title: Non-Tg SAM24325787

city: South San Francisco

first: Brad

middle: A

last: Friedman

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: RNA from sorted brain myeloid cells

extract_protocol: Cells were centrifuged at 2,600 rcf for 7 minutes (neurons) or 6,600 rcf for 7 minutes (other cell types) and the supernatant was discarded. RNA was extracted from the cell pellet using Qiagen RNeasy Plus Micro kit in a final volume of 25 μl. We typically obtained 200-300 ng RNA from neurons, 10-20 ng from microglia, and 2-5 ng from astrocytes. RNA quality was quantified using the Bioanalyzer.

value: brain Cd11b+ myeloid cells

value: 6 month old

value: Non-Transgenic littermate

tag: gender

value: male


title: aSTAT4_STAT4KO_STIM_3_INPUT

status: Public on Dec 20 2017

type: SRA

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

country: USA

institute: Cornell University

library_source: genomic

data_processing:
BCL files were converted to fastq using bcl2fastq (v1.8.3 and v1.8.4)
ChIP-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.36) and aligned to the mm10 genome assembly using Bowtie2 (v2.2.9).
Peak-calling was done on concordantly aligned paired reads using MACS2 (2.1.1.20160309).
BigWig files were generated by converting BAM files to size-normalized BEDGRAPH files using bedtools (v2.26.0) and converted to bigWig using UCSC's bedGraphToBigWig (v4).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files normalized by size factors calculated by DESeq2 among all ChIP (non-input) samples in peak regions or flank regions (see manuscript)

molecule: genomic DNA

organism: Mus musculus

source_name: splenic NK cells

extract_protocol:
Protein was cross-linked to DNA with 0.75% formaldehyde. Clarified supernatant from sonicated nuclei were applied to antibody-bound beads. After de-crosslinking and elution, DNA was isolated using Qiagen Gel Extraction Kit. Input samples were clarified supernatant that were not applied to antibody-bound beads.
Immunoprecipitated DNA was quantified by Picogreen and size was evaluated on a HighSense BioAnalyzer chip. When possible, fragments between 100 and 600 bp were size selected and Illumina Hiseq libraries were prepared using the Kapa DNA library preparation chemistry (Kapa Biosystems) using 12-15 cycles of PCR. Adaptors were diluted 1/10 or  1/50 depending on the starting amount of material available. Barcoded libraries were run on Hiseq 2500 1T in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina). An average of 57 million paired reads were generated per sample.

tag: genotype

tag: chip antibody

tag: condition

tag: cell type

value: splenic NK cells


title: hMAPT-P301S SAM24325790

library_source: transcriptomic

molecule: total RNA

tag: age


title: aSTAT4_STAT4WT_UNSTIM_2_INPUT

value: unstim


title: aSTAT4_STAT4WT_STIM_2_INPUT


title: Non-Tg SAM24325788


title: Non-Tg SAM24325786


title: Non-Tg SAM24325783


title: hMAPT-P301S SAM24325793


title: STAT4WT_HNEG_D0_002

description: STAT4KOChimera_MCMV_Stat4HposHneg_rawCounts_knownGene.txt

data_processing:
BCL files were converted to fastq using bcl2fastq (v2.16-2.19)
RNA-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.36) and aligned to the mm10 genome assembly using Bowtie2 (v2.2.9).
Genome_build: mm10
Supplementary_files_format_and_content: Text files are raw counts (1 count per pair of reads) calculated using the summarizeOverlaps function from the GenomicAlignments R package (v10.10.1)

extract_protocol:
Cells were sorted directly into Trizol and total RNA underwent amplification using SMART-seq V4 (Clontech) Ultra Low Input RNA kit.
Subsequently, 10 ng of amplified cDNA was used to prepare Illumina hiseq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using 8 cycles of PCR. Samples were barcoded and run on Hiseq 2500 1T, in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina). An average of 47 million paired reads were generated per sample and the percent of mRNA bases was over to 72% on average.

tag: replicate

value: HNEG


title: aSTAT4_STAT4WT_STIM_1_INPUT


title: Tg SAM24308123

value: 11-12 months-old

value: Brain Cd11b+ myeloid cells

tag: Sex

value: Male

value: Tau-P301L transgenic mice

tag: samid


title: Non-Tg SAM24325784


title: hMAPT-P301S SAM24325791


title: Tg SAM24308125


title: hMAPT-P301S SAM24325794


title: hMAPT-P301S SAM24325792


title: WT_F1

description: RUNX1KOChimera_MCMV_F1M1M2_rawCounts_knownGene.txt

value: HPOS


title: WT SAM24308118

value: wild type


title: Non-Tg SAM24325785


title: opaque cell crosses biological rep 2

city: Providence

first: Christine

middle: Maria

last: Scaduto

state: RI

address: 171 Meeting Street

department: Molecular Microbiology and Immunology

institute: Brown University

description: mix of a cells and alpha cells

data_processing:
base calling by Illumina HiSeq software
sequenced reads were mapped to C. albicans genome (Assembly 21) using TopHat2
fragments per kilobase of transcript per million mapped reads (FPKM) values were calculated using Cufflinks
Genome_build: C albicans SC5314 Assembly 21
Supplementary_files_format_and_content: tab delimited text files of FPKM values for each sample

molecule: polyA RNA

organism: Candida albicans

source_name: C. albicans opaque a and alpha cells grown on Spider medium

growth_protocol: Spider agar for 8 hours

extract_protocol:
Cells were scraped off plates after 8 hours on mating media and flash frozen in liquid nitrogen. RNA was extracted using the RiboPure RNA purificaiton kit for yeast (Thermo Scientific).
Libraries were constructed using the Illumina TrueSeq Stranded mRNA Library Prep Kit (cat # RS-122-2103).

tag: strain

tag: cell state

value: opaque

value: WT


title: hMAPT-P301S SAM24325789


title: MAA3 RNAseq

city: Vancouver

first: Annie

middle: Vogel

last: Ciernia

state: British Columbia

address: 2215 Wesbrook Mall room 4550, Centre for Brain Health

country: Canada

institute: University of British Columbia

description: Mother given maternal allergic asthma inflammation on gestation day 9,12, and 17

data_processing:
RNA-seq reads were analyzed for both quality and adapter contamination using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
All reads were trimmed using Trimmomatic using Illuminaclip single end adapter trimming, a removal of the first three bp from the 5’ as recommended for SMARTer libraries, and a 4 bp sliding window trim for quality scores less than 15.  All remaining reads greater than 15 bp were then reanalyzed using FASTQC to verify quality.
RNA-seq reads were aligned to mouse genome mm10 using the splicing-aware aligner Tophat2 (v2.0.14/bowtie2.2.5, stranded, Single End) and reads aligning to each gene will were counted using FeatureCounts with exclusion of multimapping reads
Genome_build: mm10
Supplementary_files_format_and_content: FeatureCounts raw counts per gene

source_name: acutely isolated microglia, P35 brain

extract_protocol:
P35 female mice were deeply anaesthetized with CO2 and then quickly perfused intracardially with ice-cold PBS. Whole brains were removed and stored on ice in HBSS w/out Ca/Mg until processed. Each brain was gently homogenized to a single cell solution using a dounce, then added to 1.8ml of isotonic Percoll to form a 30% isotonic Percoll solution.  Isotonic Percoll gradients were then constructed with layers of 70% with 1x phenol red, 37% and the top layer of brain/30%.  The resulting gradients were spun in a swinging bucket centrifuge for 30min at 500xg at room temperature. The top layer of myelin and non-microglial cells were discarded and the microglia at the interface between the 37% and 70% layers were collected. The resulting microglia were then washed in HBSS and counted.  An additional animal was run in parallel and harvested microglia were used to assess purity by flow cytometry for CD45.2 and CD11b. The collected cells were immediately flash frozen for RNA/DNA extraction.
Duet RNA/DNA kit (Zymo, D7001) with on-column DNase digestion (Qiagen, 79254) for RNA extraction.  RNA and DNA were quantified using Qubit High Sensitivity assays.  RNA quality was assessed by Bioanalyzer and only samples with RIN scores greater than 7 were used for library preparation.  60-100 ng of input RNA per sample were used for RiboGone rRNA removal (Clonetech, 634847).  2 ng of rRNA depleted RNA per sample was then used for library construction using the SMARTer Stranded RNA-Seq kit (Clontech, 634836) and 14 cycles of PCR amplification.  Library quality was assessed using a bioanalyzer and quantified by Qubit high sensitivity assay.
All samples were barcoded, pooled, and run on a single sequencing lane of a HiSeq3000 to generate 50 bp single end reads.

treatment_protocol: Briefly, on postnatal day (P) 42 and 49 sexually naive female C57Bl/6J mice were sensitized with a single intraperitoneal injection of 10μg ovalbumin (OVA, Sigma, St. Louis, MO USA) in 1mg (Al)OH3 (InvivoGen, San Diego, CA USA) dissolved in 200μl phosphate buffered saline (PBS). One week following the second sensitization treatment, female mice were mated overnight and checked daily for the presence of a seminal plug, noted as gestational day 0.5 (G0.5). Pregnant mice were randomly assigned to either the allergic asthma or control group and exposed to either an aerosolized solution of 1% (wt/vl) OVA in PBS (maternal allergic asthma (MAA) group) or vehicle control for three 45-minute induction on gestational days 9.5, 12.5, and 17.5, to correspond with early, middle, and late gestation.  Following the final induction, mice were returned to their home cages, single housed, and left undisturbed until the birth of their litters. Pups remained with their mother until weaning on P21, at which time the offspring were group housed with same-sex littermates.

value: postnatal day 35

value: female

tag: index

value: TTAGGC

tag: group


title: WT SAM24308114

value: Female


title: Tg SAM24308124


title: Tg SAM24308122


title: Tg SAM24308120


title: sample15: PS2APP

source_name: RNA from sorted microglia (Cx3cr1::GFP+)

extract_protocol: See manuscript for details on extraction. Briefly, RNA was extracted from GFP+ cells using Qiagen RNeasy Plus Micro kit. RNA quality was quantified using the Bioanalyzer.

tag: tissue

value: cortex

value: sorted microglia (Cx3cr1::GFP+)

value: 15 months


title: sample13: non-Tg

value: 14 months

value: non-transgenic wild type


title: sample14: PS2APP


title: WT SAM24308116

value: 11-12 months-old


title: Id3hi Treg rep2

city: Freiburg

first: Kristina

last: Schachtrup

address: Breisacher Str. 117

department: Center for Chronic Immunodeficiency

country: Germany

institute: University Medical Center Freiburg

data_processing:
Reads mapped against mouse (mm10) genome using the STAR aligner application on Illumina BaseSpace
Differential gene analaysis performed using DeSeq2 application on Illumina BaseSpace.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts of sequencing reads

source_name: splenic Treg cells (CD4+CD25+CD45RBlo)

extract_protocol:
Treg cells were FACS sorted directly into RLT lysis buffer and RNA extracted using RNAeasy MicroKit (Qiagen) according to manufacturer’s recommendations. cDNA was generated using Ovation RNA-seq system V2 (NuGEN).
Libraries were constructed with Ovation Ultralow System V2 1-16 (NuGEN) according to the manufacturer’s instructions.
The libraries were subjected to 50 cycles of NextSeq 500 sequencing from 2-3 samples per cell type.

value: splenic Treg cells (CD4+CD25+CD45RBlo)


title: noTF-condition_RBMX-siRNA_rep1

status: Public on Dec 21 2017

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

data_processing:
Samples were demultiplexed (bcl2fastq using BaseSpace) to produce FASTQ files.
Sequenced reads were aligned to the hg19 Refseq gene model, in a strand-specific manner, using TopHat v2.0.11 (parameters: --b2-very-sensitive --library-type fr-firststrand).
To generate genome coverage tracks, BED files were first pooled between biological replicates. Reads aligning to genomic regions longer than the sequencing length (75 bp), due to spanning of splice junctions, were discarded. Pooled BED files were then converted to BedGraph files using genomeCoverageBed (bedtools v2.20.1) and normalized to the number of millions of reads sequenced, to correct for lane or sample biases. The resulting subtracted BedGraph was converted to a bigWig file using bedGraphToBigWig (v4).
Genome_build: hg19
Supplementary_files_format_and_content: bigWIg

organism: Homo sapiens

source_name: BJ foreskin fibroblasts

growth_protocol: Human BJ foreskin fibroblasts were obtained from Stemgent (08-0027) at passage 6 and cultured in Eagle’s Minimum Essential Medium (Sigma M2279) supplemented with 10% fetal bovine serum (FBS, Hyclone SH30071) and 2mM L-glutamine (Gibco) at 37°C and 5% CO2.

extract_protocol:
RNA was purified using the ZR-96 Quick-RNA kit (Zymo Research R1052) and was polyA-selected using Oligo(dT)25 Dynabeads (Thermo Fisher Scientific, #61002).
NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, #E7420S)

treatment_protocol: Cells were treated with two rounds of transfection with 10nM Silencer Silect siRNAs (Thermo Fisher Scientific) and 2.5 μl Lipofectamine RNAiMAX (Thermo Fisher #13778150), for 3 days per transfection. RNA was harvested at day 6 after the first transfection. For samples in the "hepatic TF" protocol, cells were first infected with lentiviruses delivering the human hepatic transcription factors FOXA3, HNF1A, and HNF4A (MOI 1.25 per virus) the day before the first siRNA transfection (day -1), or 7 days before RNA harvest.

tag: viral infection

tag: sirna

value: RBMX/RBMXL1 (10nM Silencer Select s56035)


title: sample10: PS2APP


title: sample9: non-Tg


title: sample5: non-Tg


title: sample4: PS2APP


title: sample8: PS2APP


title: WT SAM24308117

value: Brain Cd11b+ myeloid cells

value: Male


title: sample11: non-Tg


title: sample3: PS2APP


title: sample7: PS2APP


title: sample6: PS2APP


title: sample12: non-Tg


title: U87MG shFUBP1 1

city: Cambridge

first: Silvia

last: Buonamici

state: MA

address: 300 Technology Square #5

institute: H3 Biomedicine

description:
GS044836
Junction PSI

data_processing:
Raw data were aligned to hg19 using the STAR alignment package
Junction counts and reads across exon-intron boundaries are converted to percent spliced-in (PSI)
Genome_build: hg19
Supplementary_files_format_and_content: PSI values for each junction within each sample

source_name: GBM

extract_protocol:
Total RNA was harvested and Poly A selected
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: biomaterial provider

value: ATCC

tag: genotype/variation

value: FUBP1 knockdown via shRNA


title: Nalm-6 K700E H3B-8800 13nM 6hr 3

value: B-cell precursor

value: SF3B1 K700E mutant

tag: treated with

value: 13nM H3B-8800 for 6hrs


title: sample1: PS2APP

tag: genotype


title: sample2: non-Tg

tag: cell type


title: Nalm-6 K700E H3B-8800 13nM 6hr 2


title: Nalm-6 K700E H3B-8800 13nM 6hr 1


title: H3_D2_rep5_ChIPSeq

first: Siu

middle: Sylvia

last: Lee

state: NY

address: 520 Campus road

description:
glp-1 stands for the mutant abnormal Germ Line Proliferation
processed data file:
subtract_D2K4rep5ChIP_vs_H3_rmdup.bw.gz

data_processing:
Basecalls performed using CASAVA version 1.8
For RNAseq: tRNA and rRNA reads were first filtered out using Bowtie2 (2.2.6)  using the parameters --un-gz --al-gz -x–U –S. Libraries were stranded. RNA-seq reads  were further aligned to WBcel235 transcript annotation by TopHat2 (v2.1.0) (--min-segment-intron 20 --library-type fr-secondstrand --no-novel-juncs --transcriptome-index=transcriptome_data/known) with no novel junctions allowed
For ChIPseq: Sequencing reads were filtered by FASTX_toolkit (-q 20 –p 80) and mapped to C. elegans reference genome ce10 by bowtie2 (2.2.6) with the default setting (bowtie2 -x ce10 –U –S). Mapped reads were extracted (samtools view -hS -F 4) and PCR duplicates were removed with samtools (samtools rmdup -s). aligned reads were expressed as normalized bigwig using the deepTools utility bamCompare using the parameters --binSize 25 --fragmentLength 200 --missingDataAsZero no --ratio subtract --scaleFactorsMethod readCount --normalizeUsingRPKM
Genome build: ce10, WBcel235
Processed data files format and content: for ChIP-seq,bigwig files were generated to present H3K4me3 enrichment normalized to H3 by subtraction (Deeptools, bamCompare function). For ribo-RNAseq, tab-delimited text files include FPKM values from Cuffdiff (v2.1.1) analysis are used to present expression level.

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: C. elegans strain glp-1(e2141)  stocks were kept at 16°C and grown under standard growth condition (Brenner 1974).  For ChIP-seq and ribo-RNAseq experiments, embryos prepared from 16°C glp-1(e2141)  stocks by bleaching were hatched and cultured at 25°C with about 3,000 embryos per 15 cm Nematode Growth Media (NGM) plate seeded with concentrated E. coli OP50 (1.5 mL 30 x overnight culture) with carbenicillin (50 μg/mL) and tetracycline (15 μg/mL).  For day 12 samples, worms were re-fed once on day 4.

extract_protocol:
For ChIP-seq,chromatin immunoprecipitation was performed as described (Ercan et al. 2007; Landt et al. 2012).  Chromatin extract was incubated with H3 antibody, H3K4me3 antibodies overnight at 4°C.  Antibodies used were prescreened for specificity using dot blots.  The optimal amounts of antibodies used were determined by titration in preliminary experiment with ChIP-qPCR.  5-15 ng precipitated DNA from each sample was used for illumina sequencing library preparation.  DNA from ChIP was first end-repaired to generate blunt end, followed by adding single adenine base for adaptor ligation. Ligation product with adaptor was size selected and amplified by PCR with primers targeting adaptor.
Worms at L3,adult day 2, and adult day 12 stages were washed with ice cold M9 three times.  Worm pellets were stored at -80°C before chromatin immunoprecipitation and RNA extraction. For ChIP-seq, chromatin immunoprecipitation was performed as described (Ercan et al. 2007; Landt et al. 2012).  Worm pellet was grinded with mortar/pestle and cross-linked with 1% formaldehyde in PBS at room temperature for 10 min.  Worm fragments were collected by spinning at 3,000 g for 5 min and resuspended in FA buffer followed by sonication with Bioruptor. For ribo-RNAseq, total RNA was extracted from worms harvested at the same stages at adult day 2 and day 12 as ChIP-seq sample preparation.

tag: age

value: D2 young adult

value: whole animal

tag: chip-antibody

tag: antibody source

value: H3 (ab1791, Abcam)


title: Nalm-6 K700E E7107 15nM 6hr 3

value: 15nM  E7107 for 6hrs


title: NMyc_CD532

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

data_processing:
Fastq files were generated using Illumina's CASAVA software and overall sequencing quality was analyzed with the FastQC script.
For RNA-seq, reads were mapped to hg19 with Tophat2 and Bowtie1 with default settings.
Reads per gene were counted using the countOverlaps function from the R package {GenomicRanges}.
Weakly expressed genes were removed(mean count over all samples <1.5) and differentially expressed genes were called using EdgeR.
Genome_build: hg19
Supplementary_files_format_and_content: txt files containing Ensembl gene ID, gene symbol, gene description, log2FC, p-value and q-value (FDR) for all comparisons. A matrix file containing raw read counts for all samples.
For ChIP-seq, fastq files were mapped to the human genome (hg19) using Bowtie v1.1.1. and normalized to the sample with the smallest number of mapped reads.
Wiggle files were generated using MACS v1.4.2 with default parameters but a p-value cutoff of 1e-6.
Genome_build: hg19
Supplementary_files_format_and_content: Fixed step wiggle files with a resolution of 10bp.

growth_protocol: Neuroblastoma cells were grown in RPMI-1640 (Sigma). Medium was supplemented with 10% fetal calf serum (Biochrom) and penicillin/streptomycin (Sigma).

extract_protocol:
Cells were treated with 1% formaldehyde for 10 min at 37 °C. After cell lysis, nuclei were re-suspended in RIPA buffer (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% NP40, 1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA) and DNA was fragmented to a size <500 bp using a Branson sonifier. Chromatin was eluted with 1% SDS and crosslinking was reverted overnight. For purification, chloroform/phenol extraction was used.
Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (200 bp) and purified with Qiagen gel extraction kit. DNA fragments were amplified by 18 cycles of PCR and library size was tested with the Biorad Experion system. The amount of library DNA was quantified using a picogreen assay

treatment_protocol: For siRNA transfections, cells were transfected using the RNAiMAX reagent and OptiMem medium (LifeTechnologies) according to the manufacturer's instructions. Cells were harvested 48 h after transfection. Cells were treated with CD532 (1µM) or DMSO for 4 (ChIP-seq) or 4 and 8 (RNA-seq) hours.

tag: treatment

tag: antibody

value: N-MYC (B8.4.B, Santa Cruz, sc-53993)


title: SUM159OE1_IgG

city: Houston

first: Jenny

last: Chang

state: TX

address: 6670 Bertner Ave.

department: Houston Methodist Cancer Center

institute: Houston Methodist Hospital

data_processing:
Basecalls performed using HOMER’s findPeaks tool
We utilized the Burrows-Wheeler Aligner (BWA) MEM algorithm to align the sequence reads against the human genome GRCh37/hg19 Assembly.Peak calling identifies the regions in the genome where a significant number of sequencing reads are found. These peaks were visualized in bigWig track file format in the UCSC genome browser. This UCSC-accepted file was created by first running HOMER’s makeUCSCfile tool followed by UCSC’s bedGraphToBigWig script.
HOMER’s annotatePeaks.pl program was used to associate peaks with nearby genes.
To confirm the peaks found by HOMER’s findPeaks tool, and to check for additional peaks, we used another peak-finding algorithm, the Model-based Analysis for ChIP-Seq (MACS) program, to find peaks in our sample. Following this, we used the online tool PAVIS to annotate these peaks.
peaks were called using HOMER's findpeaks with the following setting: fold enrichment over input tag count 4.0, fold enrichment over local tag count 4.0, fold enrichment limit of expected unique tag positions 2.0.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: .txt file was generated using HOMER's findPeaks, peak score represents position adjusted reads from initial peak region - reads per position may be limited

source_name: Breast cancer

growth_protocol: Triple-negative breast cancer cell line were cultured in DMEM (Invitrogen, Grand Island, NY) with 10% FBS (Thermos Scientific Hyclone, Rockford, IL) in a humidified 5% CO2 incubator at 37ºC.

extract_protocol:
ChIP was carried out using EZ-ChIP kit (EMD Millipore, #17-371) following the manufacturer’s protocol.
DNA libraries were prepared for sequencing using the Illumina TruSeq Sample preparation kit.

treatment_protocol: SUM159 cells were transfected with a HN1L plasmid tagged with Myc-DDK (with DDK encoding a FLAG sequence) (Origene #RC209294) using TurboFectin transfection reagent (Origene). Transfected cells were selected using 3mg/ml G418 (Invitrogen) for 3 days.

value: Breast cancer

value: Passage 8

value: Triple negative


title: Nalm-6 K700E E7107 15nM 6hr 1


title: Nalm-6 K700E E7107 15nM 6hr 2


title: TF3C5_DMSO

value: DMSO

value: GTF3C5 (Bethyl, A301-242A)


title: NMyc_DMSO


title: Nalm-6 K700E 3

source_name: Nalm-6 K700E

value: none (untreated control)


title: STAT4WT_HPOS_D2_003

tag: replicate

value: HPOS

tag: condition

value: splenic NK cells


title: K562 SF3B1 K700E DMSO 3

source_name: K562 SF3B1 K700E DMSO

tag: disease state

value: Myelogenous leukemia

value: SF3B1 K700E

tag: agent

value: control


title: K562 SF3B1 K700E DMSO 1


title: K562 SF3B1 WT 38800 1xGI50 3

value: SF3B1 WT


title: Nalm-6 K700E 2

value: B-cell precursor

value: SF3B1 K700E mutant


title: input


title: wildtype mouse fetal liver small RNA replicate 2

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

country: Australia

institute: John Curtin School of Medical Research, The Australian National University

data_processing:
3' adapter sequences were  trimmmed using the cutadapt utility
reads < 17nt in size were filtered
identical read sequences were collapsed using the fastq_collapser utility
Supplementary_files_format_and_content: read count table files (columns are read sequence and number of reads)

source_name: mouse fetal liver

extract_protocol:
wildtype and Ago2 catalytic dead mouse fetal livers were dissected and flash frozen in liquid nitrogen. Total RNA was extracted using Trizol as per manufacturer's instructions.
For Illumina HiSeq Library: Libraries were created with the Illumina truseq small RNA cloning kit using a modified protocol (PMID: 25490151). All enzymatic reactions and oligos were used as indicated by manufacturer.

tag: tissue

value: fetal liver


title: K562 SF3B1 K700E DMSO 2


title: K562 SF3B1 K700E 38800 1xGI50 2


title: K562 SF3B1 K700E 38800 1xGI50 1


title: K562 SF3B1 WT DMSO 3

source_name: K562 SF3B1 WT DMSO


title: K562 SF3B1 WT 38800 1xGI50 1


title: DK_FP-Repl2

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: GKVK Campus, Bellary road

department: Plant epigenetics

country: India

institute: National Center for Biological Sciences

data_processing:
3’ adapter (5’-TGGAATTCTCGGGTGCCAAGG-3’) was removed from sequenced reads using UEA small RNA workbench.
The small RNA reads of length 16nt-35nt filtered and were analyzed.
Supplementary_files_format_and_content: Text file containing 16nt-35nt long unique reads and their raw abundance after removal of adapter.

organism: Vitis vinifera

source_name: Fruit peels

extract_protocol:
Total RNA from young leaves and fruits peels were extracted using the RNeasy Plant Mini Kit according to manufacters’ instructions with slight modifications
Size fractionation

tag: cultivar

value: Dilkhush

value: Fruit peels


title: K562 SF3B1 WT DMSO 2

tag: cell line


title: SUM159OE1_HN1L

value: Breast cancer


title: Tpre-Xyl-1

city: Adelphi

first: Matthew

last: Perisin

state: MD

address: 2800 Powder Mill Rd

department: Biotechnology Branch

institute: US Army Research Laboratory

data_processing:
Pooled libraries were 1 x 75 bp sequenced on a NextSeq 500 (Illumina, San Diego, CA, USA) in two sequencing runs. Tpre and T15 in one run. T30 and T60 in another run.
Base calling with RTA version 2.4.11
Concatenate and compress reads from different lanes with zcat and gzip
Quality filter and trim reads with Trimmomatic-0.36 (parameters: ILLUMINACLIP:Trimmomatic-0.36/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
Reverse complement reads with FASTX toolkit version 0.0.13 (fastx_reverse_complement -Q33)
Determine gene expression levels with EDGE-pro version 1.3.1
Genome_build: GCF_000008765.1_ASM876v1
Supplementary_files_format_and_content: Concatenate mapped read counts for all genes and samples into table (pentose_hierarchy_EdgePro_Reads_table.csv)
Supplementary_files_format_and_content: Differential expression testing with DESeq2 version 1.10.1 in R version 3.4.0 (default parameters, rlog transformed counts in: pentose_hierarchy_EdgePro_rlog_Reads_table.csv)
Supplementary_files_format_and_content: RPKM values calculated using R (pentose_hierarchy_EdgePro_RPKM_table.csv)

organism: Clostridium acetobutylicum ATCC 824

source_name: cell culture

growth_protocol: Clostridium acetobutylicum ATCC 824 was utilized for all studies. All growth was conducted anaerobically in a Coy anaerobic chamber (Coy Lab Products) at 37°C in an atmosphere containing 5% H2, 5% CO2, and 90% N2. Cells were maintained as spore suspensions in potato glucose medium (PGM) containing, per liter: 150 g potato (shredded, boiled 1 hour, and filtered through cheesecloth), 1% glucose, 30 mM CaCO3, and 4 mM (NH4)2SO4. Experimental cultures were grown in clostridium growth medium (CGM) containing, per liter: 0.5% yeast extract, 15 mM (NH4)2SO4, 15 mM L-Asparagine, 17 mM NaCl, 5 mM KH2(PO4), 3 mM Mg(SO4)*H2O, 0.7 mM Mn(SO4)*H2O, 0.4 mM Fe(SO4)*7H2O.

extract_protocol:
Total RNA was isolated using the miRNeasy Mini Kit (Qiagen; 217004) according to the manufacturer’s protocol, with an additional homogenization and mechanical disruption step using a bead beater (BioSpec, Bartlesville, OK, USA) with Zirconia/Silica beads (BioSpec; 11079101z). RNA quality was assessed using the 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and quantified using a spectrophotometer (DeNovix, Wilmington, DE, USA) and was stored at -80°C until DNase treatment. DNA was removed using the TURBO DNA-free kit (Life Technologies; AM1907) according to the manufacturer’s protocol. RNA was quantified and quality assessed, as stated above, and genomic DNA depletion was confirmed using qPCR with 16S rRNA gene primers [19] and iQ SYBR Green Supermix (Bio-Rad; 170-8882) according to the manufacturer’s instructions. Ribosomal RNA was removed using the Ribo-Zero rRNA Removal Kit (Gram-Positive Bacteria) (Illumina; MRZGP126) according to the manufacturer’s protocol. The quality of rRNA depleted samples was assessed using a 2100 BioAnalyzer prior to processing for sequencing library generation.
TruSeq Stranded mRNA Sample Preparation Kit (Illumina; RS-122-2101) was used to prepare the rRNA depleted RNA for sequencing according to the manufacturer’s protocol. Libraries were quantified using the Kapa Library Quantification Kit (KapaBiosystems; KK4854) according to the manufacturer’s instructions, then normalized and pooled for sequencing according to the Denature and Dilute Libraries Guide for the NextSeq 500 (Illumina; Doc No – 15048776 v02).

treatment_protocol: All cultures were incubated at 37°C under anaerobic conditions open to the environment of the anaerobe chamber, without shaking. Spores were heat shocked at 80°C for 10 minutes and inoculated into CGM supplemented with 0.5% xylose. Starter cultures were subcultured into 0.5% xylose CGM and incubated overnight. At OD600 = 0.2 the culture was aliquoted into milk dilutions bottles (70 mL each; four conditions in triplicate independent biological replicates ) and incubated until OD600 = 0.4. Pre-carbohydrate supplementation RNA and metabolite analysis samples were collected. Cultures were then supplemented with arabinose (0.25% final), glucose (0.25% final), or xylose (0.25% final), from a 50% stock solution of the respective sugars in water, or equal volume of water (control). RNA, metabolites, and OD600 readings were taken at 0 min, 15 min, 30 min, and 60 min. Cultures were monitored for an additional 9 hours and metabolites and OD600 reading were taken every hour. Final OD600 readings and metabolite samples were taken the following day at 21 hours post supplemental sugar addition. Samples collected for RNA isolation were immediately incubated with 0.03 mg/mL rifampicin (final concentration) on ice, pelleted and treated with RNA Protect (Qiagen, Valencia, CA) according to the manufacturer’s protocol, and stored at -80°C until RNA extraction.

tag: media

value: CGM + 0.5% xylose

tag: added sugar

value: 0.25% xylose

tag: time (min)


title: Tpre-Xyl-3


title: Tpre-Xyl-2


title: DK_FP-Repl1


title: RG_FP-Repl2

value: Red globe


title: Nalm-6 K700E 1

tag: genotype/variation

tag: treated with


title: K562 SF3B1 K700E 38800 1xGI50 3


title: Tpre-None-2

value: water


title: Tpre-None-1


title: RG_FP-Repl1


title: TF3C5_CD532

value: GTF3C5 (Bethyl, A301-242A)


title: DK_YL-Repl2

source_name: Young leaves

value: Young leaves


title: BB_FP-Repl2

value: Bangalore blue


title: K562 SF3B1 WT 38800 1xGI50 2

value: Myelogenous leukemia


title: DK_YL-Repl1


title: BB_FP-Repl1


title: Tpre-Glu-3

value: 0.25% glucose


title: Tpre-Ara-3

value: 0.25% arabinose


title: Tpre-Glu-1


title: Tpre-Glu-2


title: RG_YL-Repl2


title: Tpre-None-3


title: input_L3_rep2_ChIPSeq

description: glp-1 stands for the mutant abnormal Germ Line Proliferation

tag: strain

tag: age

value: whole animal


title: Tpre-Ara-2


title: DK_FP-Repl2

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads.
The processed reads were aligned to grape transcriptome using TopHat (v2.1.1).
Gene expressions were calculated using CuffLinks (v2.2.1) as mentioned in Cole Trapnell et al, 2012.
Genome_build: grape transcriptome Genoscope 12X v2
Supplementary_files_format_and_content: Text delimited files including RPKM for each sample.

extract_protocol:
Total RNA from young leaves and fruits peels were extracted using the RNeasy Plant Mini Kit according to manufacters’ instructions with slight modifications
Transcriptome library for sequencing was constructed according to the NEXTflex Rapid Directional mRNA-Seq Bundle library protocol outlined in “NEXTflexTM Rapid Directional mRNA-Seq Sample Preparation Guide” (Cat # 5138-10)


title: H3_L3_rep1_ChIPSeq

description:
glp-1 stands for the mutant abnormal Germ Line Proliferation
processed data file:
subtract_L3K4me3ChIP_vs_H3_rmdup.bw

tag: chip-antibody

tag: antibody source

value: H3 (ab1791, Abcam)


title: input_L3_rep1_ChIPSeq


title: H3K4me3_L3_rep1_ChIPSeq

value: H3K4me3 (ab9050, Abcam)


title: T60-Xyl-2


title: T60-Xyl-1


title: H3_L3_rep2_ChIPSeq


title: RG_FP-Repl2


title: H3K4me3_L3_rep2_ChIPSeq

value: H3K4me3 (17-614,millipore)


title: RG_YL-Repl1


title: DK_FP-Repl1

value: Dilkhush


title: RG_FP-Repl1

value: Fruit peels


title: T60-None-2


title: DK_YL-Repl2


title: T60-None-1


title: T60-Glu-1


title: T60-Xyl-3


title: DK_YL-Repl1


title: BB_FP-Repl2


title: RG_YL-Repl1


title: BB_FP-Repl1


title: RG_YL-Repl2


title: T60-Glu-3


title: T60-Ara-3


title: BB_YL-Repl1


title: T60-None-3


title: BB_YL-Repl2


title: Tpre-Ara-1


title: T60-Ara-2


title: BB_YL-Repl1


title: PG (regular RNA seq) 1

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

data_processing:
For the RNA-seq data, all the pair-end reads were mapped to the zebrafish genome  using TopHat (version 2.0.11). Genome annotation files with GTF format for known genes were downloaded from Ensembl. FPKM and RPKM values were calculated for each miRNA and gene respectively using Cufflinks software (version 2.2.1) with default parameters.
Genome_build: Zv9 (Ensembl release 79)
Supplementary_files_format_and_content: tab-delimited text files include FFKM for each mRNA transcript; tab-delimited text files include RFKM for each miRNA.

organism: Danio rerio

source_name: Ovarian follicle

growth_protocol: AB fish was housed under a stable flow-through condition at 28°C on a 14L:10D photoperiod with the light on at 0800 and off at 2200. Fish were fed regularly twice a day with live brine shrimp with supplement of commercial tropical fish food at a fixed time basis.

extract_protocol:
RNA was extracted with miRNeasy and RNAeasy extraction kits (Qiagen)
RNA-Seq libraries were constructed according to Illumima TrueSeq and small RNA-seq protocol, and sequenced with the Illumina Hiseq 2000
Single-end sequencing and pair-end sequencing were used for small RNA-seq library and RNA-seq library, respectively

treatment_protocol: Ovaries from 3-month old adult zebrafish were dissected in 60% medium of Leibovitz L-15 and follicles (PG,PV) were sorted out according to the size and morphology.

value: AB

tag: cell type

value: Primary growth follicle

value: from ovary of 3-month zebrafish


title: PG (regular RNA seq) 2

value: Pre-vitellogenic follicle


title: T30-Xyl-2

value: CGM + 0.5% xylose

value: 0.25% xylose

tag: replicate


title: T30-None-3

value: water


title: PG (small RNA seq) 2


title: T30-Xyl-1


title: T30-None-2


title: T60-Glu-2


title: T30-Glu-3


title: T30-Glu-2


title: T30-Ara-3


title: T30-Ara-2


title: T30-None-1


title: T15-Xyl-2


title: T15-Xyl-1


title: T30-Ara-1


title: T60-Ara-1


title: T15-None-2


title: T15-Glu-3


title: T15-Glu-2


title: T30-Glu-1


title: T30-Xyl-3


title: T15-Xyl-3


title: PG (small RNA seq) 1


title: T15-Glu-1


title: BB_YL-Repl2

value: Bangalore blue

value: Young leaves


title: T15-Ara-2


title: T15-None-3


title: T15-Ara-3


title: T15-None-1


title: Dsim_20

status: Public on Dec 19 2017

city: Woodbury

first: Philippe

last: Batut

address: 500 Sunnyside Blvd.

institute: CSHL

data_processing:
Sequences corresponding to the library identification barcode (first 6 bases of read 1) and the reverse-transcription primer (first 15 bases of read 2) were trimmed prior to mapping.
Trimmed reads were mapped with STAR, with parameters as follows (--outSAMattributes All --outFilterScoreMinOverLread 0.85 --outFilterMatchNminOverLread 0.85 —outFilterMultimapNmax 50 --outFilterIntronMotifs None --seedSearchStartLmax 30 —outSAMunmapped Within --outFilterType BySJout --outFilterMismatchNmax 10 —clip5pNbases 6 15). All uniquely mapping reads were kept. As a rescue strategy for multiply mapping reads, if all alignments for those reads started within an annotated transposon and overlapped the same gene annotation, the alignment starting in the closest transposon insertion was selected. All non-rescued multi-mappers were discarded.
PCR duplicates, defined as reads sharing the same alignment coordinates (start, end and splice sites), were removed from the individual datasets. To avoid over-collapsing, we took advantage of the fact that the long random sequence (15-mer) of our reverse-transcription primer often primes with mismatches. We used this sequence as a pseudo-random barcode allowing us to distinguish between true duplicates (same barcode) and independent identical inserts.
Custom scripts were used to extract the 5'-most position of each RAMPAGE read, which corresponds to the TSS used for the transcription of the original RNA molecule.
All collapsed datasets in the time series were  combined prior to peak calling. The density of cDNA 5' ends across the genome was determined from this combined dataset, as well as the density of coverage by second (i.e., downstream) sequencing reads. Peaks were called by a sliding window algorithm that assesses the significance of local signal enrichment given a null distribution. Downstream read coverage in the same window was used to correct for local transcript abundance, by subtracting from the raw signal a pseudocount proportional to this coverage. After FDR correction, significant windows in close proximity to each other were merged into peaks, and those were trimmed at the edges down to the first base with signal. (Parameters: window width 15 bases, null distribution negative binomial with k=0.5, background weight 0.5, FDR 0.1, merging range 150 bases).
Individual peaks were connected to annotated genes based on cDNA structure information. For each peak, if we could find at least 2 inserts having their 5' in the peak and overlapping an annotated exon of a gene, the peak was functionally linked to that gene. If a peak could potentially be linked to several genes, ties were broken by removing all links that were 5-fold weaker than the strongest one. For quantification, the signal for each peak and each timepoint was derived from the uncollapsed datasets, and normalized to dataset size (defined as the total number of reads attributed to any genic TSS). Expression valuesin the matrix files are thus in reads per milion (RPM). Expression values for genes are the sum of expression values for all TSCs attributed to the gene (in RPM).
Gene expression matrices were upsampled 5-fold, subjected to Gaussian smoothing (width parameter=10), and converted to Z-scores using the GTEM package (see Goltsev et al., BMC Bioinformatics 2009). The time series was globally aligned to the D. melanogaster replicate 1 series using the MAlign tool in GTEM.
Genome_build: dsim r1.4 (FlyBase)
Supplementary_files_format_and_content: Signal density tracks (bigWig) were generated after collapsing PCR duplicates, and represent the density of RAMPAGE read 5' ends (i.e., the 5' mapping position) over each base across the genome.
Supplementary_files_format_and_content: Peak calls (i.e., TSCs) for the combined time series datasets are annotated in BED6 file format. Scores correspond to the total number of collapsed read 5' ends supporting the peak.
Supplementary_files_format_and_content: TSC expression and Gene expression matrices combine expression values for individual features, normalized by the total number of uniquely mapped reads per time point (in reads per million, RPM).
Supplementary_files_format_and_content: The aligned gene expression matrix represents expression values as Z-scores of the original RPM values, after upsampling, smoothing and global alignment of the time series.

organism: Drosophila simulans

source_name: Whole embryos (staged)

growth_protocol: Stocks were maintained on standard cornmeal medium. Embryo collections were performed in population cages. 2- to 7-day-old flies were left to acclimatize to the cage for at least 48h and regularly fed with grape juice-agar plates generously loaded with fresh yeast paste. After two 2-hour pre-lays, embryos were collected in 1-hour windows and aged appropriately (22 time points, 0-22h). Embryos were washed with deionized water, dechorionated for 90 sec with 50% bleach, rinsed abundantly with water, and snap-frozen in liquid nitrogen.

extract_protocol:
Total RNA was extracted from embryos using a Beadbeater (Biospec, Cat. #607) with 1.0 mm zirconia beads (Biospec, #11079110zx) and the RNAdvance Tissue kit (Agencourt #A32649) according to the manufacturer’s instructions, including DNaseI treatment. We systematically checked on a Bioanalyzer RNA Nano chip (Agilent) that the RNA was of very high quality.
Libraries were prepared as described in Batut et al., Genome Research 2012. In brief, 5’-monophosphate transcripts were depleted by TEX digest (Epicentre #TER51020). For every time series, each sample was labeled with a different sequence barcode during reverse-transcription, and all samples for the series were then pooled and processed together as a single library. The 5'-complete cDNA selection strategy relies on the combination of two orthogonal enrichment methods: reverse-transcriptase template-switching, and cap-trapping. The template-switching approach is based on the ability of reverse-transcriptase to add linker sequences to the ends of 5'-complete cDNAs – preferentially if they are made from capped transcripts. Cap-trapping relies on the biotinylation of capped RNA molecules and specific pulldown of their associated 5'-complete cDNAs. Quality control and library quantification were carried out on a Bioanalyzer DNA High Sensitivity chip. Each library was sequenced on one lane of an Illumina HiSeq 2000.
reference: Batut, P., Dobin, A., Plessy, C., Carninci, P. & Gingeras, T.R. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Res (2012).
reference: Batut, P. & Gingeras, T.R. RAMPAGE: Promoter Activity Profiling by Paired-End Sequencing of 5'-Complete cDNAs. Curr Protoc Mol Biol 104, 25B 11 1-25B 11 16 (2013).

value: w[501] (reference genome strain)

tag: ucsd stock #

tag: Stage

value: 19-20 hours after egg laying


title: Dsim_17

value: 16-17 hours after egg laying


title: Dsim_19

value: 18-19 hours after egg laying


title: Dsim_22

value: 21-22 hours after egg laying


title: Dsim_16

value: 15-16 hours after egg laying


title: Dsim_18

value: 17-18 hours after egg laying


title: Dsim_21

value: 20-21 hours after egg laying


title: Dsim_15

value: 14-15 hours after egg laying


title: Dsim_14

value: 13-14 hours after egg laying


title: Dsim_13

value: 12-13 hours after egg laying


title: Dsim_11

value: 10-11 hours after egg laying


title: Dsim_10

value: 9-10 hours after egg laying


title: Dsim_12

value: 11-12 hours after egg laying


title: Dsim_09

value: 8-9 hours after egg laying


title: Dsim_07

value: 6-7 hours after egg laying


title: Dsim_06

value: 5-6 hours after egg laying


title: Dsim_08

value: w[501] (reference genome strain)

value: 7-8 hours after egg laying


title: T15-Ara-1

value: CGM + 0.5% xylose

value: 0.25% arabinose


title: Dsim_04

value: 3-4 hours after egg laying


title: Dsim_05

value: 4-5 hours after egg laying


title: Dsim_03

value: 2-3 hours after egg laying


title: Dsim_02

value: 1-2 hours after egg laying


title: Dsim_01

value: 0-1 hour after egg laying


title: Dmel2_20

data_processing:
Sequences corresponding to the library identification barcode (first 6 bases of read 1) and the reverse-transcription primer (first 15 bases of read 2) were trimmed prior to mapping.
Trimmed reads were mapped with STAR, with parameters as follows (--outSAMattributes All --outFilterScoreMinOverLread 0.85 --outFilterMatchNminOverLread 0.85 —outFilterMultimapNmax 50 --outFilterIntronMotifs None --seedSearchStartLmax 30 —outSAMunmapped Within --outFilterType BySJout --outFilterMismatchNmax 10 —clip5pNbases 6 15). All uniquely mapping reads were kept. As a rescue strategy for multiply mapping reads, if all alignments for those reads started within an annotated transposon and overlapped the same gene annotation, the alignment starting in the closest transposon insertion was selected. All non-rescued multi-mappers were discarded.
PCR duplicates, defined as reads sharing the same alignment coordinates (start, end and splice sites), were removed from the individual datasets. To avoid over-collapsing, we took advantage of the fact that the long random sequence (15-mer) of our reverse-transcription primer often primes with mismatches. We used this sequence as a pseudo-random barcode allowing us to distinguish between true duplicates (same barcode) and independent identical inserts.
Custom scripts were used to extract the 5'-most position of each RAMPAGE read, which corresponds to the TSS used for the transcription of the original RNA molecule.
All collapsed datasets in the time series were  combined prior to peak calling. The density of cDNA 5' ends across the genome was determined from this combined dataset, as well as the density of coverage by second (i.e., downstream) sequencing reads. Peaks were called by a sliding window algorithm that assesses the significance of local signal enrichment given a null distribution. Downstream read coverage in the same window was used to correct for local transcript abundance, by subtracting from the raw signal a pseudocount proportional to this coverage. After FDR correction, significant windows in close proximity to each other were merged into peaks, and those were trimmed at the edges down to the first base with signal. (Parameters: window width 15 bases, null distribution negative binomial with k=0.5, background weight 0.5, FDR 0.1, merging range 150 bases).
Individual peaks were connected to annotated genes based on cDNA structure information. For each peak, if we could find at least 2 inserts having their 5' in the peak and overlapping an annotated exon of a gene, the peak was functionally linked to that gene. If a peak could potentially be linked to several genes, ties were broken by removing all links that were 5-fold weaker than the strongest one. For quantification, the signal for each peak and each timepoint was derived from the uncollapsed datasets, and normalized to dataset size (defined as the total number of reads attributed to any genic TSS). Expression valuesin the matrix files are thus in reads per milion (RPM). Expression values for genes are the sum of expression values for all TSCs attributed to the gene (in RPM).
Gene expression matrices were upsampled 5-fold, subjected to Gaussian smoothing (width parameter=10), and converted to Z-scores using the GTEM package (see Goltsev et al., BMC Bioinformatics 2009). The time series was globally aligned to the D. melanogaster replicate 1 series using the MAlign tool in GTEM.
Genome_build: dm3 (FlyBase r5.49)
Supplementary_files_format_and_content: Signal density tracks (bigWig) were generated after collapsing PCR duplicates, and represent the density of RAMPAGE read 5' ends (i.e., the 5' mapping position) over each base across the genome.
Supplementary_files_format_and_content: Peak calls (i.e., TSCs) for the combined time series datasets are annotated in BED6 file format. Scores correspond to the total number of collapsed read 5' ends supporting the peak.
Supplementary_files_format_and_content: TSC expression and Gene expression matrices combine expression values for individual features, normalized by the total number of uniquely mapped reads per time point (in reads per million, RPM).
Supplementary_files_format_and_content: The aligned gene expression matrix represents expression values as Z-scores of the original RPM values, after upsampling, smoothing and global alignment of the time series.

organism: Drosophila melanogaster

growth_protocol: Stocks were maintained on standard cornmeal medium. Embryo collections were performed in population cages. 2- to 7-day-old flies were left to acclimatize to the cage for at least 48h and regularly fed with grape juice-agar plates generously loaded with fresh yeast paste. After two 2-hour pre-lays, embryos were collected in 1-hour windows and aged appropriately (23 time points, 0-23h). Embryos were washed with deionized water, dechorionated for 90 sec with 50% bleach, rinsed abundantly with water, and snap-frozen in liquid nitrogen.

value: y; cn bw sp

value: 19-20 hours after egg laying


title: Dmel2_19

value: 18-19 hours after egg laying


title: Dmel2_21

value: 20-21 hours after egg laying


title: Dmel2_23

value: 22-23 hours after egg laying


title: Dmel2_22

value: 21-22 hours after egg laying


title: Dmel2_18

value: 17-18 hours after egg laying


title: Dmel2_13

value: 12-13 hours after egg laying


title: Dmel2_15

value: 14-15 hours after egg laying


title: Dmel2_17

value: 16-17 hours after egg laying


title: Dmel2_16

value: 15-16 hours after egg laying


title: Dmel2_14

value: 13-14 hours after egg laying


title: Dmel2_10

value: 9-10 hours after egg laying


title: Dmel2_07

value: 6-7 hours after egg laying


title: Dmel2_11

value: 10-11 hours after egg laying


title: Dmel2_09

value: 8-9 hours after egg laying


title: Dmel2_06

value: 5-6 hours after egg laying


title: Dmel2_08

value: y; cn bw sp

value: 7-8 hours after egg laying


title: Dmel2_05

value: 4-5 hours after egg laying


title: Dmel2_02

value: 1-2 hours after egg laying


title: Dmel2_03

value: 2-3 hours after egg laying


title: Dmel2_01

value: 0-1 hour after egg laying


title: Te05-W-s94R

city: Hangzhou

first: Hongshan

last: Guo

state: Zhejiang Province

address: No.1369, Wenyixi Road

department: School of Medicine, Zhejiang University

country: China

institute: Liangzhu Laboratory

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
All sequencing reads were first trimmed to remove adaptors and low quality bases using trim_galore (RefXXX) (parameters: --quality 20 --phred33 –length 50 --paired).
Next, reads passed quality control were mapped to human or mouse reference genome (version: hg19 or mm9) using bismark (version: 0.7.6) for bisulfite sequencing reads with paired-end alignment mode (parameters: --non-directional --fastq) and tophat for RNA-seq reads. To rescue more bisulfite sequencing reads, unmapped reads were realigned to the same reference genome in single-end alignment mode.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: For bisulfite sequencing samples, the processed files include the DNA methylation levels of cytosines in CpG, CHH and CHG context, in bed format. Processed data of RNA-seq samples were gene expression tables obtained from cufflinks.

extract_protocol:
single cell or small amounts of cells were seeded into the lysis buffer using the mouth pipette, and DNAs were released after proteinase treatment at 50C and then bisulfite converted.
After purification, DNAs were complemented with the biotinated random primer (5’-biotin-CTACACGACGCTCTTCCGATCTNNNNNNNNN-3’) and 50 units of klenow polymerase (3’ to 5’exo-, New England Biolabs). This random priming was repeated 5 times in total. The second strands were synthesized using another random primer (5’-AGACGTGTGCTCTTCCGATCTNNNNNNNNN-3’) and the final libraries were generated after 8-12 cycles PCR amplification with the Illumina universal PCR primer and Illumina indexed primer. For RNA-Seq, transcriptome of single cells or low amount of cells were amplified using a modified Smart-seq2. We reversely transcribed RNA molecules using a oligo (dT) primer anchored with 8bp unique molecular identifiers (UMI). Amplified cDNAs were fragmented into around 300 bp using a Covaris S2 and the sequencing libraries were constructed using a Kapa Hyper Prep Kit (Kapa Biosystems).

value: TE

tag: gender

value: male

tag: bulk or single cell

value: single cell


title: NG-G1

source_name: Peripheral Blood

value: Peripheral Blood

value: female

value: bulk cells


title: Te05-W-s93R


title: Te11-Q-s106R


title: Te13-Q-s119R


title: Dmel2_04

value: 3-4 hours after egg laying


title: NG-G2


title: Dmel2_12

value: 11-12 hours after egg laying


title: Te05-W-s92R


title: Te05-W-s91R


title: Te05-W-s88R


title: Te05-W-s90R


title: Te05-W-s89R


title: K562 SF3B1 WT DMSO 1

tag: disease state

value: Myelogenous leukemia

value: SF3B1 WT

tag: agent

value: control


title: Te05-W-b172R


title: Te05-W-b173R


title: Te04-W-s72R


title: Te05-W-s87R


title: Te04-W-s73R


title: Te04-W-s74R


title: Te04-W-s67R


title: Te04-W-s69R


title: Te04-W-s70R


title: Te04-W-s68R


title: Te04-W-b169R


title: Te03-W-s50R


title: Te03-W-s52R


title: Te03-W-s51R


title: Te03-W-s48R


title: Te03-W-s47R


title: Te03-W-s46R


title: Te02-W-s31R


title: Te03-W-b177R


title: Te03-W-b178R


title: Te03-W-s45R


title: Te02-W-s30R


title: Te02-W-s29R


title: Te02-W-s28R


title: Te04-W-s71R


title: Te02-W-s26R


title: Te02-W-b188R


title: Te02-W-s27R


title: Te01-W-s09R


title: Te02-W-b187R


title: Te01-W-s10R


title: Te01-W-s08R


title: Te01-W-s07R


title: Te02-W-s25R


title: Te01-W-s05R


title: CTCF_5-3hfp_A

city: Dunedin

first: Michael

last: Meier

address: 1st Floor Hercus Building, Dunedin School of Medicine, Great King Street

department: Pathology

country: New Zealand

institute: University of Otago

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Zebrafish genome danRer7[Zv9] using TopHat2 (version 2.0.9) with parameters tophat2 --GTF genes.gtf --library-type fr-firststrand -p 24 --mate-inner-dist -8 --mate-std-dev 6 zv9
Transcriptomes were assembled with Cufflinks (version 2.2.0) using options: ‘cufflinks -p 32 --GTF genes.gtf’ and differential expression analysis between control and knockdown embryos was performed using Cuffdiff
Genome_build: Zv9
Supplementary_files_format_and_content: xls spread sheet file including differentially expressed transcripts from pairwise comparisons between conditions at each stage and tab delimited txt file with FPKM values for each Sample

source_name: whole embryos

extract_protocol:
Morpholino injected and control embryos were stage matched by eye and collected at defined stage. 100 pooled embryos were put in RA1 buffer (NucleoSpin® RNAII Kit, Macherey-Nagel) and flash frozen with LN. Illumina TruSeq stranded total RNA-ribozero kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: AB/PS

tag: tissue

value: whole embryos

value: 5.3 hpf

tag: genotype

value: CTCF MO


title: CTCF_5-3hfp_B


title: CTCF_10hfp_A

value: 10 hpf


title: Te01-W-s06R


title: Te02-W-s32R


title: CTCF_10hfp_C


title: Te01-W-s04R


title: CTCF_4-5hpf_C

value: 4.5 hpf


title: Te01-W-s03R

value: TE


title: Te01-W-b11R

value: male


title: CTCF_4-5hpf_B


title: CTCF_4-5hpf_A


title: Icm11-Q-s111R

value: ICM

value: single cell


title: CTCF_3-3hfp_C

value: 3.3 hpf


title: CTCF_3-3hfp_B


title: Icm10-Q-s258

value: female


title: Icm05-W-s99R


title: CTCF_5-3hfp_C


title: CTCF_10hfp_B


title: CTCF_2-5hpf_A

value: 2.5 hpf


title: Icm05-W-s97R


title: CTCF_2-5hpf_B


title: Icm05-W-s98R


title: CTCF_2-5hpf_C


title: Rad21_10hfp_C

value: Rad21 MO


title: Icm05-W-s95R


title: Rad21_10hfp_B


title: Rad21_10hfp_A


title: Te01-W-b12R

value: bulk cells


title: Icm13-Q-s123R


title: Rad21_5-3hfp_C


title: Icm05-W-s104R


title: Icm05-W-s102R


title: Icm05-W-s101R


title: Rad21_5-3hfp_A


title: Rad21_4-5hpf_C


title: CTCF_3-3hfp_A


title: Rad21_4-5hpf_B


title: Rad21_4-5hpf_A


title: Icm05-W-s100R


title: Icm05-W-b174R


title: Icm05-W-b175R


title: Icm04-W-s83R


title: Icm05-W-s96R


title: Icm04-W-s84R


title: Rad21_3-3hfp_B


title: Rad21_3-3hfp_A


title: Icm04-W-s82R


title: Rad21_3-3hfp_C


title: Icm04-W-s81R


title: Icm04-W-s80R


title: Icm05-W-s103R


title: Rad21_2-5hpf_B


title: Rad21_2-5hpf_C


title: Rad21_5-3hfp_B


title: Rad21_2-5hpf_A


title: WT_10hfp_C

value: wild type


title: Icm04-W-s78R


title: WT_10hfp_B


title: Icm04-W-b171R


title: Icm04-W-s77R


title: WT_5-3hfp_C


title: WT_10hfp_A


title: WT_5-3hfp_B


title: Icm04-W-b170R


title: WT_4-5hpf_C


title: Icm03-W-s59R


title: Icm03-W-s58R


title: WT_4-5hpf_B


title: WT_3-3hfp_C


title: WT_4-5hpf_A


title: WT_3-3hfp_A


title: Icm03-W-s56R


title: Icm03-W-s57R


title: Icm03-W-b190R


title: Icm04-W-s79R


title: WT_2-5hpf_C


title: Icm03-W-b180R


title: WT_3-3hfp_B


title: Icm03-W-s55R


title: 10_hpf_CTCF_2

data_processing:
After adapter and quality trimming, reads were aligned to the Zv9 genome assembly using bowtie2 (version 2.2.1.) with default settings. 85% of the raw reads could be aligned except for Rad21 ChIP samples from 2.5 hpf, which had a 40% mapping rate
Peak finding and downstream data analysis was performed using HOMER. Peaks were defined at a 0.1% estimated false discovery rate
Genome_build: Zv9
Supplementary_files_format_and_content: peak files in bed format from HOMER analysis,

extract_protocol:
Chromatin was prepared from two independent collections of pooled embryos (n=2000) for 2.5 hpf stage embryos and (n=1000) for 4.5 hpf and 10 hpf embryos.Briefly, embryos were dechorionated using a syringe with a 21G needle, fixed in 1% formaldehyde 10 minutes at room temperature. Fixation was stopped by adding glycine to a final concentration to 0.125 M and incubation on ice for 5 minutes. Fixed embryos were then washed three times in ice cold 1x PBS, snap frozen and stored at -80 °C until use. After cell lysis, chromatin was sheared to 200-500 base pairs using a S220 Focused-ultrasonicator (Covaris) with the following settings per cycle: peak power = 70, duty factor = 5, cycles of bursts = 200, time=30 s. Individual cycle numbers were optimized for each stage. Chromatin from pre-MZT embryos needed 6 cycles of sonication to reach the desired 200-500 bp range, whereas chromatin isolated from 4.5 hpf and 10 hpf stages required 10 cycles.  Cell debris was removed by centrifugation. To provide standardized input for each ChIP experiment, chromatin was diluted to A260=0.25. For each ChIP, 6 µg of Rad21 antibody per 10 µl Dynabeads and 100 µl chromatin was incubated overnight at 4 °C. After elution, ChIP DNA and input controls were purified and precipitated with ethanol.
The ThruPLEX® DNA-seq Kit (Rubicon Genomics, USA) was used to prepare the 2.5 hpf sample libraries for sequencing. 125-bp paired-end sequencing was performed to a depth of 20-50 million reads per library on an Illumina HiSeq 2500TM by New Zealand Genomics Limited, NZ. Libraries for the 4.5 hpf and 10 hpf samples were constructed and sequenced at the Beijing Genomics Institute (China), yielding 20 million 50 bp single-end reads per sample

tag: chip antibody

value: CTCF (custom made by GenScript Corporation, USA)


title: Icm02-W-s39R


title: WT_2-5hpf_A

value: AB/PS


title: WT_5-3hfp_A

value: whole embryos


title: Icm02-W-s37R


title: Icm02-W-s36R


title: Icm02-W-s35R


title: Icm02-W-s41R


title: Icm02-W-s42R


title: WT_2-5hpf_B


title: 10_hpf_Rad21_1

value: Rad21 (custom made by GenScript Corporation, USA)


title: Icm02-W-s38R


title: 10_hpf_Rad21_2


title: Icm02-W-s40R


title: 10_hpf_Input_2

value: no antibody input control


title: 10_hpf_CTCF_1

value: 10 hpf


title: Icm02-W-b189R


title: Icm03-W-b179R


title: 10_hpf_Input_1


title: Icm01-W-s22R


title: 4.5_hpf_Rad21_1

value: 4.5 hpf


title: Icm01-W-s17R


title: Icm01-W-s18R


title: Icm01-W-s19R


title: 4.5_hpf_Input_2


title: 4.5_hpf_Rad21_2


title: Icm01-W-s15R


title: Icm01-W-s16R


title: Icm01-W-b186R


title: Bst12-Q-s403

value: Blastocyst


title: Bst12-Q-s406


title: Bst12-Q-s367


title: Bst12-Q-s402


title: Bst12-Q-s366


title: Icm01-W-b185R

value: male


title: Bst12-Q-s405


title: Bst12-Q-s404


title: Bst12-Q-s365


title: atac-seq_wt_rep2

data_processing:
After adapter and quality trimming, reads were aligned to the Zv9 genome assembly using bowtie2 (version 2.2.1.) with default settings.
Peak finding and downstream data analysis was performed using MACS2.
macs2 callpeak -t ./paired/wt_2.5_dec7_paired.bam -n wt_2.5_dec7 --outdir ./macs2_out/ -f BAM --nomodel --extsize 147 -g 1.37e+09 -B -q 0.01
Genome_build: Zv9
Supplementary_files_format_and_content: peak files in bed format from MACS2 analysis,

extract_protocol:
Embryos were collected at the 256-cell stage and dechorionated using pronase and yolk was removed.
75,000 cells were used to prepare the libraries. Libraries were pooled and sequenced on an Illumina HiSeq.


title: atac-seq_wt_rep1


title: R2-HLCs-2

city: Cleveland

first: Xianfang

last: Wu

state: Ohio

address: 9500 Euclid Avenue/NE20, Office NE2-308, Office NE2-308

department: Infection Biology

institute: Cleveland Clinic

data_processing:
The single end, stranded reads were mapped to the Ensembl human genome assembly GRCh37 (also known as hg19) using Tophat2 (version 2.0.12; Bowtie version 2.2.7) with first strand library type, no novel junctions, and otherwise default options
Mapped reads were counted using featureCounts (from subread version 1.4.6) with default options
Gene length-corrected counts were calculated as reads per kilobase per million (RPKM) with edgeR and transcripts per million (TPM),using the gene lengths returned with the feature Counts read summarization output.
Analyses were done with the R statistical framework
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: genomic features

source_name: Hepatocyte-like cells

growth_protocol:
Human ES/iPS cells were cultured on growth factor reduced Matrigel according to manufacturer recommendations in feeder-independent mTeSR1 medium
hES-derived endoderm cells were routinely generated by treating hESCs with 100ng/ml Activin-A and 3μM CHIR99021 for one day and then with 0.25ng/ml BMP4, 5ng/ml bFGF and 100ng/ml Activin-A for three more days
hES-derived mesoderm cells were routinely generated by treating hESCs with 10μM CHIR-98014 for four days
hES-derived ectoderm cells were routinely generated by treating hESCs with 10μM SB431542 and 200nM Noggin for five to seven days
hES-derived mesenchymal stem cells were routinely generated by treating mesoderm cells with MSC medium (knockout-DMEM, 10% KOSR, 1% sodium pyruvate, 1% Insulin-Transferrin-Selenium-X (ITS-X), and 0.1% β-mercaptoethanol, 5ng/ml bFGF, 10ng/ml PDGF-AB, and 10ng/ml EGF)
hES-derived neural stem cells were routinely generated by treating ectoderm cells with with 10μM SB431542 and 200nM Noggin for one week and cultured in neural progenitor medium (DMEM/F12, 2% StemPro Neural Supplement, and 1% GlutaMax, 20ng/ml bFGF and 20ng/ml EGF
hES-derived pancreatic stem cells were routinely generated by treating endoderm cells in BLAR medium (custom formulated as described) supplemented with 0.5% BSA, 10mM glucose, 0.25mM ascorbic acid, 50ng/ml FGF7 for one day and with additional supplement ( 2% BSA, 0.25μM SANT-1, 1μM retinoid acid, 100nM LDN193189, and 0.5% ITS-X) for two more days. Cells were then exposed to the same medium with reduced FGF7 (2ng/ml) for three days. Finally, cells were cultured in BLAR medium with 20mM glucose, 2% BSA, 0.25μM SANT-1, 0.05μM retinoid acid, 100nM LDN193189, and 0.5% ITS-X, 1μM T3, 10μM ALK5 inhibitor II (Enzo Life Science), 10μM zinc sulfate and 10μg/ml heparin for four days.
hES-derived neuron-like cells were routinely generated by treating neural stem cells with neuronal differentiation medium (BrainPhys basal medium, 2% SM1 neuronal supplement, 1% N2 supplement-A, 200nM ascorbic acid, 1mM dibutyryl cAMP, 20ng/ml BDNF and 20ng/ml GDNF.
hES-derived myofibroblast-like cells were routinely generated by treating mesenchymal stem cells with differentiation medium (DMEM/F12, 2% FBS, and 1% GlutaMax) supplemented with 1μM retinoid acid, 30ng/ml VEGF, and 10ng/ml PDGF-AB for two weeks
hES-derived immature pancreatic β-like cells were routinely generated by treating pancreatic stem cells with maturation medium (DMEM/F12, 0.2% BSA, 0.5×N2, 0.5×B-27, 1% GlutaMax) supplemented with 1% ITS, 10ng/ml bFGF, 10mM nicotinamide, 50ng/ml Exendin-4, and 10ng/ml BMP4 for seven to nine days
hES-derived hepatic stem cells were routinely generated by treating endoderm cells with RPMI/B-27 supplemented with 20ng/ml BMP4 and 10ng/ml bFGF and replace medium daily for five days
hES-derived immature hepatocytes were routinely generated by treating hepatic stem cells with RPMI/B-27 containing 20ng/ml HGF for five days
hES-derived mature hepatocytes were routinely generated by further maturing immature hepatocytes in Lonza hepatocyte culture medium containing ascorbic acid, BSA-FAF, hydrocortisone, transferrin, insulin, GA-1000 and 20ng/ml OSM for additional one to two weeks. HLCs cultures were replenished with fresh medium every two days.
hES-derived hematopoietic stem cells were routinely generated by sequentially culturing hESCs in SFM (IMDM/Ham’s F12 (1:1), 5mg/ml BSA, 1x insulin-transferrin-selenium, 1x synthetic lipids, 50μg/ml of ascorbic acid and 2mM GlutaMax) supplemented with 10ng/ml BMP4, 10ng/ml bFGF, and 10μM ROCK inhibitor (Y-27632) for two days. SFM supplemented with 10ng/ml BMP4, 10ng/ml bFGF, and 20ng/ml VEGF was added to cultures (50μl/well) every three days. On day 8, half of the culture medium was removed and fresh SFM medium containing 10ng/ml bFGF, 10ng/ml VEGF, and 50ng/ml SCF was added every three days until day 14
hES-derived basophilic erythroblast-like cells were routinely generated by culturing hematopoietic stem cells with stage-one medium (IMDM, 2% human plasma, 3% human AB serum, 200 mg/ml Holo human transferrin, 3 IU/ml heparin, and 10 mg/ml insulin) supplemented with 10ng/ml SCF, 1ng/ml IL-3, and 3IU/ml EPO for one week. Cells were then exposed to stage-two medium supplemented with 10ng/ml SCF and 3IU/ml EPO for five days
Primary MSCs were maintained in Lonza MSC basal medium supplemented with MSCGMTM SinglequotsTM according to the manufacturer’s instructions

extract_protocol:
Total RNA was isolated from cell lysates using the RNAeasy Mini Kit (Qiagen, Cat No./ID: 74104) , together with on-column digestion of DNA (Qiagen Cat No./ID: 79254)
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA LT Sample Prep Kit (Catalog IDs: RS-122-2101, RS-122-2102  ).Briefly, 100ng total RNA was used for library preparation

value: ex vivo derived cells

tag: age/passage

value: hES-derived hepatocyte-like cells

value: Hepatocyte-like cells


title: pMSC-1

source_name: mesenchymal stem cells

value: Bone marrow

value: Natal, P3

value: Primary human cells

value: mesenchymal stem cells


title: R2-HepSC-2

source_name: Hepatic stem cells

value: hES-derived hepatic stem cells

value: Hepatic stem cells


title: pMSC-2

value: Natal, P4


title: Bst12-Q-s323

value: female

value: single cell


title: R2-Immature-Hep-1

source_name: Immature hepatocyte

value: hES-derived immature hepatocytes

value: Immature hepatocyte


title: Bst12-Q-s322


title: 4.5_hpf_Input_1

value: AB/PS

value: whole embryos

value: 4.5 hpf

value: no antibody input control


title: Bst12-Q-s321

value: Blastocyst


title: R2-HepSC-1

value: ex vivo derived cells


title: R2-Immature-Hep-2


title: R2-MES-2

source_name: Mesoderm cells

value: hES-derived mesoderm cells

value: Mesoderm cells


title: R2-ECT-1

source_name: Ectoderm cells

value: hES-derived ectoderm cells

value: Ectoderm cells


title: R2-ECT-2


title: R2-MES-1


title: Bst12-Q-s319


title: R2-END-2

source_name: Endoderm cells

value: hES-derived endoderm cells

value: Endoderm cells


title: R2-HLCs-1

value: hES-derived hepatocyte-like cells

value: Hepatocyte-like cells


title: Bst12-Q-s324

value: female

value: single cell


title: Bst12-Q-s316


title: Bst12-Q-s315


title: Bst12-Q-s318


title: Bst12-Q-s317


title: Bst07-W-s132

value: male


title: Bst07-W-s134


title: Te13-Q-s409

value: TE


title: Te13-Q-s408


title: Bst07-W-s131


title: Te13-Q-s407


title: H9-MYF-2

source_name: Myofibroblast

value: hES-derived myofibroblasts

value: Myofibroblast


title: R2-END-1


title: H9-Neuron-3

source_name: Neuron-like cells

value: hES-derived neuron-like cells

value: Neuron-like cells


title: H9-Beta-2

source_name: Pancreatic beta-like cells

value: ex vivo derived cells

value: hES-derived pancreatic beta-like cells

value: Pancreatic beta-like cells


title: H9-MYF-3


title: H9-Beta-3


title: H9-Neuron-2


title: H9-Neuron-1


title: H9-PanSC-2

source_name: Pancreatic stem cells

value: hES-derived pancreatic stem cells

value: Pancreatic stem cells


title: H9-NSC-3

source_name: Neural stem cell

value: hES-derived nerual stem cells

value: Neural stem cell


title: H9-PanSC-3


title: Te11-Q-s281


title: Te13-Q-b411

value: bulk cells


title: Te11-Q-b284


title: Te10-Q-s276


title: Te10-Q-s275


title: H9-Beta-1


title: H9-MYF-1


title: Te10-Q-s274


title: H9-NSC-2


title: H9-NSC-1


title: H9-MSC-2

value: hES-derived mesenchymal stem cells

value: mesenchymal stem cells


title: H9-PanSC-1


title: H9-MSC-1


title: Te10-Q-s243

value: female

value: single cell


title: Te10-Q-s244

value: TE


title: Te10-Q-s273


title: Te10-Q-s271


title: Te10-Q-s242


title: Te10-Q-s238


title: Te10-Q-s236


title: H9-ECT-3

value: hES-derived ectoderm cells

value: Ectoderm cells


title: H9-ECT-2


title: Te10-Q-s237


title: Te10-Q-s233


title: Te10-Q-s234


title: H9-MSC-3


title: Te10-Q-s228


title: H9-MES-1

value: hES-derived mesoderm cells

value: Mesoderm cells


title: H9-END-2

value: ex vivo derived cells

value: hES-derived endoderm cells

value: Endoderm cells


title: H9-END-3


title: LVID2-iPS-2

source_name: Induced pluripotent stem cells

value: foreskin fibroblast (mRNA transfection)

value: Human induced pluripotent stem cells

value: Induced pluripotent stem cells


title: H9-END-1


title: Te10-Q-s227


title: Te10-Q-s225


title: LVID2-iPS-1


title: C3A-iPS-2

value: foreskin fibroblast (lentiviral transduction)


title: C3A-iPS-1


title: H9-ECT-1


title: Te10-Q-s224


title: Te10-Q-s218


title: Te10-Q-s222


title: R2-ESC-3

source_name: Embryonic stem cells

value: Inner cell mass

value: Human embryonic stem cells

value: Embryonic stem cells


title: Te10-Q-s229

value: female


title: H9-MES-2


title: Te10-Q-s219

value: single cell


title: Te10-Q-s216

value: TE


title: Te10-Q-s235


title: Te10-Q-s215


title: Te10-Q-s214


title: Te10-Q-s212


title: Te10-Q-s213


title: Te10-Q-s209


title: Te10-Q-s207


title: ID9048-Ortho

source_name: Orthochromatic normoblast

value: fetal liver

value: 17 weeks

value: Primary human cells

value: Orthochromatic normoblast


title: ID9048-Poly

source_name: Polychromatic normoblast

value: Polychromatic normoblast


title: ID9048-CD34

source_name: Hematopoietic stem cells

value: Hematopoietic stem cells


title: ID9048-Pro

source_name: Pro-erythrocyte

value: Pro-erythrocyte


title: ID9048-EB

source_name: Early basophilic-erythrocyte

value: Early basophilic-erythrocyte


title: H9-ESC-3


title: ID9048-LB

source_name: Late basophilic-erythrocyte

value: Late basophilic-erythrocyte


title: H9-ESC-1


title: H9-ESC-2


title: Te10-Q-s206


title: Te10-Q-s217


title: ID9047-Poly


title: ID9047-Ortho


title: R2-ESC-2


title: R2-ESC-1


title: Te10-Q-s208


title: Te10-Q-s203


title: Te10-Q-s202


title: Te10-Q-s204


title: Te10-Q-s197


title: ID9047-CD34


title: ID9047-EB


title: ID9047-Pro


title: ID9852-Poly

value: 18 weeks


title: Te10-Q-s201


title: ID9852-Ortho


title: Te10-Q-s205


title: Te10-Q-s200


title: Te05-W-s96

value: male


title: Te05-W-s95


title: Te05-W-s94


title: Te05-W-s91


title: ID9852-CD34


title: ID9852-EB


title: ID9852-Pro


title: ID9852-LB


title: Te05-W-s92


title: Te05-W-s93


title: Te05-W-s98


title: Te05-W-s97


title: Te04-W-s74


title: Te04-W-s72


title: Te05-W-b100

value: bulk cells


title: Te05-W-b99


title: Te04-W-s75


title: Te04-W-s66


title: Te04-W-b76


title: Te03-W-s53


title: Te03-W-s52


title: Te03-W-s54


title: Te10-Q-s196


title: Te03-W-s51


title: mouse_PS-4C-5-4


title: Te04-W-s67


title: Te03-W-s48


title: mouse_PS-4C-5-3


title: Te03-W-b57


title: mouse_PS-4C-4-1


title: mouse_PS-4C-5-1


title: Te03-W-s47


title: mouse_PS-4C-3-3


title: mouse_PS-4C-4-4


title: mouse_PS-4C-4-3


title: mouse_PS-4C-5-2


title: Te03-W-s49


title: mouse_PS-4C-3-2


title: Te02-W-s32


title: mouse_PS-4C-4-2


title: Te02-W-s31


title: Te03-W-b56


title: mouse_PS-4C-3-4


title: Te02-W-s30


title: Te02-W-s29


title: Te03-W-s50


title: mouse_PS-4C-2-3


title: mouse_PS-4C-2-2


title: Te02-W-s28


title: mouse_PS-4C-2-4


title: mouse_PS-4C-2-1


title: mouse_PS-4C-1-3


title: Te02-W-s24


title: mouse_PS-4C-1-1


title: Te02-W-s23


title: Te01-W-s10


title: mouse_PS-4C-1-2


title: Te01-W-s09


title: Te02-W-s25


title: Te01-W-s06


title: mouse_F-4C-4-2


title: Te01-W-s02


title: mouse_F-4C-4-1


title: mouse_F-4C-4-3


title: Te01-W-s05


title: mouse_F-4C-4-4


title: mouse_PS-4C-3-1


title: Te01-W-b11


title: Te02-W-s27


title: mouse_F-4C-3-4


title: mouse_F-4C-3-2


title: Icm13-Q-s417

value: ICM


title: mouse_F-4C-3-3


title: mouse_F-4C-3-1


title: mouse_PS-4C-1-4


title: Te01-W-s01


title: Icm13-Q-s414


title: Icm13-Q-s413


title: mouse_F-4C-2-4


title: mouse_F-4C-2-3


title: Te02-W-b33


title: mouse_F-4C-2-2


title: Icm11-Q-s287


title: Icm11-Q-s286


title: mouse_F-4C-2-1


title: Icm13-Q-b424


title: mouse_F-4C-1-2


title: mouse_F-4C-1-3


title: mouse_F-4C-1-4


title: mouse_F-4C-1-1


title: Icm10-Q-s314


title: Icm11-Q-b293


title: ID9047-LB


title: Diploid_F121-9_early S fraction_2

city: Tallahassee

first: David

middle: M

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Biology

institute: Florida State University

data_processing:
Library strategy: repli-seq
Reads are mapped on mm10 using bowtie2.
Reads were converted to reads per million.
Coverage data in 50 kb bins are calculated from mapped reads using samtools and bedtools.
Base 2 log of early to late coverage ratio is calculated on 50kb windows.
Genome_build: mm10
Supplementary_files_format_and_content: The proceesed data file ("Population_repli-seq.txt") is the replication timing calculated as the base 2 log ratio between early and late S fraction. Column 1 and 2 are CHR and POS. Column 3 is the average replication timing between 2 biological replicates.

source_name: mouse ESC

growth_protocol: F121-9 (diploid) mouse embryonic cells were cultured in N2B27+2i+LIF media.

extract_protocol:
Genome-wide replication timing profiles were constructed as previously described (Hiratani et al. 2008; Ryba et al. 2011). Briefly, cells were pulse labeled with BrdU and separated into early and late S-phase fractions by flow cytometry and processed by NGS.
Sequencing libraries of BrdU-substituted DNA from early and late fractions were prepared by NEBNext Ultra DNA Library Prep Kit for Illumina (E7370).

value: ESC

tag: ploidy

value: diploid

value: hybrid cas/129

tag: s-phase fraction

value: Early S fraction


title: Diploid_F121-9_late S fraction_2

tag: strain

value: Late S fraction


title: Diploid_F121-9_early S fraction_1


title: Diploid_F121-9_late S fraction_1


title: Icm10-Q-s312

value: female

value: single cell


title: Icm13-Q-b425


title: Icm13-Q-s412


title: Icm11-Q-s285


title: Diploid_F121-18_S6

description:
Processed data file:
singlecell_normalized_smoothed.txt
singlecell_binarized.txt

data_processing:
Library strategy: replication profiling
Reads are mapped on mm10 using bowtie2. F121-9 cells are also been parsed, between cas and 129 genome. Reads with WGA adpator universal seqeunces were trimmed using tagcleaner package before mapping.
Coverage data in 50 kb bins are calculated from mapped reads using samtools and bedtools.
S-phase cell coverage was normalzied using G1/G2 cell coverage, outliers bins were removed and data smoothed using median filter (span=15) as explained in supplementary methods (singlecell_normalized_smoothed.txt).
Normalized smooth data was binarized to reflect replicated vs. un-replicated bins as explained in supplementary methods (singlecell_bianrized.txt).
Binaraized data from diploid cells were further parsed into cas and 129 homologue specific binary singnal based on the cas and 129 homolouge read coverage as descirbed in supplementary methods.
Genome_build: mm10
Supplementary_files_format_and_content: There are two proceesed data files. The first one is the normalized and smoothed single cell data (singlecell_normalized_smoothed.txt) and the other is the binarized data (singlecell_binarized.txt). In the binarized file 1 indicates a replicated bin and 0 indicates the bin has not replicated. The first 2 columns are CHR and POS. The rest of the columns are the single cells. For diploid cells, each cell has 2 columns in the binarized file representing the cas and 129 homologue.  The processed data files are available on series GSE102074.

extract_protocol:
Single cells from G1 or S-phase were sorted using AriaII FACS sorter based on DNA content after DAPI staining. Next, we performed whole genome single-cell sequencing as described in Baslan et al. 2012. Briefly, we performed whole genome amplification using WGA4 kit (WGA4-50RXN). Purified amplified products were sonicated to remove ends with WGA adaptors.
Illumina library preparation was performed on the sonicated WGA products using NEBNext Ultra DNA Library Prep Kit for Illumina (E7370).

value: hybrid cas /129

tag: cell number

value: Single cell

tag: cell cycle stage

value: S-phase


title: Icm10-Q-s311

tag: cell type


title: Diploid_F121-17_S5


title: Icm10-Q-s308


title: Icm10-Q-s307


title: Diploid_F121-15_S3


title: Te03-W-s46

value: TE


title: Diploid_F121-14_S2


title: Icm10-Q-s306


title: Icm10-Q-s305


title: Icm11-Q-b294


title: Diploid_F121-16_S4


title: Diploid_F121-13_S1

description:
Removed at quality control steps
Processed data file: NA


title: Icm10-Q-s304


title: Icm10-Q-s313


title: Diploid_F121-12_G2.2


title: Diploid_F121-11_G2.1

description:
G2 cell used for normalization
Processed data file: NA


title: Diploid_F121-19_S7


title: Diploid_F121-10_G1.2


title: Icm10-Q-s303


title: Icm10-Q-s301


title: Icm10-Q-s300


title: Icm10-Q-s299


title: Icm10-Q-s309


title: Haploid_H129-2_H7

description:
G1 cell used for normalization
processed data file:
NA

data_processing:
Library strategy: replication-profiling
Reads were parsed into single-cell specific reads using the unique barcodes. Parsed reads are mapped on mm10 using bowtie2. F121-9 diploid cells are also parsed, between cas and 129 genome.
Coverage data in 50 kb bins are calculated from mapped reads using samtools and bedtools.
S-phase cell coverage was normalzied using G1/G2 cell coverage, outliers bins were removed and data smoothed using median filter (span=15) as explained in supplementary methods (singlecell_normalized_smoothed.txt).
Normalized smooth data was binarized to reflect replicated vs. un-replicated bins as explained in supplementary methods (singlecell_bianrized.txt).
Binaraized data from F121-9 diploid cells were further parsed into cas and 129 homologue specific binary singnal based on the cas and 129 homolouge read coverage as descirbed in supplementary methods.
Genome_build: mm10
Supplementary_files_format_and_content: There are two proceesed data files. The first one is the normalized and smoothed single cell data (singlecell_normalized_smoothed.txt) and the other is the binarized data (singlecell_binarized.txt). In the binarized file 1 indicates a replicated bin and 0 indicates the bin has not replicated. The first 2 columns are CHR and POS. The rest of the columns are the single cells. For diploid cells, each cell has 2 columns in the binarized file representing the cas and 129 homologue.

growth_protocol: F121-9 (diploid) and H129-2 (haploid) mouse embryonic cells were cultured in N2B27+2i+LIF media.

extract_protocol:
Single cells from G1 or S-phase were sorted using AriaII FACS sorter based on DNA content after DAPI staining. Next, we performed whole genome single-cell sequencing as described in Baslan et al. 2015. Briefly, the cells were lysed and amplified using the Sigma SeqPlex kit (SEQXE-50RXN). The WGA products were purified and the WGA universal adaptor sequences were removed as per the kit protocol, leaving NN overhangs.
Uniquely barcoded illumina adaptors with NN overhangs were ligated to purified amplfied DNA with NN overhangs. Upto 96 uniquely barcoded cells were pooled together and re-amplified. Samples were then quantified using the Bioanalyzer and qPCR and sequenced on Hiseq 2500 sequencer using 50 bp single-end read format.

value: haploid


title: Haploid_H129-2_H9


title: Haploid_H129-2_H6


title: Te04-W-s73


title: Haploid_H129-2_H8


title: Haploid_H129-2_H5


title: Haploid_H129-2_H4


title: Haploid_H129-2_H3

description:
processed data file:
singlecell_normalized_smoothed.txt
singlecell_binarized.txt


title: Icm10-Q-s295


title: Icm10-Q-s296


title: Icm10-Q-s297


title: Haploid_H129-2_H2

description:
Removed at quality control steps
processed data file:
NA


title: Diploid_F121-9_G1.1

description:
G1 cell used for normalization
Processed data file: NA


title: Icm10-Q-s269


title: Haploid_H129-2_H1


title: Icm10-Q-s268


title: Icm10-Q-s270


title: Icm10-Q-s264


title: Haploid_H129-2_G11


title: Icm10-Q-s263


title: Icm10-Q-s302


title: Haploid_H129-2_G10


title: Haploid_H129-2_G9


title: Icm10-Q-s298


title: Haploid_H129-2_G12


title: Haploid_H129-2_G8


title: Icm10-Q-s277


title: Icm10-Q-s262


title: Haploid_H129-2_G6


title: Icm10-Q-s261


title: Icm10-Q-s260


title: Icm10-Q-s278


title: Icm10-Q-s256


title: Icm10-Q-s259


title: Icm10-Q-s255


title: Haploid_H129-2_G5


title: Haploid_H129-2_G4


title: Haploid_H129-2_G3


title: Haploid_H129-2_G2


title: Icm10-Q-s253


title: Haploid_H129-2_F11


title: Haploid_H129-2_G1


title: Icm10-Q-s252


title: Icm10-Q-s251


title: Icm10-Q-s247


title: Haploid_H129-2_F10


title: Icm10-Q-s246


title: Haploid_H129-2_F9


title: Haploid_H129-2_F8


title: Haploid_H129-2_F7


title: Haploid_H129-2_F6


title: Icm05-W-s110


title: Icm10-Q-s257


title: Icm05-W-s89


title: Haploid_H129-2_F5


title: Icm05-W-s108


title: Icm05-W-s106


title: Haploid_H129-2_F4


title: Icm05-W-s107


title: Icm05-W-s105


title: Haploid_H129-2_F2


title: Icm05-W-s104


title: Haploid_H129-2_E12


title: Haploid_H129-2_F1


title: Icm05-W-s102


title: Icm05-W-s101


title: Haploid_H129-2_E11


title: Haploid_H129-2_E10


title: Icm05-W-b112


title: Icm05-W-b111


title: Haploid_H129-2_E8


title: Icm04-W-s86


title: Icm04-W-s85


title: Haploid_H129-2_E7


title: Haploid_H129-2_E9


title: Haploid_H129-2_G7


title: Icm04-W-s84


title: Icm04-W-s83


title: Haploid_H129-2_E6


title: Haploid_H129-2_E5


title: Haploid_H129-2_E3


title: Icm05-W-s103


title: Haploid_H129-2_F3


title: Icm04-W-b88


title: Icm04-W-b87


title: Haploid_H129-2_E2


title: Haploid_H129-2_E1


title: Haploid_H129-2_D12


title: Icm04-W-s78


title: Icm03-W-s64


title: Icm03-W-s63


title: Icm03-W-s61


title: Icm03-W-s60


title: Icm03-W-s59


title: Haploid_H129-2_D11


title: Haploid_H129-2_D9


title: Haploid_H129-2_D8


title: Haploid_H129-2_D7


title: Icm03-W-b65


title: Haploid_H129-2_E4


title: Icm03-W-s58


title: Haploid_H129-2_D5


title: Icm02-W-s42


title: Icm02-W-s37


title: Haploid_H129-2_D4


title: Haploid_H129-2_D2


title: Haploid_H129-2_D1


title: Haploid_H129-2_D6


title: Icm02-W-s38


title: Icm02-W-s35


title: Icm02-W-s36


title: Icm02-W-s34


title: Haploid_H129-2_D3


title: Haploid_H129-2_C12


title: Icm02-W-s14


title: Haploid_H129-2_D10


title: Haploid_H129-2_C11


title: Icm02-W-b45


title: Haploid_H129-2_C10


title: Icm02-W-b44


title: Haploid_H129-2_C9


title: Icm02-Q-s41


title: Haploid_H129-2_C8


title: Haploid_H129-2_C7


title: Icm02-Q-s40


title: Icm02-Q-s39


title: Icm01-W-s21


title: Haploid_H129-2_C5


title: Icm01-W-s20


title: Haploid_H129-2_C3


title: Icm01-W-s18


title: Haploid_H129-2_C1


title: Haploid_H129-2_B12


title: Icm01-W-s17


title: Icm01-W-s12


title: Icm01-W-s13


title: Mor09-W-s180

value: Morula


title: Mor09-W-s185


title: Haploid_H129-2_B11


title: Icm01-W-b22


title: Haploid_H129-2_C6


title: Mor09-W-s179


title: Mor09-W-s178


title: Haploid_H129-2_B8


title: Haploid_H129-2_B5


title: Haploid_H129-2_B6


title: Icm01-W-s19


title: Haploid_H129-2_C4


title: Mor09-Q-s193


title: Haploid_H129-2_B4


title: Mor09-Q-s192


title: Haploid_H129-2_C2


title: Mor09-Q-s191


title: Haploid_H129-2_B2


title: Haploid_H129-2_B9


title: Haploid_H129-2_B1


title: Haploid_H129-2_A12


title: Haploid_H129-2_B10


title: Haploid_H129-2_F12


title: Haploid_H129-2_A11


title: Mor09-Q-s190


title: Haploid_H129-2_A9


title: Mor09-Q-s186


title: Mor09-Q-s183


title: Haploid_H129-2_B7


title: Mor09-Q-s194


title: Haploid_H129-2_B3


title: Haploid_H129-2_A8


title: Mor09-Q-s182


title: Mor09-Q-s181


title: Haploid_H129-2_A7


title: Mor09-Q-s177


title: Mor09-Q-s184


title: Mor08-Q-s175


title: Mor08-Q-s176


title: Haploid_H129-2_A4


title: Mor08-Q-s174


title: Haploid_H129-2_A5


title: Haploid_H129-2_A3


title: Mor09-Q-s187


title: Haploid_H129-2_A2


title: Haploid_H129-2_A1


title: Diploid_F121-9_H12


title: Mor08-Q-s173


title: Mor08-Q-s171


title: Mor08-Q-s172


title: Mor08-Q-s170


title: Mor08-Q-s168


title: Diploid_F121-9_H8


title: Mor08-Q-s166


title: Diploid_F121-9_H6


title: Haploid_H129-2_A6


title: Diploid_F121-9_H7


title: Mor08-Q-s164


title: Mor08-Q-s167


title: Mor08-Q-s165


title: Diploid_F121-9_H10


title: Diploid_F121-9_H3


title: Diploid_F121-9_H5


title: Diploid_F121-9_H2


title: Mor08-Q-s163


title: Mor08-Q-s162


title: Mor08-Q-s160


title: Mor08-Q-s159


title: Diploid_F121-9_H4


title: Diploid_F121-9_H1


title: Diploid_F121-9_H11


title: Mor08-Q-s158


title: Diploid_F121-9_H9


title: Diploid_F121-9_G10


title: Diploid_F121-9_G11


title: Mor06-Q-s129


title: Mor06-Q-s130


title: Mor06-Q-s128


title: Mor08-Q-s161


title: Diploid_F121-9_G8


title: Diploid_F121-9_G7


title: Diploid_F121-9_G6


title: Mor06-Q-s127


title: Diploid_F121-9_G5


title: Mor06-Q-s126


title: Mor06-Q-s124


title: Mor06-Q-s123


title: Diploid_F121-9_G12


title: Diploid_F121-9_G2


title: Diploid_F121-9_G1


title: Mor06-Q-s121


title: Diploid_F121-9_G9


title: Mor06-Q-s122


title: Mor06-Q-s120


title: Diploid_F121-9_F12


title: Mor06-Q-s119


title: Diploid_F121-9_F11


title: Icm05-W-s90


title: Mor06-Q-s118


title: Diploid_F121-9_F10


title: Mor06-Q-s117


title: Mor06-Q-s125


title: Mor06-Q-s115


title: Diploid_F121-9_F9


title: Mor06-Q-s116


title: Diploid_F121-9_F7


title: Diploid_F121-9_G3


title: Mor06-Q-s114


title: Mor06-Q-s113


title: Diploid_F121-9_F5


title: Diploid_F121-9_F4


title: Diploid_F121-9_F6


title: Diploid_F121-9_F3


title: scBS-ZHB-Sp6

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
All bisulfite sequencing reads were first trimmed to remove adaptors and low quality bases using trim_galore (RefXXX) (parameters: --quality 20 --phred33 –length 50 --paired).
Next, reads passed quality control were mapped to human reference genome (version: hg19) using bismark (version: 0.7.6) (RefXXX) with paired-end alignment mode (parameters: --non-directional --fastq). To rescue more sequencing reads, unmapped reads were realigned to the same reference genome in single-end alignment mode (RefXXX).
Genome_build: hg19
Supplementary_files_format_and_content: For bisulfite sequencing samples, the processed files include the DNA methylation levels of cytosines in CpG, CHH and CHG context, in bed format.

source_name: sperm donor1

extract_protocol:
single cell or small amounts of cells were seeded into the lysis buffer using the mouth pipette, and DNAs were released after proteinase treatment at 50C and then bisulfite converted.
After purification, DNAs were complemented with the biotinated random primer (5’-biotin-CTACACGACGCTCTTCCGATCTNNNNNNNNN-3’) and 50 units of klenow polymerase (3’ to 5’exo-, New England Biolabs). This random priming was repeated 5 times in total. The second strands were synthesized using another random primer (5’-AGACGTGTGCTCTTCCGATCTNNNNNNNNN-3’) and the final libraries were generated after 8-12 cycles PCR amplification with the Illumina universal PCR primer and Illumina indexed primer.

value: sperm


title: Diploid_F121-9_F1


title: scBS-ZHB-Sp8


title: scBS-ZHB-Sp7


title: scBS-ZHB-Sp5


title: scBS-ZHB-Sp4


title: scBS-ZHB-Sp3


title: Diploid_F121-9_E12


title: Diploid_F121-9_F8


title: Diploid_F121-9_F2


title: scBS-ZHB-Sp2


title: Diploid_F121-9_E10


title: Diploid_F121-9_E9


title: scBS-ZHB-Sp1


title: Diploid_F121-9_E8


title: Diploid_F121-9_E7


title: Diploid_F121-9_E6


title: scBS-ZHB-Sp15


title: scBS-ZHB-Sp9


title: scBS-ZHB-Sp13


title: scBS-ZHB-Sp14


title: scBS-ZHB-Sp11


title: scBS-ZHB-Sp12


title: scBS-ZHB-Sp16


title: Diploid_F121-9_E3


title: Diploid_F121-9_E2


title: Diploid_F121-9_E1


title: scBS-Morula-5bulk

source_name: Morula embryo#5


title: scBS-ZHB-Sp10


title: Diploid_F121-9_E5


title: scBS-Morula-3-5

source_name: Morula embryo#3


title: Diploid_F121-9_D10


title: Diploid_F121-9_D11


title: Diploid_F121-9_G4


title: scBS-Morula-3-3


title: Diploid_F121-9_E4


title: scBS-Morula-1-9

source_name: Morula embryo#1


title: scBS-Morula-3-4


title: scBS-Morula-1-1


title: scBS-Morula-1-2


title: Diploid_F121-9_D6


title: Diploid_F121-9_D4


title: Diploid_F121-9_D7


title: scBS-8C-9-6

source_name: 8-cell embryo#9


title: Diploid_F121-9_D2


title: Diploid_F121-9_D8


title: Diploid_F121-9_D12


title: scBS-8C-9-5


title: Diploid_F121-9_D1


title: scBS-Morula-3bulk


title: scBS-8C-9-8


title: scBS-8C-9-4


title: scBS-8C-9-3


title: Diploid_F121-9_D9


title: Diploid_F121-9_E11


title: Diploid_F121-9_D5


title: Diploid_F121-9_C9


title: Diploid_F121-9_C7


title: Diploid_F121-9_C8


title: Diploid_F121-9_C12


title: Diploid_F121-9_C10


title: scBS-8C-9-7


title: scBS-8C-6-6

source_name: 8-cell embryo#6


title: Diploid_F121-9_C6


title: scBS-8C-6-7


title: Diploid_F121-9_C11


title: Diploid_F121-9_D3


title: Diploid_F121-9_C5


title: scBS-8C-6-3


title: scBS-8C-6-4


title: Diploid_F121-9_C3


title: Diploid_F121-9_C2


title: Diploid_F121-9_C4


title: scBS-8C-6-2


title: scBS-8C-6-1


title: scBS-8C-9-2


title: Diploid_F121-9_B12


title: Diploid_F121-9_C1


title: scBS-8C-9-1


title: scBS-8C-2-2

source_name: 8-cell embryo#2


title: scBS-8C-2-1


title: Diploid_F121-9_B11


title: scBS-8C-6-8


title: scBS-8C-1-8

source_name: 8-cell embryo#1


title: Diploid_F121-9_B10


title: scBS-8C-1-7


title: Diploid_F121-9_B9


title: scBS-8C-6-5


title: scBS-8C-1-6


title: scBS-8C-1-4


title: Diploid_F121-9_B7


title: Diploid_F121-9_B5


title: Diploid_F121-9_B6


title: scBS-8C-1-3


title: Diploid_F121-9_B8


title: scBS-8C-1-5


title: Diploid_F121-9_B3


title: scBS-Sp13

source_name: sperm


title: scBS-Sp11


title: Diploid_F121-9_B2


title: scBS-P-MII-2

source_name: metaphase II oocyte

value: metaphase II oocyte


title: scBS-8C-1-1


title: Diploid_F121-9_B4


title: scBS-8C-1-2


title: scBS-O-TE-14s5

source_name: TE

value: blastocyst


title: Diploid_F121-9_A9


title: scBS-P-MII-1


title: scBS-O-TE-14s4


title: Diploid_F121-9_A10


title: Diploid_F121-9_A11


title: scBS-O-TE-14s3


title: scBS-O-TE-14s2


title: Diploid_F121-9_A12


title: Diploid_F121-9_A8


title: scBS-O-TE-14s1


title: scBS-O-TE-14b

value: bulk cells


title: Diploid_F121-9_A6

value: ESC


title: scBS-O-ICM-5s5

source_name: ICM


title: Diploid_F121-9_A4

value: diploid


title: Diploid_F121-9_A3

value: hybrid cas/129


title: Diploid_F121-9_A2


title: scBS-O-ICM-14s4


title: scBS-O-ICM-5s1


title: scBS-O-ICM-5s2


title: Diploid_F121-9_B1


title: scBS-O-ICM-14s3


title: scBS-O-ICM-14s5


title: scBS-O-ICM-5s3


title: scBS-O-ICM-14s2


title: scBS-O-ICM-14s1


title: Diploid_F121-9_A1


title: scBS-O-ICM-5b


title: scBS-O-ICM-14b