title: D17-2762

first: Myriam

last: Heiman

state: Massachusetts

address: The Picower Institute of Learning & Memory

institute: MIT

description: BACHD + Foxp2 2

data_processing:
The raw fastq data of 50-bp single-end sequencing reads were aligned to the mouse mm10 reference genome using the STAR 2.4.0 RNA-Seq aligner
The mapped reads were processed by htseq-count of HTSeq software with mm10 gene annotation to count the number of reads mapped to each gene.
Gene differential expression test between different animal groups was performed using DESeq2 package with the assumption of negative binomial distribution for RNA-Seq data
Genes with adjusted p-value <0.05 were chosen as differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: count files, DEG statistics tables

source_name: BACHD + Foxp2

extract_protocol:
Qiagen RNeasy Lipid Tissue Kit
Clontech SMARTer
The quality of prepared bar-coded libraries was assessed using an Advanced Analytical-fragment Analyzer before mixing for sequencing on the Illumina HiSeq 2000 platform at the MIT BioMicro Center.

tag: injected virus

value: Foxp2 OX

tag: age at harvest

value: 13 months

value: BACHD

value: striatum


title: D17-2764

status: Public on Dec 05 2017

type: SRA

city: Cambridge

country: USA

description: BACHD + Foxp2 4

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: genotype

tag: tissue


title: D17-2761

description: BACHD + Foxp2 1


title: D17-2763

description: BACHD + Foxp2 3


title: D17-2759

description: BACHD + Con 3

source_name: BACHD + Con

value: Control


title: D17-2760

description: BACHD + Con 4


title: BM_LCM_03_EM_rep1

city: Stockholm

first: Cheng

last: Zhao

state: Stockholm

address: H9 Klinisk vetenskap,171 77 Stockholm

department: Clinical Science

country: Sweden

institute: Karolinska institute

data_processing:
Illumina Casava1.7 software used for basecalling.
The clean reads (quality checked by FastQC) were aligned to the reference genome twice. At first, clean reads were mapped to B73 reference using Tophat aligner(with 4 mismatch) and the unmapped reads were remapped to SNPs-substituted reference (B73 reference substituted to MO17 reference by replacing SNPs between B73 and MO17) using the Tophat aligner (with 2 mismatches). Reads with no more than five best mapped positions were retained for further analysis. After combining above mapping results, read counts of annotated genes (filtered gene set version 5b.60) were summarized by HTSeq-count. Gene expression [Reads per kilobase of transcript per million fragments mapped] (FPKM) was estimated by Cufflinks (V2.2.1) software.
Genome_build: REL5b.60
Supplementary_files_format_and_content: Tab-delimited text file include Reads and FPKM values for 48 Samples .

organism: Zea mays

source_name: LCM 03DAP Embryo

growth_protocol: The two inbred lines B73 and Mo17 were grown in the China Agriculture university experiment station of Beijing, and they were used as two parental lines for reciprocal crosses. Before pollination, the ear and the tassel of B73 and Mo17 were bagged with kraft paper on the day before pollination. The next day, each paper bag was patted to collect the pollens from one parental, which were used to pollinate the ear of the other parental.

extract_protocol:
As described above, 15 kinds of embryo samples and one endosperm sample were collected for RNA-seq analysis. For each sample, hundreds(9DAP,11DAP,13DAP) or thousands(5DAP,7DAP) individual embryos were put into one tube containing RNA storing liquid buffer (Hueyueyang, China) (three replicates). The embryo and endosperm were collected from at least three ears in each replicate. RNA samples were isolated by Quick RNA isolation Kit (Huayueyang, China) and were checked on 1% agarose gels to avoid possible degradation and contamination. Then examined by a Nano Photometer spectrophotometer (IMPLEN, CA, USA) for RNA purity and sent to the Novogene for mRNA library construction and high-throughput sequencing using the Illumina HiSeq2500 platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: This was followed by two kinds of treatments during the pollination:(1) the B73 inbred lines as the female treatment, before pollination, the ear of B73 and the tassel of Mo17 were bagged with kraft paper on the day before pollination. The next day, each paper bag of Mo17 was patted to collect the pollens to pollinate the ear of B73. (2) the Mo17 inbred lines as the female treatment, before pollination, the ear of Mo17 and the tassel of B73 were bagged with kraft paper on the day before pollination. The next day, each paper bag of B73 was patted to collect the pollens to pollinate the ear of Mo17.

tag: age


title: Seed rep1

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

country: China

institute: Tsinghua University

data_processing:
After removing bacodes, adapters and low-quality reads, clean reads of size 18-28 nt were mapped to the Arabidopsis genome (TAIR10 version) with Bowtie (Langmead et al., Genome Biology, 2009, 10, R25) allowing no mismatches. sRNA abundance was calculated as reads per million (RPM).
Genome_build: TAIR10
Supplementary_files_format_and_content: Genome-matched unique reads

organism: Arabidopsis thaliana

source_name: 24 hours on moist paper

growth_protocol: Plants were grown in a standard chamber under long-day conditions (16 h of light/8 h of darkness, 22°C).

extract_protocol:
Total RNA were extracted by Trizol reagent (Invitrogen) followed by PEG precipitation to enrich low molecular-weight sRNAs. The resulting sRNAs were resolved on a 17% denaturing PAGE gel, and visualized by SYBR-Gold (Invitrogen) staining. Gel slices within the range of 18-28nt were excised, and the RNAs were eluted and purified for small RNA library contruction.
Small RNA libraries were constructed as previously described (Mi et al., Cell, 2008, 133, 116-175).

value: Wild type

tag: ecotype

value: Columbia

value: 24 hours on moist paper


title: MazF_mRNA_5m_rep1

city: Boston

first: Peter

last: Culviner

state: MA

address: 677 Huntington Ave

department: IID

institute: Harvard School of Public Health

description:
RNA with rRNA subtracted
[processed data file: ]
5m_ribozero_counts_cleavage_ratio.csv.gz

data_processing:
Paired-end reads mapped to MG1655 genome using bowtie2 with default settings. Any adapter sequences were removed prior to mapping.
For each uniquely mapped fragment (ribozero treated samples) or all mapped fragments (total RNA samples), at all aligned positions a count was added.
Counts were depth normalized to a pseudo-reference sample calculated from all samples (ribozero treated samples) or using counts per million counts (total RNA samples).
For ribozero treated samples, counts at all positions were log2 transformed and a cleavage ratio was calculated (+ MazF - empty vector) for assessing MazF cleavage in transcripts.
Genome_build: NCBI reference sequence: NC_000913.2
Supplementary_files_format_and_content: 5m_ribozero_counts_cleavage_ratio.csv.gz is a log-transformed list of sequencing depth-normalized counts for every genomic position at both strands for each ribozero treated sample as well as the average cleavage ratio calculated from all samples. total_RNA_rpm.csv.gz is a list of sequencing depth-normalized counts for every genomic position at both strans for all total RNA samples.

organism: Escherichia coli

source_name: Bacterial liquid culture

growth_protocol: Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM. Cultures were centrifuged, washed, and back diluted into media lacking glucose. After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2%. Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge. Pellets were immediately flash frozen in lN2.

extract_protocol:
RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo).
See publication for complete protocol. Briefly, samples with rRNA subtraction with treated with bacterial Ribo-Zero kit (Illumina). Next, RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Libraries were extracted from an acrylamide gel and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols.

tag: strain

value: MG1655 delta_mazF

tag: plasmid

tag: ribozero

value: Yes

tag: ercc spike-in

value: No

tag: time induction

value: 5 minutes


title: emptyvec_totalRNA_5m_rep1

description:
[processed data file: ]
total_RNA_rpm.csv.gz

value: Prior to extraction


title: MazF_mRNA_5m_rep2


title: D17-2758

description: BACHD + Con 2


title: emptyvec_mRNA_5m_rep2


title: D17-2757

description: BACHD + Con 1


title: Root rep1

source_name: Seven-days-old seedlings

value: Seven-days-old


title: SAM rep1


title: Seedling rep1-2


title: Seedling rep1-1


title: D17-2756

description: Con + Foxp2 4

source_name: Con + Foxp2


title: Hi-C_E6.5VE_rep2

city: Beijing

first: Wei

last: Xie

address: Zhongguancun north street

description: Processed data file: Hi-C_processed_data_files.tar.gz.

library_source: genomic

data_processing:
Basecalls were performed using CASAVA version 1.8.
Sequencing reads were mapped, processed and iteratively corrected using HiC-Pro, a pipeline developed by Servant et al. Briefly, the read pairs were mapped to the mm9 reference genome in a two-step approach with Bowtie2. Next, the invalid read pairs including dangling end, self-circle ligation and duplicates were discarded. The genome was divided into bins of specific length to generate the contact maps. For global detection of contacts, a 100Kb bin size was used and a 40Kb bin size was used for examination of local domain level contacts. The raw contact counts were normalized with iterative correction.
Genome build: mm9.
Processed data files format and content: The compartment files contain the values which indicate compartment A (more than 0) or compartment B (less than 0) in 100kb bin in the genome. The matrix txt file includes the interaction frequency between the two bins (represented by the number in the bed file) in first two columns. These files are available in a tar archive on the series record.

molecule: genomic DNA

source_name: Embryo

extract_protocol: After trypsin and pancreatic enzyme digestion followed by mechanical dissection to separate epiblast and visceral endoderm, embryonic cells were washed with PBS and incubated in lysis buffer. Hi-C libraries were prepared using a protocol described in Du et al., Nature, 2017, 547(7662):232.

treatment_protocol: C57BL/6N female mice were induced for superovulation by injections of 5 IU of pregnant mare’s serum gonadotrophin and 5 IU of human chorionic gonadotrophin (44-48 hours apart) and mated to DBA/2N males.

value: C57BL/6N x PWK/PhJ

tag: developmental stage

value: Visceral endoderm


title: MazF_totalRNA_30m_rep2

value: 30 minutes


title: D17-2755

description: Con + Foxp2 3

value: Foxp2 OX


title: emptyvec_totalRNA_30m_rep2


title: emptyvec_mRNA_5m_rep1


title: Hi-C_E6.5VE_rep1


title: D17-2754

description: Con + Foxp2 2

value: 13 months


title: D17-2753

description: Con + Foxp2 1


title: Hi-C E7.5Ect_rep1

description: HI-C processed data file: Hi-C_processed_data_files.tar.gz

value: C57BL/6N x DBA

value: Ectoderm


title: D17-2768

description: Con + Con 4

source_name: Con + Con

value: Control

value: striatum


title: Hi-C E3.5ICM_rep1

description:
HI-C
processed data file: Hi-C_processed_data_files.tar.gz.

value: Inner cell mass


title: Hi-C E3.5ICM_rep2


title: Bent torpedo embryo rep1

source_name: Seven-weeks-old seedlings

value: Wild type

value: Columbia

value: Seven-weeks-old


title: Green leaf embryo rep1-1


title: D17-2767

description: Con + Con 3


title: D17-2766

description: Con + Con 2


title: Flower stage 12 rep1-3

source_name: Five-weeks-old seedlings

value: Five-weeks-old


title: D17-2765

description: Con + Con 1


title: Flower carpel 13 rep1


title: total_input_kcl

city: London

first: Luca

last: Crepaldi

address: Gower Street

department: MRC Laboratory for Molecular Cell Biology

country: United Kingdom

institute: University College London

description: cells stimulated with 50 mM KCl, 45 min

data_processing:
Reads were aligned to the mouse genome (GRCm38/mm10) using Bowtie2
Reads were  filtered for alignment quality (MAPQ > 10).
MACS2 was employed to identify regions of ChIPseq enrichment.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files encode the ChIPseq profile obtained by merging sequencing reads from three separate biological replicates. Narrowpeak files encode the regions of enrichment obtained by merging sequencing reads from three separate biological replicates

source_name: Primary cortical neurons, DIV6

growth_protocol: Primary cortical neurons were dissected and cultured as described in Crepaldi et al. (2013). PLoS Genet. 9, e1003699.

extract_protocol:
Crosslinking buffer (0.1 M NaCl, 1 mM EDTA, 0.5 mM EGTA and 25 mM HEPES-KOH, pH 8.0) containing 1% formaldehyde was added to cultured cells for 10 min at room temperature. The cross-linking reaction was stopped by adding glycine to a final concentration of 125 mM. Cells were rinsed three times with ice-cold PBS containing protease inhibitor cocktail and 1mM PMSF), collected by scraping and centrifuged at 3000rpm at 4°C for 5 minutes. Cell pellets were transferred to 1.5 ml tubes and lysed with 20 cell pellet volumes (CPVs) of buffer 1 (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, pH 8.0, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100 and complete protease inhibitor cocktail) for 10 min at 4 °C. Nuclei were pelleted by centrifugation at 3000 rpm for 10 min at 4 °C,  incubated with 20 CPVs of buffer 2 (200 mM NaCl, 1 mM EDTA, pH 8.0, 0.5 mM EGTA, pH 8.0, 10 mM Tris-HCl, pH 8.0, and complete protease inhibitor cocktail) for 10 min at RT and re-pelleted.  4 CPVs of buffer 3 (1 mM EDTA, pH 8.0, 0.5 mM EGTA, pH 8.0, 10 mM Tris-HCl, pH 8.0, and complete protease inhibitor cocktail) were added to the nuclei, and sonication was carried out by applying 30 pulses, 30 seconds each, at 30 seconds intervals. Insoluble materials were removed by centrifugation at 14000 rpm for 10 min at 4 °C, the supernatant was transferred to a new tube and the final volume of the nuclear lysate was adjusted to 1 mL by adding buffer 3 supplemented with 0.3 M NaCl, 1% Triton X-100 and 0.1% deoxycholate. The lysates were pre-cleared with 70μL of Protein A-Sepharose beads (1 hour at 4°C) and subjected to immunoprecipitation. One tenth of the chromatin was saved for input control, while the remaining fraction was incubated with 3-5μg of antibody and rotated overnight at 4°C. Immune complexes were purified by incubating the lysates with 80μl of Protein A-Sepharose beads for 1 hour at 4°C. Beads were pelleted and washed twice with each of the following buffers: low-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, and 150 mM NaCl), high-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris- HCl, pH 8.1, and 500 mM NaCl) and LiCl buffer (0.25 M LiCl, 1% IGEPAL CA630, 1% deoxycholic acid (sodium salt), 1 mM EDTA and 10 mM Tris, pH 8.1). For each wash, the beads were incubated for 10 min at 4 °C while rotating. Beads were rinsed once with 1× TE buffer (10 mM Tris-HCl, pH 8.0, and 1 mM EDTA) and the immunoprecipitated material was eluted by vortexing the beads twice for 15 min at RT in elution buffer (0.1 M NaHCO3 pH 8.0, 1% SDS). Crosslinking was reversed by adding 10μl 5M NaCl and incubating the samples at 65°C over night. DNA was purified using PCR purification columns (Qiagen) according to the manufacturer’s instructions.
Libraries were prepared for sequencing using NEBNext ChIP-Seq Library Prep Master Mix (NEB) or Microplex Library preparation kit (Diagenode)

treatment_protocol: Prior to stimulation, neurons were culture overnight in reduced serum (3%). Cells were either left untrated or stimulated wit 50 mM KCl for 45 min.

tag: cell type

value: primary cortical neurons


title: RNA-seq IVC+4d VE rep1

description:
Processed data file: FPKM_IVC.txt.gz
Processed data file: FPKM_replicates.txt.gz

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

molecule: polyA RNA

source_name: In vitro culture embryo

extract_protocol: After trypsin and pancreatic enzyme digestion followed by mechanical dissection to separate epiblast and visceral endoderm, embryonic cells were washed with PBS and incubated in lysis buffer. RNA-Seq libraries were prepared using Smart-Seq2 protocol with slightly modification.

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

value: C57BL/6N x DBA/2N


title: Flower stage 12 rep1-1


title: RNA-seq IVC+4d VE rep2


title: RNA-seq IVC+4d Epi rep2

value: Epiblast


title: Flower_stage_13 rep1


title: Flower stage 10_11 rep1


title: Flower stage 12 rep1-2


title: Hi-C_E6.5Epi_rep2

source_name: Postimplantation embryo_E6.5 Epiblast

value: C57BL/6N x PWK/PhJ


title: H3K27ac_ctrl

description: unstimulated cells


title: Flower stage 9 rep1


title: RNA-seq IVC+4d Epi rep1


title: MethylC-seq mESC bulk TT2 cell line

description: Processed data file: stage.bed.gz in STEM-seq_methylation_bedgraph_files.tar.gz.

data_processing:
Base calls were performed using CASAVA version 1.8. Early embryo STEM-seq reads were aligned to the mm9 genome using BSseeker2.0.8. Replicates of same stage were pooled together and methylation values in wiggle files were computed for each single base. ES cell STEM-seq and MethylC-seq reads were aligned to the mm9 genome using BSseeker2.0.8. Replicates of same stage were pooled together and methylation values in wiggle files were computed by the number of reads falling into 1,000bp bin in the genome.
 Genome_build: mm9.
Supplementary_files_format_and_content: The bedgraph files counted the number of reads falling on each base or 1,000bp bin in the genome.

source_name: Embryonic stem cell

growth_protocol: mESCs were cultured routinely in LIF and serum medium.

extract_protocol:
Embryonic stem cells were washed with PBS and incubated in lysis buffer.
MethylC-seq libraries were prepared using methylC-seq method.

tag: cell line

value: Embryonic stem cell


title: H3K27ac_kcl

description: cells stimulated with 50 mM KCl, 45 min


title: Green leaf embryo rep1-2


title: Hi-C_E6.5Epi_rep1


title: H3K4me1_ctrl

description: unstimulated cells


title: H3K4me1_kcl

description: cells stimulated with 50 mM KCl, 45 min


title: Green leaf embryo rep1-3


title: STEM-seq mESC (10ng)

extract_protocol: Embryos were washed with PBS and incubated in lysis buffer. STEM-seq libraries were constructed following the protocol described in this study (Zhang et al., Nature Genetics, 2017).


title: Flower carpel 12 rep1


title: Rpc155_kcl

description: cells stimulated with 50 mM KCl, 45 min


title: total_input_ctrl

description: unstimulated cells


title: Flower stamen 12 rep1


title: STEM-seq mESC (100ng)

description: processed data file: stage.bed.gz in STEM-seq_methylation_bedgraph_files.tar.gz.


title: Flower petal 12 rep1


title: Rpc155_ctrl

description: unstimulated cells


title: MethylC-seq mESC bulk R1 cell line


title: Gtf3c1_ctrl

description: unstimulated cells


title: STEM-seq IVC+4d Epi rep2


title: STEM-seq IVC+4d VE rep1

value: Visceral endoderm


title: Hypocotyl rep1

value: Seven-days-old


title: Stem first node rep1

source_name: Four-weeks-old seedlings

value: Four-weeks-old


title: Inflorescence rep1


title: Flower sepal 12 rep1


title: Cauline leaf rep1


title: STEM-seq IVC+4d VE rep2


title: Gtf3c1_kcl

description: cells stimulated with 50 mM KCl, 45 min


title: STEM-seq IVC+4d Epi rep1


title: cKO-MLIC rep1

city: Washington

first: Yang

last: Liu

state: DC

address: 111 Michigan Ave NW

department: Center for Cancer and Immunology Research

institute: Childrens' National Medical Center

data_processing:
Basecalls performed using CASAVA version 1.8.2
Clean reads were respectively aligned to the reference genome and transcriptome (mm10) using Tophat2.  No more than 5 mismatches were allowed in the alignment for each read.
Reads that could be uniquely mapped to a gene were used to calculate the expression level. The gene expression level was measured by RPKM and was calculated by DEGseq.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: CD11b(+)Gr-1(-) BM cells

growth_protocol: Primary bone marrow cells were isolated from mice.

extract_protocol:
Total RNA was isolated using TRIzol Reagent (Life Technologies) according to manufacturer’s instructions.
The cDNA libraries were constructed following the standard Illumina protocols by TruSeq RNA and DNA sample preparation kits (Illumina).

treatment_protocol: No treatment for isolated bone marrow cells.

tag: strain background

tag: genotype/variation

value: Raptor F/F, Mx1-Cre (cKO)

value: Bone marrow

tag: surface markers

value: Sorted CD11b(+)Gr-1(-) BM


title: cKO-MLIC rep2


title: Ctrl-WBM rep2

source_name: Whole Bone Marrow cells

value: Raptor F/F (Ctrl)

value: No sorting, whole BM


title: Ctrl-WBM rep1


title: cKO-MLIC rep3


title: STEM-seq E7.5End rep1

description:
Processed data file: stage.mCG.gz in STEM-seq-methylC_mCG.tar.gz.
The format for mCG files is as below:
chr position methylated_crick, un-methylated_crick, methylated_watson, un-methylated watson.

source_name: postimplantation embryo_E7.5 Endoderm

value: Endoderm


title: STEM-seq E7.5End rep2


title: Ctrl-WBM rep3


title: Cotyledon rep1

value: Wild type

value: Columbia


title: Adult leaf 2 rep1


title: Adult leaf 1 rep1


title: STEM-seq E7.5Mes rep2

source_name: postimplantation embryo_E7.5 Mesoderm

value: Mesoderm


title: STEM-seq E7.5PS rep2

source_name: postimplantation embryo_E7.5 Primitive streak

value: Primitive streak


title: STEM-seq E7.5PS rep1

extract_protocol:
Embryos were washed with PBS and incubated in lysis buffer.
STEM-seq libraries were prepared using TELP developed by PengXu et al. with slight modification.

value: C57BL/6N x DBA/2N


title: Silique 7d rep1

source_name: Six-weeks-old seedlings

value: Six-weeks-old


title: STEM-seq E7.5Mes rep1


title: STEM-seq E7.5Ect rep2

source_name: postimplantation embryo_E7.5 Ectoderm

value: Ectoderm


title: Silique 5d rep1


title: Silique 3d rep1


title: Silique 2d rep1


title: STEM-seq E6.5VE rep1

source_name: Postimplantation embryo_E6.5 Visceral endoderm


title: nos-1(gv5) nos-2(RNAi) ATAC-seq

city: Baltimore

first: Geraldine

last: Seydoux

state: MD

address: 725 N. wolfe St. PCTB 706

department: MBG

institute: Johns Hopkins University

description: Transpoase-treated genomic DNA

data_processing:
Base calling and demultiplexing was performed at UC reverside IIGB Genomics Core facility with CASAVA 1.8.
Raw reads of two biological samples were first merged using “cat” command in Unix environment followed by bowtie2 (v2.1.0, using default parameter setting) alignment using C. elegans ce10 as the reference genome.
The callpeak function in MACS2 package is used to identify locus with nos-1/2 –dependent features (peaks). Uasage of MACS2: macs2 callpeak -t  < nos-1/2 aligned reads.sam>  -c < wild type aligned reads.sam> --nomodel --extsize 200 -f SAM -g ce -n -B -q 0.05.
PAVIS (https://manticore.niehs.nih.gov/pavis2/) uses the output file NAME_summits.bed from MACS2 for peak annotation. Identification of genes with nos-1/2-dependent peaks at their upstream was extracted and gene IDs were cross-referenced with RNA-seq analysis
Genome_build: ce10
Supplementary_files_format_and_content: nanos-dependent ATACseq peak.xls. is a tabular file which contains information about called peaks. MACS package stores the fragment pileup in nanos-dependent_ATACseq_peak_treat_pileup.bdg

organism: Caenorhabditis elegans

source_name: Sorted L1 PGCs

growth_protocol: Embryos were collected from adult worms and cultured for overnight in M9 solution. Synchronized L1 were collected and used for PGC isolation.

extract_protocol:
Worm were dissociated with pronase solution. Cell suspensions were subjected to FACS to isolated PGL-1::GFP marked primordial germ cells (PGCs)
Library construction was performed as described in Buenrostro et al. 2015. In brief, 30,000 sorted PGCs were used for ATAC-seq library construction. The transposition reaction was performed with a 50l reaction mixture (25l TD, 2.5l TDE, 22.5 l nuclease-free H2O. Illumina, Nextera DNA library preparation Kit FC-121-1030) at 37C for 30 min. Transposed DNA was purified using Qiagen MinElute kit and saved in -20C. qPCR was used to determine appropriate PCR cycle number for PCR amplification as detailed in Buenrostro et al. 6-7 cycles of PCR amplification were used. Final cDNA libraries (150bp to 700bp) were selected using Agencourt AMPure beads (Beckman-Coulter A63880).

treatment_protocol: All worms were grown on HT115 bacteria containing either empty vector(L4440) or nos-2(RNAi) plasmid.

value: Starved L1


title: nos-1(gv5) nos-2(RNAi) ATAC-seq (Replicate)

description: Transpoase-treated genomic DNA


title: Wild-type ATAC-seq (Replicate)

description: Transpoase-treated genomic DNA


title: STEM-seq E7.5Ect rep1


title: STEM-seq E6.5Epi rep1

value: Epiblast


title: STEM-seq E6.5Epi rep2


title: STEM-seq E5.5VE rep2

source_name: Postimplantation embryo_E5.5 Visceral endoderm

value: Visceral endoderm


title: Wild-type ATAC-seq

description: Transpoase-treated genomic DNA


title: STEM-seq E5.5Epi rep1

source_name: Postimplantation embryo_E5.5 Epiblast

treatment_protocol: EC57BL/6N female mice were induced for superovulation by injections of 5 IU of pregnant mare’s serum gonadotrophin and 5 IU of human chorionic gonadotrophin (44-48 hours apart) and mated to DBA/2N males.


title: STEM-seq E4.0ICM rep2

source_name: Periimplantation embryo_E4.0 Inner cell mass

value: Inner cell mass


title: STEM-seq E5.5VE rep1


title: Juvenile leaf rep1

value: Four-weeks-old


title: STEM-seq E4.0ICM rep1


title: STEM-seq E3.5TE rep2

value: Trophectoderm


title: STEM-seq E3.5TE rep1


title: STEM-seq E3.5ICM

source_name: Preimplantation embryo_E3.5 Inner cell mass


title: RNA-Seq End rep2

description:
Processed data file: FPKM_stage.txt.gz
Processed data file: FPKM_replicates.txt.gz

extract_protocol: Total RNAs of E5.5 to E7.5 embryos were extracted by RNeasy Plus Micro Kit according to the manufacturer’s protocol. RNA-Seq libraries were prepared using Smart-Seq2 protocol with slight modification.

treatment_protocol: Embryos were collected from C57BL/6N female mice mated naturally to DBA/2N males. The day when vaginal plug was observed was considered to be E0.5.


title: RNA-Seq Mes rep1


title: RNA-Seq End rep1


title: RNA-Seq PS rep2


title: STEM-seq E6.5VE rep2


title: RNA-Seq Ect rep1


title: RNA-Seq Ect rep2


title: RNA-Seq E6.5VE rep2

source_name: postimplantation embryo_E6.5 Visceral endoderm


title: RNA-Seq E6.5Epi rep2

source_name: postimplantation embryo_E6.5 Epiblast


title: RNA-Seq E6.5Epi rep1

description:
processed data file: FPKM_stage.txt.gz
Processed data file: FPKM_replicates.txt.gz

data_processing:
Basecalls performed using CASAVA version 1.8
Early embryo BS-TELP reads were aligned to the mm9 genome using BSseeker2.0.8, replicates of same stage were pooled together and methylation value in wiggle files were counted by single base; ES cells BS-TELP and MethylC-seq reads were aligned to the mm9 genome using BSseeker2.0.8, replicates of same stage were pooled together and methylation value in wiggle files were counted by the number of reads falling into 1000bp bin in the genome
RNA-Seq reads were aligned to the mm9 genome assembly using tophat2 version 2.0.11, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2
Genome_build: mm9
Supplementary_files_format_and_content: The bedgraph files counted by the number of reads falling into base resolution and 1000bp bin in the genome.  Bedgraph files are available in a tar archive on the series record. A tab-delimited text file includes RPKM values for each sample

extract_protocol:
Total RNAs of E5.5 to E7.5 embryos were extracted by RNeasy Plus Micro Kit according to the manufacturer’s protocol.
RNA-Seq libraries were prepared using Smart-Seq2 protocol with slight modification.

treatment_protocol: Embryos were collected from C57BL/6N female mice mated naturally to DBA/2N males. The day when vaginal plug was observed was considered to be E0.10.


title: STEM-seq E5.5Epi rep2


title: RNA-Seq E5.5Epi rep1

source_name: postimplantation embryo_E5.5 Epiblast


title: RNA-Seq E5.5VE rep1

source_name: postimplantation embryo_E5.5 Visceral endoderm


title: RNA-Seq E5.5Epi rep2


title: RNA-Seq E4.0ICM rep2

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

treatment_protocol: Embryos were collected from C57BL/6N mice induced for superovulation by injections of 5 IU of pregnant mare’s serum gonadotrophin and 5 IU of human chorionic gonadotrophin (44-48 hours apart) and mated to DBA/2N males.


title: RNA-Seq E5.5VE rep2


title: RNA-Seq E3.5TE rep2

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


title: RNA-Seq E4.0ICM rep1

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


title: RNA-Seq E3.5ICM rep2


title: RNA-Seq E3.5TE rep1


title: RNA-Seq PS rep1


title: RNA-Seq Mes rep2


title: RNA-Seq E3.5ICM rep1


title: 7d_Sm_rep1

city: Ames

first: Andrew

middle: J

last: Severin

email: severin@iastate.edu, csiva@iastate.edu

state: IA

address: 2200 Osborn Drive

department: Office of Biotechnology

institute: Iowa State University

description:
7dphSm6-26
PolyA RNA
Processed data file: genes.counts.matrix
Processed data file: isoforms.counts.matrix

data_processing:
de novo transcript assembly using Trinity (version r20140717).
Abundance estimation was done using RSEM and bowtie2 (2.2.0).
Counts table was generated using the estimated abundances.
DESeq2 (1.2.10) was used for differential gene expression analysis.
Trinotate (r20140708) was used to annotate the transcripts.
Genome_build: de novo assembly
Supplementary_files_format_and_content: genes.counts.matrix: Tab-delimited text file includes gene counts for each sample.
Supplementary_files_format_and_content: isoforms.counts.matrix: Tab-delimited text file includes isoform counts for each sample.
Supplementary_files_format_and_content: Trinity.fasta: FASTA of assembled transcripts.
Supplementary_files_format_and_content: Trinotate_report.xls: Excel file includes annotation information for transcripts.

organism: Seriola lalandi dorsalis

source_name: Larvae, 7 dph, small

extract_protocol:
Larvae from the common rearing tanks were transferred in small batches to the wet lab where they could be measured under a microscope camera setup. Depending on developmental stage, one to several larvae were placed on a microscope slide and euthanized with a lethal dose of MS-222. The larvae were quickly photographed, measured, and sorted by size into vials containing RNAlater® (Ambion). The length of time from the point when the larvae were removed from the water to the point of being placed in RNAlater® was under two minutes. The vials of RNAlater® were kept on ice until being placed in -20°C storage at the NMFS laboratory.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Larvae

value: 7 days post hatching

tag: phenotype

value: Small


title: 2d_Sm_rep3

description:
2dphSm8-15
PolyA RNA
Processed data file: genes.counts.matrix
Processed data file: isoforms.counts.matrix

source_name: Larvae, 2 dph, small

value: 2 days post hatching


title: 7d_Lg_rep2

description:
7dphLg7-09
PolyA RNA
Processed data file: genes.counts.matrix
Processed data file: isoforms.counts.matrix

source_name: Larvae, 7 dph, large

value: Large


title: 7d_Lg_rep1

description:
7dphLg6-26
PolyA RNA
Processed data file: genes.counts.matrix
Processed data file: isoforms.counts.matrix


title: 7d_Sm_rep3

description:
7dphSm8-14
PolyA RNA
Processed data file: genes.counts.matrix
Processed data file: isoforms.counts.matrix


title: RNA-Seq E6.5VE rep1


title: E1010

city: Pirassununga

first: Mario

last: Binelli

state: SP

address: Rua Duque de Caxias Norte, 255

department: department of animal reproduction

country: Brazil

institute: University of Sao Paulo (USP)

data_processing:
CASAVA v1.8.2
The 100bp paired end (PE) reads were filtered using a perl script which removed all reads with a mean quality under 26. The reads were mapped with Bowtie2 v2.1.0 on the masked bovine genome assembly (Bos taurus UMD 3.1, NCBI).
The mapping file was sorted using SAMTools v 0.1.18 and read counts were obtained using the script from HTSeq-count v0.5.4p2 (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html).
The differential expression analysis was performed with package DESEq v1.12.1, from R. Using the function estimateSizeFactors, the normalized counts were obtained (baseMean values, which are the number of reads divided by the size factor or normalization constant). The standard deviation along the baseMean values was also calculated for each transcript.
In order to avoid artifacts caused by low expression profiles and high expression variance, only transcripts that had an average of baseMean > 5 and the mean greater than the standard variation were analyzed. The threshold for evaluating significance was obtained by applying a p-value of 0.05 FDR-Benjamini-Hochberg.
Genome_build:  Bos taurus (assembly Bos_taurus_UMD_3.1.1)

organism: Bos indicus

source_name: Endometrium

extract_protocol:
Approximately 30 mg of endometrial tissue were ground in liquid nitrogen using a stainless steel apparatus and immediately mixed with buffer RLT from the RNeasy Mini columns kit (Qiagen, São Paulo, SP, Brazil), as per manufacturer’s instructions. To maximize lysis, tissue suspension was passed at least ten times through a 21 G needle, and centrifuged at 13,000 x g for 3 minutes for removal of debris, prior to supernatant loading and processing in RNeasy columns. Columns were eluted with 40 l of RNase free water, and elution was repeated using the same 40 l initially used to increase RNA concentration. Concentration of total RNA on extracts was measured by a spectrophotometer (NanoDrop, Thermo Scientific, Wilmington, USA). Prior to reverse-transcription, 1 g of total RNA was treated with DNAse I (Life Technologies, São Paulo, SP, Brazil) for 15 minutes at room temperature in a 10 l reaction, followed by addition of 1l of EDTA (25mM) and heating at 65C for 10 minutes to inactivate DNase I. DNase I treatment was immediately followed by reverse-transcription (High Capacity cDNA Reverse Transcription Kit, Life Technologies) according to manufacturer’s instructions. Briefly, 9 l of master mix containing RT buffer, dNTP mix, random primers, RNase inhibitor and reverse transcriptase were added to the 11 l of DNase I treatment reaction. Immediately, samples were incubated at 25 C for 10 minutes, followed by incubation at 37 C for 2 hours and reverse-transcriptase inactivation at 85C for 5 minutes and storage at -20C.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A total of 12 suckled cows presenting absence of corpus luteum detected by ultrasound received 2 mg of estradiol benzoate im and an intravaginal P4 device. Eight days later, P4 devices were removed, and the cows received 500 mg of sodium cloprostenol IM. Cows were blocked according to body condition score and the diameter of largest follicle (LF) at P4 device removal and were randomly assigned to receive an im treatment with 1mg of ECP (ECP, n=6) or not (CON, n=6) at the P4 device removal. All cows received 10μg of buserelin acetate 48 h after the P4 device removal and were timed artificially inseminated immediately after. Cows presenting a new corpus luteum formed 6 d after the GnRH treatment had an endometrial fragment collected by transcervical biopsy

value: multiparous cows

tag: health status

value: Healthy

tag: breed

value: Nelore

tag: treatment

value: Estradiol cypionate supplemented

tag: pregnant status

value: Pregnant

tag: progesterone (ng/ml) at sample collection

value: endometrium


title: X156

tag: tissue


title: 2d_Sm_rep2

description:
2dphSm8-09
PolyA RNA
Processed data file: genes.counts.matrix
Processed data file: isoforms.counts.matrix


title: E0952

value: Non-pregnant


title: SD3_2 Steroid Model Day 3 Post Infection

city: Blacksburg

first: Shiv

middle: D.

last: Kale

state: VA

address: 1015 Steger Hall, Life Science Circle

department: Biocomplexity Institute

institute: Virginia Tech

data_processing:
Adaptor sequences were trimmed and filtered based on phred score (>33) and length (> 36) using Trimmomatic-0.35. Non-paired reads were also filtered out.
A master GTF was created using the GRCm38 mouse genome build and the Af1163 genome scaffolds
Filtered pair-ended RNA-Seq reads were mapped to the merged reference genome using the splice-aware short read mapping tool TopHat 2.1.0 with Bowtie2 2.2.7118
Abundance estimation and differential expression analysis for the reference genes and transcripts were performed using Cufflinks 2.2.1 and visualized in part via CummRbund120
Abundance estimation and differential expression analysis for fungal genes  and transcripts were performed using HTSeq-DeSeq2 1.12.4
Genome_build: GRCm38, EnsembleFungi:  Aspergillus fumigatus A1163
Supplementary_files_format_and_content: tab-delimited text containing standard Cufflinks and DeSeq2 output for abundance measurement and differential expression

organism:
Mus musculus
Aspergillus fumigatus

source_name: whole mouse lungs

extract_protocol:
Whole mouse lung tissue was lyophilized and processed through triazol extraction followed by Qiagen clean-up
Library preparation was performed using the TruSeq RNA preparation kit (Illumina, FC-122-1001/1002) from purified RNA (100 ng-1 mg of total RNA with RIN ≥ 8.0).

tag: mouse strain

tag: a. fumigatus strain

tag: model

value: Steroid

tag: time point

value: day 3


title: 7d_Sm_rep2

description:
7dphSm7-09
PolyA RNA
Processed data file: genes.counts.matrix
Processed data file: isoforms.counts.matrix

tag: developmental stage


title: D160


title: 2d_Lg_rep3

description:
2dphLg8-15
PolyA RNA
Processed data file: genes.counts.matrix
Processed data file: isoforms.counts.matrix

source_name: Larvae, 2 dph, large


title: SD2_5 Steroid Model Day 2 Post Infection

value: day 2


title: 7d_Lg_rep3

description:
7dphLg8-14
PolyA RNA
Processed data file: genes.counts.matrix
Processed data file: isoforms.counts.matrix


title: B0646


title: C317


title: 2d_Lg_rep2

description:
2dphLg8-09
PolyA RNA
Processed data file: genes.counts.matrix
Processed data file: isoforms.counts.matrix


title: SD2_2 Steroid Model Day 2 Post Infection


title: X228

value: Non estradiol cypionate supplemented


title: 2d_Lg_rep1

description:
2dphLg6-21
PolyA RNA
Processed data file: genes.counts.matrix
Processed data file: isoforms.counts.matrix


title: 17d_Sm_rep1

description:
17dhSm7-06
PolyA RNA
Processed data file: genes.counts.matrix
Processed data file: isoforms.counts.matrix

source_name: Larvae, 17 dph, small

value: 17 days post hatching


title: 17d_Sm_rep3

description:
17dhSm8-24
PolyA RNA
Processed data file: genes.counts.matrix
Processed data file: isoforms.counts.matrix

value: Larvae


title: 17d_Sm_rep2

description:
17dhSm7-09
PolyA RNA
Processed data file: genes.counts.matrix
Processed data file: isoforms.counts.matrix


title: LD3_5 Chemotherapeutic Model Day 3 Post Infection

value: Chemotherapeutic


title: SD2_1 Steroid Model Day 2 Post Infection


title: E0406


title: E0819


title: SD3_3 Steroid Model Day 3 Post Infection


title: LD3_1 Chemotherapeutic Model Day 3 Post Infection


title: E0040


title: 17d_Lg_rep3

description:
17dhLg8-24
PolyA RNA
Processed data file: genes.counts.matrix
Processed data file: isoforms.counts.matrix

source_name: Larvae, 17 dph, large


title: LD2_4 Chemotherapeutic Model Day 2 Post Infection


title: 17d_Lg_rep2

description:
17dhLg7-09
PolyA RNA
Processed data file: genes.counts.matrix
Processed data file: isoforms.counts.matrix


title: B1042


title: 1814


title: SD3_1 Steroid Model Day 3 Post Infection


title: 17d_Lg_rep1

description:
17dhLg7-06
PolyA RNA
Processed data file: genes.counts.matrix
Processed data file: isoforms.counts.matrix


title: LD2_2 Chemotherapeutic Model Day 2 Post Infection


title: RNA_D7_siSATB1_Exp2

status: Public on Dec 04 2017

city: Odense M

first: Susanne

last: Mandrup

state: Fyn

address: Campusvej 55

department: Department of Biochemistry and Molecular Biologi

country: Denmark

institute: University of Southern Denmark

description:
processed data file: Gene_expression_Knockdowns.txt
SATB1_D7_E2_SM2511.sam

data_processing:
Alignment: RNA-seq reads were mapped to hg19 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21) using default parameters.
quantification: RNA-seq reads in exons were quantified using iRNA-seq (Madsen, J. et al., Nucleic Acid Research, 2015, 43(6), e40). Differentially expressed genes were identified using edgeR (Robinson et al. 2010, Bioinformatics 26: 139-140).
Genome_build: hg19
Supplementary_files_format_and_content: Abundance or occupancy measures

organism: Homo sapiens

growth_protocol: Immortalized human mesenchymal stem cells, hMSC-TERT4, were cultured and differentiated essentially as previously described (Simonsen et al. 2002). Briefly, two days post-confluency, cells were induced to undergo adipogenesis by switching the cells to DMEM supplemented with 10% fetal serum, 10ug/mL insulin, 1µM rosiglitazone, 100 mM dexamethasone, and 500 µM isobutylmethylxanthine.

extract_protocol:
Cells were lyzed using Isol-RNA lysis Reagent® (5-Prime), and total RNA was purified using EconoSpin (Epoc Life) columns.
Libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014, Methods in Enzymology 2014, Vol. 537, pp. 261-279).

treatment_protocol: Knock down of selected TFs was done 3 days prior to induction of the differentiation using revers transfection with DharmaFECT (Thermo Fisher) and a pool of three different siRNA sequences (MISSION® Sigma).

tag: differentiation stage


title: RNA_D0_siSATB1_Exp2

description:
processed data file: Gene_expression_Knockdowns.txt
SATB1_D0_E2_SM2507.sam

tag: cell line


title: RNA_D1_siSATB1_Exp1

description:
processed data file: Gene_expression_Knockdowns.txt
SATB1_D1_E1_SM2508.sam


title: RNA_D1_siSATB1_Exp2

description:
processed data file: Gene_expression_Knockdowns.txt
SATB1_D1_E2_SM2509.sam


title: RNA_D7_siSATB1_Exp1

description:
processed data file: Gene_expression_Knockdowns.txt
SATB1_D7_E1_SM2510.sam


title: RNA_D0_siSATB1_Exp1

description:
processed data file: Gene_expression_Knockdowns.txt
SATB1_D0_E1_SM2506.sam


title: RNA_D1_siTSHZ1_Exp2

description:
processed data file: Gene_expression_Knockdowns.txt
TSHZ1_D1_E2_SM2533.sam


title: RNA_D1_siTSHZ1_Exp1

description:
processed data file: Gene_expression_Knockdowns.txt
TSHZ1_D1_E1_SM2532.sam


title: LD3_3 Chemotherapeutic Model Day 3 Post Infection


title: RNA_D0_siTSHZ1_Exp2

description:
processed data file: Gene_expression_Knockdowns.txt
TSHZ1_D0_E2_SM2531.sam


title: RNA_D7_siTSHZ1_Exp2

description:
processed data file: Gene_expression_Knockdowns.txt
TSHZ1_D7_E2_SM2535.sam


title: RNA_D0_siTSHZ1_Exp1

description:
processed data file: Gene_expression_Knockdowns.txt
TSHZ1_D0_E1_SM2530.sam


title: RNA_D7_siMAZ_Exp1

description:
processed data file: Gene_expression_Knockdowns.txt
MAZ_D7_E1_SM2522.sam

value: siMAZ


title: RNA_D1_siMAZ_Exp2

description:
processed data file: Gene_expression_Knockdowns.txt
MAZ_D1_E2_SM2521.sam


title: RNA_D0_siMAZ_Exp2

description:
processed data file: Gene_expression_Knockdowns.txt
MAZ_D0_E2_SM2519.sam


title: RNA_D7_siTSHZ1_Exp1

description:
processed data file: Gene_expression_Knockdowns.txt
TSHZ1_D7_E1_SM2534.sam


title: RNA_D7_siMAZ_Exp2

description:
processed data file: Gene_expression_Knockdowns.txt
MAZ_D7_E2_SM2523.sam


title: RNA_D7_siNFIL3_Exp2

description:
processed data file: Gene_expression_Knockdowns.txt
NFIL3_D7_E2_SM2505.sam


title: RNA_D1_siMAZ_Exp1

description:
processed data file: Gene_expression_Knockdowns.txt
MAZ_D1_E1_SM2520.sam


title: RNA_D0_siNFIL3_Exp1

description:
processed data file: Gene_expression_Knockdowns.txt
NFIL3_D0_E1_SM2500.sam


title: RNA_D7_siNFIL3_Exp1

description:
processed data file: Gene_expression_Knockdowns.txt
NFIL3_D7_E1_SM2504.sam


title: RNA_D0_siMAZ_Exp1

description:
processed data file: Gene_expression_Knockdowns.txt
MAZ_D0_E1_SM2518.sam


title: RNA_D7_siMYBL1_Exp2

description:
processed data file: Gene_expression_Knockdowns.txt
MYBL1_D7_E2_SM2529.sam


title: RNA_D7_siMYBL1_Exp1

description:
processed data file: Gene_expression_Knockdowns.txt
MYBL1_D7_E1_SM2528.sam


title: RNA_D0_siNFIL3_Exp2

description:
processed data file: Gene_expression_Knockdowns.txt
NFIL3_D0_E2_SM2501.sam


title: 2d_Sm_rep1

description:
2dphSm6-21
PolyA RNA
Processed data file: genes.counts.matrix
Processed data file: isoforms.counts.matrix

value: 2 days post hatching

value: Small


title: RNA_D0_siMYBL1_Exp1

description:
processed data file: Gene_expression_Knockdowns.txt
MYBL1_D0_E1_SM2524.sam


title: RNA_D7_siHSF1_Exp2

description:
processed data file: Gene_expression_Knockdowns.txt
HSF1_D7_E2_SM2517.sam


title: RNA_D1_siMYBL1_Exp2

description:
processed data file: Gene_expression_Knockdowns.txt
MYBL1_D1_E2_SM2527.sam


title: RNA_D1_siMYBL1_Exp1

description:
processed data file: Gene_expression_Knockdowns.txt
MYBL1_D1_E1_SM2526.sam


title: RNA_D7_siHSF1_Exp1

description:
processed data file: Gene_expression_Knockdowns.txt
HSF1_D7_E1_SM2516.sam


title: RNA_D1_siHSF1_Exp2

description:
processed data file: Gene_expression_Knockdowns.txt
HSF1_D1_E2_SM2515.sam


title: RNA_D0_siHSF1_Exp1

description:
processed data file: Gene_expression_Knockdowns.txt
HSF1_D0_E1_SM2512.sam


title: mir-71(n4115) Day 5, replicate 3 [small RNA]

city: New Haven

first: Sachi

last: Inukai

state: Connecticut

address: 219 Prospect St

institute: Yale University

description:
smRNA_m71_Day5_rep3
Small RNA-seq; size selected for small RNA.
Processed data file: small_RNA-seq_combined_counts_normalized.txt
Processed data file: small_RNA-seq_combined_counts_normalized_log2.txt

data_processing:
Sequencing reads were mapped to the C. elegans genome using STAR (version 2.4.0h) (Dobin et al., Bioinformatics, 2013) using default parameters.
For small RNA-seq, miRNAs were annotated against miRBase release 20 using SeqBuster (Pantano et al., Nucleic Acids Res., 2010) and then manually curated to match annotations in miRBase release 21.
Differential expression for small RNA-seq was tested using DESeq2 (Love et al., Genome Biol., 2014). For small RNA-seq, size factor calculation was conducted against the number of sequences excluding those mapping to rRNA and repeat sequences.
Genome_build: WBcel235
Supplementary_files_format_and_content: small_RNA-seq_combined_counts_normalized.txt: Tab-delimited text file contains normalized read counts for each gene in each sample.
Supplementary_files_format_and_content: small_RNA-seq_combined_counts_normalized_log2.txt: Tab-delimited text file contains log2-transformed normalized counts for each gene in each sample.

source_name: whole animal, mir-71 mutant, day 5 adulthood

growth_protocol: Animals cultured at 20C and moved shortly after L4/adult molt to plates containing 0.1mg/mL 5-fluorodeoxyuridine.

extract_protocol:
Whole animals were collected by washing with M9 buffer and flash frozen on liquid nitrogen. RNA was extracted using TRIzol reagent followed by phenol:chloroform extraction.
RNA libraries were prepared using standard Illumina protocols following size selection.

tag: strain/background

tag: age

value: day 5 adulthood

value: whole body


title: RNA_D0_siHSF1_Exp2

description:
processed data file: Gene_expression_Knockdowns.txt
HSF1_D0_E2_SM2513.sam

tag: genotype/variation


title: N2 Day 0, replicate 3 [small RNA]

description:
smRNA_N2_Day0_rep3
Small RNA-seq; size selected for small RNA.
Processed data file: small_RNA-seq_combined_counts_normalized.txt
Processed data file: small_RNA-seq_combined_counts_normalized_log2.txt

source_name: whole animal, wildtype, day 0 adulthood

value: wildtype

value: day 0 adulthood


title: RNA_D1_siNFIL3_Exp1

description:
processed data file: Gene_expression_Knockdowns.txt
NFIL3_D1_E1_SM2502.sam


title: RNA_D7_siControl_Exp2

description:
processed data file: Gene_expression_Knockdowns.txt
UNI_D7_E2_SM2499.sam

value: siControl


title: N2 Day 5, replicate 3 [small RNA]

description:
smRNA_N2_Day5_rep3
Small RNA-seq; size selected for small RNA.
Processed data file: small_RNA-seq_combined_counts_normalized.txt
Processed data file: small_RNA-seq_combined_counts_normalized_log2.txt

source_name: whole animal, wildtype, day 5 adulthood


title: RNA_D1_siNFIL3_Exp2

description:
processed data file: Gene_expression_Knockdowns.txt
NFIL3_D1_E2_SM2503.sam


title: RNA_D1_siHSF1_Exp1

description:
processed data file: Gene_expression_Knockdowns.txt
HSF1_D1_E1_SM2514.sam


title: RNA_D1_siControl_Exp2

description:
processed data file: Gene_expression_Knockdowns.txt
Uni_D1_E2_SM2497.sam


title: mir-71(n4115) Day 0, replicate 2 [small RNA]

description:
smRNA_m71_Day0_rep2
Small RNA-seq; size selected for small RNA.
Processed data file: small_RNA-seq_combined_counts_normalized.txt
Processed data file: small_RNA-seq_combined_counts_normalized_log2.txt

source_name: whole animal, mir-71 mutant, day 0 adulthood


title: mir-71(n4115) Day 5, replicate 2 [small RNA]

description:
smRNA_m71_Day5_rep2
Small RNA-seq; size selected for small RNA.
Processed data file: small_RNA-seq_combined_counts_normalized.txt
Processed data file: small_RNA-seq_combined_counts_normalized_log2.txt


title: RNA_D7_siControl_Exp1

description:
processed data file: Gene_expression_Knockdowns.txt
Uni_D7_E1_SM2498.sam


title: N2 Day 5, replicate 2 [small RNA]

description:
smRNA_N2_Day5_rep2
Small RNA-seq; size selected for small RNA.
Processed data file: small_RNA-seq_combined_counts_normalized.txt
Processed data file: small_RNA-seq_combined_counts_normalized_log2.txt


title: RNA_D0_siMYBL1_Exp2

description:
processed data file: Gene_expression_Knockdowns.txt
MYBL1_D0_E2_SM2525.sam


title: N2 Day 0, replicate 2 [small RNA]

description:
smRNA_N2_Day0_rep2
Small RNA-seq; size selected for small RNA.
Processed data file: small_RNA-seq_combined_counts_normalized.txt
Processed data file: small_RNA-seq_combined_counts_normalized_log2.txt


title: mir-71(n4115) Day 5, replicate 1 [small RNA]

description:
smRNA_m71_Day5_rep1
Small RNA-seq; size selected for small RNA.
Processed data file: small_RNA-seq_combined_counts_normalized.txt
Processed data file: small_RNA-seq_combined_counts_normalized_log2.txt


title: RNA_D0_siControl_Exp2

description:
processed data file: Gene_expression_Knockdowns.txt
UNI_D0_E2_SM2495.sam


title: RNA_D1_siControl_Exp1

description:
processed data file: Gene_expression_Knockdowns.txt
UNI_D1_E1_SM2496.sam


title: mir-71(n4115) Day 0, replicate 1 [small RNA]

description:
smRNA_m71_Day0_rep1
Small RNA-seq; size selected for small RNA.
Processed data file: small_RNA-seq_combined_counts_normalized.txt
Processed data file: small_RNA-seq_combined_counts_normalized_log2.txt


title: N2 Day 5, replicate 1 [small RNA]

description:
smRNA_N2_Day5_rep1
Small RNA-seq; size selected for small RNA.
Processed data file: small_RNA-seq_combined_counts_normalized.txt
Processed data file: small_RNA-seq_combined_counts_normalized_log2.txt


title: RNA_D0_siControl_Exp1

description:
processed data file: Gene_expression_Knockdowns.txt
UNI_D0_E1_SM2494.sam


title: mir-71(n4115) Day 0, replicate 3 [small RNA]

description:
smRNA_m71_Day0_rep3
Small RNA-seq; size selected for small RNA.
Processed data file: small_RNA-seq_combined_counts_normalized.txt
Processed data file: small_RNA-seq_combined_counts_normalized_log2.txt


title: rox2_rnadamid_msl2_mutant2

first: Andrea

last: Brand

address: Tennis Court Rd

institute: The Gurdon Institute

description:
DamID
rox2_rnadamid_msl2_mutant_normalised_average.bedgraph

data_processing:
FASTQ files were processed with damidseq_pipeline.
Processed data from the damidseq_pipeline software in bedgraph format were used for peak calling. Peaks common to both replicates were considered. For data representation replicates were averaged and the three rox1 dataset for different tissues were quantile normalised.
Genome_build: DMBDGP6
Supplementary_files_format_and_content: bedgraph files were generated using the damidseq_pipeline software, at GATC fragment resolution.  Score represents the normalised log2(lncRNA-3xMS2,MCP Dam over control) foldenrichment.  Processed files are provided as averaged bedgraphs

organism: Drosophila melanogaster

source_name: 3rd instar larval larvae

extract_protocol:
gDNA was extracted using the QuiAmp® DNA Micro. The gDNA was digested with DpnI, adaptors were ligated and then digested with DpnII and pcr amplified.
DNA was sonicated to an average size of 300bp using a Diagenode Bioruptor and DamID adaptors removed with AlwI digestion.  Sonnicated material was end-repaired, A-tailed, sequencing adaptors ligated and PCR amplified.

value: 3rd instar larval larvae

tag: Sex

value: female

tag: gal4 driver

value: tubulin-GAL4, tubulin-GAL80ts


title: mir-71(n4115) Day 5, replicate 3 [poly(A) RNA]

description:
mRNA_mir71_Day5_rep3
Poly(A) selected
Processed data file: RNA-seq_combined_counts.txt
Processed data file: RNA-seq_combined_counts_normalized_rlog.txt

data_processing:
Sequencing reads were mapped to the C. elegans genome using STAR (version 2.4.0h) (Dobin et al., Bioinformatics, 2013) using default parameters.
For RNA-seq, sequence data processing and analysis were performed primarily using the bcbio-nextgen pipeline (https://bcbio-nextgen.readthedocs.org/).
Differential expression for RNA-seq was tested using DESeq2 (Love et al., Genome Biol., 2014).
Genome_build: WBcel235
Supplementary_files_format_and_content: RNA-seq_combined_counts.txt: Tab-delimited text file contains raw read counts for each gene in each sample.
Supplementary_files_format_and_content: RNA-seq_combined_counts_normalized_rlog.txt: Tab-delimited text file contains regularized log-transformed, normalized read counts for each gene in each sample.

extract_protocol:
Whole animals were collected by washing with M9 buffer and flash frozen on liquid nitrogen. RNA was extracted using TRIzol reagent followed by phenol:chloroform extraction.
RNA libraries were prepared using standard Illumina protocols. For RNA library construction, RNA was poly(A)-selected.


title: rox2_rnadamid_msl2_mutant1


title: control_rnadamid_msl2_mutant2

description: DamID


title: control_rnadamid_msl2_mutant1

description: DamID


title: N2 Day 5, replicate 3 [poly(A) RNA]

description:
mRNA_N2_Day5_rep3
Poly(A) selected
Processed data file: RNA-seq_combined_counts.txt
Processed data file: RNA-seq_combined_counts_normalized_rlog.txt


title: N2 Day 0, replicate 3 [poly(A) RNA]

description:
mRNA_N2_Day0_rep3
Poly(A) selected
Processed data file: RNA-seq_combined_counts.txt
Processed data file: RNA-seq_combined_counts_normalized_rlog.txt


title: mir-71(n4115) Day 0, replicate 3 [poly(A) RNA]

description:
mRNA_mir71_Day0_rep3
Poly(A) selected
Processed data file: RNA-seq_combined_counts.txt
Processed data file: RNA-seq_combined_counts_normalized_rlog.txt


title: rox2_rnadamid_f2

description:
DamID
rox2_rnadamid_female_normalised_average.bedgraph

value: 3rd instar larvae


title: mir-71(n4115) Day 5, replicate 2 [poly(A) RNA]

description:
mRNA_mir71_Day5_rep2
Poly(A) selected
Processed data file: RNA-seq_combined_counts.txt
Processed data file: RNA-seq_combined_counts_normalized_rlog.txt


title: mir-71(n4115) Day 0, replicate 2 [poly(A) RNA]

description:
mRNA_mir71_Day0_rep2
Poly(A) selected
Processed data file: RNA-seq_combined_counts.txt
Processed data file: RNA-seq_combined_counts_normalized_rlog.txt


title: rox2_rnadamid_f1


title: N2 Day 5, replicate 2 [poly(A) RNA]

description:
mRNA_N2_Day5_rep2
Poly(A) selected
Processed data file: RNA-seq_combined_counts.txt
Processed data file: RNA-seq_combined_counts_normalized_rlog.txt


title: control_rnadamid_f2

description: DamID


title: MED1_D14_Exp1

description: processed data file: MED1_occupancy_Differentiation.txt

data_processing:
Alignment: ChIP-seq reads were mapped to hg19 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21)  specifying --alignIntronMax 1 to avoid potentially aligning across exon-exon junctions.
peak detection: Regions enriched for MED1 ChIP-seq signal against pooled input were identified using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589) with the “-factor” setting. Merged peak files were generated from the individual MED1 peak files if the center of two or more peaks were within 200 bp. Merged peaks were only included if they are within 100kb of the nearest TSS.
quantification: ChIP-seq reads were quantified and normalized in a 400bp window using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589).
Genome_build: hg19
Supplementary_files_format_and_content: Abundance or occupancy measures

extract_protocol:
ChIP experiments were performed according to standard protocol as described in (Siersbæk et al. 2012, MCB, 32: 3452-3463)
Libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014, Methods in Enzymology 2014, Vol. 537, pp. 261-279).

tag: chip antibody

value: MED1/TRAP220 antibody (M-255) Cat# SC-8998


title: N2 Day 0, replicate 2 [poly(A) RNA]

description:
mRNA_N2_Day0_rep2
Poly(A) selected
Processed data file: RNA-seq_combined_counts.txt
Processed data file: RNA-seq_combined_counts_normalized_rlog.txt


title: N2 Day 0, replicate 1 [small RNA]

description:
smRNA_N2_Day0_rep1
Small RNA-seq; size selected for small RNA.
Processed data file: small_RNA-seq_combined_counts_normalized.txt
Processed data file: small_RNA-seq_combined_counts_normalized_log2.txt


title: control_rnadamid_f1

description: DamID


title: mir-71(n4115) Day 5, replicate 1 [poly(A) RNA]

description:
mRNA_mir71_Day5_rep1
Poly(A) selected
Processed data file: RNA-seq_combined_counts.txt
Processed data file: RNA-seq_combined_counts_normalized_rlog.txt


title: mir-71(n4115) Day 0, replicate 1 [poly(A) RNA]

description:
mRNA_mir71_Day0_rep1
Poly(A) selected
Processed data file: RNA-seq_combined_counts.txt
Processed data file: RNA-seq_combined_counts_normalized_rlog.txt


title: control_rnadamid_sg2

description: DamID

source_name: dissected 3rd instar larval salivary gland

value: male

value: inscuteable-GAL4, tubulin-GAL80ts


title: N2 Day 0, replicate 1 [poly(A) RNA]

description:
mRNA_N2_Day0_rep1
Poly(A) selected
Processed data file: RNA-seq_combined_counts.txt
Processed data file: RNA-seq_combined_counts_normalized_rlog.txt


title: control_rnadamid_sg1

description: DamID

value: dissected 3rd instar larval salivary gland


title: MED1_D7_Exp1


title: HLHS12-lon2

city: Newcastle upon Tyne

first: Majlinda

last: Lako

address: Central Parkway

institute: Newcastle University

data_processing:
BCL-to-Fastq conversion performed using Illumina’s bcl2fastq software, version 2.17.1.14
Reads were pseudo-aligned to the human transcriptome GRCh38, release 79 using Kallisto (v0.43.0).  This then quantified the abundance of transcripts and genes within each sample
Genome_build: GRCh38
Supplementary_files_format_and_content: Abundance measurements: excel files listing genes, transcripts and their abundance in TPM.

source_name: carodiomyocytes

growth_protocol: iPS-derived CMs were cultured with RPMI 1640 medium plus 1x B27

extract_protocol:
RNA was harvested using Trizol reagent from Life Technologies
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: iPS-derived cardiomyocytes

tag: Stage

value: day 30 of differentiation

tag: status

value: purified


title: Input_D1

data_processing:
Alignment: ChIP-seq reads were mapped to hg19 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21)  specifying --alignIntronMax 1 to avoid potentially aligning across exon-exon junctions.
Genome_build: hg19
Supplementary_files_format_and_content: Abundance or occupancy measures


title: SB Neo3


title: Input_D0


title: MED1_D3_Exp2


title: F2-FiPSC-RNA-seq

city: Stanford

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

description:
F2-FiPSC-RNA-seq
processed data file:
RNA-seq_DESeq2_vsd_exp.txt

data_processing:
ChIP-seq: bowtie -p 4 -q -m 1 -v 3 --sam --best --strata /data/bowtie_index/hg38
RNA-seq: hisat -x hg38 -1 R1.fq.gz -2 R2.fq.gz  -S R.sam
Genome_build: hg38
Supplementary_files_format_and_content: Text files. ChIP-seq: Raw read counts for specific loci. RNA-seq: DESeq2 normalized log2 transformed reads.

growth_protocol: Human induced pluripotent stem cells (iPSCs) were maintained in mTeSR-1 medium (STEMCELL Technologies) on Matrigel-coated plates. Endothelial cells (ECs) were maintained on 0.1% gelatin-coated plates with EGM-2 medium (Lonza). Cardiac progenitor cells (CPCs) were cultured on 0.1% gelatin-coated dishes in M199 (Gibco)/EGM-2  (3:1) medium supplemented with 10% FBS, 10 ng/ml basic fibroblast growth factor (bFGF, PeproTech), 5 ng/ml epithelial growth factor (EGF, PeproTech), 5 ng/mL insulin-like growth factor (IGF-1, PeproTech), and 5 ng/ml hepatocyte growth factor (HGF, PeproTech). Fibroblast cells (FBs) were cultured in DMEM medium (Gibco) supplemented with 10% FBS (Hyclone) and GlutaMax (Gibco).

extract_protocol:
Total RNAs were extracted by RNeasy Plus Mini kit (Qiagen) according to the manufacturer’s protocol.
RNA-seq libraries were generated using the NuGEN Encore Complete RNA-seq Library Systems (Part No. 0311, NuGEN). Chromatin immunoprecipitation were performed using approximately 1x10^7 cells of human iPSCs, fibroblasts, endothelial cells, and cardiac progenitor cells. Cells were first cross-linked with 1% formaldehyde for 10 min at RT, and formaldehyde was quenched by glycine with a final concentration of 0.125 M. Chromatin was broken into small pieces with an average size of 0.5-2 kb using the Bioruptor (Diagenode). The sonicated chromatin was then incubated with 3-5 μg of primary antibodies overnight at 4°C. A small portion (10%) of chromatin without antibody incubation was kept as input DNA for each ChIP reaction. Subsequently, 75 μl of Dynabeads Protein A or Protein G were added and incubator for 4 h at 4°C with overhead shaking. Magnetic beads were then washed away and chromatin was eluted. Crosslink was then reversed and precipitated DNA was purified and resuspended in nuclease-free water. Sequencing libraries of immunoprecipitated DNA and input DNA were constructed according to an Illumina DNA library preparation protocol.

treatment_protocol: Different human cell types: CiPSCs, EiPSCs, FiPSCs, CPCs, ECs, and FBs.

value: Induced pluripotent stem cells (iPSCs)

tag: passage


title: MED1_D3_Exp1


title: MED1_D14_Exp2


title: F2-FB-RNA-seq

description:
F2-FB-RNA-seq
processed data file:
RNA-seq_DESeq2_vsd_exp.txt

value: Fibroblast cells (FBs)


title: rox1_rnadamid_sg1

description:
DamID
rox1_rnadamid_sg_normalised_average.bedgraph

tag: tissue


title: MED1_D1_Exp2


title: F2-EiPSC-RNA-seq

description:
F2-EiPSC-RNA-seq
processed data file:
RNA-seq_DESeq2_vsd_exp.txt


title: HLHS12-lon1


title: F2-EC-RNA-seq

description:
F2-EC-RNA-seq
processed data file:
RNA-seq_DESeq2_vsd_exp.txt

value: Endothelial cells (ECs)


title: control_rnadamid_nsc2

description: DamID

source_name: dissected 3rd instar larval brain

value: dissected 3rd instar larval brain


title: MED1_D7_Exp2


title: F2-CPC-RNA-seq

description:
F2-CPC-RNA-seq
processed data file:
RNA-seq_DESeq2_vsd_exp.txt

value: Cardiac progenitor cells (CPCs)


title: N2 Day 5, replicate 1 [poly(A) RNA]

description:
mRNA_N2_Day5_rep1
Poly(A) selected
Processed data file: RNA-seq_combined_counts.txt
Processed data file: RNA-seq_combined_counts_normalized_rlog.txt

value: wildtype

value: day 5 adulthood

value: whole body


title: MED1_D1_Exp1


title: F2-CiPSC-RNA-seq

description:
F2-CiPSC-RNA-seq
processed data file:
RNA-seq_DESeq2_vsd_exp.txt


title: control_rnadamid_nsc1

description: DamID


title: MED1_4h_Exp2


title: F1-FiPSC-RNA-seq

description:
F1-FiPSC-RNA-seq
processed data file:
RNA-seq_DESeq2_vsd_exp.txt


title: F1-FB-RNA-seq

description:
F1-FB-RNA-seq
processed data file:
RNA-seq_DESeq2_vsd_exp.txt


title: F1-EiPSC-RNA-seq

description:
F1-EiPSC-RNA-seq
processed data file:
RNA-seq_DESeq2_vsd_exp.txt


title: MED1_4h_Exp1

description: processed data file: MED1_occupancy_Differentiation.txt


title: F1-EC-RNA-seq

description:
F1-EC-RNA-seq
processed data file:
RNA-seq_DESeq2_vsd_exp.txt


title: rox1_rnadamid_nsc2

description:
DamID
rox1_rnadamid_nsc_normalised_average.bedgraph


title: rox1_rnadamid_sg2


title: MED1_D0_Exp2


title: rox1_rnadamid_nsc1


title: F1-CPC-RNA-seq

description:
F1-CPC-RNA-seq
processed data file:
RNA-seq_DESeq2_vsd_exp.txt


title: msl3_tada

description:
DamID
msl3_tada_normalised.bedgraph

value: 3rd instar larval larvae

value: tubulin-GAL4, tubulin-GAL80ts


title: F2-FiPSC-Pol2

description:
F2-FiPSC-Pol2
processed data file:
ChIP-seq_enhancer_Pol2_vsd_exp.txt
ChIP-seq_promoter_Pol2_counts.txt

value: Anti-RNA Polymerase II antibody, CTD (clone 8WG16)

tag: chip antibody vendor

value: EMD Millipore

tag: chip antibody cat. #


title: MED1_D0_Exp1

value: MED1/TRAP220 antibody (M-255) Cat# SC-8998


title: F2-FiPSC-p300

description:
F2-FiPSC-p300
processed data file:
ChIP-seq_enhancer_p300_vsd_exp.txt
ChIP-seq_promoter_p300_counts.txt

value: p300 antibody (C-20)

value: Santa Cruz Biotechnology


title: F2-FiPSC-K4me3

description:
F2-FiPSC-K4me3
processed data file:
ChIP-seq_enhancer_K4me3_vsd_exp.txt
ChIP-seq_promoter_K4me3_counts.txt

value: Histone H3K4me3 antibody (pAb)

value: Active Motif


title: RNA_D14_Exp3

description:
processed data file: Gene_expression_Differentiation.txt
D14_Rep3.fq.gz.sam


title: rox2_rnadamid_m2

description:
DamID
rox2_rnadamid_male_normalised_average.bedgraph

value: male


title: F2-FiPSC-K27me3

description:
F2-FiPSC-K27me3
processed data file:
ChIP-seq_enhancer_K27me3_vsd_exp.txt
ChIP-seq_promoter_K27me3_counts.txt

value: Induced pluripotent stem cells (iPSCs)

value: Histone H3K27me3 antibody (clone:7B11)


title: RNA_D14_Exp2

description:
processed data file: Gene_expression_Differentiation.txt
D14_Rep2.fq.gz.sam


title: rox2_rnadamid_m1


title: F2-FB-Pol2

description:
F2-FB-Pol2
processed data file:
ChIP-seq_enhancer_Pol2_vsd_exp.txt
ChIP-seq_promoter_Pol2_counts.txt

value: Fibroblast cells (FBs)


title: F2-FiPSC-Input


title: F2-FiPSC-K27ac

description:
F2-FiPSC-K27ac
processed data file:
ChIP-seq_enhancer_K27ac_vsd_exp.txt
ChIP-seq_promoter_K27ac_counts.txt

value: Histone H3K27ac antibody (pAb)


title: rox1_rnadamid_m2

description:
DamID
rox1_rnadamid_normalised_average.bedgraph


title: RNA_D14_Exp1

description:
processed data file: Gene_expression_Differentiation.txt
D14_Rep1.fq.gz.sam


title: F2-FB-p300

description:
F2-FB-p300
processed data file:
ChIP-seq_enhancer_p300_vsd_exp.txt
ChIP-seq_promoter_p300_counts.txt


title: rox1_rnadamid_m1


title: RNA_D7_Exp2

description:
processed data file: Gene_expression_Differentiation.txt
D7_Rep2.fq.gz.sam


title: RNA_D7_Exp3

description:
processed data file: Gene_expression_Differentiation.txt
D7_Rep3.fq.gz.sam


title: F2-FB-K4me1

description:
F2-FB-K4me1
processed data file:
ChIP-seq_enhancer_K4me1_vsd_exp.txt
ChIP-seq_promoter_K4me1_counts.txt

value: Anti-histone H3 (mono methyl K4) antibody

value: Abcam


title: F1-CiPSC-RNA-seq

description:
F1-CiPSC-RNA-seq
processed data file:
RNA-seq_DESeq2_vsd_exp.txt


title: F2-FB-K27me3

description:
F2-FB-K27me3
processed data file:
ChIP-seq_enhancer_K27me3_vsd_exp.txt
ChIP-seq_promoter_K27me3_counts.txt


title: F2-FB-K4me3

description:
F2-FB-K4me3
processed data file:
ChIP-seq_enhancer_K4me3_vsd_exp.txt
ChIP-seq_promoter_K4me3_counts.txt


title: F2-FB-Input


title: F2-FiPSC-K4me1

description:
F2-FiPSC-K4me1
processed data file:
ChIP-seq_enhancer_K4me1_vsd_exp.txt
ChIP-seq_promoter_K4me1_counts.txt


title: control_rnadamid_m2

description: DamID


title: F2-FB-K27ac

description:
F2-FB-K27ac
processed data file:
ChIP-seq_enhancer_K27ac_vsd_exp.txt
ChIP-seq_promoter_K27ac_counts.txt


title: control_rnadamid_m1

description: DamID


title: F2-EiPSC-Pol2

description:
F2-EiPSC-Pol2
processed data file:
ChIP-seq_enhancer_Pol2_vsd_exp.txt
ChIP-seq_promoter_Pol2_counts.txt


title: RNA_D3_Exp3

description:
processed data file: Gene_expression_Differentiation.txt
D3_Rep3.fq.gz.sam


title: dam_tada

description: DamID


title: RNA_D3_Exp2

description:
processed data file: Gene_expression_Differentiation.txt
D3_Rep2.fq.gz.sam


title: F2-EiPSC-p300

description:
F2-EiPSC-p300
processed data file:
ChIP-seq_enhancer_p300_vsd_exp.txt
ChIP-seq_promoter_p300_counts.txt


title: RNA_D3_Exp1

description:
processed data file: Gene_expression_Differentiation.txt
D3_Rep1.fq.gz.sam


title: G005_96h_T8

city: Riverside

first: Daniel

last: Schlenk

state: CA

address: 900 University Ave

institute: University of California, Riverside

description:
Sample collected at 96hpf after source oil exposure
96hG005matrixfinal, 96_G005_results

data_processing:
Adaptor sequences were trimmed off using the FASTX toolkit (Cambridge, UK), to obtain a mean Phred score ≥30.
The processed reads were blasted against the fugu (Fugu rubripes) genome using miRDeep (2.0.0.8) mapper
Then both known and novel miRNAs were identified using miRDeep (2.0.0.8).
Differential expression analysis using DESeq2 Release (3.5)
Genome_build: Fugu rubripes (fr3.fa.gz)
Supplementary_files_format_and_content: matrixfinal: Raw read counts
Supplementary_files_format_and_content: results: Differential expression

organism: Coryphaena hippurus

source_name: whole embryo

growth_protocol:
Mahi-mahi broodstock were captured off the coast of Miami, FL using hook and line angling techniques and subsequently transferred to the University of Miami Experimental Hatchery (UMEH) where they were acclimated in 80 m3 fiberglass maturation tanks (typically 5-7 per tank).  Tanks were equipped with recirculating aquaculture systems for water quality and temperature control.  All embryos used in experiments were collected <8 h following a volitional (non-induced) spawn using standard UMEH methods (Stieglitz et al 2012).
Mahi-mahi broodstock were captured off the coast of Miami, FL using hook and line angling techniques and subsequently transferred to the University of Miami Experimental Hatchery (UMEH) where they were acclimated in 80 m3 fiberglass maturation tanks (typically 5-7 per tank).  Tanks were equipped with recirculating aquaculture systems for water quality and temperature control.  All embryos used in experiments were collected <8 h following a volitional (non-induced) spawn using standard UMEH methods (Stieglitz et al 2012).

extract_protocol:
Thirty pooled embryos or larvae per replicate were homogenized with a Kontes Pellet Pestle Cordless Motor (Sigma-Aldrich, St. Louis, Missouri) in Qiazol. Samples were isolated using the miRNeasy mini kit and RNeasy Mini Elute Cleanup Kit from Qiagen (Valenica, CA).
miRNA libraries were made using the New England Biolabs NEBNext Multiplex Small RNA Sample Prep kit (Ipswich, MA) following the manufacturer’s protocol.  The PCR amplified cDNA libraries were then purified using the Qiagen QIAQuick PCR Purification Kit (Valencia, CA) according to the manufacturer’s manual. The purified libraries were size-selected using Beckman Coulter SPRIselect beads (Indianapolis, IN).  The size distribution and concentration of the libraries were determined using the Agilent High Sensitivity DNA Assay Chip (Santa Clara, CA).
Thirty pooled embryos or larvae per replicate were homogenized with a Kontes Pellet Pestle Cordless Motor (Sigma-Aldrich, St. Louis, Missouri) in Qiazol. Samples were isolated using the miRNeasy mini kit and RNeasy Mini Elute Cleanup Kit from Qiagen (Valenica, CA).
miRNA libraries were made using the New England Biolabs NEBNext Multiplex Small RNA Sample Prep kit (Ipswich, MA) following the manufacturer’s protocol.  The PCR amplified cDNA libraries were then purified using the Qiagen QIAQuick PCR Purification Kit (Valencia, CA) according to the manufacturer’s manual. The purified libraries were size-selected using Beckman Coulter SPRIselect beads (Indianapolis, IN).  The size distribution and concentration of the libraries were determined using the Agilent High Sensitivity DNA Assay Chip (Santa Clara, CA).

treatment_protocol:
Bulk dilutions were prepared by adding the appropriate volume of slick or source oil HEWAF to 1 µm filtered, UV-sterilized seawater in 5 L glass bottles,  vigorously spinning for several minutes with a stir bar followed by decanting into each of the replicate 1 L glass beakers.   Freshly fertilized embryos were then gently added to each replicate using a glass transfer pipette and each beaker covered with a glass petri dish.  All exposures were static, non-renewal and performed in a temperature controlled environmental chamber at 27°C with a light cycle of 16:8 h light:dark.
Bulk dilutions were prepared by adding the appropriate volume of slick or source oil HEWAF to 1 µm filtered, UV-sterilized seawater in 5 L glass bottles,  vigorously spinning for several minutes with a stir bar followed by decanting into each of the replicate 1 L glass beakers.   Freshly fertilized embryos were then gently added to each replicate using a glass transfer pipette and each beaker covered with a glass petri dish.  All exposures were static, non-renewal and performed in a temperature controlled environmental chamber at 27°C with a light cycle of 16:8 h light:dark.

value: whole embryo

tag: concentration

tag: agent

value: source oil


title: foxg1_04

city: Santa Cruz

first: Bin

last: Chen

address: 1156 High St.

department: MCD Biology

institute: University of California Santa Cruz

data_processing:
The raw 51x51bp pairedEnd reads were paired-end mapped to mm9 with bowtie, and only uniquely mapping reads were retained.
The mappings of the two input dna samples, which were derived from the same sample, were concatenated with samtools merge before duplicate removal.
Duplicate pairedEnd mappings were removed with samtools rmdup.
The mapped paired-end reads of the ChIP samples were used to estimate the MACS shiftsize parameter
The read1 mappings were input to MACS 1.4.0 for peak calling, using the merged input sample as a control for each ChIP sample.
Genome_build: mm9
Supplementary_files_format_and_content: MACS peaks are in tsv (Excel compatible) format.

source_name: cortex

growth_protocol: timed pregnant CD1 mice were ordered from Charles River Laboratory

extract_protocol:
Lysate from sonicated cortices were cleared after centrifugation. Foxg1-DNA complexes were isolated using a Foxg1 antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).
ChIP-Seq library was sequenced for pair-end sequencing (51 nt per end) on an Illumina Genome Analyzer II platform

treatment_protocol: Cerebral cortex were dissected out from E14-15 embryos, fixed in 1% formadehyde, neutralized using 2% glycine,  and processed for chromatin IP using Foxg1 antibody.

tag: developmental stage

value: embryonic day 14-15

value: Foxg1 antibody

value: cortex

tag: strain


title: foxg1_05


title: G005_96h_T9


title: input_11


title: input_01


title: F2-EiPSC-K4me3

description:
F2-EiPSC-K4me3
processed data file:
ChIP-seq_enhancer_K4me3_vsd_exp.txt
ChIP-seq_promoter_K4me3_counts.txt


title: RNA_D1_Exp3

description:
processed data file: Gene_expression_Differentiation.txt
D1_Rep3.fq.gz.sam

tag: cell line

tag: differentiation stage


title: G005_96h_T7


title: F2-EiPSC-K4me1

description:
F2-EiPSC-K4me1
processed data file:
ChIP-seq_enhancer_K4me1_vsd_exp.txt
ChIP-seq_promoter_K4me1_counts.txt


title: RNA_D7_Exp1

description:
processed data file: Gene_expression_Differentiation.txt
D7_Rep1.fq.gz.sam


title: RNA_D1_Exp2

description:
processed data file: Gene_expression_Differentiation.txt
D1_Rep2.fq.gz.sam


title: F2-EiPSC-K27me3

description:
F2-EiPSC-K27me3
processed data file:
ChIP-seq_enhancer_K27me3_vsd_exp.txt
ChIP-seq_promoter_K27me3_counts.txt


title: G005_48h_T5

description:
Sample collected at 48hpf after source oil exposure
48hG005matrixfinal, 48_G005_results


title: RNA_D1_Exp1

description:
processed data file: Gene_expression_Differentiation.txt
D1_Rep1.fq.gz.sam


title: G005_48h_T4


title: F2-EiPSC-Input


title: RNA_4h_Exp3

description:
processed data file: Gene_expression_Differentiation.txt
H4_Rep3.fq.gz.sam


title: G005_24h_T3

description:
Sample collected at 24hpf after source oil exposure
24hG005matrixfinal, 24_G005_results


title: F2-EC-Pol2

description:
F2-EC-Pol2
processed data file:
ChIP-seq_enhancer_Pol2_vsd_exp.txt
ChIP-seq_promoter_Pol2_counts.txt

value: Endothelial cells (ECs)

value: Anti-RNA Polymerase II antibody, CTD (clone 8WG16)

value: EMD Millipore


title: RNA_4h_Exp2

description:
processed data file: Gene_expression_Differentiation.txt
H4_Rep2.fq.gz.sam


title: 10557X17

city: Salt Lake City

first: Russell

last: Butterfield

state: UT

department: Pediatric Neurology

institute: University of Utah

description: Sample 16

data_processing:
Sequenced reads were processed for quality using FASTX toolkit version 0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/) to clip adapter sequences and filter for minimum quality score of 15 or greater in 80% of bases per read.
Alignment of filtered/clipped reads to the reference sequence was performed using Tophat2 (v2.0.10) with default parameters.
Transcript abundances were estimated and normalized for transcript length and for read depth and reported as fragments per kb (in the transcript model) per million reads mapped (FPKM) using Cufflinks (v2.2.1).
Differential expression was determined using Cuffdiff2 with pairwise comparisons for 1) control vs. dominant negative mutants, 2) control vs. null mutants, and 3) dominant negative mutants vs. null mutants.  Our analysis used the –G option to restrict the analysis to the reference genome, -u to correct for multi-reads, and–b option to implement the fragment bias correction algorithm.
Genome_build: GRCv37 / UCSC hg19
Supplementary_files_format_and_content: cufflinks gene.fpkm.tracking

source_name: dermal fibroblast

growth_protocol: Fibroblasts were grown in Dulbecco’s modified Eagle medium with 10% FBS and 1% Penicillin/Streptomycin in a 6-well plate in 5% CO2 at 37°C until 80% confluence. Cells were continuously cultured in the presence of 25ug/ml L-ascorbic acid phosphate (Wako, Osaka, Japan) for 72 hours and then changed to medium without L-ascorbic acid phosphate for 16 hours.

extract_protocol:
Total RNA was obtained from existing cultured fibroblasts using RNeasy Mini Kit (QIAGEN, cat# 74106)
Poly-A purified sequencing libraries were produced from total RNA using the Illumina TruSeq RNA Sample Prep Kit (Illuminia, Inc., San Diego, CA) according to the manufacturer’s protocol. Sequencing was performed using the Illumina HiSeq 2000 instrument with a 50 cycle single-end protocol at the University of Utah Microarray and Genomic Analysis Core

tag: condition

value: control

value: dermal fibroblast

tag: genotype


title: 10557X18

description: Sample 17


title: 10557X12

description: Sample 14


title: G005_24h_T2


title: F2-EC-p300

description:
F2-EC-p300
processed data file:
ChIP-seq_enhancer_p300_vsd_exp.txt
ChIP-seq_promoter_p300_counts.txt

value: p300 antibody (C-20)

value: Santa Cruz Biotechnology


title: F2-EC-K4me3

description:
F2-EC-K4me3
processed data file:
ChIP-seq_enhancer_K4me3_vsd_exp.txt
ChIP-seq_promoter_K4me3_counts.txt

value: Histone H3K4me3 antibody (pAb)

value: Active Motif


title: G005_48h_T6


title: 10557X10

description: Sample 12


title: G005_24h_T1


title: G004_96h_T9

description:
Sample collected at 96hpf after Slick oil exposure
96hG004matrixfinal, 96_G004_results

value: Slick oil


title: 8498X2

description: Sample 1


title: F2-EC-K27me3

description:
F2-EC-K27me3
processed data file:
ChIP-seq_enhancer_K27me3_vsd_exp.txt
ChIP-seq_promoter_K27me3_counts.txt

value: Histone H3K27me3 antibody (clone:7B11)


title: RNA_D0_Exp2

description:
processed data file: Gene_expression_Differentiation.txt
D0_Rep2.fq.gz.sam


title: F2-EiPSC-K27ac

description:
F2-EiPSC-K27ac
processed data file:
ChIP-seq_enhancer_K27ac_vsd_exp.txt
ChIP-seq_promoter_K27ac_counts.txt

value: Induced pluripotent stem cells (iPSCs)

value: Histone H3K27ac antibody (pAb)


title: G004_96h_T8

value: whole embryo


title: RNA_D0_Exp1

description:
processed data file: Gene_expression_Differentiation.txt
D0_Rep1.fq.gz.sam


title: 10557X9

description: Sample 11

value: collagen VI related muscular dystrophy

value: Null mutant


title: RNA_D0_Exp3

description:
processed data file: Gene_expression_Differentiation.txt
D0_Rep3.fq.gz.sam


title: G004_96h_T7


title: RNA_4h_Exp1

description:
processed data file: Gene_expression_Differentiation.txt
H4_Rep1.fq.gz.sam


title: F2-EC-K27ac

description:
F2-EC-K27ac
processed data file:
ChIP-seq_enhancer_K27ac_vsd_exp.txt
ChIP-seq_promoter_K27ac_counts.txt


title: 10557X8

description: Sample 10


title: 10557X11

description: Sample 13


title: 10557X16

description: Sample 15


title: G004_48h_T6

description:
Sample collected at 48hpf after Slick oil exposure
48hG004matrixfinal, 48_G004_results


title: 10557X7

description: Sample 9


title: F2-EC-K4me1

description:
F2-EC-K4me1
processed data file:
ChIP-seq_enhancer_K4me1_vsd_exp.txt
ChIP-seq_promoter_K4me1_counts.txt

value: Anti-histone H3 (mono methyl K4) antibody

value: Abcam


title: F2-EC-Input

value: Endothelial cells (ECs)


title: G004_48h_T5


title: G004_48h_T4


title: F2-CPC-Pol2

description:
F2-CPC-Pol2
processed data file:
ChIP-seq_enhancer_Pol2_vsd_exp.txt
ChIP-seq_promoter_Pol2_counts.txt

value: Cardiac progenitor cells (CPCs)

value: Anti-RNA Polymerase II antibody, CTD (clone 8WG16)

value: EMD Millipore


title: 10557X6

description: Sample 8

value: dermal fibroblast


title: F2-CPC-p300

description:
F2-CPC-p300
processed data file:
ChIP-seq_enhancer_p300_vsd_exp.txt
ChIP-seq_promoter_p300_counts.txt

value: p300 antibody (C-20)

value: Santa Cruz Biotechnology


title: 10557X20

description: Sample 19

value: Dominant negative mutant_glycine missense


title: G004_24h_T3

description:
Sample collected at 24hpf after Slick oil exposure
24hG004matrixfinal, 24_G004_results

value: Slick oil


title: F2-CPC-K4me1

description:
F2-CPC-K4me1
processed data file:
ChIP-seq_enhancer_K4me1_vsd_exp.txt
ChIP-seq_promoter_K4me1_counts.txt


title: F2-CPC-K4me3

description:
F2-CPC-K4me3
processed data file:
ChIP-seq_enhancer_K4me3_vsd_exp.txt
ChIP-seq_promoter_K4me3_counts.txt

value: Histone H3K4me3 antibody (pAb)

value: Active Motif


title: G004_24h_T2


title: 10557X19

description: Sample 18


title: 8498X12

description: Sample 7


title: G004_24h_T1


title: 8498X11

description: Sample 6


title: F2-CPC-K27me3

description:
F2-CPC-K27me3
processed data file:
ChIP-seq_enhancer_K27me3_vsd_exp.txt
ChIP-seq_promoter_K27me3_counts.txt

value: Histone H3K27me3 antibody (clone:7B11)


title: 8498X10

description: Sample 5

value: Dominant negative mutant_exon skipping


title: G004_96h_C8

description:
Control sample for 96hpf
96hG004matrixfinal, 96hG005matrixfinal, 96_G004_results, 96_G005_results

value: whole embryo


title: G004_96h_C9


title: F2-CPC-Input


title: 8498X9

description: Sample 4

value: collagen VI related muscular dystrophy


title: G004_48h_C6

description:
Control sample for 48hpf
48hG004matrixfinal, 48hG005matrixfinal, 48_G004_results, 48_G005_results


title: G004_96h_C7


title: 8498X8

description: Sample 3


title: F2-CiPSC-Pol2

description:
F2-CiPSC-Pol2
processed data file:
ChIP-seq_enhancer_Pol2_vsd_exp.txt
ChIP-seq_promoter_Pol2_counts.txt

value: Induced pluripotent stem cells (iPSCs)


title: G004_48h_C5


title: G004_48h_C4


title: F2-CiPSC-K4me1

description:
F2-CiPSC-K4me1
processed data file:
ChIP-seq_enhancer_K4me1_vsd_exp.txt
ChIP-seq_promoter_K4me1_counts.txt

value: Anti-histone H3 (mono methyl K4) antibody

value: Abcam


title: F2-CiPSC-K4me3

description:
F2-CiPSC-K4me3
processed data file:
ChIP-seq_enhancer_K4me3_vsd_exp.txt
ChIP-seq_promoter_K4me3_counts.txt


title: G004_24h_C3

description:
Control sample for 24hpf
24hG004matrixfinal, 24hG005matrixfinal, 24_G004_results, 24_G005_results


title: G004_24h_C2


title: F2-CiPSC-K27ac

description:
F2-CiPSC-K27ac
processed data file:
ChIP-seq_enhancer_K27ac_vsd_exp.txt
ChIP-seq_promoter_K27ac_counts.txt

value: Histone H3K27ac antibody (pAb)


title: F2-CiPSC-p300

description:
F2-CiPSC-p300
processed data file:
ChIP-seq_enhancer_p300_vsd_exp.txt
ChIP-seq_promoter_p300_counts.txt


title: F2-CiPSC-Input


title: F1-FiPSC-Pol2

description:
F1-FiPSC-Pol2
processed data file:
ChIP-seq_enhancer_Pol2_vsd_exp.txt
ChIP-seq_promoter_Pol2_counts.txt

value: Anti-RNA Polymerase II antibody, CTD (clone 8WG16)


title: WM266.4 shJMJD2C

city: Berlin

first: Maja

last: Milanovic

address: Augustenburgerplatz 1

department: Hematology and Oncology

country: Germany

institute: Charite University Medicine, Berlin

data_processing:
Computational rRNA depletion using SortMeRNA version 2.1
RNA-seq reads were aligned to the GRCh38 Ensembl release 88 reference genome using STAR RNA-seq aligner 2.5.2b with --twopassMode Basic
sam files were converted to BAM format using Samtools version 0.18
Transcript abundance was quantified using the summarizeOverlaps function in the  R/Bioconductor package GenomicAlignments. Counting mode was set to "Union"
Raw transcript counts were transformed to log2-scale using the rlog function from the R/Bioconductor package DESeq2
Genome_build: GRCh38 Ensembl release 88
Supplementary_files_format_and_content: F17FTSEUHT0688_human_Counts.txt.gz contains a data matrix of raw transcript counts; F17FTSEUHT0688_human_RLOG.txt.gz contains log2 expression values generated by rlog from the DESeq2 package in R/Bioconductor. Both files are tab-delimited with samples in columns and features in rows.

source_name: WM266.4 melanoma cell line

growth_protocol: Cells were cultured in DMEM medium with 10% FBS and penicillin/streptomycin in 37°C incubator.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plus Mini Kit.
Libraries were prepared by BGI (Hongkong).

treatment_protocol: Cells were transduced with shLSD1, shJMJD2C or scrambled shRNA construct as control.

tag: treatment

value: melanoma


title: WM266.4 shLSD1


title: F1-FiPSC-p300

description:
F1-FiPSC-p300
processed data file:
ChIP-seq_enhancer_p300_vsd_exp.txt
ChIP-seq_promoter_p300_counts.txt

tag: chip antibody


title: F2-CPC-K27ac

description:
F2-CPC-K27ac
processed data file:
ChIP-seq_enhancer_K27ac_vsd_exp.txt
ChIP-seq_promoter_K27ac_counts.txt

tag: cell type

value: Cardiac progenitor cells (CPCs)


title: PVC39

city: New York

first: Karen

last: Duff

state: NY

address: 630 West 168th Street, P & S 12-440

department: Pathology and Cell Biology

institute: Columbia University Medical Center

data_processing:
generated 149bp single end sequences using an Illumina Hi-Seq sequencer
aligned the fastq files to the mm9 mouse reference genome using Tophat (v2.0.6) and Bowtie (v2.0.2.0)
annotated and quantified the reads to specific genes using Python module HT-SEQ with a modified NCBIM37.61 (containing only protein coding genes) gtf to provide reference boundaries
compared aligned reads across samples using the R/Bioconductor package DESeq2 (v1.10.1)
Genome_build: mm9
Supplementary_files_format_and_content: text file with DESeq2 output. Each tissue analyzed individually.

source_name: Primary Visual Cortex

extract_protocol:
Trizol
TruSeq RNA Sample Prep Kit v2

value: brain

tag: tissue compartment

value: Primary Visual Cortex

tag: gender

value: Male

tag: age

value: 14-15 months


title: PVC35

tag: tissue


title: WM266.4 shControl

value: shControl


title: A375 shJMJD2C

source_name: A375 melanoma cell line


title: F1-FiPSC-K4me3

description:
F1-FiPSC-K4me3
processed data file:
ChIP-seq_enhancer_K4me3_vsd_exp.txt
ChIP-seq_promoter_K4me3_counts.txt

tag: passage

value: Histone H3K4me3 antibody (pAb)

tag: chip antibody vendor

value: Active Motif


title: 8498X5

description: Sample 2

value: dermal fibroblast

value: Dominant negative mutant_exon skipping


title: F1-FiPSC-K4me1

description:
F1-FiPSC-K4me1
processed data file:
ChIP-seq_enhancer_K4me1_vsd_exp.txt
ChIP-seq_promoter_K4me1_counts.txt

tag: chip antibody cat. #


title: PVC34


title: PVC33

description: same library run multiple times for depth


title: A375 shControl


title: PVC20


title: PVC19


title: F1-FiPSC-K27ac

description:
F1-FiPSC-K27ac
processed data file:
ChIP-seq_enhancer_K27ac_vsd_exp.txt
ChIP-seq_promoter_K27ac_counts.txt


title: F1-FiPSC-K27me3

description:
F1-FiPSC-K27me3
processed data file:
ChIP-seq_enhancer_K27me3_vsd_exp.txt
ChIP-seq_promoter_K27me3_counts.txt

value: Histone H3K27me3 antibody (clone:7B11)


title: G004_24h_C1

value: whole embryo

tag: concentration

tag: agent


title: F1-FiPSC-Input

value: Induced pluripotent stem cells (iPSCs)


title: B16F10 shJMJD2C

data_processing:
Computational rRNA depletion using SortMeRNA version 2.1
RNA-seq reads were aligned to the GRCm38 Ensembl release 88 reference genome using STAR RNA-seq aligner 2.5.2b with --twopassMode Basic
sam files were converted to BAM format using Samtools version 0.18
Transcript abundance was quantified using the summarizeOverlaps function in the  R/Bioconductor package GenomicAlignments. Counting mode was set to "Union"
Raw transcript counts were transformed to log2-scale using the rlog function from the R/Bioconductor package DESeq2
Genome_build: GRCm38 Ensembl release 88
Supplementary_files_format_and_content: F17FTSEUHT0688_mouse_Counts.txt.gz contains a data matrix of raw transcript counts; F17FTSEUHT0688_mouse_RLOG.txt.gz contains log2 expression values generated by rlog from the DESeq2 package in R/Bioconductor. Both files are tab-delimited with samples in columns and features in rows.

source_name: B16F10 melanoma cell line


title: B16F10 shLSD1


title: PVC16

tag: strain


title: B16F10 shControl

tag: cell line


title: PVC15


title: PVC17


title: F2-CiPSC-K27me3

description:
F2-CiPSC-K27me3
processed data file:
ChIP-seq_enhancer_K27me3_vsd_exp.txt
ChIP-seq_promoter_K27me3_counts.txt


title: F1-FB-K4me3

description:
F1-FB-K4me3
processed data file:
ChIP-seq_enhancer_K4me3_vsd_exp.txt
ChIP-seq_promoter_K4me3_counts.txt

value: Fibroblast cells (FBs)


title: A375 shLSD1


title: F1-FB-K4me1

description:
F1-FB-K4me1
processed data file:
ChIP-seq_enhancer_K4me1_vsd_exp.txt
ChIP-seq_promoter_K4me1_counts.txt

value: Anti-histone H3 (mono methyl K4) antibody

value: Abcam


title: F1-FB-K27me3

description:
F1-FB-K27me3
processed data file:
ChIP-seq_enhancer_K27me3_vsd_exp.txt
ChIP-seq_promoter_K27me3_counts.txt


title: Donor 3_∆UL138 6dpi SS

city: Tucson

first: Janko

last: Nikolich-Zugich

state: AZ

address: 1656 E. Mabel St.

institute: University of Arizona

description:
∆UL138 HCMV infected 6 days
Raw_donor_NSSS14.txt

data_processing:
Raw sequencing data was de-multiplexed and fastq files generated using either built-in software (MiSeq) or CASAVA (HiSeq).
Raw sequence data were first evaluated using FastQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and preprocessed for quality through a combination of  trimming and filtering using Trim Galore (v0.4.0, 15 bases were trimmed off from the 5'-end of the reads and 5 bases were trimmed off from the 3'-end, Phred score threshold of 20 and minimum length of 50 bp, Paired, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Quality reads were then uniquely mapped to HHCMV (strain TB40/E, GenBank: EF999921.1) and human (GRCh38) genomes, respectively, both using Tophat2 (v2.1.1) with strand-specific alignment of fr-firststrand. For HHCMV alignment, the maximum intron size was set to 5kb as described on Tophat2 manual, and the uniquely mapped HCMV, but not human, reads were used for all subsequent analyses.
Raw read counts for each sample were obtained by mapping reads at the gene-level using HTSeq-count tool from the Python package HTSeq, with a stranded-reverse setting. DESeq2 R-package (v1.8.2) was then used to perform differential expression (DE) and statistical analysis, with a biological sample from  SS and NS libraries of same cell donor grouped.
Raw read counts for genes over a group of six biological samples of fibroblast or CD34+ HPC infection were normalized through a regularized logarithm transformation (rlog) implemented in DESeq2, and kernel density estimates (KDE) were then obtained using the density R function with default parameters. The six density curves were overlaid on one plot. The featured density variation, associated with fibroblast or CD34+ HPC infection, was further evaluated using an extended group comprised of total four time points of post infection in fibroblasts (12, 24, 48, 72hpi, total 12 samples) and all NS/SS replicates from different cell donors of CD34+ HPC infection (total 24 samples).  Density variation across samples was accessed by different bandwidth settings (0.5, 0.75, 1 and 1.25), which determine the degree of smoothing in the estimate of the density function of statistical software package R (http://www.r-project.org/). In addition, density variation across samples was assessed by the comparison between real and random samples, where raw read count for each gene in each sample was the mean value of 100 permutations of involved real samples and rlog normalization was performed.
Variability with respect to transcriptomes from infection in fibroblasts or CD34+ HPCs was assessed by the squared coefficient of variation (CV2), i.e., the variance in expression of rlog normalized counts (σ2) divided by the squared mean expression (μ2) and then multiplied by 100.  The cumulative CV2 was also obtained as a final squared coefficient of variation representing the variability in different cell types.
In addition to rlog normalized counts, we quantified expression level of genes by merging annotated isoforms' FPKM values from Cufflinks (v2.2.1).
Genome_build: EF999921.1 (HCMV), GRCh38 (Human)
Supplementary_files_format_and_content: [Raw_Fb16.txt] Raw HCMV reads counts for fibroblast infection
Supplementary_files_format_and_content: [Raw_NSSS12.txt] Raw HCMV reads counts for CD34+ HPC infection from donor 1
Supplementary_files_format_and_content: [Raw_donor_NSSS14.txt] Raw HCMV reads counts for CD34+ HPC infection from donor 2 and donor 3
Supplementary_files_format_and_content: [Raw_natural.txt] Raw HCMV reads counts for natural infection
Supplementary_files_format_and_content: [FPKM13.txt] Abundance measurements of HCMV genes for CD34+ HPC infection (donor 1) and natural infection

organism: Human betaherpesvirus 5

source_name: Hematopoietic Stem Cells, ∆UL138 HCMV infected 6 days

growth_protocol: MRC-5 lung fibroblasts were maintained with DMEM (Gibco) supplemented with 10% FBS, 100 U/mL penicillin and streptomycin, 2mM L-alanyl-glutamine, 1 mM sodium pyruvate, 0.1 mM nonessential amino acids, and 10 mM HEPES

extract_protocol:
RNA was extracted using a ZR-Duet DNA/RNA miniprep kit (Zymo Research, Irvine, CA)
RNA libraries were prepared for Illumina sequencing using either Agilent's SureSelect Strand Specific RNA Library Preparation Kit or Kapa Biosystem's KAPA Stranded mRNA-seq kit

tag: host cell type

value: CD34+ Hematopoietic Stem Cells

tag: isolate

value: initial isolate

tag: selection

value: SureSelect Targeted enrichment


title: PVC10

value: brain

value: Primary Visual Cortex

tag: genotype


title: F1-FB-K27ac

description:
F1-FB-K27ac
processed data file:
ChIP-seq_enhancer_K27ac_vsd_exp.txt
ChIP-seq_promoter_K27ac_counts.txt

tag: chip antibody

value: Histone H3K27ac antibody (pAb)


title: Natural_Adult HCMV High

description:
Clinical samples pooled from four adults (avg. age 40) with high HCMV ab titers
Raw_natural.txt
FPKM13.txt

source_name: peripheral blood mononuclear cells, Clinical samples pooled from four adults (avg. age 40) with high HCMV ab titers

value: Total PBMC

value: Clinical isolates


title: PVC8

value: Male

value: 14-15 months


title: PVC9