title: Low Feeder Pop 2, G10 Males, Biological Rep 1

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

data_processing:
Demultiplexing: Barcoded sequence reads were demultiplexed using the Illumina pipeline v1.9.
Filtering Contaminant Sequences: Adapter sequences were trimmed using cutadapt v1.6 and trimmed sequences shorter than 50bp were discarded from further analysis. Trimmed sequences were then filtered for ribosomal RNA sequences by aligning against a database containing the complete 5S, 18S-5p8S-2S-28S, mt:lrRNA, and mt:srRNA sequences using BWA v0.7.10 (MEM algorithm with parameters ‘-v 2 –t 4’).
Alignment: The remaining sequences were aligned to the D. melanogaster genome (BDGP5) and known transcriptome (FlyBase v5.57) using STAR v2.4.0e.
Read Counting: Read counts were computed for known gene models using HTSeq-count with the ‘intersection-nonempty’ assignment method.
Genome_build: BDGP5/FlyBase5.57
Supplementary_files_format_and_content: Raw read counts for each gene feature in each sample provided as a single table (tab-delimited text). EXPRESSED column indicates whether gene feature met our minimum expression requirements for analysis.

source_name: adult whole body

growth_protocol: We created an advanced intercross outbred population (AIP) from 37 of the 205 sequenced, wild-derived, inbred DGRP lines. These 37 lines are minimally related (polygenic relatedness < 0.08), maximally homozygous (genome-wide heterozygosity < 5%), have the standard karyotype for all common polymorphic inversions, and are not infected with Wolbachia. The lines were first crossed in a round robin design to ensure equal representation of each genotype. At generation (G) zero, one virgin F1 female and one F1 male from each of the 37 lines was placed into each of 10 bottles. The AIP was maintained by random mating by mixing progeny from all bottles and distributing 40 females and 40 males into each of 10 new bottles, for a census population size of 800. To minimize natural selection via larval competition, egg-laying was restricted to 24 hours. The first divergent selection replicate population was initiated (G0) at AIP G24, the second at AIP G25, and the control population at AIP G27. The AIP and selection lines were reared in bottles on cornmeal/molasses/agar medium under standard culture conditions (25°C, 12:12 hour light/dark cycle).

extract_protocol:
We flash froze at -80 °C three-to-five day-old virgin flies at generations nine and ten, with at least thirty flies per replicate and two replicates per sex per selected population per generation (32 samples) such that each generation of each population and each sex had two biological replicates that were processed separately. All flies were collected between 1 PM and 3 PM. Total RNA was extracted with Trizol using the RNAeasy Mini Kit (Qiagen, Inc.). rRNA was depleted using the Ribo-Zero™ Gold Kit (Epicentre, Inc.) with 5ug total RNA input.
Depleted mRNA was fragmented and converted to first strand cDNA. During the synthesis of second strand cDNA, dUTP instead of dTTP was incorporated to label the second strand cDNA. cDNA from each RNA sample was used to produce barcoded cDNA libraries using NEXTflex™ DNA Barcodes (Bioo Scientific, Inc.) with an Illumina TrueSeq compatible protocol. Library size was selected using Agencourt Ampure XP Beads (Beckman Coulter, Inc.) and centered around 250 bp with the insert size ~130 bp. Second strand DNA was digested with Uracil-DNA Glycosylase before amplification to produce directional cDNA libraries. Libraries were quantified using Qubit dsDNA HS Kits (Life Technologies, Inc.) and Bioanalyzer (Agilent Technologies, Inc.) to calculate molarity. Libraries were then diluted to equal molarity and re-quantified. Two pools of 16 libraries were made, one of the 16 libraries from replicate 1 high and low lines; and one of the 16 libraries from replicate 2 high and low lines. Pooled library samples were quantified again to calculate final molarity and then denatured and diluted to 14pM. Pooled library samples were clustered on Illumina cBot; each pool was sequenced on one lane of Illumina Hiseq2500 using 125 bp single-read v4 chemistry.

treatment_protocol: We used virgin 3-7 day old flies in all assays, placing each fly in an individual vial with food following CO2 anesthesia. After a minimum recovery period of 24 hours, we placed each fly into individual vials containing 2 mL 1.5% agar medium and one 5 µL capillary tube (Kimble Glass Inc.) containing a 4% sucrose solution (w/v) inserted through a foam plug. Beginning at G8, we inserted two capillaries per vial for the high consumption replicate populations. Our modified version of the CAFE assay includes the agar medium to prevent desiccation from affecting food consumption. We placed the CAFE vials in a transparent plastic container in which high humidity is maintained with open containers of water to minimize evaporation from the capillary tubes. In addition, we assessed evaporation by placing CAFE vials with capillary tubes containing 4% sucrose but without flies in the same humid chamber. We measured total food consumption in each CAFE vial after 24 hours, between 10 A.M. and 12 P.M, and then transferred the flies into individual vials containing food to allow them to continue eating while we determined which individuals to select. We adjusted the total amount of food consumed by the average evaporation that occurred in the negative control vials to give the phenotype of each fly. Mass selection using the CAFE assay was performed as follows: At G0 for each of the divergent selection replicates, we scored 100 virgin females and males, and selected the 20 individuals of each sex with the highest and lowest food consumption to establish the two high (H1, H2) and two low (L1, L2) selection lines. In each subsequent generation, we selected the 20 highest (or lowest) males and females from 100 scored of each sex as parents of the next generation. We established a control population (C) maintained with 20 unselected males and females each generation. We scored 100 males and females from the control line every two generations. Selection was continued for 10 generations. We estimated h2, the narrow sense (realized) heritability, for each selection replicate as the regression of the cumulative response to selection (ΣR) on the cumulative selection differential (ΣS). At G9 and G10, we assessed correlated responses to selection for body mass, molecular metabolites, and genome wide genetic and gene expression divergence for all selection lines.

tag: selection

value: Low Feeding Behavior

tag: population replicate

tag: generation

value: Male

tag: biological replicate


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 72

status: Public on Dec 07 2016

type: SRA

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

country: USA

institute: Penn State University

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_72
esc1_12h_72_rsem

library_source: transcriptomic

data_processing:
Basecall conversion to fastq files was performed using bcl2fastq for HiSeq runs and Picard fpr NextSeq runs.
We quantified gene expression (transcripts per million) in each library as previously described (Shalek et al., 2013). We filtered out low quality cells where we detected less than 2,000 unique genes, which typically had poor transcriptomics alignment rates (<30%, as compared to 65% for successful cells). We first ran a principal component analysis (PCA), as previously described (Shalek et al., 2013) using all detected genes, and saw that the first component perfectly separated the two experimental batches. We therefore subtracted the first PC from the data in order to remove this batch effect.
Single cell RNA-seq: Data pre-processing and filtration: We quantified gene expression (transcripts per million) in each library as previously described (Shalek et al., 2013). We filtered out low quality cells where we detected less than 2,000 unique genes, which typically had poor transcriptomics alignment rates (<30%, as compared to 65% for successful cells). We first ran a principal component analysis (PCA), as previously described (Shalek et al., 2013) using all detected genes, and saw that the first component perfectly separated the two experimental batches. We therefore subtracted the first PC from the data in order to remove this batch effect.
Calculating developmental trajectories and ‘pseudotime’: As trajectory analysis is sensitive to gene input list, we first sought to identify a set of genes whose expression changes with biological time (the timepoint during the differentiation series when the cells were collected). We used a strategy similar to (Trapnell et al., 2014), constructing a linear model for each gene as a function of its biological time. We identified 458 genes where the linear model explained a significant (p<1e-5 after Bonferroni correction) of the variance in gene expression. We next used these 458 genes as input to a diffusion map, a non-linear dimensional reduction technique that has been shown to be well-suited to reconstructing developmental trajectories for single cell data. We assigned each cell a ‘pseudotime’ value, reflecting its progression through the differentiation process, by projecting a principal curve through the first two diffusion map dimensions.
Genome_build: mm10
Supplementary_files_format_and_content: gene expression table summarizing processed per-gene read counts across all submitted experiments

molecule: total RNA

organism: Mus musculus

growth_protocol: Generation of inducible lines: NIL (Ngn2-Isl1-Lhx3)-V5 and Flag-Ngn2 inducible ESC lines were generated as previously described (Mazzoni et al. 2013, Mazzoni et al. 2011). To generate IL (Isl1-Lhx3)-V5 inducible ESC lines, Isl1-Lhx3 open reading frames were amplified from p2Lox-NIL-V5 and inserted into the p2Lox-V5 plasmid (Iacovino M. et al., 2011). Phusion polymerase (New England Biolabs) was used to minimize the introduction of mutations during PCR amplification. Inducible cell lines were generated by treating the recipient ESCs for 16 h with 1 µg/ml Dox to induce Cre followed by electroporation of p2Lox-IL-V5 plasmid. After G418 selection (250ng/ml, Cellgro), four resistant clones were picked, characterized and expanded.   Cell culture and differentiation: All the inducible ESC lines were grown in 2-inhibitors medium (Advanced DMEM/F12:Neurobasal (1:1) Medium (Gibco), supplemented with 2.5% ESC-grade fetal bovine serum (vol/vol, Corning), N2 (Gibco), B27 (Gibco), 2mM L-glutamine (Gibco), 0.1 mM β-mercaptoethanol (Gibco), 1000 U/ml leukemia inhibitory factor (Millipore), 3µM CHIR (BioVision) and 1 µM PD0325901 (Sigma). For ChIP experiments, 3 x 10^6 cells were plated in each square dish (245mm x 245mm).

extract_protocol:
Cells were collected at different time points after NIL induction. Differentiating embryoid bodies were washed with phosphate-buffered saline and then dissociated by mild trypsinization followed by mechanical dissociation into single cell suspension. Viable cells were labeled by incubating with 1 µM Fluorescein diacetate (Sigma) at 37°C for 10 minutes. Single cells were FACS-sorted into 96-well plates containing 10 µl of 1% beta-mercaptoethanol in TCL buffer (Qiagen). Once sorting was completed, plates were sealed, centrifuged 1 min at 800 g at RT and immediately frozen on dry ice. Plates were kept at -80°C until lysate cleanup and reverse transcription of mRNA.
Single cell libraries were prepared in two overall batches using a custom version of the SMART-Seq2 protocol (Picelli et al., 2013), as previously described (Satija et al., 2015), without the use of Random Molecular Tags. Cells were sequenced with 50bp single end reads on a HiSeq 2500 at an average sequencing depth of 325,000 reads per cell.

treatment_protocol: To obtain Embryoid bodies (EBs) ESC were trypsinized (Gibco) and seeded in AK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout SR (vol/vol) (Gibco), Pen/Strep (Gibco), 2mM L-glutamine and 0.1 mM 2-mercaptoethanol) (day -2).  After 2 days, EBs were passed 1:2 and the inducible cassette was induced by adding 3 µg/ml of Doxycycline (Sigma) to the culture medium (EBs 0h).

tag: strain

tag: treatment

tag: cell type

value: ES-derived embryoid bodies with induced transcription factors


title: wt_3

city: Lausanne

first: Jean-Yves

last: Roignant

address: genopode building

country: Switzerland

institute: University of Lausanne

data_processing:
Libraries were sequenced on  Illumina HiSeq 2500 on 2 High output flowcells. Basecalling was done using CASAVA 1.8.4. Readlength was 71 bp paired end.
Mapping was done using Star (v. 2.4.0h), secondary alignments were filtered. Mapping was done against BDGP6 (ensembl release 79).
Mapped reads were filtered for mitochondiral and rRNA reads before counting (reference rDNA and dmel_mitochondrion_genome).
Read on genes were counted using HtSeq count (v. 0.6.1.p1)
Differential expression analysis was done using DESeq2 (v. 1.6.3)
Differential splicing analysis was done using rMATS (v. 3.0.9)
Genome_build: BDGP6 ensembl release 79
Supplementary_files_format_and_content: htseq count counted reads are provided as processed data files

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: wt, 1-2 day old female adult heads

growth_protocol: Flies raised on standard conditions (25 °C, 60% humidity)

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen). mRNA was purified by using two rounds of purification with Dynabeads Oligo (dT)25 (Invitrogen)
Libraries were made following NEBNext Ultra directional RNA kit protocol

treatment_protocol: Heterozygous and homozygous flies for Ime4 were compared to control flies

tag: gender

value: female

tag: age

value: 1-2 days old

tag: developmental stage

value: adult

tag: tissue

value: head

tag: genotype/variation

value: control


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 73

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_73
esc1_12h_73_rsem


title: Low Feeder Pop 2, G10 Females, Biological Rep 2

tag: Sex

value: Female


title: Low Feeder Pop 2, G10 Males, Biological Rep 2


title: Low Feeder Pop 2, G10 Females, Biological Rep 1


title: Low Feeder Pop 2, G9 Males, Biological Rep 2


title: Low Feeder Pop 2, G9 Males, Biological Rep 1


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 71

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_71
esc1_12h_71_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 70

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_70
esc1_12h_70_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 69

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_69
esc1_12h_69_rsem


title: Low Feeder Pop 2, G9 Females, Biological Rep 2


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 68

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_68
esc1_12h_68_rsem


title: Low Feeder Pop 2, G9 Females, Biological Rep 1


title: Low Feeder Pop 1, G10 Males, Biological Rep 2


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 65

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_65
esc1_12h_65_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 63

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_63
esc1_12h_63_rsem


title: Low Feeder Pop 1, G10 Females, Biological Rep 1


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 64

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_64
esc1_12h_64_rsem


title: Low Feeder Pop 1, G9 Males, Biological Rep 1


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 62

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_62
esc1_12h_62_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 61

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_61
esc1_12h_61_rsem


title: Low Feeder Pop 1, G9 Males, Biological Rep 2


title: Low Feeder Pop 1, G9 Females, Biological Rep 1


title: Low Feeder Pop 1, G10 Males, Biological Rep 1


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 59

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_59
esc1_12h_59_rsem


title: Low Feeder Pop 1, G9 Females, Biological Rep 2


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 57

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_57
esc1_12h_57_rsem


title: High Feeder Pop 2, G10 Males, Biological Rep 2

value: High Feeding Behavior


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 58

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_58
esc1_12h_58_rsem


title: High Feeder Pop 2, G10 Males, Biological Rep 1


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 60

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_60
esc1_12h_60_rsem


title: High Feeder Pop 2, G9 Males, Biological Rep 2


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 67

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_67
esc1_12h_67_rsem


title: Low Feeder Pop 1, G10 Females, Biological Rep 2


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 55

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_55
esc1_12h_55_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 66

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_66
esc1_12h_66_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 54

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_54
esc1_12h_54_rsem


title: High Feeder Pop 2, G9 Males, Biological Rep 1


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 53

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_53
esc1_12h_53_rsem


title: High Feeder Pop 1, G10 Males, Biological Rep 2


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 52

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_52
esc1_12h_52_rsem


title: High Feeder Pop 2, G9 Females, Biological Rep 1


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 51

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_51
esc1_12h_51_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 50

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_50
esc1_12h_50_rsem


title: High Feeder Pop 1, G10 Males, Biological Rep 1


title: High Feeder Pop 1, G9 Males, Biological Rep 2


title: High Feeder Pop 1, G9 Males, Biological Rep 1


title: High Feeder Pop 1, G10 Females, Biological Rep 2


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 49

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_49
esc1_12h_49_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 48

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_48
esc1_12h_48_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 46

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_46
esc1_12h_46_rsem


title: High Feeder Pop 2, G10 Females, Biological Rep 1


title: High Feeder Pop 1, G9 Females, Biological Rep 2


title: High Feeder Pop 1, G10 Females, Biological Rep 1


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 56

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_56
esc1_12h_56_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 45

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_45
esc1_12h_45_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 44

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_44
esc1_12h_44_rsem


title: High Feeder Pop 1, G9 Females, Biological Rep 1


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 47

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_47
esc1_12h_47_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 40

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_40
esc1_12h_40_rsem


title: High Feeder Pop 2, G10 Females, Biological Rep 2


title: High Feeder Pop 2, G9 Females, Biological Rep 2


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 36

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_36
esc1_12h_36_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 42

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_42
esc1_12h_42_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 41

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_41
esc1_12h_41_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 34

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_34
esc1_12h_34_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 39

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_39
esc1_12h_39_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 32

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_32
esc1_12h_32_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 30

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_30
esc1_12h_30_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 35

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_35
esc1_12h_35_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 31

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_31
esc1_12h_31_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 37

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_37
esc1_12h_37_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 26

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_26
esc1_12h_26_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 43

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_43
esc1_12h_43_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 27

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_27
esc1_12h_27_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 33

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_33
esc1_12h_33_rsem


title: Small RNAs from ovaries of H90 transgenic strain

city: Moscow

first: Sergei

last: Ryazansky

address: Kurchatov sq., 2

department: Department of Molecular Genetics of Cell

country: Russia

institute: Institute of Molecular Genetics

data_processing:
The reads with clipped 3'-adapter were passed through length (>18 nt), quality (80% of nt should contain >=20 Phred score) and artefacts filters, and mapped by bowtie to dm3 genome assembly with requiring of perfect mathcing.
Genome_build: dm3
Supplementary_files_format_and_content: Tab-delimited files include the frequencies of clipped read occurrences in each library.

source_name: ovaries

growth_protocol: Flies were grown according to standard protocols.

extract_protocol:
Total RNA was isolated by Trizol (Invitrogene) and size-fractioned by PAGE (19-29 nt)
Libraries of small RNAs 19-29 nt were constructed as previously described in (Muerdter et al. 2012)

value: ovaries


title: Small RNAs from ovaries of H95 transgenic strain


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 29

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_29
esc1_12h_29_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 25

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_25
esc1_12h_25_rsem


title: DNase-seq from inferior parietal cortex (ENCLB038LYE)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR986YWZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR986YWZ
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB038LYE
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

library_source: genomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens inferior parietal cortex tissue male adult (84 years)

value: inferior parietal cortex

value: tissue

tag: biosample encode accession

tag: dev stage

value: male

value: 84 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: link

value: ENCBS894OTI at ENCODE; https://www.encodeproject.org/ENCBS894OTI/

value: Derived from ENCODE donor ENCDO240JUB; https://www.encodeproject.org/ENCDO240JUB/


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 28

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_28
esc1_12h_28_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 38

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_38
esc1_12h_38_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 23

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_23
esc1_12h_23_rsem


title: DNase-seq from H9 (ENCLB215KJM)

description:
https://www.encodeproject.org/experiments/ENCSR964WHY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR964WHY
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-08-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB215KJM

source_name: Homo sapiens H9 stem cell G1 phase transiently expressing N-terminal eGFP fusion protein, C-terminal eGFP fusion protein

value: stem cell

value: unknown

value: not collected

tag: phase

value: ENCBS375GFI at ENCODE; https://www.encodeproject.org/ENCBS375GFI/

value: Derived from ENCODE donor ENCDO488VKC; https://www.encodeproject.org/ENCDO488VKC/

value: ENCODE dbxrefs Cellosaurus CVCL_9773; http://web.expasy.org/cellosaurus/CVCL_9773


title: DNase-seq from trophoblast cell (ENCLB195SGC)

description:
https://www.encodeproject.org/experiments/ENCSR964MZQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR964MZQ
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB195SGC
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens trophoblast primary cell fetal (40 weeks)

value: trophoblast cell

value: primary cell

value: fetal

value: 40 week

value: ENCBS162CVS at ENCODE; https://www.encodeproject.org/ENCBS162CVS/

value: Derived from ENCODE donor ENCDO204REL; https://www.encodeproject.org/ENCDO204REL/


title: DNase-seq from trophoblast cell (ENCLB425LBY)

description:
https://www.encodeproject.org/experiments/ENCSR964MZQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR964MZQ
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB425LBY
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens trophoblast primary cell fetal (39 weeks)

value: 39 week

value: ENCBS943QPE at ENCODE; https://www.encodeproject.org/ENCBS943QPE/

value: Derived from ENCODE donor ENCDO671XTD; https://www.encodeproject.org/ENCDO671XTD/


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 21

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_21
esc1_12h_21_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 22

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_22
esc1_12h_22_rsem


title: DNase-seq from SK-N-DZ (ENCLB799DVF)

description:
https://www.encodeproject.org/experiments/ENCSR946MVP/
***************
biological replicate number: 1
technical replicate number: 1,2
description:
experiment encode accession: ENCSR946MVP
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-08-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB799DVF
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Homo sapiens SK-N-DZ immortalized cell line

tag: line

value: SK-N-DZ

value: immortalized cell line

value: child

value: female

value: 2 year

value: John Stamatoyannopoulos, UW

value: ENCBS439FDS at ENCODE; https://www.encodeproject.org/ENCBS439FDS/

value: Derived from ENCODE donor ENCDO340AAA; https://www.encodeproject.org/ENCDO340AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1701; http://web.expasy.org/cellosaurus/CVCL_1701


title: DNase-seq from H9 (ENCLB666KBT)

description:
https://www.encodeproject.org/experiments/ENCSR964WHY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR964WHY
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-08-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB666KBT

value: stem cell

value: unknown

value: not collected

value: ENCBS853WXF at ENCODE; https://www.encodeproject.org/ENCBS853WXF/

value: Derived from ENCODE donor ENCDO488VKC; https://www.encodeproject.org/ENCDO488VKC/

value: ENCODE dbxrefs Cellosaurus CVCL_9773; http://web.expasy.org/cellosaurus/CVCL_9773


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 20

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_20
esc1_12h_20_rsem


title: Small RNAs from ovaries of H111 transgenic strain

value: ovaries


title: DNase-seq from H9 (ENCLB902KQC)

description:
https://www.encodeproject.org/experiments/ENCSR943SYS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR943SYS
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-08-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB902KQC

source_name: Homo sapiens H9 stem cell G2 phase transiently expressing N-terminal eGFP fusion protein, C-terminal eGFP fusion protein

value: ENCBS692FVF at ENCODE; https://www.encodeproject.org/ENCBS692FVF/


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 19

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_19
esc1_12h_19_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: DNase-seq from H9 (ENCLB458DKR)

description:
https://www.encodeproject.org/experiments/ENCSR943SYS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR943SYS
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-08-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB458DKR

value: ENCBS417MAQ at ENCODE; https://www.encodeproject.org/ENCBS417MAQ/


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 17

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_17
esc1_12h_17_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 16

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_16
esc1_12h_16_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 18

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_18
esc1_12h_18_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 15

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_15
esc1_12h_15_rsem


title: DNase-seq from thyroid gland (ENCLB933HHQ)

description:
https://www.encodeproject.org/experiments/ENCSR902XFY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR902XFY
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-23
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB933HHQ
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens thyroid gland tissue male adult (54 years)

value: thyroid gland

value: tissue

value: adult

value: male

value: 54 year

value: ENCBS702NUN at ENCODE; https://www.encodeproject.org/ENCBS702NUN/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: DNase-seq from sigmoid colon (ENCLB047DHV)

description:
https://www.encodeproject.org/experiments/ENCSR907VOR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR907VOR
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB047DHV
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens sigmoid colon tissue female adult (53 years)

value: sigmoid colon

value: female

value: 53 year

value: John Stamatoyannopoulos, UW

value: ENCBS138ZSN at ENCODE; https://www.encodeproject.org/ENCBS138ZSN/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 24

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_24
esc1_12h_24_rsem


title: genetic modification DNase-seq from K562 (ENCLB042ZME)

description:
https://www.encodeproject.org/experiments/ENCSR901BRM/
***************
biological replicate number: 1
technical replicate number: 1
description: TALEN-mediated homozygous DHS deletion in K562.
experiment encode accession: ENCSR901BRM
assay title: genetic modification DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-07-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB042ZME

source_name: Homo sapiens K562 immortalized cell line genetically modified (deletion) using TALEs

value: immortalized cell line

tag: description

tag: health state

value: chronic myelogenous leukemia (CML)

value: ENCBS461TCT at ENCODE; https://www.encodeproject.org/ENCBS461TCT/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 13

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_13
esc1_12h_13_rsem

tag: strain

value: ES-derived embryoid bodies with induced transcription factors


title: DNase-seq from occipital lobe (ENCLB077BDT)

description:
https://www.encodeproject.org/experiments/ENCSR859CZM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR859CZM
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB077BDT
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens occipital lobe tissue male adult (84 years)

value: occipital lobe

value: tissue

value: adult

value: 84 year

value: ENCBS312LJS at ENCODE; https://www.encodeproject.org/ENCBS312LJS/

value: Derived from ENCODE donor ENCDO240JUB; https://www.encodeproject.org/ENCDO240JUB/


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 11

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_11
esc1_12h_11_rsem

tag: treatment


title: DNase-seq from adrenal gland (ENCLB027HVL)

description:
https://www.encodeproject.org/experiments/ENCSR865ICK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR865ICK
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB027HVL

source_name: Homo sapiens adrenal gland tissue female adult (51 year)

value: adrenal gland

value: female

value: 51 year

value: ENCBS548ULT at ENCODE; https://www.encodeproject.org/ENCBS548ULT/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 9

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_9
esc1_12h_9_rsem

tag: cell type


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 8

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_8
esc1_12h_8_rsem


title: DNase-seq from retina (ENCLB151OHK)

description:
https://www.encodeproject.org/experiments/ENCSR820ICX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR820ICX
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB151OHK
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Homo sapiens retina tissue female fetal (89 days)

value: retina

value: fetal

value: 89 day

value: John Stamatoyannopoulos, UW

value: ENCBS941TEO at ENCODE; https://www.encodeproject.org/ENCBS941TEO/

value: Derived from ENCODE donor ENCDO685SWK; https://www.encodeproject.org/ENCDO685SWK/


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 7

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_7
esc1_12h_7_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: DNase-seq from limb (ENCLB817QBG)

description:
https://www.encodeproject.org/experiments/ENCSR818JGZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR818JGZ
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB817QBG
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens limb tissue fetal (53 days)

value: limb

value: tissue

value: not collected

value: 53 day

value: ENCBS930THP at ENCODE; https://www.encodeproject.org/ENCBS930THP/

value: Derived from ENCODE donor ENCDO733WDT; https://www.encodeproject.org/ENCDO733WDT/


title: DNase-seq from H4 (ENCLB979PFL)

description:
https://www.encodeproject.org/experiments/ENCSR809CEA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR809CEA
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-08-18
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB979PFL
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Homo sapiens H4 immortalized cell line

value: immortalized cell line

value: 37 year

value: adult

value: male

value: ENCBS381KGR at ENCODE; https://www.encodeproject.org/ENCBS381KGR/

value: Derived from ENCODE donor ENCDO337AAA; https://www.encodeproject.org/ENCDO337AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1239; http://web.expasy.org/cellosaurus/CVCL_1239


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 6

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_6
esc1_12h_6_rsem


title: DNase-seq from HT-29 (ENCLB540APO)

description:
https://www.encodeproject.org/experiments/ENCSR814KRX/
***************
biological replicate number: 2
technical replicate number: 1
description: DNase-seq on immortalized cell line HT-29, epithelial cells from a 44 year old female adult human colon with a colorectal adenocarcinoma.
experiment encode accession: ENCSR814KRX
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-10-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB540APO
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens HT-29 immortalized cell line

value: adenocarcinoma colon cells

value: female

value: 44 year

value: colorectal adenocarcinoma

value: John Stamatoyannopoulos, UW

value: ENCBS668UDT at ENCODE; https://www.encodeproject.org/ENCBS668UDT/

value: Derived from ENCODE donor ENCDO347AAA; https://www.encodeproject.org/ENCDO347AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0320; http://web.expasy.org/cellosaurus/CVCL_0320

value: ATCC sample source; http://www.atcc.org/products/all/HTB-38.aspx


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 5

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_5
esc1_12h_5_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: DNase-seq from heart (ENCLB423WYN)

description:
https://www.encodeproject.org/experiments/ENCSR804RSI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR804RSI
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB423WYN
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Homo sapiens heart tissue fetal (80 days)

value: heart

value: tissue

value: fetal

value: not collected

value: 80 day

value: ENCBS913ULP at ENCODE; https://www.encodeproject.org/ENCBS913ULP/

value: Derived from ENCODE donor ENCDO662IIE; https://www.encodeproject.org/ENCDO662IIE/


title: genetic modification DNase-seq from K562 (ENCLB198IDA)

description:
https://www.encodeproject.org/experiments/ENCSR914PJE/
***************
biological replicate number: 1
technical replicate number: 1
description: TALEN-mediated homozygous DHS deletion in K562.
experiment encode accession: ENCSR914PJE
assay title: genetic modification DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-11-02
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB198IDA

value: immortalized cell line

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS064ELJ at ENCODE; https://www.encodeproject.org/ENCBS064ELJ/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 4

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_4
esc1_12h_4_rsem


title: DNase-seq from adrenal gland (ENCLB469LLY)

description:
https://www.encodeproject.org/experiments/ENCSR848XIY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR848XIY
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB469LLY

source_name: Homo sapiens adrenal gland tissue male adult (54 years)

value: adrenal gland

value: male

value: 54 year

value: John Stamatoyannopoulos, UW

value: ENCBS942WBM at ENCODE; https://www.encodeproject.org/ENCBS942WBM/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: DNase-seq from amniotic stem cell (ENCLB908AVO)

description:
https://www.encodeproject.org/experiments/ENCSR820WLP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR820WLP
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB908AVO
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Homo sapiens amniotic stem cell male fetal (15 weeks)

value: amniotic stem cell

value: stem cell

value: Dedifferentiated Mesenchymal Stem Cells from Amniotic Fluid

value: fetal

value: 15 week

value: ENCBS469CDX at ENCODE; https://www.encodeproject.org/ENCBS469CDX/

value: Derived from ENCODE donor ENCDO942PSS; https://www.encodeproject.org/ENCDO942PSS/


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 14

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_14
esc1_12h_14_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: DNase-seq from right kidney (ENCLB500XLJ)

description:
https://www.encodeproject.org/experiments/ENCSR768OLL/
***************
biological replicate number: 1
technical replicate number: 1,2
description:
experiment encode accession: ENCSR768OLL
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB500XLJ
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Homo sapiens right kidney tissue male fetal (91 day)

value: right kidney

value: tissue

value: 91 day

value: ENCBS816VUN at ENCODE; https://www.encodeproject.org/ENCBS816VUN/

value: Derived from ENCODE donor ENCDO245RIZ; https://www.encodeproject.org/ENCDO245RIZ/


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 3

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_3
esc1_12h_3_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 1

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_1
esc1_12h_1_rsem


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 96

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_96
esc1_6h_96_rsem


title: DNase-seq from heart (ENCLB965FSO)

description:
https://www.encodeproject.org/experiments/ENCSR705CNJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR705CNJ
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-11-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB965FSO
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Homo sapiens heart tissue male fetal (72 days)

value: heart

value: male

value: 72 day

value: ENCBS486AQS at ENCODE; https://www.encodeproject.org/ENCBS486AQS/

value: Derived from ENCODE donor ENCDO300THQ; https://www.encodeproject.org/ENCDO300THQ/


title: DNase-seq from midbrain (ENCLB033CJI)

description:
https://www.encodeproject.org/experiments/ENCSR706IDL/
***************
biological replicate number: 2
technical replicate number: 1
description: DNase-seq on 78 year old male human adult midbrain tissue
experiment encode accession: ENCSR706IDL
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-08-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB033CJI
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens midbrain tissue male adult (84 years)

value: midbrain

value: adult

value: 84 year

value: John Stamatoyannopoulos, UW

value: ENCBS804RUL at ENCODE; https://www.encodeproject.org/ENCBS804RUL/

value: Derived from ENCODE donor ENCDO240JUB; https://www.encodeproject.org/ENCDO240JUB/


title: DNase-seq from transverse colon (ENCLB242YSP)

description:
https://www.encodeproject.org/experiments/ENCSR790FIS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR790FIS
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB242YSP

source_name: Homo sapiens transverse colon tissue male adult (54 years)

value: transverse colon

value: 54 year

value: ENCBS409AIP at ENCODE; https://www.encodeproject.org/ENCBS409AIP/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 2

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_2
esc1_12h_2_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: DNase-seq from heart (ENCLB417ZPE)

description:
https://www.encodeproject.org/experiments/ENCSR664PKM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR664PKM
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-09-22
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB417ZPE
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Homo sapiens heart tissue female fetal (76 days)

value: tissue

value: fetal

value: female

value: 76 day

value: ENCBS953MIB at ENCODE; https://www.encodeproject.org/ENCBS953MIB/

value: Derived from ENCODE donor ENCDO237NAG; https://www.encodeproject.org/ENCDO237NAG/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 94

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_94
esc1_6h_94_rsem


title: DNase-seq from NAMALWA (ENCLB214IOO)

description:
https://www.encodeproject.org/experiments/ENCSR662HMO/
***************
biological replicate number: 1
technical replicate number: 1,2
description:
experiment encode accession: ENCSR662HMO
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-11-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB214IOO
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000,Illumina NextSeq 500

source_name: Homo sapiens NAMALWA immortalized cell line

value: NAMALWA

value: immortalized cell line

value: child

value: 3 year

value: ENCBS105ISO at ENCODE; https://www.encodeproject.org/ENCBS105ISO/

value: Derived from ENCODE donor ENCDO993XLR; https://www.encodeproject.org/ENCDO993XLR/

value: ENCODE dbxrefs Cellosaurus CVCL_0067; http://web.expasy.org/cellosaurus/CVCL_0067


title: DNase-seq from H9 (ENCLB579XJQ)

description:
https://www.encodeproject.org/experiments/ENCSR754LIN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR754LIN
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-08-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB579XJQ

source_name: Homo sapiens H9 stem cell G1 phase transiently expressing N-terminal eGFP fusion protein, C-terminal eGFP fusion protein

value: stem cell

value: unknown

value: not collected

value: John Stamatoyannopoulos, UW

value: ENCBS741LLD at ENCODE; https://www.encodeproject.org/ENCBS741LLD/

value: Derived from ENCODE donor ENCDO488VKC; https://www.encodeproject.org/ENCDO488VKC/

value: ENCODE dbxrefs Cellosaurus CVCL_9773; http://web.expasy.org/cellosaurus/CVCL_9773


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 93

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_93
esc1_6h_93_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 92

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_92
esc1_6h_92_rsem


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 95

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_95
esc1_6h_95_rsem


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 90

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_90
esc1_6h_90_rsem


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 91

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_91
esc1_6h_91_rsem


title: DNase-seq from HAP-1 (ENCLB760TOD)

description:
https://www.encodeproject.org/experiments/ENCSR620QNS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR620QNS
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-11
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB760TOD

source_name: Homo sapiens HAP-1 immortalized cell line

value: male

value: ENCBS912MMS at ENCODE; https://www.encodeproject.org/ENCBS912MMS/

value: Derived from ENCODE donor ENCDO188XMG; https://www.encodeproject.org/ENCDO188XMG/

value: ENCODE dbxrefs Cellosaurus CVCL_Y019; http://web.expasy.org/cellosaurus/CVCL_Y019


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 89

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_89
esc1_6h_89_rsem


title: DNase-seq from NAMALWA (ENCLB748BZC)

description:
https://www.encodeproject.org/experiments/ENCSR662HMO/
***************
biological replicate number: 2
technical replicate number: 1,2
description:
experiment encode accession: ENCSR662HMO
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-11-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB748BZC
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

value: NAMALWA

value: immortalized cell line

value: child

value: female

value: ENCBS499IUK at ENCODE; https://www.encodeproject.org/ENCBS499IUK/


title: DNase-seq from HAP-1 (ENCLB949CJA)

description:
https://www.encodeproject.org/experiments/ENCSR620QNS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR620QNS
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-11
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB949CJA
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

value: ENCBS217AEF at ENCODE; https://www.encodeproject.org/ENCBS217AEF/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 88

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_88
esc1_6h_88_rsem


title: DNase-seq from RPMI8226 (ENCLB123CIH)

description:
https://www.encodeproject.org/experiments/ENCSR594NOE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR594NOE
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-11-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB123CIH
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens RPMI8226 immortalized cell line

value: adult

value: 61 year

value: ENCBS604KZU at ENCODE; https://www.encodeproject.org/ENCBS604KZU/

value: Derived from ENCODE donor ENCDO624OGB; https://www.encodeproject.org/ENCDO624OGB/

value: ENCODE dbxrefs Cellosaurus CVCL_0014; http://web.expasy.org/cellosaurus/CVCL_0014


title: DNase-seq from H9 (ENCLB139ECN)

description:
https://www.encodeproject.org/experiments/ENCSR754LIN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR754LIN
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-08-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB139ECN

value: stem cell

value: unknown

value: not collected

value: John Stamatoyannopoulos, UW

value: ENCBS140HIH at ENCODE; https://www.encodeproject.org/ENCBS140HIH/

value: Derived from ENCODE donor ENCDO488VKC; https://www.encodeproject.org/ENCDO488VKC/

value: ENCODE dbxrefs Cellosaurus CVCL_9773; http://web.expasy.org/cellosaurus/CVCL_9773


title: genetic modification DNase-seq from K562 (ENCLB634TEY)

description:
https://www.encodeproject.org/experiments/ENCSR605SNG/
***************
biological replicate number: 1
technical replicate number: 1
description: TALEN-mediated homozygous DHS deletion in K562.
experiment encode accession: ENCSR605SNG
assay title: genetic modification DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-11-02
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB634TEY
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Homo sapiens K562 immortalized cell line genetically modified (deletion) using TALEs

value: immortalized cell line

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS021EGH at ENCODE; https://www.encodeproject.org/ENCBS021EGH/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 86

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_86
esc1_6h_86_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: DNase-seq from trophoblast cell (ENCLB699ZAP)

description:
https://www.encodeproject.org/experiments/ENCSR593LTJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR593LTJ
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB699ZAP
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens trophoblast primary cell fetal (18 weeks)

value: trophoblast cell

value: primary cell

value: fetal

value: 18 week

value: ENCBS626CAG at ENCODE; https://www.encodeproject.org/ENCBS626CAG/

value: Derived from ENCODE donor ENCDO070KYQ; https://www.encodeproject.org/ENCDO070KYQ/


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 10

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_10
esc1_12h_10_rsem


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 87

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_87
esc1_6h_87_rsem


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 85

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_85
esc1_6h_85_rsem


title: DNase-seq from sigmoid colon (ENCLB369VGO)

description:
https://www.encodeproject.org/experiments/ENCSR592DQC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR592DQC
assay title: DNase-seq
assembly: hg19, GRCh38
encode release date: 2016-08-10
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB369VGO
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens sigmoid colon tissue male adult (37 years)

value: sigmoid colon

value: tissue

value: adult

value: male

value: 37 year

value: ENCBS682JHS at ENCODE; https://www.encodeproject.org/ENCBS682JHS/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 84

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_84
esc1_6h_84_rsem


title: DNase-seq from RPMI8226 (ENCLB167OQH)

description:
https://www.encodeproject.org/experiments/ENCSR594NOE/
***************
biological replicate number: 2
technical replicate number: 1,2
description:
experiment encode accession: ENCSR594NOE
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-11-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB167OQH
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

value: immortalized cell line

value: 61 year

value: John Stamatoyannopoulos, UW

value: ENCBS457ZNO at ENCODE; https://www.encodeproject.org/ENCBS457ZNO/

value: Derived from ENCODE donor ENCDO624OGB; https://www.encodeproject.org/ENCDO624OGB/

value: ENCODE dbxrefs Cellosaurus CVCL_0014; http://web.expasy.org/cellosaurus/CVCL_0014


title: DNase-seq from esophagus squamous epithelium (ENCLB660ZZS)

description:
https://www.encodeproject.org/experiments/ENCSR579BNV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR579BNV
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB660ZZS
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens esophagus squamous epithelium tissue female adult (53 years)

value: esophagus squamous epithelium

value: female

value: 53 year

value: ENCBS783WNF at ENCODE; https://www.encodeproject.org/ENCBS783WNF/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: DNase-seq from placenta (ENCLB078EIG)

description:
https://www.encodeproject.org/experiments/ENCSR575VMI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR575VMI
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB078EIG
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens placenta tissue male fetal (105 days)

value: placenta

value: tissue

value: fetal

value: 105 day

value: ENCBS545ZET at ENCODE; https://www.encodeproject.org/ENCBS545ZET/

value: Derived from ENCODE donor ENCDO005BVN; https://www.encodeproject.org/ENCDO005BVN/


title: DNase-seq from hematopoietic multipotent progenitor cell (ENCLB809BBZ)

description:
https://www.encodeproject.org/experiments/ENCSR564JUY/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq on 25 year old human adult male hematopoietic multipotent progenitor cell line
experiment encode accession: ENCSR564JUY
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-08-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB809BBZ
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Homo sapiens hematopoietic multipotent progenitor primary cell male adult (25 years) treated with interleukin-3 , kit ligand , hydrocortisone succinate , erythropoietin

value: primary cell

value: Day 6 (T6)

value: adult

tag: treatments

value: treatment_term_id:UniprotKB:P08700; treatment_term_name:interleukin-3; treatment_type:protein; treatment_term_id:UniprotKB:P21583; treatment_term_name:kit ligand; treatment_type:protein; treatment_term_id:CHEBI:31677; treatment_term_name:hydrocortisone succinate; treatment_type:chemical; treatment_term_id:CHEBI:81579; treatment_term_name:erythropoietin; treatment_type:chemical;

value: male

value: 25 year

value: ENCBS200EQQ at ENCODE; https://www.encodeproject.org/ENCBS200EQQ/

value: Derived from ENCODE donor ENCDO937OUY; https://www.encodeproject.org/ENCDO937OUY/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 80

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_80
esc1_6h_80_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: genetic modification DNase-seq from K562 (ENCLB460QAM)

description:
https://www.encodeproject.org/experiments/ENCSR632CQZ/
***************
biological replicate number: 1
technical replicate number: 1
description: TALEN-mediated heterozygous DHS deletion in K562.
experiment encode accession: ENCSR632CQZ
assay title: genetic modification DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-07-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB460QAM
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

value: immortalized cell line

value: female

tag: age

value: 53 year

value: chronic myelogenous leukemia (CML)

value: John Stamatoyannopoulos, UW

value: ENCBS624RXT at ENCODE; https://www.encodeproject.org/ENCBS624RXT/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004


title: genetic modification DNase-seq from K562 (ENCLB755MMP)

description:
https://www.encodeproject.org/experiments/ENCSR527IGO/
***************
biological replicate number: 1
technical replicate number: 1
description: TALEN-mediated homozygous DHS deletion in K562
experiment encode accession: ENCSR527IGO
assay title: genetic modification DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-07-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB755MMP
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

value: TALEN-mediated homozygous DHS deletion in K562.

value: ENCBS889MQU at ENCODE; https://www.encodeproject.org/ENCBS889MQU/


title: DNase-seq from limb (ENCLB188HLU)

description:
https://www.encodeproject.org/experiments/ENCSR532CRI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR532CRI
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB188HLU
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens limb tissue fetal (58 days)

value: limb

value: tissue

value: fetal

value: not collected

value: 58 day

value: ENCBS872QKU at ENCODE; https://www.encodeproject.org/ENCBS872QKU/

value: Derived from ENCODE donor ENCDO234CBV; https://www.encodeproject.org/ENCDO234CBV/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 79

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_79
esc1_6h_79_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 77

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_77
esc1_6h_77_rsem


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 78

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_78
esc1_6h_78_rsem


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 76

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_76
esc1_6h_76_rsem


title: genetic modification DNase-seq from K562 (ENCLB716UXG)

description:
https://www.encodeproject.org/experiments/ENCSR518HJD/
***************
biological replicate number: 1
technical replicate number: 1
description: TALEN-mediated heterozygous DHS deletion in K562.
experiment encode accession: ENCSR518HJD
assay title: genetic modification DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-11-02
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB716UXG

value: immortalized cell line

value: adult

value: female

value: ENCBS386ISE at ENCODE; https://www.encodeproject.org/ENCBS386ISE/


title: DNase-seq from body of pancreas (ENCLB469NCD)

description:
https://www.encodeproject.org/experiments/ENCSR522WLH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR522WLH
assay title: DNase-seq
assembly: hg19, GRCh38
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB469NCD
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens body of pancreas tissue male adult (37 years)

value: body of pancreas

value: male

value: 37 year

value: John Stamatoyannopoulos, UW

value: ENCBS962ETL at ENCODE; https://www.encodeproject.org/ENCBS962ETL/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 75

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_75
esc1_6h_75_rsem


title: Single-cell RNA-seq in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) cell 12

description:
EB+12hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_12
esc1_12h_12_rsem


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 83

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_83
esc1_6h_83_rsem


title: DNase-seq from LoVo (ENCLB058OPC)

description:
https://www.encodeproject.org/experiments/ENCSR503BEM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR503BEM
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-11
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB058OPC
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens LoVo immortalized cell line

value: LoVo

value: 56 year

value: ENCBS080BPN at ENCODE; https://www.encodeproject.org/ENCBS080BPN/

value: Derived from ENCODE donor ENCDO828APO; https://www.encodeproject.org/ENCDO828APO/

value: ENCODE dbxrefs Cellosaurus CVCL_0399; http://web.expasy.org/cellosaurus/CVCL_0399


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 73

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_73
esc1_6h_73_rsem


title: genetic modification DNase-seq from K562 (ENCLB648QNH)

description:
https://www.encodeproject.org/experiments/ENCSR514EOB/
***************
biological replicate number: 1
technical replicate number: 1
description: TALEN-mediated heterozygous DHS deletion in K562.
experiment encode accession: ENCSR514EOB
assay title: genetic modification DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-07-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB648QNH

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS829VJO at ENCODE; https://www.encodeproject.org/ENCBS829VJO/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 82

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_82
esc1_6h_82_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 71

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_71
esc1_6h_71_rsem


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 72

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_72
esc1_6h_72_rsem


title: DNase-seq from placenta (ENCLB356SYJ)

description:
https://www.encodeproject.org/experiments/ENCSR499IFY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR499IFY
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB356SYJ
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens placenta tissue fetal (53 days)

value: placenta

value: tissue

value: fetal

value: not collected

value: 53 day

value: ENCBS138QHR at ENCODE; https://www.encodeproject.org/ENCBS138QHR/

value: Derived from ENCODE donor ENCDO870GPO; https://www.encodeproject.org/ENCDO870GPO/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 81

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_81
esc1_6h_81_rsem


title: DNase-seq from putamen (ENCLB558ETM)

description:
https://www.encodeproject.org/experiments/ENCSR493VDS/
***************
biological replicate number: 1
technical replicate number: 1,2
description:
experiment encode accession: ENCSR493VDS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB558ETM
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Homo sapiens putamen tissue male adult (78 years)

value: putamen

value: adult

value: male

value: 78 year

value: John Stamatoyannopoulos, UW

value: ENCBS163MRT at ENCODE; https://www.encodeproject.org/ENCBS163MRT/

value: Derived from ENCODE donor ENCDO317XRR; https://www.encodeproject.org/ENCDO317XRR/


title: DNase-seq from testis (ENCLB532SAN)

description:
https://www.encodeproject.org/experiments/ENCSR475SYH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR475SYH
assay title: DNase-seq
assembly: hg19, GRCh38
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB532SAN

source_name: Homo sapiens testis tissue male adult (37 years)

value: testis

value: 37 year

value: ENCBS197JOA at ENCODE; https://www.encodeproject.org/ENCBS197JOA/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: DNase-seq from heart left ventricle (ENCLB699DLF)

description:
https://www.encodeproject.org/experiments/ENCSR501FWC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR501FWC
assay title: DNase-seq
assembly: hg19, GRCh38
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB699DLF

source_name: Homo sapiens heart left ventricle tissue female fetal (136 days)

value: heart left ventricle

value: tissue

value: female

value: 136 day

value: ENCBS936JZF at ENCODE; https://www.encodeproject.org/ENCBS936JZF/

value: Derived from ENCODE donor ENCDO294LOE; https://www.encodeproject.org/ENCDO294LOE/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 70

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_70
esc1_6h_70_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 69

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_69
esc1_6h_69_rsem


title: DNase-seq from limb (ENCLB514OLY)

description:
https://www.encodeproject.org/experiments/ENCSR532CRI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR532CRI
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB514OLY

source_name: Homo sapiens limb tissue fetal (59 days)

value: limb

value: fetal

value: not collected

value: 59 day

value: ENCBS301NVB at ENCODE; https://www.encodeproject.org/ENCBS301NVB/

value: Derived from ENCODE donor ENCDO041UTR; https://www.encodeproject.org/ENCDO041UTR/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 68

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_68
esc1_6h_68_rsem


title: DNase-seq from prostate gland (ENCLB659ICY)

description:
https://www.encodeproject.org/experiments/ENCSR456SOX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR456SOX
assay title: DNase-seq
assembly: hg19, GRCh38
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB659ICY
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens prostate gland tissue male adult (54 years)

value: prostate gland

value: adult

value: male

value: 54 year

value: John Stamatoyannopoulos, UW

value: ENCBS524RBS at ENCODE; https://www.encodeproject.org/ENCBS524RBS/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 67

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_67
esc1_6h_67_rsem


title: DNase-seq from embryonic facial prominence (ENCLB322LRH)

description:
https://www.encodeproject.org/experiments/ENCSR435NHO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR435NHO
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB322LRH

source_name: Homo sapiens embryonic facial prominence tissue fetal (53 days)

value: embryonic facial prominence

value: tissue

value: 53 day

value: ENCBS353VAH at ENCODE; https://www.encodeproject.org/ENCBS353VAH/

value: Derived from ENCODE donor ENCDO870GPO; https://www.encodeproject.org/ENCDO870GPO/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 74

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_74
esc1_6h_74_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: genetic modification DNase-seq from K562 (ENCLB278AQO)

description:
https://www.encodeproject.org/experiments/ENCSR447ULX/
***************
biological replicate number: 1
technical replicate number: 1
description: TALEN-mediated heterozygous DHS deletion in K562.
experiment encode accession: ENCSR447ULX
assay title: genetic modification DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-11-02
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB278AQO
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

value: immortalized cell line

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS640ATO at ENCODE; https://www.encodeproject.org/ENCBS640ATO/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 66

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_66
esc1_6h_66_rsem


title: DNase-seq from RKO (ENCLB741CNW)

description:
https://www.encodeproject.org/experiments/ENCSR429RHR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR429RHR
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-08-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB741CNW

source_name: Homo sapiens RKO immortalized cell line

value: RKO

value: unknown

value: not collected

value: ENCBS740UAH at ENCODE; https://www.encodeproject.org/ENCBS740UAH/

value: Derived from ENCODE donor ENCDO035MMY; https://www.encodeproject.org/ENCDO035MMY/

value: ENCODE dbxrefs Cellosaurus CVCL_0504; http://web.expasy.org/cellosaurus/CVCL_0504


title: DNase-seq from LoVo (ENCLB644CCC)

description:
https://www.encodeproject.org/experiments/ENCSR503BEM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR503BEM
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-11
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB644CCC
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

value: LoVo

value: adult

value: male

value: 56 year

value: John Stamatoyannopoulos, UW

value: ENCBS024NHD at ENCODE; https://www.encodeproject.org/ENCBS024NHD/

value: Derived from ENCODE donor ENCDO828APO; https://www.encodeproject.org/ENCDO828APO/

value: ENCODE dbxrefs Cellosaurus CVCL_0399; http://web.expasy.org/cellosaurus/CVCL_0399


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 65

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_65
esc1_6h_65_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: DNase-seq from RKO (ENCLB307RIV)

description:
https://www.encodeproject.org/experiments/ENCSR429RHR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR429RHR
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-08-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB307RIV
instrument models: Illumina HiSeq 2500,Illumina HiSeq 4000,Illumina NextSeq 500

value: immortalized cell line

value: ENCBS954LTA at ENCODE; https://www.encodeproject.org/ENCBS954LTA/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 64

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_64
esc1_6h_64_rsem


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 63

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_63
esc1_6h_63_rsem


title: DNase-seq from CD1c-positive myeloid dendritic cell (ENCLB958JIU)

description:
https://www.encodeproject.org/experiments/ENCSR373BIX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR373BIX
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-11
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB958JIU

source_name: Homo sapiens CD1c-positive myeloid dendritic primary cell

value: CD1c-positive myeloid dendritic cell

value: primary cell

value: ENCBS514YGQ at ENCODE; https://www.encodeproject.org/ENCBS514YGQ/

value: Derived from ENCODE donor ENCDO820BXZ; https://www.encodeproject.org/ENCDO820BXZ/


title: DNase-seq from superior temporal gyrus (ENCLB306SUY)

description:
https://www.encodeproject.org/experiments/ENCSR382JUJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR382JUJ
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB306SUY
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens superior temporal gyrus tissue male adult (84 years)

value: superior temporal gyrus

value: tissue

value: 84 year

value: ENCBS833HUD at ENCODE; https://www.encodeproject.org/ENCBS833HUD/

value: Derived from ENCODE donor ENCDO240JUB; https://www.encodeproject.org/ENCDO240JUB/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 61

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_61
esc1_6h_61_rsem


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 62

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_62
esc1_6h_62_rsem


title: DNase-seq from hepatocyte (ENCLB636PSO)

description:
https://www.encodeproject.org/experiments/ENCSR364MFN/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq on 5 day embryonic female human IV-differentiated hepatocyte
experiment encode accession: ENCSR364MFN
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-06-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB636PSO
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens hepatocyte in vitro differentiated cells female embryo (5 days) derived from H9

value: hepatocyte

value: in vitro differentiated cells

value: Frozen or fixed, in vitro differentiated hepatocyte-like cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: 5 day

value: embryonic

value: female

value: healthy

value: Richard Myers, HAIB

value: ENCBS520VFV at ENCODE; https://www.encodeproject.org/ENCBS520VFV/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 60

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_60
esc1_6h_60_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: DNase-seq from CD1c-positive myeloid dendritic cell (ENCLB334ICF)

description:
https://www.encodeproject.org/experiments/ENCSR373BIX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR373BIX
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-11
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB334ICF

value: CD1c-positive myeloid dendritic cell

value: primary cell

value: unknown

value: not collected

value: John Stamatoyannopoulos, UW

value: ENCBS450MZJ at ENCODE; https://www.encodeproject.org/ENCBS450MZJ/

value: Derived from ENCODE donor ENCDO820BXZ; https://www.encodeproject.org/ENCDO820BXZ/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 58

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_58
esc1_6h_58_rsem


title: DNase-seq from hepatocyte (ENCLB437ZLJ)

description:
https://www.encodeproject.org/experiments/ENCSR364MFN/
***************
biological replicate number: 2
technical replicate number: 1
description: DNase-seq on 5 day embryonic female human IV-differentiated hepatocyte
experiment encode accession: ENCSR364MFN
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-06-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB437ZLJ

value: hepatocyte

value: in vitro differentiated cells

value: ENCBS077RUJ at ENCODE; https://www.encodeproject.org/ENCBS077RUJ/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 59

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_59
esc1_6h_59_rsem


title: DNase-seq from middle frontal gyrus (ENCLB166BCX)

description:
https://www.encodeproject.org/experiments/ENCSR318PRQ/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq on 78 year old male human middle frontal gyral tissue
experiment encode accession: ENCSR318PRQ
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-08-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB166BCX
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Homo sapiens middle frontal gyrus tissue male adult (78 years)

value: middle frontal gyrus

value: tissue

value: adult

value: male

value: 78 year

value: ENCBS299RKW at ENCODE; https://www.encodeproject.org/ENCBS299RKW/

value: Derived from ENCODE donor ENCDO317XRR; https://www.encodeproject.org/ENCDO317XRR/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 57

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_57
esc1_6h_57_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: DNase-seq from middle frontal gyrus (ENCLB524IQB)

description:
https://www.encodeproject.org/experiments/ENCSR318PRQ/
***************
biological replicate number: 2
technical replicate number: 1
description: DNase-seq on 78 year old male human middle frontal gyral tissue
experiment encode accession: ENCSR318PRQ
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-08-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB524IQB
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000,Illumina NextSeq 500

value: ENCBS568MCE at ENCODE; https://www.encodeproject.org/ENCBS568MCE/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 56

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_56
esc1_6h_56_rsem


title: 26S rRNA tail seq from eri-1 after cold shock

city: Hefei

first: Shouhong

last: Guang

state: Anhui

address: 443 HuangShan Road

department: School of Life Sciences

country: China

institute: University of Science & Technology of China

data_processing:
The Illumina-generated raw reads were first filtered to remove adaptors, low quality tags as well as contaminants to get clean reads at BGI Shenzhen. Clean reads targeting 26S rRNA were de-multiplexed. The number of reads with distinct 3'-end modifications were counted by custom Perl scripts.
The Illumina-generated raw reads were first filtered to remove adaptors, low quality tags as well as contaminants to get clean reads at BGI Shenzhen. Clean reads ranging from 20 to 30 nt were mapped to the C. elegans genome and the transcriptome assembly WS243, respectively, using Bowtie2 with default parameters (Langmead and Salzberg Nat Methods 9: 357-359. (2012)). The number of reads targeting each gene was counted by custom Perl scripts and displayed by IGV (Thorvaldsdottir et al. Brief Bioinform 14: 178-192. (2013)). Total mappable reads excluding sense rRNA were used for normalization.
The data processing pipeline for 26S rRNA tail-seq was included as an additional column of the SAMPLES section.
Genome_build: WS243
Supplementary_files_format_and_content: text files; the reads were aligned to C. elegans transcriptome WS243 version by Bowtie2 and counted the number of reads targeting each transcript by Perl script. For tail-seq, the reads were aligned to 26S rRNA and the extra nucleotides at 3'-ends were counted; Gene_ID. sense_counts, antisense_counts, Classification, Gene_description .

organism: Caenorhabditis elegans

source_name: embryo

growth_protocol: C. elegans strains were cultured on NGM plates with E. coli OP50 as the food source in a temperature controlled incubator. Worms were maintained at 20°C prior to the experiment. Worms were synchronized by using the standard egg-prep protocol. L1s were released onto 10 cm NGM concentrated OP50 plate (approximately 3000 L1s per plate). Synchronized embryos were incubated at 20°C, 15°C, or 4°C for 12 hours, then grown at 20°C for 2 hours before RNA extraction.

extract_protocol:
Total RNAs were isolated from bleached embryos. Briefly, embryos were harvested and dounced on ice with pestle B in TRIzol reagent (Invitrogen) followed by isopropanol precipitation. The RNA were digested with DNase I and re-purified by TRIzol reagent. Total RNAs were ligated to the 3' RNA linkers with T4 RNA ligase (Thermo #EL0021) (300 ng total RNAs, 2μl 3' RNA linker (10 ng/μl), 1μl 10x T4 RNA ligation buffer, 2μl T4 RNA ligase, 37°C, 30min ). 3' RNA linker-1: 5'-pGATCCACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3'. 3' RNA linker-2: 5'-pGTACCACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3'. 3' RNA linker-3: 5'-pCGACACACTCGGGCACCAAGG-NH2-3'. The RNAs were reverse transcribed with the following primers: 3' linker RT-1: 5'-GCTGGAATTCGCGGTTAAATCCTTGGTGCCCGAGTGTGGATC-3'. 3' linker RT-2: 5'-GCTGGAATTCGCGGTTAAATCCTTGGTGCCCGAGTGTGGTAC-3'. 3' linker RT-3: 5'-GCTGGAATTCGCGGTTAAATCCTTGGTGCCCGAGTGTGTCG-3'. The cDNAs were PCR amplified with the primers 26S rRNA-202-F: 5'-CATCTCTATCTCGTGGCAACACGAG-3' and linker-R: 5'-GCTGGAATTCGCGGTTAAATCCTTG-3' and gel purified.
Small RNAs were cloned and deep sequenced using an Illumina platform, according to the manufacturer's instructions, by the Beijing Genomics Institute (BGI Shenzhen). sRNAs ranging from 20 to 30 nt were gel-purified and ligated to a 3’ adaptor (5’-pUCGUAUGCCGUCUUCUGCUUGidT-3’; p, phosphate; idT, inverted deoxythymidine) and a 5’ adaptor (5’-GUUCAGAGUUCUACAGUCCGACGAUC-3’). The ligation products were gel-purified, reverse transcribed, and amplified using Illumina’s sRNA primer set (5’-CAAGCAGAAGACG GCATACGA-3’; 5’-AATGATACGGCGACCACCGA-3’). The samples were sequenced using an Illumina Hiseq platform.

tag: strain background

tag: genotype

tag: temperature

value: 20oC, then 4°C for 12 hours, then 20°C for 2 hours

tag: molecule subtype

value: tail of 26S rRNA


title: 26S rRNA tail seq from eri-1;susi-1(ust1)

growth_protocol: C. elegans strains were cultured on NGM plates with E. coli OP50 as the food source in a temperature controlled incubator. Worms were maintained at 20°C prior to the experiment. Worms were synchronized by using the standard egg-prep protocol. L1s were released onto 10 cm NGM concentrated OP50 plate (approximately 3000 L1s per plate).


title: DNase-seq from NCI-H226 (ENCLB013BNK)

description:
https://www.encodeproject.org/experiments/ENCSR265TEK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR265TEK
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-11-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB013BNK

source_name: Homo sapiens NCI-H226 immortalized cell line

value: immortalized cell line

tag: biosample encode accession

value: unknown

tag: Sex

value: John Stamatoyannopoulos, UW

value: ENCBS986NWY at ENCODE; https://www.encodeproject.org/ENCBS986NWY/

value: Derived from ENCODE donor ENCDO337XRW; https://www.encodeproject.org/ENCDO337XRW/

value: ENCODE dbxrefs Cellosaurus CVCL_1544; http://web.expasy.org/cellosaurus/CVCL_1544


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 55

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_55
esc1_6h_55_rsem


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 54

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_54
esc1_6h_54_rsem


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 53

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_53
esc1_6h_53_rsem


title: DNase-seq from ACHN (ENCLB078PAT)

description:
https://www.encodeproject.org/experiments/ENCSR257BGZ/
***************
biological replicate number: 2
technical replicate number: 1,2
description: DNase-seq on cell line ACHN (epithelial cell from 22 year old male human kidney, renal cell adenocarcinoma)
experiment encode accession: ENCSR257BGZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2015-08-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB078PAT
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Homo sapiens ACHN immortalized cell line

value: ACHN

tag: dev stage

value: 22 year

tag: lab

value: ENCBS569UYK at ENCODE; https://www.encodeproject.org/ENCBS569UYK/

value: Derived from ENCODE donor ENCDO627NDO; https://www.encodeproject.org/ENCDO627NDO/

value: ENCODE dbxrefs Cellosaurus CVCL_1067; http://web.expasy.org/cellosaurus/CVCL_1067


title: 26S rRNA tail seq from N2

value: wild type


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 52

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_52
esc1_6h_52_rsem


title: total small RNA in eri-1 with UV

data_processing:
The Illumina-generated raw reads were first filtered to remove adaptors, low quality tags as well as contaminants to get clean reads at BGI Shenzhen. Clean reads ranging from 20 to 30 nt were mapped to the C. elegans genome and the transcriptome assembly WS243, respectively, using Bowtie2 with default parameters (Langmead and Salzberg Nat Methods 9: 357-359. (2012)). The number of reads targeting each gene was counted by custom Perl scripts and displayed by IGV (Thorvaldsdottir et al. Brief Bioinform 14: 178-192. (2013)). Total mappable reads excluding sense rRNA were used for normalization.
The data processing pipeline for 26S rRNA tail-seq was included as an additional column of the SAMPLES section.
Genome_build: WS243
Supplementary_files_format_and_content: text files; the reads were aligned to C. elegans transcriptome WS243 version by Bowtie2 and counted the number of reads targeting each transcript by Perl script. For tail-seq, the reads were aligned to 26S rRNA and the extra nucleotides at 3'-ends were counted; Gene_ID. sense_counts, antisense_counts, Classification, Gene_description .

growth_protocol: C. elegans strains were cultured on NGM plates with E. coli OP50 as the food source in a temperature controlled incubator. Worms were maintained at 20°C prior to the experiment. Worms were synchronized by using the standard egg-prep protocol. L1s were released onto 10 cm plates without food. Bleached embryos were exposed to 50 mJ/cm2 UV irradiation by Ultraviolet (HL-2000 HybriLinker) and recover for 2 hours.

extract_protocol:
Total small RNAs were isolated from bleached embryos. Briefly, embryos were harvested and dounced on ice with pestle B in TRIzol reagent (Invitrogen) followed by isopropanol precipitation. The precipitates were treated with calf intestinal alkaline phosphatase (CIAP, Invitrogen), re-extracted with TRIzol, and treated with T4 polynucleotide kinase (T4 PNK, New England Biolabs) in the presence of 1 mM ATP.
Small RNAs were cloned and deep sequenced using an Illumina platform, according to the manufacturer's instructions, by the Beijing Genomics Institute (BGI Shenzhen). sRNAs ranging from 20 to 30 nt were gel-purified and ligated to a 3’ adaptor (5’-pUCGUAUGCCGUCUUCUGCUUGidT-3’; p, phosphate; idT, inverted deoxythymidine) and a 5’ adaptor (5’-GUUCAGAGUUCUACAGUCCGACGAUC-3’). The ligation products were gel-purified, reverse transcribed, and amplified using Illumina’s sRNA primer set (5’-CAAGCAGAAGACG GCATACGA-3’; 5’-AATGATACGGCGACCACCGA-3’). The samples were sequenced using an Illumina Hiseq platform.

value: 20oC, then 50 mJ/cm2 UV, then 20oC for 2 hours

value: total small RNAs


title: DNase-seq from body of pancreas (ENCLB338MHP)

description:
https://www.encodeproject.org/experiments/ENCSR228IKB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR228IKB
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB338MHP
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens body of pancreas tissue male adult (54 years)

value: body of pancreas

value: tissue

value: adult

value: male

value: 54 year

tag: link

value: ENCBS268HAX at ENCODE; https://www.encodeproject.org/ENCBS268HAX/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: DNase-seq from uterus (ENCLB299WAF)

description:
https://www.encodeproject.org/experiments/ENCSR237WJY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR237WJY
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB299WAF
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens uterus tissue female adult (53 years)

value: uterus

value: female

value: 53 year

value: John Stamatoyannopoulos, UW

value: ENCBS310EYM at ENCODE; https://www.encodeproject.org/ENCBS310EYM/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: total small RNA in eri-1 without UV

growth_protocol: C. elegans strains were cultured on NGM plates with E. coli OP50 as the food source in a temperature controlled incubator. Worms were maintained at 20°C prior to the experiment. Worms were synchronized by using the standard egg-prep protocol. L1s were released onto 10 cm plates without food.


title: DNase-seq from medulla oblongata (ENCLB955BGY)

description:
https://www.encodeproject.org/experiments/ENCSR224IYD/
***************
biological replicate number: 2
technical replicate number: 1,2
description:
experiment encode accession: ENCSR224IYD
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-08-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB955BGY
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Homo sapiens medulla oblongata tissue male adult (78 years)

value: medulla oblongata

value: 78 year

value: ENCBS433NBX at ENCODE; https://www.encodeproject.org/ENCBS433NBX/

value: Derived from ENCODE donor ENCDO317XRR; https://www.encodeproject.org/ENCDO317XRR/


title: DNase-seq from body of pancreas (ENCLB756SVX)

description:
https://www.encodeproject.org/experiments/ENCSR228IKB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR228IKB
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB756SVX
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

value: body of pancreas