep2

source_name: acc1-5 H3K9ac rep2

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
10 ng of ChIP DNA immunoprecipitated by anti-H3K9ac antibody was used for ChIP-seq library construction. Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol. Illumina Hiseq 2500 was used for high-throughput sequencing of the ChIP-seq library.

value: H3K9ac (Millipore 07-352)


title: acc1-5 H3K18ac rep2

source_name: acc1-5 H3K18ac rep2


title: VA-ES-BJ_empty_H3K27me3

description: VA-ES-BJ empty anti-H3K27me3 ChIP-seq


title: MEF+Ascl1_22d_B2_rep2

source_name: MEF+Ascl1 22d, Tau::EGFP+

value: E13.5 fibroblast

value: 22 days


title: WT H3K9ac rep2

source_name: WT H3K9ac rep2

value: WT


title: VA-ES-BJ_empty_H3K27ac

description: VA-ES-BJ empty anti-H3K27ac ChIP-seq


title: MEF+Ascl1_22d_B2_rep1


title: VA-ES-BJ_empty_BAF155

description: VA-ES-BJ empty anti-BAF155 ChIP-seq


title: WT H3K27me3

source_name: WT H3K27me3

value: H3K27me3 (Millipore 07-449)


title: acc1-5 H3K27me3

source_name: acc1-5 H3K27me3


title: WT H3K27ac rep2

source_name: WT H3K27ac rep2

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
10 ng of ChIP DNA immunoprecipitated by anti-H3K27ac antibody was used for ChIP-seq library construction. Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol. Illumina Hiseq 2500 was used for high-throughput sequencing of the ChIP-seq library.

value: H3K27ac (Millipore 07-360)


title: MEF+Ascl1_22d_B1_rep1


title: VA-ES-BJ_empty_BRG1

description: VA-ES-BJ empty anti-BRG1 ChIP-seq


title: MEF+Ascl1_13d_B2_rep1

source_name: MEF+Ascl1 13d, Tau::EGFP+

value: 13 days


title: MEF+Ascl1_13d_B2_rep2


title: acc1-5 H3K27ac rep2

source_name: acc1-5 H3K27ac rep2


title: HS-ES-2M_BAF47_Input

description: HS-ES-2M BAF47 Input ChIP-seq

source_name: HS-ES-2M (EpS)


title: MEF+Ascl1_13d_B1_rep2


title: MEF+Ascl1_13d_B1_rep1


title: acc1-5 acla-1i-1induced H3K27ac rep1

source_name: acc1-5 acla-1i-1induced H3K27ac rep1

value: acc1-5 acla-1i-1


title: KD_3

description:
Infected with Tet-On-neo-anti-BORIS-shRNA lentivirus (KD).
Processed data file: difference.txt

data_processing:
The image file obtained by sequencing was converted into raw FASTQ file. After interpretation of quality coding marks, clean FASTQ files were generated.
Alignment using TopHat2 with the parameters: --segment-length 20 -G GRCh38
Cufflinks 2.0.0, parameter settings: -g GRCh38
Cuffmerge, parameters: -p 8 -o -g GRCh38 -s
Cuffdiff, parameters: -p 8 -L -b -M, loci over 500k filtered out.
Genome_build: hg38
Supplementary_files_format_and_content: difference.txt: Tab-delimited text file; matrix includes fields: gene_id, gene, locus, sample_1, sample_2, status, value_1, value_2, log2(fold_change), test_stat, p_value, q_value, significant.

source_name: bone marrow, chronic myelogenous leukemia (CML)

growth_protocol: K562 cells and stably infected derivatives were grown in IMDM with 10% or 20% Tet-On certified FBS. BORIS knockdown (KD) vectors were constructed to express either of the two shRNA templates, GGAAATACCACGATGCAAATT (Site_1) or GGTGTGAAATGCTCCTCAACA (Site_2) cloned into the pLKO-Tet-On-neo vector. K562 infected with lentivirus stock were selected for 4 weeks or more in media supplemented with 600µg/ml G418, followed by the selection of individual clones.

extract_protocol:
Trizol standard.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For BORIS knockdown and/or empty vector (EV) control, the stably infected cells were induced with 200ng/ml doxycycline for 96 hours.

value: immortalized tumor cells

tag: transgene

value: Tet-On-neo-anti-BORIS-shRNA


title: KD_2


title: MEF+Ascl1_5d_negative_B1_rep2

source_name: MEF+Ascl1 5d, Tau::EGFP-

value: 5 days


title: KD_1


title: MEF+Ascl1_5d_B2_rep2

source_name: MEF+Ascl1 5d, Tau::EGFP+


title: KD_0


title: HS-ES-2M_empty_Input

description: HS-ES-2M empty Input ChIP-seq

value: epithelioid sarcoma


title: HS-ES-2M_BAF47_H3K27ac

description: HS-ES-2M BAF47 anti-H3K27ac ChIP-seq


title: HS-ES-2M_BAF47_H3K27me3

description: HS-ES-2M BAF47 anti-H3K27me3 ChIP-seq


title: HS-ES-2M_BAF47_SUZ12

description: HS-ES-2M BAF47 anti-SUZ12 ChIP-seq


title: HS-ES-2M_BAF47_BRG1

description: HS-ES-2M BAF47 anti-BRG1 ChIP-seq


title: acc1-5 H4K16ac rep2

source_name: acc1-5 H4K16ac rep2


title: HS-ES-2M_BAF47_BAF155

description: HS-ES-2M BAF47 anti-BAF155 ChIP-seq


title: MEF+Ascl1_5d_B1_rep1


title: MEF+Ascl1_5d_B2_rep1


title: EV_1

description:
Infected with pLKO-Tet-On-neo lentivirus (EV).
Processed data file: difference.txt

value: pLKO-Tet-On-neo


title: EV_0


title: MEF+Ascl1_48hr_B2_rep2

description:
merged_macspeaks_all_wo.new.rtta_RPKM.quantile.filtered.stepminer.annotated.txt
merged_macspeaks_early_wo.new.rtta_RPKM.quantile.filtered.stepminer.reordered.annotated.txt

source_name: MEF+Ascl1 48hr

value: 48 hours


title: MEF+Ascl1_48hr_B2_rep1


title: acc1-5 acla-1i-1 mock H3K27ac rep1

source_name: acc1-5 acla-1i-1mock H3K27ac rep1

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
10 ng of ChIP DNA immunoprecipitated by anti-H3k27ac antibody was used for ChIP-seq library construction. Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol. Illumina Hiseq 2500 was used for high-throughput sequencing of the ChIP-seq library.

value: acc1-5 acla-1i

value: seedlings

value: 12 days after germination


title: HS-ES-2M_empty_H3K27ac

description: HS-ES-2M empty anti-H3K27ac ChIP-seq

extract_protocol:
Chromatin immunoprecipitation (ChIP) experiments were performed per standard protocols (Millipore, Billerica, MA) with minor modifications. Briefly, 10M cells were crosslinked with 1% formaldehyde for 10 min at 37 °C. This reaction was subsequently quenched with 0.125M glycine.
All library prep and sequencing were 75bp single end on Illuminia Nextseq 500


title: HS-ES-2M_empty_BAF155

description: HS-ES-2M empty anti-BAF155 ChIP-seq


title: [delta]cre-1[delta]clr-3 10h Starvation Biological Replicate 3

source_name: Neurospora crassa mycelia

extract_protocol:
Mycelia were filtered using Whatman paper #1 and flash frozen using liquid nitrogen. RNA was isolated by bead beating in Trizol reagent and then cleaned up using the Qiagen RNeasy kit.
RNA were prepared for sequencing using standard Illumina protocols

tag: media

value: Vogel's minimal media lacking a carbon source


title: MEF+Ascl1_48hr_B1_rep2

value: E13.5 fibroblast


title: MEF+Ascl1_5d_negative_B1_rep1


title: MEF+Ascl1_36hr_B2_rep2

source_name: MEF+Ascl1 36hr

value: 36 hours


title: [delta]cre-1[delta]clr-3 10h Starvation Biological Replicate 2


title: TTC1240_BAF47_SUZ12

description: TTC1240 BAF47 anti-SUZ12 ChIP-seq

source_name: TTC1240 (MRT)

value: Malignant rhabdoid tumor


title: TTC1240_BAF47_Input

description: TTC1240 BAF47 Input ChIP-seq


title: MEF+Ascl1_48hr_B1_rep1


title: [delta]cre-1[delta]clr-3 10h Starvation Biological Replicate 1


title: MEF+Ascl1_36hr_B2_rep1


title: [delta]os-2[delta]clr-3 10h Starvation Biological Replicate 3


title: EV_2


title: TTC1240_BAF47_H3K27me3

description: TTC1240 BAF47 anti-H3K27me3 ChIP-seq


title: MEF+Ascl1_36hr_B1_rep2


title: [delta]os-2[delta]clr-3 10h Starvation Biological Replicate 1


title: TTC1240_BAF47_H3K27ac

description: TTC1240 BAF47 anti-H3K27ac ChIP-seq


title: [delta]os-2[delta]clr-3 10h Starvation Biological Replicate 2


title: MEF+Ascl1_36hr_B1_rep1


title: HS-ES-2M_empty_SUZ12

description: HS-ES-2M empty anti-SUZ12 ChIP-seq


title: HS-ES-2M_empty_H3K27me3

description: HS-ES-2M empty anti-H3K27me3 ChIP-seq


title: MEF+Ascl1_24hr_B2_rep2

source_name: MEF+Ascl1 24hr

value: 24 hours


title: TTC1240_BAF47_BAF155

description: TTC1240 BAF47 anti-BAF155 ChIP-seq


title: [delta]os-1[delta]clr-3 10h Starvation Biological Replicate 3


title: MEF+Ascl1_24hr_B2_rep1


title: TTC1240_empty_Input

description: TTC1240 empty Input ChIP-seq


title: TTC1240_BAF47_BRG1

description: TTC1240 BAF47 anti-BRG1 ChIP-seq


title: TTC1240_empty_SUZ12

description: TTC1240 empty anti-SUZ12 ChIP-seq


title: [delta]os-1[delta]clr-3 10h Starvation Biological Replicate 2


title: MEF+Ascl1_24hr_B1_rep2


title: HS-ES-2M_empty_BRG1

description: HS-ES-2M empty anti-BRG1 ChIP-seq


title: [delta]os-1[delta]clr-3 10h Starvation Biological Replicate 1


title: [delta]cre-1 10h Starvation Biological Replicate 3


title: MEF+Ascl1_24hr_B1_rep1


title: [delta]cre-1 10h Starvation Biological Replicate 2


title: TTC1240_empty_H3K27me3

description: TTC1240 empty anti-H3K27me3 ChIP-seq


title: MEF+Ascl1_12hr_B2_rep2

source_name: MEF+Ascl1 12hr

value: 12 hours


title: TTC1240_empty_H3K27ac

description: TTC1240 empty anti-H3K27ac ChIP-seq


title: MEF+Ascl1_12hr_B2_rep1


title: [delta]cre-1 10h Starvation Biological Replicate 1


title: [delta]os-2 10h Starvation Biological Replicate 3


title: TTC1240_empty_BAF155

description: TTC1240 empty anti-BAF155 ChIP-seq


title: MEF+Ascl1_12hr_B1_rep2


title: MEF+Ascl1_12hr_B1_rep1


title: G401_BAF47_Input

description: G401 BAF47 Input ChIP-seq


title: [delta]os-2 10h Starvation Biological Replicate 1


title: [delta]os-2 10h Starvation Biological Replicate 2


title: G401_BAF47_SUZ12

description: G401 BAF47 anti-SUZ12 ChIP-seq


title: TTC1240_empty_BRG1

description: TTC1240 empty anti-BRG1 ChIP-seq


title: MEF+rtTA_B1_rep1

source_name: MEF+rtTA 48hr


title: G401_BAF47_H3K27me3

description: G401 BAF47 anti-H3K27me3 ChIP-seq


title: [delta]os-1 10h Starvation Biological Replicate 3


title: MEF+rtTA_B1_rep2


title: [delta]os-1 10h Starvation Biological Replicate 2


title: MEF

source_name: MEF 48hr


title: myoblast_dicr_2

source_name: skeletal muscle from dICR/dICR

extract_protocol:
RNA was isolated from primary myoblast and 24-hour-differentiated myotube cells using Tripure (Roche) followed by the RNeasy Micro kit (Qiagen). Samples with RNA Integrity numbers >9 were used for sequencing. Ribosomal RNA was depleted from 1-5 μg total RNA using the RiboZero Gold kit (Illumina).
Library preparation for the Illumina HiSeq 2000 was performed using the TruSeq RNA Sample Prep V2 kit (Illumina). Pooled barcoded libraries were sequenced to generate paired-end 101 bp reads. For the ABI SOLiD sequencing, libraries were prepared using the SOLiD Whole Transcriptome Analysis kit (Thermo Fisher Scientific). Pooled barcoded libraries were sequenced to generate paired-end 35 x 75 bp reads.

value: mixed

value: primary myoblast

value: dICR/dICR


title: G401_BAF47_BAF155

description: G401 BAF47 anti-BAF155 ChIP-seq


title: G401_BAF47_H3K27ac

description: G401 BAF47 anti-H3K27ac ChIP-seq


title: [delta]os-1 10h Starvation Biological Replicate 1


title: myoblast_dicr_1


title: G401_BAF47_BRG1

description: G401 BAF47 anti-BRG1 ChIP-seq


title: [delta]clr-3 10h Starvation Biological Replicate 2


title: [delta]clr-3 10h Starvation Biological Replicate 3


title: myotube_wt_3

source_name: skeletal muscle from wild type

value: 24-hour differentiated myotube

value: wild type


title: G401_empty_Input

description: G401 empty Input ChIP-seq


title: Wild type 10h Starvation Biological Replicate 3

value: FGSC 2489


title: [delta]clr-3 10h Starvation Biological Replicate 1


title: myotube_wt_1


title: G401_empty_H3K27me3

description: G401 empty anti-H3K27me3 ChIP-seq


title: G401_empty_SUZ12

description: G401 empty anti-SUZ12 ChIP-seq


title: myoblast_wt_2


title: myoblast_wt_1


title: Wild type 10h Starvation Biological Replicate 2


title: Wild type 10h Starvation Biological Replicate 1


title: IMR90_DEX_60min_2

status: Public on Sep 24 2017

city: Rehovot

first: Yehoshua

last: Enuka

address: Herzl 234

department: Biological Regulation

country: Israel

institute: Weizmann Institute of Science

data_processing:
sixty base-pair long, single-end, RNA-Seq reads were aligned to the human genome with STAR (Dobin et al., 2013).
Reads per gene were counted using the summarizeOverlaps function from the GenomicAlignments package in R with the Refseq transcriptome as reference. Reads per gene were normalized across samples using the DESeq2 package.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized (according to library size) reads for all Refseq genes

growth_protocol: MCF7 and IMR90 cells were grown in DME medium supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
RNA was extracted using the 5-prime kit and poly-A selected on magnetic beads using the TruSeq RNA Library Preparation Kit v2
Library were constructed using the TruSeq RNA Library Preparation Kit v2

treatment_protocol: Cells were starved overnight in medium without serum and then stimulated with EGF or DEX for 60 minutes before sequencing

tag: treatment

value: DEX

tag: duration


title: IMR90_DEX_60min_1


title: G401_empty_BAF155

description: G401 empty anti-BAF155 ChIP-seq

tag: cell line


title: IMR90_EGF_60min_2

value: EGF


title: IMR90_starve_2

value: untreated


title: MCF7_DEX_60min_2


title: MCF7_DEX_60min_1


title: H3K27Ac_ed240

data_processing:
Chromatin immunoprecipitation (ChIP) sequencing reads were mapped to the hg19 genome assembly using Bowtie2 (Langmead and Salzberg, 2012)
Genome_build: hg19
Supplementary_files_format_and_content: Tag read densities were generated by the makeTagDirectory from the Homer suite

growth_protocol: MCF10A cells were cultured as described (Tarcic et al., 2012) in DME:F12 medium (Gibco BRL, Grand Island, NY) supplemented with 10 µg ml-1 insulin, 0.1 µg ml-1 cholera toxin, 0.5 µg ml-1 hydrocortison, 5% heat-inactivated horse serum (Biological Industries, Beit-Haemek, Israel) and 10 ng ml-1 EGF.

extract_protocol:
Cell fixation and chromatin immunoprecipitation were performed as described (Blecher-Gonen et al., 2013)
Library construction and sequencing were performed as described (Blecher-Gonen et al., 2013)

treatment_protocol: Cells were starved overnight in medium without additives and then stimulated with EGF (e), DEX (d) or the combination (ed) for the indicated time intervals (minutes) before sequencing

value: Histone 3 K27 Acetylation - (ab4729, abcam)

value: EGF + DEX

tag: treatemtn time

value: 240 min


title: H3K27Ac_ed120

value: 120 min


title: H3K27Ac_ed60

value: 60 min


title: H3K27Ac_e120


title: H3K27Ac_ed40

value: 40 min


title: H3K27Ac_ed20

value: 20 min


title: MCF7_starve_1


title: MCF7_starve_2


title: G401_empty_H3K27ac

description: G401 empty anti-H3K27ac ChIP-seq

value: Malignant rhabdoid tumor


title: MCF7_EGF_60min_2


title: H3K27Ac_e240


title: myotube_wt_2

tag: strain/background

value: mixed

tag: cell type


title: IMR90_EGF_60min_1


title: IMR90_starve_1


title: H3K27Ac_untreated_2

value: 1 hour


title: H3K27Ac_d20

value: dexamethasone (DEX)


title: H3K27Ac_d240


title: H3K27Ac_e20


title: H3K27Ac_d40


title: H3K27Ac_e40


title: H3K27Ac_d60


title: H3K27Ac_d120


title: DKO_EGF_60min_2

growth_protocol: HCT116 cells were cultured in McCoy’s 5a Medium supplemented with 10% fetal bovine serum

treatment_protocol: Cells were starved overnight in medium without serum and then stimulated with EGF for 60 minutes before sequencing

tag: genotype

value: DNMT1a and DNMT3b double-knockout

tag: treatment duration


title: DKO_starve_1


title: DKO_starve_2


title: WT_starve_2

value: WT


title: WT_EGF_60min_1


title: MCF7_EGF_60min_1


title: H3K27Ac_e60


title: WT_starve_1


title: DKO_EGF_60min_1


title: H3K27Ac_untreated_1


title: RHB044

first: Gokce

last: OGUZ

address: 60 Biopolis St, GENOME, #02-01

department: Bioinformatics Consulting and Training Platform

institute: Genome Institute of Singapore

data_processing:
Illumina 100 bp paired-end sequenced reads were aligned to reference human genome 19 using Bowtie 2 and TopHat 2.
All further analysis were performed using R Statistical Programming. summarizeOverlap function from Genomic Alignments package is used to count aligned reads in gene with the default from mode of “Union”.
DESeqDataSetFromMatrix  and Deseq function from DESeq2 package is used to obtain the count matrix input. Further on  AnnotationDbi package is used to annotate the genes.
The differential gene expression analysis was conducted using DESeq2 package. To visualize the data read counts are normalized by rlog function.
Genome_build: hg19
Supplementary_files_format_and_content: [Rawcount_12patientER.txt] tab-delimited text file containing raw count RNA-Seq data where each row represents a gene and each column represents a sample.
Supplementary_files_format_and_content: [RLDNormalizedCount_12patientER.txt] tab-delimited text file containing normalized count RNA-Seq data

source_name: Patient 5 - Sphere

growth_protocol: Surgical samples were collected from consenting breast cancer patients at Tan Tock Seng Hospital (Singapore) according to human subject research protocols approved by the Ethics Committee. Samples were washed with cold PBS with antibiotics three times, chopped with a sterile blade, and incubated by using MACS Tissue Dissociation Kits (Miltenyi Biotec) according to protocol. The resulting cell suspension were passed through 70 μm (BD Falcon, San Jose, CA, USA) and centrifuged at 800 rpm for 5 min at 4°C. Cells were seeded in Single-cell suspensions (10,000 cells/well) were plated in 6-well ultra-low attachment plates (Corning) in DMEM/F12 medium containing 1X B27 (Invitrogen, cat. 12587-010), 50 ng/ml EGF, and 20 ng/ml βFGF for up to 1 months.

extract_protocol:
Snap frozen human breast cancer tissues were disrupted using TissueLyser II (Qiagen). Total RNA including small RNAs from both human breast cancer tissue as well as the cell lines were isolated using miRNeasy Mini Kit (Qiagen, cat. 217004) according manual.
RNA-seq libraries were generated by using the cDNA amplification kit SMARTer® Ultra™ Low RNA Kit (Cat. No. 634935,  Clontech Laboratories, Inc. Mountain View, USA) for small amount of RNA or less than 200 cells according to manufacturer's manual followed by DNA library construction using the NEBNext® DNA Library Prep Master Mix Set for Illumina® kit (Cat. No. E6040S, New England Biolabs). In brief, c.a. 50 ng of total RNAs or 200 tumor cells were first lysed in reverse transcription buffer and the reaction is initiated with oligodT containing primer. Complete first strand synthesis is followed by template switching and the incorporation of SMARTer oligonucleotide. Full-length cDNAs are amplified using PCR to obtain DNA. Fragmentation and adapter introduction was performed using acoustic shearing to approximately 200 to 500 bp length and NEBNext® DNA Library Prep kit incorporating multiplex index primers. A pooled multiplexed library consisting equal amount of 6 individual libraries were sequenced on The HiSeq 2500 System by core facility.

tag: individual

value: Patient 5

tag: sample type

value: Sphere

tag: disease state

value: breast cancer

tag: er status

value: ER Positive


title: RHB344

source_name: Patient 8 - Sphere

value: Patient 8


title: WT_EGF_60min_2

value: EGF


title: RHB348

source_name: Patient 11 - Sphere

value: Patient 11


title: RHB347

source_name: Patient 10 - Sphere

value: Patient 10


title: RHB047

source_name: Patient 7 - Sphere

value: Patient 7


title: RHB032

source_name: Patient 2 - Sphere

value: Patient 2


title: RHB031

source_name: Patient 1 - Sphere

value: Patient 1


title: RHB035

source_name: Patient 3 - Sphere

value: Patient 3


title: RHB349

source_name: Patient 12 - Sphere

value: Patient 12


title: RHB046

source_name: Patient 6 - Sphere

value: Patient 6


title: RHB355

source_name: Patient 12 - Primary Tumor

value: Primary Tumor


title: RHB353

source_name: Patient 10 - Primary Tumor


title: RHB350

source_name: Patient 8 - Primary Tumor


title: RHB043

source_name: Patient 4 - Sphere

value: Patient 4


title: RHB050

source_name: Patient 5 - Primary Tumor


title: RHB041

source_name: Patient 3 - Primary Tumor


title: RHB351

source_name: Patient 9 - Primary Tumor

value: Patient 9


title: RHB037

source_name: Patient 1 - Primary Tumor


title: RHB345

source_name: Patient 9 - Sphere


title: RHB052

source_name: Patient 6 - Primary Tumor


title: RHB038

source_name: Patient 2 - Primary Tumor


title: RHB053

source_name: Patient 7 - Primary Tumor


title: CA1_veh_mm_rna_sr_5

city: Goettingen

first: Eva

last: Benito Garagorri

state: Niedersachsen

address: Von Siebold Strasse 3A

department: Epigenetics of Aging

country: Germany

institute: DZNE Goettingen

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were aligend to mm10 using STAR with following parameters: outStd SAM; outFilterMismatchNmax 2; outSAMstrandField intronMotif; sjdbOverhang 49
Gene counts were generated using htseq in the "intersection non-empty" mode
Data were analyzed using the tophat-cufflinks-cuffdiff standard pipeline with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: txt file containing gene counts or fpkm values

source_name: CA1 hippocampal region

extract_protocol:
CA1 was microdissected under a microscope and snap-frozen in liquid nitrogen. RNA was extracted with Tri reagent (Sigma) and treated with DNAse I (Life Technologies) according to manufacturer's instructions.
Libraries were constructe from 500ng of RNA according to standard Illumina protocols.

tag: strain

value: 3 months

tag: tissue

value: CA1 hippocampal subregion

tag: drug treatment

value: vehicle (10% DMSO),i.p. 13 days


title: CA1_veh_mm_rna_sr_7

tag: age


title: CA1_veh_mm_rna_sr_6


title: CA1_veh_mm_rna_sr_8


title: RHB049

source_name: Patient 4 - Primary Tumor

value: breast cancer

value: ER Positive


title: RHB354

source_name: Patient 11 - Primary Tumor


title: CA1_veh_mm_rna_sr_4


title: CA1_veh_mm_rna_sr_2


title: CA1_veh_mm_rna_sr_1


title: CA1_jq1_mm_rna_sr_8

value: JQ1 50mg/kg i.p., 13 days


title: CA1_jq1_mm_rna_sr_3


title: CA1_jq1_mm_rna_sr_7


title: CA1_jq1_mm_rna_sr_5


title: Pol2_ed20_2

tag: chip antibody

value: Rpb1 NTD - 14958S cell signaling


title: Pol2_ed60_2


title: CA1_jq1_mm_rna_sr_4


title: Pol2_e60_1


title: Pol2_ed60_1


title: Pol2_e60_2


title: CA1_jq1_mm_rna_sr_2


title: CA1_jq1_mm_rna_sr_6


title: Pol2_e20_1


title: WT_veh_mm_rna_sr_5

value: APP/PS1-21 in a C57B/6 background

value: 8-10 months

value: vehicle (10% DMSO) i.p., 10 days


title: Pol2_d60_2


title: Pol2_e20_2


title: CA1_jq1_mm_rna_sr_1


title: Pol2_d60_1


title: WT_veh_mm_rna_sr_4


title: WT_veh_mm_rna_sr_2


title: Pol2_untreated_2


title: WT_veh_mm_rna_sr_3


title: APP_veh_mm_rna_sr_6


title: Pol2_d20_2


title: CA1_veh_mm_rna_sr_3


title: WT_veh_mm_rna_sr_1


title: Pol2_ed20_1


title: Pol2_d20_1


title: Pol2_untreated_1


title: APP_veh_mm_rna_sr_3


title: APP_veh_mm_rna_sr_5


title: Mouse calvaria Runx2+/- -MS275 3

city: Seoul

first: Han-sol

last: Bae

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Molecular Genetics

country: South Korea

institute: School of Dentistry, Seoul National University

description: Sample 12 (4-3)

data_processing:
Trimmomatic was used (Bolger et al. 2014) with following option : PE -phred33 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 MINLEN:75 2 for generating clean reads.
We mapped such clean reads into genome reference (GRCh38.p7) from Ensembl database using Bowtie2, implemented inTophat2.
For making the SAM file from the BAM file, we used SAMtools.
Gene expression was quantified by using HTseq package (Anders 2010) with gene annotation file of GRCH38.p7 genome.
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: *count.txt: Tab-delimited text files include raw read counts for each sample.

source_name: E17.5 calvaria, Runx2+/-, MS275

growth_protocol: None, surgical biopsy.

extract_protocol:
E17.5 mice calvariae were removed and flash frozen in liquid nitrogen. RNA was harvested using Trizol reagent.
Libraries were prepared based on Illumina instruction (TruSeq Stranded Total RNA Sample Preparation Kit).

treatment_protocol: WT and Runx2+/- mice were mated at 8 weeks of age. Pregnant mice were given twice intraperitoneal injections of MS-275 (10 mg/kg) at 14.5 and 16.5 d.p.c.

tag: genotype/variation

tag: developmental stage

value: Embryonic day 17.5

value: Calvaria

tag: treatment


title: Mouse calvaria Runx2+/- -MS275 1

description: Sample 10 (4-1)


title: Mouse calvaria WT-MS275 3

description: Sample 9 (3-3)

source_name: E17.5 calvaria, WT, MS-275

value: Wildtype


title: Mouse calvaria Runx2+/- -MS275 2

description: Sample 11 (4-2)


title: APP_jq1_mm_rna_sr_6

value: JQ1 50mg/kg i.p., 10 days


title: Mouse calvaria WT-MS275 2

description: Sample 8 (3-2)


title: APP_jq1_mm_rna_sr_5


title: APP_veh_mm_rna_sr_1


title: APP_veh_mm_rna_sr_2


title: APP_veh_mm_rna_sr_4


title: Mouse calvaria Runx2+/- -vehicle 3

description: Sample 6 (2-3)

source_name: E17.5 calvaria, Runx2+/-, vehicle

value: vehicle


title: Mouse calvaria WT-MS275 1

description: Sample 7 (3-1)


title: APP_jq1_mm_rna_sr_4


title: Mouse calvaria Runx2+/- -vehicle 2

description: Sample 5 (2-2)


title: APP_jq1_mm_rna_sr_3


title: Mouse calvaria WT-vehicle 3

description: Sample 3 (1-3)

source_name: E17.5 calvaria, WT, vehicle


title: APP_jq1_mm_rna_sr_1


title: Mouse calvaria WT-vehicle 2

description: Sample 2 (1-2)


title: Acupuncture group Pituitary gland

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

description:
A_C
expressed_gene_RPKM.txt
expressed_gene_reads.txt

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (GATCGGAAGAGC) trimmed with fastx_clipper
Clean reads assembly by trinity with default parameters
mapped using bowtie -k 2 -v 2
detecting different expression gene using edgeR
Genome_build: Rnor_5.0 (Ensembl release 79)
Supplementary_files_format_and_content: tab-delimited text files include gene RPKM values & gene reads static for each Sample

organism: Rattus norvegicus

source_name: Acupuncture group Pituitary gland

extract_protocol:
Hippocampal, frontal cortex and pituitary gland were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA 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

treatment_protocol: The rat model of depression was established by subjecting to chronic restraint stress (6h/day) for 28 days. Rats in acupuncture group were acupunctured at GV20 (Baihui) and GV29 (Yintang) one hour before the CRS procedures every day, for 28 days. Rats in fluoxetine group were administered with fluoxetine (10mg/kg) by gavage one hour before the CRS procedures every day, for 28 days.

value: Sprague-Dawley

value: Brain

tag: tissue region

value: Pituitary gland

tag: gender

value: Male

value: 6 weeks

tag: group

value: Acupuncture


title: Acupuncture group Frontal cortex

description:
A_E
expressed_gene_RPKM.txt
expressed_gene_reads.txt

source_name: Acupuncture group Frontal cortex

value: Frontal cortex


title: Mouse calvaria WT-vehicle 1

description: Sample 1 (1-1)

tag: strain/background


title: Fluoxetine group Pituitary gland

description:
F_C
expressed_gene_RPKM.txt
expressed_gene_reads.txt

source_name: Fluoxetine group Pituitary gland

value: Fluoxetine


title: Acupuncture group Hippocampus

description:
A_H
expressed_gene_RPKM.txt
expressed_gene_reads.txt

source_name: Acupuncture group Hippocampus

value: Hippocampus


title: Model group Pituitary gland

description:
M_C
expressed_gene_RPKM.txt
expressed_gene_reads.txt

source_name: Model group Pituitary gland

value: model of depression


title: Fluoxetine group Hippocampus

description:
F_H
expressed_gene_RPKM.txt
expressed_gene_reads.txt

source_name: Fluoxetine group Hippocampus


title: Model group Hippocampus

description:
M_H
expressed_gene_RPKM.txt
expressed_gene_reads.txt

source_name: Model group Hippocampus


title: Model group Frontal cortex

description:
M_E
expressed_gene_RPKM.txt
expressed_gene_reads.txt

source_name: Model group Frontal cortex


title: Control group Frontal cortex

description:
Z_E
expressed_gene_RPKM.txt
expressed_gene_reads.txt

source_name: Control group Frontal cortex

value: Control


title: Fluoxetine group Frontal cortex

description:
F_E
expressed_gene_RPKM.txt
expressed_gene_reads.txt

source_name: Fluoxetine group Frontal cortex


title: Control group Hippocampus

description:
Z_H
expressed_gene_RPKM.txt
expressed_gene_reads.txt

source_name: Control group Hippocampus


title: 34367 mESC 24h s4U Rep 3

status: Public on Sep 23 2017

city: Vienna

first: Brian

last: Reichholf

address: Doktor-Bohr-Gasse 3

country: Austria

institute: IMBA

description:
processed data file:
mESC_UTR_regions.bed
mESC_counting_windows.bed

data_processing:
Basecalls performed using RTA V.1.18.64.0
Demultiplexed reads were adapter-trimmed using Cutadapt; 12nt were trimmed from the 5' end and poly(A) stretches (>4 subsequent As at the 3´ end) were removed.
Trimmed reads were aligned using SLAMdunk v0.2.4: Reads were aligned to the full reference genome (mm10) using local alignment scoring and up to 100 alignments were reported for multimapping reads (-n 100). In the filtering step, alignments with a minimum identity of 95% and a minimum of 50% of the read bases mapped were retained. Among multimappers, reads mapping to no or ambiguously to > 1 annotated UTR sequence were discarded (-fb). If a multimapping read mapped >1 time to the same annotated UTR sequence (mESC_UTR_regions.bed), one alignment was randomly picked. SNPs exceeding a coverage cutoff of 10x and a variant fraction cutoff of 0.8 were called using VarScan2.4.1 using default parameters. Non-SNP overlapping T>C mutations with a base quality of Phred score >26 were identified. T>C containing reads and total reads aligning within the custom defined counting windows (mESC_counting_windows.bed) were reported. T>C conversion rate was determined for each position along the custom defined counting windows by normalizing to genomic T content and coverage of each position and averaged per UTR.
Generation of mESC_counting_windows.bed and mESC_UTR_regions.bed is described in detail in submitted manuscript (Herzog, VA, et al., submitted manuscript)
Genome_build: mm10
Supplementary_files_format_and_content: mESC_UTR_regions.bed: UTR regions defined as a basis to reconciliate UTR multimappers during mapping/filtering step; mESC_counting_windows.bed: Counting windows defined as a basis to count 3' end isoform specific expression and T>C conversions. *.tsv files: Count file output from SLAMdunk containing the chromosomal coordinates, Gene Name and Strand of the counting windows, T>C conversion rate, Expression (ReadsCPM), T content of the counting window, Coverage on Ts within counting window, T>C Conversion Rate on Ts, Read Count, T>C Read Count and Multimap Counts

source_name: AN3-12 wt_mESC 24h s4U

growth_protocol: Mouse embryonic stem (mES) cells (clone AN3-12) were cultured in 15 % FBS (Gibco), 1x Penicillin-Streptomycin solution (100 U/ml Penicillin, 0.1 mg/ml Streptomycin, Sigma), 2 mM L-Glutamine (Sigma), 1x MEM Non-essential amino acid solution (Sigma), 1 mM sodium pyruvate (Sigma), 50 µM 2-Mercaptoethanol (Gibco) and 20 ng/ml LIF (in-house produced). Cells were maintained at 37°C with 5% CO2 and passaged every second day.

extract_protocol:
total RNA extraction and IAA-derivatization
3' end sequencing (QuantSeq, Lexogen)

treatment_protocol: Mouse embryonic stem cells were incubated with 100 µM s4U for 24h; followed by a wash out with incubation with standard medium supplemented with 10 mM uridine for the times indicated before they were directly lysed in Trizol® (Ambion).

tag: cell line/clone

tag: cell type

value: Mouse embryonic stem (mES) cells

value: 24h s4U treatment


title: 34506 mESC 24h s4U Rep 1


title: 31703 mESC -IAA no s4U Rep 3

data_processing:
Basecalls performed using RTA V.1.18.64.0
Demultiplexed reads were adapter-trimmed using Cutadapt; 12nt were trimmed from the 5' end and poly(A) stretches (>4 subsequent As at the 3´ end) were removed.
Trimmed reads were aligned using SLAMdunk v0.2.4. Briefly, reads were aligned to the full reference genome (mm10) using local alignment scoring and up to 100 alignments were reported for multimapping reads (-n 100). In the filtering step, alignments with a minimum identity of 95% and a minimum of 50% of the read bases mapped were retained. Among multimappers, reads mapping to no or ambiguously to > 1 annotated UTR sequence were discarded (-fb). If a multimapping read mapped >1 time to the same annotated UTR sequence, one alignment was randomly picked.
Genome_build: mm10
Supplementary_files_format_and_content: *.tsv files: Count file output from SLAMdunk containing the chromosomal coordinates, Gene Name and Strand of the counting windows, T>C conversion rate, Expression (ReadsCPM), T content of the counting window, Coverage on Ts within counting window, T>C Conversion Rate on Ts, Read Count, T>C Read Count and Multimap Counts

source_name: AN3-12 wt_mESC -IAA no s4U

extract_protocol:
Total RNA was extracted and RNA was treated with (+IAA) or without (-IAA) iodoacetamide to alkylate thiol-containing nucleotides.
3' end sequencing (QuantSeq, Lexogen)

treatment_protocol: Mouse embryonic stem cells were directly lysed in Trizol® (Ambion)

value: no IAA treatment


title: Mouse calvaria Runx2+/- -vehicle 1

description: Sample 4 (2-1)

value: Embryonic day 17.5

value: Calvaria


title: 31697 mESC -IAA no s4U Rep 1


title: 43654 small RNA cloning Xpo5 KO #2

description:
processed data file:
Mmu_miRNA.txt
Ath_miRNA.txt

data_processing:
Basecalls performed using RTA V.1.18.64.0
Small RNA libraries were mapped to the genome (A.thaliana or M.musculus) and reads aligning to miRBase annotations were extracted as described before using Tailor algorithm (Reimão-Pinto, M. M. et al. Uridylation of RNA Hairpins by Tailor Confines the Emergence of MicroRNAs in Drosophila. Mol Cell 59, 203–216 (2015).).
Genome_build: mm10
Supplementary_files_format_and_content: *.txt files contain the expression (ppm) for each miRNA annotation and each sample.

source_name: small RNA cloning Xpo5 KO

extract_protocol:
total RNA extraction
Small RNA libraries were generated as described before (Reimão-Pinto, M. M. et al. Uridylation of RNA Hairpins by Tailor Confines the Emergence of MicroRNAs in Drosophila. Mol Cell 59, 203–216 (2015).), but adding total RNA from Arabidopsis thaliana unopened floral buds as spike-in before initial size-selection.

treatment_protocol: Mouse embryonic stem cells (wildtype or Xpo5 knockout) were directly lysed in Trizol® (Ambion).

value: mouse embryonic stem cells AN3-12

value: AN3-12 Xpo5-/- clone #2


title: 31700 mESC -IAA no s4U Rep 2


title: 31677 mESC +IAA no s4U Rep 2

source_name: AN3-12 wt_mESC +IAA no s4U

value: IAA treatment


title: APP_jq1_mm_rna_sr_2

source_name: CA1 hippocampal region

value: APP/PS1-21 in a C57B/6 background

value: 8-10 months

value: CA1 hippocampal subregion

value: JQ1 50mg/kg i.p., 10 days


title: 43653 small RNA cloning Xpo5 KO #1

value: AN3-12 Xpo5-/- clone #1


title: 43655 small RNA cloning Xpo5 KO #3

value: AN3-12 Xpo5-/- clone #3


title: 43652 small RNA cloning ctr2

source_name: small RNA cloning ctr

value: AN3-12 wt, transfected with non-targeting gRNA (ctr) #2


title: 43651 small RNA cloning ctr1

value: AN3-12 wt, transfected with non-targeting gRNA (ctr) #1


title: 26757 mESC 10h ActD Rep 3

source_name: AN3-12 wt_mESC 10h ActD

extract_protocol:
total RNA extraction
3' end sequencing (QuantSeq, Lexogen)

treatment_protocol: 5 µg/ml Actinomycin D (Sigma) was added to the medium and mES cells were harvested at 0, 0.25h, 0.5h, 1h, 3h and 10 h after addition of actinomycin D by directly lysing the cells in TRIzol® (Ambion).

value: 10h ActD treatment


title: Control group Pituitary gland

description:
Z_C
expressed_gene_RPKM.txt
expressed_gene_reads.txt

source_name: Control group Pituitary gland

value: Sprague-Dawley

value: Brain

value: Pituitary gland

value: Male

value: 6 weeks

value: Control


title: 43650 small RNA cloning wt

source_name: small RNA cloning wt

value: mouse embryonic stem cells AN3-12

value: AN3-12 wt


title: 26755 mESC 10h ActD Rep 1

value: Mouse embryonic stem (mES) cells


title: 26753 mESC 3h ActD Rep 2

source_name: AN3-12 wt_mESC 3h ActD

value: 3h ActD treatment


title: 26754 mESC 3h ActD Rep 3


title: 26756 mESC 10h ActD Rep 2


title: 34354 mESC 24h s4U Rep 2

value: 24h s4U treatment


title: 26747 mESC 0.5h ActD Rep 2

source_name: AN3-12 wt_mESC 0.5h ActD

value: 0.5h ActD treatment


title: 26750 mESC 1h ActD Rep 2

source_name: AN3-12 wt_mESC 1h ActD

value: 1h ActD treatment


title: 26752 mESC 3h ActD Rep 1


title: 26751 mESC 1h ActD Rep 3


title: 31687 mESC +IAA no s4U Rep 3

value: IAA treatment


title: 26748 mESC 0.5h ActD Rep 3


title: 26746 mESC 0.5h ActD Rep 1


title: 26745 mESC 0.25h ActD Rep 3

source_name: AN3-12 wt_mESC 0.25h ActD

value: 0.25h ActD treatment


title: 31667 mESC +IAA no s4U Rep 1


title: 26743 mESC 0.25h ActD Rep 1


title: 26744 mESC 0.25h ActD Rep 2


title: 26741 mESC no ActD Rep 2

source_name: AN3-12 wt_mESC no ActD

value: no ActD treatment


title: 26742 mESC no ActD Rep 3


title: 37065 mESC Mettl3KO #3 12h pulse

source_name: AN3-12_mESC Mettl3KO 12h pulse

growth_protocol: Mouse embryonic stem (mES) cells (wildtype or Mettl3 knock-out) were cultured in 15 % FBS (Gibco), 1x Penicillin-Streptomycin solution (100 U/ml Penicillin, 0.1 mg/ml Streptomycin, Sigma), 2 mM L-Glutamine (Sigma), 1x MEM Non-essential amino acid solution (Sigma), 1 mM sodium pyruvate (Sigma), 50 µM 2-Mercaptoethanol (Gibco) and 20 ng/ml LIF (in-house produced). Cells were maintained at 37°C with 5% CO2 and passaged every second day.

treatment_protocol: Mouse embryonic stem cells (wildtype or Mettl3 knock-out) were incubated with standard medium with or without 100 µM s4U for 0, 3h or 12h before they were directly lysed in Trizol® (Ambion)

value: AN3-12 Mettl3-/- clone #3

value: 12h s4U treatment


title: 26740 mESC no ActD Rep 1


title: 37063 mESC Mettl3KO #1 12h pulse

value: AN3-12 Mettl3-/- clone #1


title: 37062 mESC Mettl3KO #3 3h pulse

source_name: AN3-12_mESC Mettl3KO 3h pulse

value: 3h s4U treatment


title: 37064 mESC Mettl3KO #2 12h pulse

value: AN3-12 Mettl3-/- clone #2


title: 37061 mESC Mettl3KO #2 3h pulse


title: 26749 mESC 1h ActD Rep 1


title: 37057 mESC Mettl3KO #1 no s4U

source_name: AN3-12_mESC Mettl3KO no s4U

value: no s4U treatment


title: 37056 mESC ctr2 12h pulse

source_name: AN3-12_mESC ctr 12h pulse

value: AN3-12 wt, transfected with non-targeting gRNA (ctr) #2


title: 37058 mESC Mettl3KO #2 no s4U


title: 37054 mESC wt 12h pulse

source_name: AN3-12_mESC wt 12h pulse


title: 37053 mESC ctr2 3h pulse

source_name: AN3-12_mESC ctr 3h pulse


title: 37051 mESC wt 3h pulse

source_name: AN3-12_mESC wt 3h pulse


title: 37052 mESC ctr1 3h pulse

value: AN3-12 wt, transfected with non-targeting gRNA (ctr) #1


title: 37055 mESC ctr1 12h pulse


title: 37049 mESC ctr1 no s4U

source_name: AN3-12_mESC ctr no s4U


title: 37050 mESC ctr2 no s4U


title: 37048 mESC wt no s4U

source_name: AN3-12_mESC wt no s4U

value: AN3-12 wt


title: 35425 mESC Xpo5KO #1 3h pulse

source_name: AN3-12_mESC Xpo5KO #1 3h pulse

growth_protocol: Mouse embryonic stem (mES) cells (wildtype or Xpo5 knock-out) were cultured in 15 % FBS (Gibco), 1x Penicillin-Streptomycin solution (100 U/ml Penicillin, 0.1 mg/ml Streptomycin, Sigma), 2 mM L-Glutamine (Sigma), 1x MEM Non-essential amino acid solution (Sigma), 1 mM sodium pyruvate (Sigma), 50 µM 2-Mercaptoethanol (Gibco) and 20 ng/ml LIF (in-house produced). Cells were maintained at 37°C with 5% CO2 and passaged every second day.

treatment_protocol: Mouse embryonic stem cells (wildtype or Xpo5 knock-out) were incubated with standard medium with or without 100 µM s4U for 0, 3h or 12h before they were directly lysed in Trizol® (Ambion)

value: Mouse embryonic stem (mES) cells

value: AN3-12 Xpo5-/- clone #1


title: 35426 mESC Xpo5KO #2 3h pulse

source_name: AN3-12_mESC Xpo5KO #2 3h pulse

value: AN3-12 Xpo5-/- clone #2


title: 35429 mESC Xpo5KO #2 12h pulse

source_name: AN3-12_mESC Xpo5KO #2 12h pulse


title: 35430 mESC Xpo5KO #3 12h pulse

source_name: AN3-12_mESC Xpo5KO #3 12h pulse

value: AN3-12 Xpo5-/- clone #3


title: 35428 mESC Xpo5KO #1 12h pulse

source_name: AN3-12_mESC Xpo5KO #1 12h pulse


title: 35423 mESC Xpo5KO #2 no s4U

source_name: AN3-12_mESC Xpo5KO #2 no s4U


title: 35424 mESC Xpo5KO #3 no s4U

source_name: AN3-12_mESC Xpo5KO #3 no s4U


title: 35421 mESC ctr2 12h pulse

source_name: AN3-12_mESC ctr2 12h pulse


title: 35419 mESC wt 12h pulse


title: 35416 mESC wt 3h pulse


title: 35418 mESC ctr2 3h pulse

source_name: AN3-12_mESC ctr2 3h pulse


title: 35422 mESC Xpo5KO #1 no s4U

source_name: AN3-12_mESC Xpo5KO #1 no s4U


title: 37060 mESC Mettl3KO #1 3h pulse

source_name: AN3-12_mESC Mettl3KO 3h pulse


title: 35420 mESC ctr1 12h pulse

source_name: AN3-12_mESC ctr1 12h pulse


title: 35417 mESC ctr1 3h pulse

source_name: AN3-12_mESC ctr1 3h pulse


title: 35415 mESC ctr2 no s4U

source_name: AN3-12_mESC ctr2 no s4U


title: 37059 mESC Mettl3KO #3 no s4U

source_name: AN3-12_mESC Mettl3KO no s4U


title: 47759 mESC no s4U Rep 3

data_processing:
Basecalls performed using "Real Time Analysis RTA" V.1.18.64.0
Demultiplexed reads were adapter-trimmed using Cutadapt; 12nt were trimmed from the 5' end and poly(A) stretches (>4 subsequent As at the 3´ end) were removed.
Trimmed reads were aligned using SLAMdunk. Briefly, reads were aligned to the full reference genome (mm10) using local alignment scoring and up to 100 alignments were reported for multimapping reads (-n 100). In the filtering step, alignments with a minimum identity of 95% and a minimum of 50% of the read bases mapped were retained. Among multimappers, reads mapping to no or ambiguously to > 1 annotated UTR sequence were discarded (-fb). If a multimapping read mapped >1 time to the same annotated UTR sequence, one alignment was randomly picked.
Genome_build: mm10
Supplementary_files_format_and_content: *.tsv files: Count file output from SLAMdunk containing the chromosomal coordinates, Gene Name and Strand of the counting windows, T>C conversion rate, Expression (ReadsCPM), T content of the counting window, Coverage on Ts within counting window, T>C Conversion Rate on Ts, Read Count, T>C Read Count and Multimap Counts

source_name: AN3-12 wt_mESC no s4U

treatment_protocol: Mouse embryonic stem cells were incubated with standard medium with or without 100 µM s4U for 45min before they were directly lysed in Trizol® (Ambion)


title: 47761 mESC 45min pulse Rep 2

source_name: AN3-12 wt_mESC 45min pulse

value: 45min s4U treatment


title: 47760 mESC 45min pulse Rep 1


title: 35414 mESC ctr1 no s4U

source_name: AN3-12_mESC ctr1 no s4U


title: 47762 mESC 45min pulse Rep 3


title: 35427 mESC Xpo5KO #3 3h pulse

source_name: AN3-12_mESC Xpo5KO #3 3h pulse


title: 47757 mESC no s4U Rep 1


title: 25206 mESC Capseq Rep 2

data_processing:
Basecalls performed using RTA 1.17.21.3 (RNA-Seq) or 1.18.64.0 (Cap-Seq)
For standard RNA sequencing data analysis, adapters were clipped from demultiplexed reads using cutadapt v1.5 and reads were size-filter for >= 15 nucleotides. Reads were aligned to mouse genome mm10 using STAR aligner v2.5.2b. Alignments were filtered for alignment scores >= 0.3 and alignment identity >= 0.3 was normalized to read length. Only alignments with >=30 matches were reported and chimeric alignments with an overlap >= 15 bp were allowed. 2-pass mapping was used. Introns < 200 kb were filtered and alignments containing non-canonical junctions were filtered. Alignment with a mismatch to mapped bases ratio >= 0.1 or with a max. number of 10 mismatches were excluded. The max number of gaps allowed for junctions by 1,2,3,N reads was set to 10 kb, 20kb, 30kb and 50 kb, respectively. The minimum overhang length for splice junctions on both sides for (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif was set to 20, 12, 12, 12, respectively. “Spurious” junction filtering was used and the maximum number of multiple alignments allowed for a read was set to 1. Exonic reads (Gencode) were quantified using FeatureCounts.
For Cap analysis gene expression (Cap-Seq), the first 4nt of the demultiplexed reads were trimmed using seqtk. Reads were screened for ribosomal RNA by aligning with BWA (v0.6.1) against known rRNA sequences (RefSeq). The rRNA subtracted reads were aligned with TopHat (v1.4.1) against the Mus musculus genome (mm10). Maximum multihits was set to 1, segment-length to 18 and segment-mismatch to 1. Additionally, a gene model was provided as GTF (Gencode VM4).
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq_tpm.txt contains expression values (tpm) for each replicated determined by RNAseq

source_name: AN3-12 wt_mESC Capseq

extract_protocol:
RNA was extracted using Trizol® (Ambion)  according to manufacturer's instructions
Standard RNA seq libraries were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB) following the instructions of the manufacturer. Cap-seq libraries were prepared as previously described in Mohn, F., Sienski, G., Handler, D. & Brennecke, J. The rhino-deadlock-cutoff complex licenses noncanonical transcription of dual-strand piRNA clusters in Drosophila. Cell 157, 1364–1379 (2014).


title: 35413 mESC wt no s4U

source_name: AN3-12_mESC wt no s4U


title: 25207 mESC Capseq Rep 3


title: 25205 mESC Capseq Rep 1


title: 47758 mESC no s4U Rep 2


title: 18195 mESC RNAseq Rep 3

description:
processed data file:
RNAseq_tpm.txt

source_name: AN3-12 wt_mESC RNAseq


title: 18194 mESC RNAseq Rep 2

description:
processed data file:
RNAseq_tpm.txt


title: 18193 mESC RNAseq Rep 1

description:
processed data file:
RNAseq_tpm.txt


title: 34525 mESC 12h chase Rep 1

source_name: AN3-12 wt_mESC 12h chase

value: 24h s4U treatment; 12h uridine chase


title: 34526 mESC 12h chase Rep 2


title: 34524 mESC 6h chase Rep 3

source_name: AN3-12 wt_mESC 6h chase

value: 24h s4U treatment; 6h uridine chase


title: 34528 mESC 24h chase Rep 1

source_name: AN3-12 wt_mESC 24h chase

value: 24h s4U treatment; 24h uridine chase


title: 34527 mESC 12h chase Rep 3


title: 34529 mESC 24h chase Rep 2


title: 34530 mESC 24h chase Rep 3


title: 34520 mESC 3h chase Rep 2

source_name: AN3-12 wt_mESC 3h chase

value: 24h s4U treatment; 3h uridine chase


title: 34522 mESC 6h chase Rep 1


title: 34519 mESC 3h chase Rep 1


title: 34523 mESC 6h chase Rep 2


title: 34518 mESC 1h chase Rep 3

source_name: AN3-12 wt_mESC 1h chase

value: 24h s4U treatment; 1h uridine chase


title: 34517 mESC 1h chase Rep 2


title: 34516 mESC 1h chase Rep 1


title: 34521 mESC 3h chase Rep 3


title: 34515 mESC 0.5h chase Rep 3

source_name: AN3-12 wt_mESC 0.5h chase

value: 24h s4U treatment; 0.5h uridine chase


title: 34513 mESC 0.5h chase Rep 1


title: 34514 mESC 0.5h chase Rep 2


title: 34507 mESC 0h chase Rep 1

source_name: AN3-12 wt_mESC 0h chase

value: 24h s4U treatment; 0h uridine chase


title: 34343 mESC no s4U Rep 2


title: 34356 mESC no s4U Rep 3


title: 34509 mESC 0h chase Rep 3


title: 34508 mESC 0h chase Rep 2


title: 34330 mESC no s4U Rep 1


title: RFP_2

city: New York

first: Qi

last: Sun

address: 550 1st Avenue, Smilow 410

department: Dermatology

institute: New York University

data_processing:
Illumna standard procedure for base-calling
Using Bowtie aligner for reads alignment
using Samtools for duplicate reads removal
reads counts with htseq-count protocol
reads normalization and comparison was done with edgeR
Genome_build: Mus_musculus.NCBIM37.67
Supplementary_files_format_and_content: Comparison of gene expression profile between normal mouse melanocyte stem cells and melanoma tumor derived from them

source_name: melanoma tumor derived from melanocyte stem cells after transplantation

extract_protocol:
For samples 1-3, mouse back skin was incubated on 0.25% Trypsin for 2 hours at RT and then separated epidermis from dermis. The epidermis was finely chopped and transferred to DMEM with 10% FBS and stirred for 20min to get single cells. For samples 4-5, melanoma tumor was harvested and finely chopped and incubated in DMEm with 10%FBS and 0.35%  Collagenase I for 35min to get single cells. Then, total RNA were isolated from all samples using RNeasy Plus Micro-Kit (Qiagen) as described by manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mixed

value: Melanoma tumor in skin

value: 47 day after transplantation

tag: genotype

value: Tyr-CreER; Braf V600E; Pten fl/fl; R26R-stop-Tomato


title: RFP_1


title: Ctrl_T7d.3

source_name: melanocyte stem cells isolated from mouse skin epidermis

value: Skin

value: 7-8 week old


title: Ctrl_T7d.1


title: R6/2_HD_Tibialis_Male_Vehicle rep4

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

data_processing:
Illumina CASAVA 1.8.2 software used for basecalling
Genome mapped via Omicsoft OSA 4.0
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using fastq-mcf sequence quality filter, clipping and processor with following settings for Omicsoft: Trimming  /Mode=TrimByQuality /ReadTrimQuality=2;  Options  /ParallelJobNumber=4 /PairedEnd=True /FileFormat=FASTQ /AutoPenalty=True /FixedPenalty=2 /Greedy=false /IndelPenalty=2 /DetectIndels=False /MaxMiddleInsertionSize=10 /MaxMiddleDeletionSize=10 /MaxEndInsertionSize=10 /MaxEndDeletionSize=10 /MinDistalEndSize=3 /ExcludeNonUniqueMapping=False /ReportCutoff=10 /WriteReadsInSeparateFiles=True /GenerateSamFiles=False /ThreadNumber=6 /InsertSizeStandardDeviation=40 /ExpectedInsertSize=300 /MatePair=False /InsertOnSameStrand=False /InsertOnDifferentStrand=True /QualityEncoding=Automatic /CompressionMethod=Gzip /Gzip=True /SearchNovelExonJunction=False /ExcludeUnmappedInBam=False /KeepFullRead=False /Replace=False /Platform=ILLUMINA /CompressBam=False;
Genome_build: Genome version Mouse.B37, gene models version Ensembl.R67
Supplementary_files_format_and_content: Excel files include FPKM and Count values for each Sample

source_name: Tibialis, Vehicle

extract_protocol:
Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the Qiagen miRNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer. A minimum of 3.75 ug of total RNA were used to collect enriched RNA subfractions for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: background

value: Tibialis

tag: Sex

value: Male

value: Vehicle

tag: treatment dose

tag: treatment administration route

value: Oral

tag: treatment frequency

value: Twice-Daily (b.i.d)


title: WT_Cortex_Female_Vehicle rep4

source_name: Cortex, Vehicle

value: Wild Type

tag: tissue

value: Cortex

value: Female


title: 14_2W6

city: Calgary

first: Benedikt

last: Hallgrimsson

state: AB

address: 3330 Hospital Dr NW

department: Cell Bio and Anatomy

country: Canada

institute: University of Calgary

data_processing:
bcl2fastq v2.17.1.14 with default parameters
Analysis was performed using Deseq2. Reads were mapped to the genome using summaize overlaps within Deseq2 on the mm8 genome.
Genome_build: mm8
Supplementary_files_format_and_content: tab delimited expression values text table for each sample

source_name: E10.5 Craniofacial

growth_protocol: Fgf8neo/wt x Fgf8neo/wt and Fgf8neo/wt x Fgf8wt/- mice were crossed and checked for post-coital plugs. Embryos were dissected at E10.5 and the craniofacial region from the 2nd branchial arch anterior.

extract_protocol:
Extraction was done using Trizol, Agilent TapeStation and RIN scores of 9-10 were obtained
Stranded mRNA libraries for sequencing were prepared from ~ 1ug of total RNA using the TruSeq Stranded mRNA library prep kit and Illumina protocol. The indexed libraries were quantitated for pooling by qPCR using a Kapa Library Quantification Kit and the pooled libraries were sequenced on two successive 75 bp high-output sequencing runs on an Illumina NextSeq 500 sequencer. An average of 46 million reads per sample were obtained.

treatment_protocol: Samples were immediately snap frozen on dry ice.

value: neo/neo


title: R6/2_HD_Liver_Male_CHDI-00390576_30mg/kg rep4

value: Liver

value: 30 mg/kg


title: 19_N9

value: wt/neo


title: 18_N5


title: 17_N4


title: 16_N10


title: 12_N6


title: 11_N3


title: R6/2_HD_Liver_Male_Vehicle rep4

source_name: Liver, Vehicle


title: Ctrl_T7d.2

tag: strain

value: Mixed

tag: age


title: R6/2_HD_Liver_Female_CHDI-00390576_100mg/kg rep3

value: 100 mg/kg


title: 9_2L6

value: wt/-


title: R6/2_HD_Liver_Male_CHDI-00390576_100mg/kg rep4


title: R6/2_HD_Liver_Female_Vehicle rep4


title: WT_Liver_Female_Vehicle rep4


title: R6/2_HD_Liver_Male_CHDI-00390576_100mg/kg rep3


title: WT_Striatum_Female_Vehicle rep4

source_name: Striatum, Vehicle

value: Striatum


title: 24_N8

value: WT


title: 7_2L2


title: 6_2L1


title: 22_2L7


title: 20_2L4


title: WT_Liver_Male_Vehicle rep3


title: R6/2_HD_Liver_Male_CHDI-00390576_100mg/kg rep2


title: 21_2L5


title: R6/2_HD_Liver_Male_CHDI-00390576_30mg/kg rep3


title: 4_iI7

value: neo/-


title: R6/2_HD_Liver_Female_CHDI-00390576_30mg/kg rep4


title: 13_N7


title: R6/2_HD_Liver_Female_CHDI-00390576_100mg/kg rep4


title: 2_I7


title: 3_iI2


title: WT_Liver_Male_Vehicle rep4

value: Male


title: R6/2_HD_Liver_Female_CHDI-00390576_30mg/kg rep3


title: 10_I6


title: WT_Liver_Female_Vehicle rep3

value: Vehicle


title: 5_2i3


title: R6/2_HD_Liver_Male_CHDI-00390576_100mg/kg rep1

value: Oral


title: R6/2_HD_Liver_Female_Vehicle rep3

value: Twice-Daily (b.i.d)


title: R6/2_HD_Liver_Female_Vehicle rep2


title: R6/2_HD_Liver_Male_Vehicle rep2


title: R6/2_HD_Liver_Male_Vehicle rep3


title: R6/2_HD_Liver_Female_CHDI-00390576_100mg/kg rep2


title: R6/2_HD_Liver_Female_CHDI-00390576_30mg/kg rep2


title: R6/2_HD_Liver_Male_CHDI-00390576_30mg/kg rep2


title: WT_Liver_Male_Vehicle rep2

value: Wild Type


title: R6/2_HD_Liver_Female_CHDI-00390576_30mg/kg rep1


title: WT_Liver_Female_Vehicle rep2


title: WT_Liver_Female_Vehicle rep1


title: R6/2_HD_Liver_Female_Vehicle rep1


title: R6/2_HD_Liver_Female_CHDI-00390576_100mg/kg rep1


title: R6/2_HD_Liver_Male_Vehicle rep1


title: WT_Heart_Male_Vehicle rep4

source_name: Heart, Vehicle

value: Heart


title: WT_Heart_Female_Vehicle rep4

value: Female


title: R6/2_HD_Heart_Female_CHDI-00390576_100mg/kg rep4


title: R6/2_HD_Heart_Male_CHDI-00390576_100mg/kg rep4


title: R6/2_HD_Liver_Male_CHDI-00390576_30mg/kg rep1


title: WT_Heart_Female_Vehicle rep3


title: R6/2_HD_Heart_Female_Vehicle rep4


title: CsDML OX3

city: Pozuelo de Alarcón (Madrid)

first: Daniel

last: Conde

address: Parque Científico y Tecnológico de la U.P.M. Campus de Montegancedo 28223

country: Spain

institute: Centre for Plant Biotechnology and Genomics U.P.M. – I.N.I.A

data_processing:
Pre-processing and assembly of sequence data were conducted using the web-based platform Galaxy at https://usegalaxy.org/which includes tools to remove reads containing N blurs, adapter sequences, and sequences shorter than 15 nucleotides. Quality control of reads was carried out with the FastQC Galaxy tool
Removal of rRNA, if needed, was performed locally with the SortMeRNA tool. The TopHat Galaxy tool was used to map clean reads to the Populus tremula x P. alba INRA clone 717-1B4 genome using the default settings
Differentially expressed gene (DEG) lists for CsDML OX versus WT were obtained using the function exactTest (edgeR package of R)
Genome_build: Populus tremula x P. alba INRA clone 717-1B4 at:
http://aspendb.uga.edu/s717
Please note that the "sPta717_v1.1.gene.gff3" (with coordinates) was used to analyze the data, similar to Populus trichocarpa available at:
https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa
Supplementary_files_format_and_content: xlsx file include log2FC in CsDMLOX respect to wild type

organism: Populus tremula x Populus alba

source_name: CsDML OX_apices

extract_protocol:
Libraries were prepared using 1 µg of RNA in the NEBNext® Ultra™ Directional RNA Library Prep Kit following the supplier's instructions (New England Biolabs, Ipswich, MA, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: clone id

tag: genotype/variation

value: CsDML overexpression

value: apices

tag: time point

value: after 28 days in SD

value: CsDML OX3


title: R6/2_HD_Heart_Male_CHDI-00390576_30mg/kg rep4

tag: treatment

value: 30 mg/kg


title: CsDML OX1

value: CsDML OX1


title: R6/2_HD_Heart_Female_CHDI-00390576_30mg/kg rep4