title: DNase-seq from L1-S8 (ENCLB950PTO)

description:
https://www.encodeproject.org/experiments/ENCSR314EZY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR314EZY
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-11
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB950PTO
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Homo sapiens L1-S8 induced pluripotent stem cell line

value: induced pluripotent stem cell line

value: L1-S8 is a partially reprogrammed cell line generated from human bone marrow mononuclear cells (BMMCs) after prestimulation with early cytokines (TPO, FL, SCF, IL-3) and transduced with Sendai viruses expressing the four factors OCT4, SOX2, KLF4 and cMYC. It originated from a single colony manually picked and clonal expanded.

value: unknown

value: not collected

value: ENCBS266IJZ at ENCODE; https://www.encodeproject.org/ENCBS266IJZ/

value: Derived from ENCODE donor ENCDO315JDK; https://www.encodeproject.org/ENCDO315JDK/


title: NRDE-3-associated small RNA in eri-1 with UV

status: Public on Dec 07 2016

type: SRA

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

library_source: transcriptomic

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 .

molecule: total RNA

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 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:
NRDE-3-associated siRNAs were isolated from embryo lysates as described (Zhou, X et al, Genetics 197, 121-32 (2014)). Briefly, the animals were sonicated in lysis buffer (20 mM Tris-HCl [pH 7.5], 200 mM NaCl, 2.5 mM MgCl2, and 0.5% NP-40); the lysate was pre-cleared with protein G-agarose beads (Roche), and incubated with anti-FLAG M2 agarose (Sigma) beads. The beads were washed extensively, and FLAG::GFP::NRDE-3 and associated RNA were eluted with 100 μg/ml 3xFLAG peptide (Sigma). The eluates were incubated with 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.

tag: strain background

tag: genotype

tag: temperature

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

tag: antibody

value: anti-FLAG M2 antibody (Sigma)

tag: molecule subtype

value: IPed small RNA


title: NRDE-3-associated 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: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 49

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+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_49
esc1_6h_49_rsem

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

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: DNase-seq from SW480 (ENCLB699TII)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR217SET/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR217SET
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB699TII
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 SW480 immortalized cell line

tag: line

value: immortalized cell line

tag: biosample encode accession

tag: dev stage

value: adult

tag: Sex

value: male

tag: age

value: 50 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: link

value: ENCBS421AQW at ENCODE; https://www.encodeproject.org/ENCBS421AQW/

value: Derived from ENCODE donor ENCDO499CXJ; https://www.encodeproject.org/ENCDO499CXJ/

value: ENCODE dbxrefs Cellosaurus CVCL_0546; http://web.expasy.org/cellosaurus/CVCL_0546


title: DNase-seq from SW480 (ENCLB090JSJ)

description:
https://www.encodeproject.org/experiments/ENCSR217SET/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR217SET
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB090JSJ
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

value: ENCBS211HGL at ENCODE; https://www.encodeproject.org/ENCBS211HGL/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 50

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_50
esc1_6h_50_rsem


title: 26S rRNA tail seq from eri-1

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 .

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).

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.

value: tail of 26S rRNA


title: total NRDE-3 bound small RNA in N2 after cold shock

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.

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


title: genetic modification DNase-seq from K562 (ENCLB236IWC)

description:
https://www.encodeproject.org/experiments/ENCSR274JIR/
***************
biological replicate number: 1
technical replicate number: 1
description: TALEN-mediated homozygous DHS deletion in K562.
experiment encode accession: ENCSR274JIR
assay title: genetic modification DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-11
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB236IWC

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

tag: description

value: female

value: 53 year

tag: health state

value: chronic myelogenous leukemia (CML)

value: ENCBS657MGB at ENCODE; https://www.encodeproject.org/ENCBS657MGB/

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

tag: strain background


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 48

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_48
esc1_6h_48_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 47

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_47
esc1_6h_47_rsem


title: genetic modification DNase-seq from K562 (ENCLB119SZN)

description:
https://www.encodeproject.org/experiments/ENCSR215FCQ/
***************
biological replicate number: 1
technical replicate number: 1
description: TALEN-mediated homozygous DHS deletion in K562.
experiment encode accession: ENCSR215FCQ
assay title: genetic modification DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-07-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB119SZN

value: immortalized cell line

value: adult

value: ENCBS751EBU at ENCODE; https://www.encodeproject.org/ENCBS751EBU/


title: total small RNAs in susi-1(R457H)

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.

tag: genotype

value: total small RNAs


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 46

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_46
esc1_6h_46_rsem


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 45

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_45
esc1_6h_45_rsem


title: total small RNAs in N2

value: wild type

tag: temperature


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 44

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_44
esc1_6h_44_rsem


title: DNase-seq from adrenal gland (ENCLB707WVL)

description:
https://www.encodeproject.org/experiments/ENCSR191FOV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR191FOV
assay title: DNase-seq
assembly: hg19, GRCh38
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB707WVL

source_name: Homo sapiens adrenal gland tissue male adult (37 years)

value: adrenal gland

value: tissue

value: male

value: 37 year

value: John Stamatoyannopoulos, UW

value: ENCBS371OZD at ENCODE; https://www.encodeproject.org/ENCBS371OZD/

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


title: total small RNAs in N2 after cold shock

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


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 51

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_51
esc1_6h_51_rsem


title: DNase-seq from gastrocnemius medialis (ENCLB765HJN)

description:
https://www.encodeproject.org/experiments/ENCSR171ETY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR171ETY
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB765HJN

source_name: Homo sapiens gastrocnemius medialis tissue male adult (54 years)

value: gastrocnemius medialis

value: 54 year

value: ENCBS921WWM at ENCODE; https://www.encodeproject.org/ENCBS921WWM/

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


title: DNase-seq from right lobe of liver (ENCLB770KGU)

description:
https://www.encodeproject.org/experiments/ENCSR174TIP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR174TIP
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB770KGU

source_name: Homo sapiens right lobe of liver tissue female adult (53 years)

value: right lobe of liver

value: female

value: 53 year

value: ENCBS220FFU at ENCODE; https://www.encodeproject.org/ENCBS220FFU/

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


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 43

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_43
esc1_6h_43_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: DNase-seq from adipocyte (ENCLB141LOR)

description:
https://www.encodeproject.org/experiments/ENCSR998KYQ/
***************
biological replicate number: 1
technical replicate number: 2,1
description:
experiment encode accession: ENCSR998KYQ
assay title: DNase-seq
assembly: mm10
encode release date: 2016-11-02
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB141LOR

source_name: Mus musculus strain C57BL/6J adipocyte in vitro differentiated cells

value: adipocyte

value: in vitro differentiated cells

value: Differentiated from 3T3-L1 (Day 8)

value: unknown

value: not collected

value: ENCBS937WUO at ENCODE; https://www.encodeproject.org/ENCBS937WUO/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: total NRDE-3 bound small RNA in eri-1 after cold shock

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

tag: antibody

value: anti-FLAG M2 antibody (Sigma)

value: IPed small RNA


title: DNase-seq from acute myeloid leukemia (ENCLB127UYP)

description:
https://www.encodeproject.org/experiments/ENCSR855ASN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR855ASN
assay title: DNase-seq
assembly: mm10
encode release date: 2015-10-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB127UYP

source_name: Mus musculus strain C57BL/6J acute myeloid leukemia in vitro differentiated cells

value: acute myeloid leukemia

value: John Stamatoyannopoulos, UW

value: ENCBS027MWX at ENCODE; https://www.encodeproject.org/ENCBS027MWX/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 42

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_42
esc1_6h_42_rsem


title: DNase-seq from acute myeloid leukemia (ENCLB151XSF)

description:
https://www.encodeproject.org/experiments/ENCSR855ASN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR855ASN
assay title: DNase-seq
assembly: mm10
encode release date: 2015-10-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB151XSF

value: ENCBS994RAP at ENCODE; https://www.encodeproject.org/ENCBS994RAP/


title: DNase-seq from adipocyte (ENCLB570PHE)

description:
https://www.encodeproject.org/experiments/ENCSR998KYQ/
***************
biological replicate number: 2
technical replicate number: 3,1
description:
experiment encode accession: ENCSR998KYQ
assay title: DNase-seq
assembly: mm10
encode release date: 2016-11-02
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB570PHE

value: ENCBS478HYO at ENCODE; https://www.encodeproject.org/ENCBS478HYO/


title: DNase-seq from thyroid gland (ENCLB745IHC)

description:
https://www.encodeproject.org/experiments/ENCSR158VAT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR158VAT
assay title: DNase-seq
assembly: hg19, GRCh38
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB745IHC
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens thyroid gland tissue male adult (37 years)

value: thyroid gland

value: tissue

value: adult

value: male

value: 37 year

value: ENCBS658GLE at ENCODE; https://www.encodeproject.org/ENCBS658GLE/

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


title: DNase-seq from thyroid gland (ENCLB145KTK)

description:
https://www.encodeproject.org/experiments/ENCSR158VAT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR158VAT
assay title: DNase-seq
assembly: hg19, GRCh38
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB145KTK
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500


title: DNase-seq from acute myeloid leukemia (ENCLB945FGZ)

description:
https://www.encodeproject.org/experiments/ENCSR855ASN/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR855ASN
assay title: DNase-seq
assembly: mm10
encode release date: 2015-10-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB945FGZ

value: in vitro differentiated cells

value: unknown

value: not collected


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 40

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_40
esc1_6h_40_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 41

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_41
esc1_6h_41_rsem


title: genetic modification DNase-seq from K562 (ENCLB034LGS)

description:
https://www.encodeproject.org/experiments/ENCSR137EEM/
***************
biological replicate number: 1
technical replicate number: 1
description: TALEN-mediated heterozygous DHS deletion in K562
experiment encode accession: ENCSR137EEM
assay title: genetic modification DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-7-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB034LGS

value: immortalized cell line

value: TALEN-mediated heterozygous DHS deletion in K562.

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS767XGD at ENCODE; https://www.encodeproject.org/ENCBS767XGD/

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 39

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_39
esc1_6h_39_rsem


title: DNase-seq from trophoblast cell (ENCLB686KFW)

description:
https://www.encodeproject.org/experiments/ENCSR121ZSL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR121ZSL
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB686KFW
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens trophoblast primary cell fetal (21 week)

value: trophoblast cell

value: primary cell

value: fetal

value: 21 week

value: John Stamatoyannopoulos, UW

value: ENCBS478CDB at ENCODE; https://www.encodeproject.org/ENCBS478CDB/

value: Derived from ENCODE donor ENCDO333OMW; https://www.encodeproject.org/ENCDO333OMW/


title: genetic modification DNase-seq from K562 (ENCLB272MDP)

description:
https://www.encodeproject.org/experiments/ENCSR087QUG/
***************
biological replicate number: 1
technical replicate number: 1
description: TALEN-mediated heterozygous DHS deletion in K562.
experiment encode accession: ENCSR087QUG
assay title: genetic modification DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-07-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB272MDP
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

value: adult

value: ENCBS852JTF at ENCODE; https://www.encodeproject.org/ENCBS852JTF/


title: DNase-seq from acute myeloid leukemia (ENCLB601CML)

description:
https://www.encodeproject.org/experiments/ENCSR855ASN/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR855ASN
assay title: DNase-seq
assembly: mm10
encode release date: 2015-10-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB601CML

value: acute myeloid leukemia

value: in vitro differentiated cells

value: unknown

value: not collected

value: ENCBS027MWX at ENCODE; https://www.encodeproject.org/ENCBS027MWX/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 38

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_38
esc1_6h_38_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: DNase-seq from kidney (ENCLB334GBK)

description:
https://www.encodeproject.org/experiments/ENCSR066WZJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR066WZJ
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB334GBK
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Homo sapiens kidney tissue fetal (80 days)

value: kidney

value: tissue

value: 80 day

value: ENCBS444KCH at ENCODE; https://www.encodeproject.org/ENCBS444KCH/

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


title: DNase-seq from PC-3 (ENCLB670JIB)

description:
https://www.encodeproject.org/experiments/ENCSR052AWE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR052AWE
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-11-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB670JIB
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens PC-3 immortalized cell line

value: immortalized cell line

value: male

value: 62 year

value: grade IV, adenocarcinoma

value: John Stamatoyannopoulos, UW

value: ENCBS420VDY at ENCODE; https://www.encodeproject.org/ENCBS420VDY/

value: Derived from ENCODE donor ENCDO349AAA; https://www.encodeproject.org/ENCDO349AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0035; http://web.expasy.org/cellosaurus/CVCL_0035


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 37

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_37
esc1_6h_37_rsem


title: DNase-seq from 3T3-L1 (ENCLB532ENM)

description:
https://www.encodeproject.org/experiments/ENCSR687EAW/
***************
biological replicate number: 2
technical replicate number: 1
description: DNase-seq on 3T3-L1 mouse cell line (mouse embryo fibroblasts)
experiment encode accession: ENCSR687EAW
assay title: DNase-seq
assembly: mm10
encode release date: 2015-10-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB532ENM

source_name: Mus musculus strain C57BL/6J 3T3-L1 immortalized cell line

value: unknown

value: not collected

value: ENCBS366WMO at ENCODE; https://www.encodeproject.org/ENCBS366WMO/

value: ENCODE dbxrefs Cellosaurus CVCL_0123; http://web.expasy.org/cellosaurus/CVCL_0123


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 36

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_36
esc1_6h_36_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 35

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_35
esc1_6h_35_rsem


title: genetic modification DNase-seq from K562 (ENCLB311GTH)

description:
https://www.encodeproject.org/experiments/ENCSR048BUO/
***************
biological replicate number: 1
technical replicate number: 1
description: TALEN-mediated heterozygous DHS deletion in K562.
experiment encode accession: ENCSR048BUO
assay title: genetic modification DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-07-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB311GTH
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS504SHW at ENCODE; https://www.encodeproject.org/ENCBS504SHW/

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 34

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_34
esc1_6h_34_rsem


title: DNase-seq from RCC 7860 (ENCLB620NUI)

description:
https://www.encodeproject.org/experiments/ENCSR037PGI/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq of RCC 7860 (human renal carcinoma cell, 58 year old male)
experiment encode accession: ENCSR037PGI
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-10-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB620NUI
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens RCC 7860 immortalized cell line

value: immortalized cell line

value: Renal cell adenocarcinmoma

value: male

value: 58 year

value: ENCBS807WMR at ENCODE; https://www.encodeproject.org/ENCBS807WMR/

value: Derived from ENCODE donor ENCDO371AEU; https://www.encodeproject.org/ENCDO371AEU/

value: ENCODE dbxrefs Cellosaurus CVCL_1051; http://web.expasy.org/cellosaurus/CVCL_1051


title: DNase-seq from RCC 7860 (ENCLB369SCD)

description:
https://www.encodeproject.org/experiments/ENCSR037PGI/
***************
biological replicate number: 2
technical replicate number: 1
description: DNase-seq of RCC 7860 (human renal carcinoma cell, 58 year old male)
experiment encode accession: ENCSR037PGI
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-10-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB369SCD
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

value: John Stamatoyannopoulos, UW

value: ENCBS413VCR at ENCODE; https://www.encodeproject.org/ENCBS413VCR/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 33

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_33
esc1_6h_33_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: DNase-seq from H9 (ENCLB094YXR)

description:
https://www.encodeproject.org/experiments/ENCSR017OZH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR017OZH
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-08-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB094YXR

source_name: Homo sapiens H9 stem cell S1 phase transiently expressing N-terminal eGFP fusion protein, C-terminal eGFP fusion protein

value: stem cell

value: unknown

value: not collected

tag: phase

value: ENCBS616QKE at ENCODE; https://www.encodeproject.org/ENCBS616QKE/

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 Muller cell (ENCLB523BNO)

description:
https://www.encodeproject.org/experiments/ENCSR666HFH/
***************
biological replicate number: 2
technical replicate number: 1
description: DNase-seq on mouse Muller cell
experiment encode accession: ENCSR666HFH
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB523BNO

source_name: Mus musculus strain B6NCrl Muller primary cell mixed sex postnatal (12 days)

value: Muller cell

value: primary cell

value: postnatal

value: pooled male and female

value: 12 day

value: ENCBS481ONS at ENCODE; https://www.encodeproject.org/ENCBS481ONS/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 32

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_32
esc1_6h_32_rsem

tag: strain


title: DNase-seq from Muller cell (ENCLB392WMV)

description:
https://www.encodeproject.org/experiments/ENCSR666HFH/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq on mouse Muller cell
experiment encode accession: ENCSR666HFH
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB392WMV

value: ENCBS040NFI at ENCODE; https://www.encodeproject.org/ENCBS040NFI/


title: DNase-seq from H9 (ENCLB542FUM)

description:
https://www.encodeproject.org/experiments/ENCSR017OZH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR017OZH
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2016-08-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB542FUM

value: John Stamatoyannopoulos, UW

value: ENCBS477SFO at ENCODE; https://www.encodeproject.org/ENCBS477SFO/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 30

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_30
esc1_6h_30_rsem

tag: treatment

value: ES-derived embryoid bodies with induced transcription factors


title: DNase-seq from 3T3-L1 (ENCLB297VSF)

description:
https://www.encodeproject.org/experiments/ENCSR687EAW/
***************
biological replicate number: 1
technical replicate number: 3
description: DNase-seq on 3T3-L1 mouse cell line (mouse embryo fibroblasts)
experiment encode accession: ENCSR687EAW
assay title: DNase-seq
assembly: mm10
encode release date: 2015-10-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB297VSF

value: immortalized cell line

value: ENCBS666CGP at ENCODE; https://www.encodeproject.org/ENCBS666CGP/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0123; http://web.expasy.org/cellosaurus/CVCL_0123


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 31

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_31
esc1_6h_31_rsem

tag: cell type


title: DNase-seq from MEL cell line (ENCLB992MJM)

description:
https://www.encodeproject.org/experiments/ENCSR446MUM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR446MUM
assay title: DNase-seq
assembly: mm10
encode release date: 2015-10-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB992MJM

source_name: Mus musculus strain MEL MEL immortalized cell line

tag: line

value: MEL cell line

value: unknown

value: not collected

value: ENCBS002NUU at ENCODE; https://www.encodeproject.org/ENCBS002NUU/

value: Derived from ENCODE donor ENCDO073AAA; https://www.encodeproject.org/ENCDO073AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_2111; http://web.expasy.org/cellosaurus/CVCL_2111


title: DNase-seq from MEL cell line (ENCLB289SLG)

description:
https://www.encodeproject.org/experiments/ENCSR446MUM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR446MUM
assay title: DNase-seq
assembly: mm10
encode release date: 2015-10-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB289SLG

tag: biosample encode accession

value: ENCBS892CGC at ENCODE; https://www.encodeproject.org/ENCBS892CGC/


title: PBNT1 rep3

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Raw reads were mapped using STAR v2.4.2a using default parameters and read counts were obtained for transcripts annotated based on Gencode v14.
Quality control measures were checked using FastQC and Picard Tools.
Differential expression (DE) analysis was performed using the exactTest module implemented in edgeR v3.8.6.
Genome_build: hg19
Supplementary_files_format_and_content: Read counts per gene, aligned by STAR, presented in the following format,  STAR_v2p4p2a_Mpd_<sample>_ReadsPerGene.out.  This is a tab delimited file.

source_name: Polar Body Nuclear Transfer

extract_protocol:
Total RNA was extracted from hESO-14 or PBNT1 cells (passage 5) using the RNeasy Lipid Tissue Mini Kit according to protocol (QIAGEN). mRNA libraries were constructed using the TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) and 4 µg total RNA according to manufacturer's instructions to confer strand specificity. mRNA was purified using the RNA Purifications Beads per Illumina protocol instructions. The mRNA was incubated in the Elute, Prime, and Fragment Mix at 94˚C for 8 min to fragment mRNA followed by first strand of cDNA and second strand synthesis.
The cDNA was ligated to adapter and enriched with PCR to create the final cDNA library per Illumina protocol specifications (15 cycles of PCR). The reaction products were purified using AMPure XP beads according to manufacturer’s specifications. RNA-seq libraries were sequenced using the Illumina HiSeq 2500 (Illumina) instrument per manufacturer’s instructions. Sequencing of libraries was performed with Single Read Cluster Kit v3, 100 cycles (Illumina).

value: pluripotent


title: hESO-14 rep1

source_name: IVF derived embryonic stem cell


title: DNase-seq from MEL cell line (ENCLB984ZML)

description:
https://www.encodeproject.org/experiments/ENCSR446MUM/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR446MUM
assay title: DNase-seq
assembly: mm10
encode release date: 2015-10-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB984ZML

tag: dev stage


title: DNase-seq from 3T3-L1 (ENCLB448GKB)

description:
https://www.encodeproject.org/experiments/ENCSR687EAW/
***************
biological replicate number: 2
technical replicate number: 2
description: DNase-seq on 3T3-L1 mouse cell line (mouse embryo fibroblasts)
experiment encode accession: ENCSR687EAW
assay title: DNase-seq
assembly: mm10
encode release date: 2015-10-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB448GKB

tag: Sex

value: ENCBS366WMO at ENCODE; https://www.encodeproject.org/ENCBS366WMO/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 28

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_28
esc1_6h_28_rsem


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 27

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_27
esc1_6h_27_rsem


title: DNase-seq from Muller cell (ENCLB605ODE)

description:
https://www.encodeproject.org/experiments/ENCSR666HFH/
***************
biological replicate number: 3
technical replicate number: 1
description: DNase-seq on mouse Muller cell
experiment encode accession: ENCSR666HFH
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB605ODE

value: Muller cell

value: primary cell

value: postnatal

value: pooled male and female

tag: age

value: 12 day

value: healthy

value: ENCBS994MCZ at ENCODE; https://www.encodeproject.org/ENCBS994MCZ/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: PBNT1 rep2


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 26

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_26
esc1_6h_26_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 29

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_29
esc1_6h_29_rsem


title: PBNT1 rep1


title: DNase-seq from MEL cell line (ENCLB433QVH)

description:
https://www.encodeproject.org/experiments/ENCSR372SMH/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR372SMH
assay title: DNase-seq
assembly: mm10
encode release date: 2015-10-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB433QVH

source_name: Mus musculus strain MEL MEL immortalized cell line treated with 125 ?M zinc dichloride for 24 hours

value: MEL cell line

value: immortalized cell line

value: unknown

tag: treatments

value: treatment_term_id:CHEBI:49976; treatment_term_name:zinc dichloride; treatment_type:chemical; duration:24; duration_units:hour;

tag: lab

value: John Stamatoyannopoulos, UW

value: ENCBS588DZE at ENCODE; https://www.encodeproject.org/ENCBS588DZE/


title: DNase-seq from MEL cell line (ENCLB762NNZ)

description:
https://www.encodeproject.org/experiments/ENCSR372SMH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR372SMH
assay title: DNase-seq
assembly: mm10
encode release date: 2015-10-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB762NNZ

value: not collected

tag: link

value: ENCBS259BOZ at ENCODE; https://www.encodeproject.org/ENCBS259BOZ/

value: Derived from ENCODE donor ENCDO073AAA; https://www.encodeproject.org/ENCDO073AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_2111; http://web.expasy.org/cellosaurus/CVCL_2111


title: DNase-seq from 3T3-L1 (ENCLB297FUH)

description:
https://www.encodeproject.org/experiments/ENCSR687EAW/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq on 3T3-L1 mouse cell line (mouse embryo fibroblasts)
experiment encode accession: ENCSR687EAW
assay title: DNase-seq
assembly: mm10
encode release date: 2015-10-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB297FUH

value: ENCBS666CGP at ENCODE; https://www.encodeproject.org/ENCBS666CGP/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0123; http://web.expasy.org/cellosaurus/CVCL_0123


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 24

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_24
esc1_6h_24_rsem


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 25

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_25
esc1_6h_25_rsem


title: hESO-14

data_processing:
Sequencing reads were first trimmed for adapter sequence using Cutadapt. All cytosines in the trimmed reads were then computationally converted to thymines and mapped twice, to a converted forward strand reference and to a converted reverse strand reference both based on the hg19 reference genome. A converted reference is created by replacing all cytosines with thymines (forward strand) or all guanines with adenines (reverse strand) in the reference FASTA file.
For mapping we used Bowtie3 with the following options: "-S","-k 1","-m 1","--chunkmbs 3072","--best","--strata","-o 4","-e 80","-l 20", and "-n 0". Any read that mapped to multiple locations was removed and one read from each starting location on each strand from each library was kept (i.e., clonal reads were removed).
To call methylated sites, we summed the number of reads that supported methylation at a site and the number of reads that did not. We used these counts to perform a binomial test with a probability of success equal to the non-conversion rate, which was determined by computing the fraction of methylated reads in the lambda genome (spiked in during library construction). The false discovery rate (FDR) for a given p-value cutoff was computed using Benjamini-Hochberg approach. Because the p-value distributions for each methylation context are different, this procedure was applied to each three nucleotide context independently (e.g., a p-value cutoff was calculated for CAT cytosines).
Genome_build: hg19
Supplementary_files_format_and_content: The processed data for the allc_<sample>_<chr>.tsv files contain a row of headers indicating the chromosome, position, strand, methylation class, methylation count, total coverage, and methylation call. This is a tab delimited file.

extract_protocol:
One microgram of genomic DNA was spiked with 5 ng unmethylated cl857 Sam7 Lambda DNA (Promega, Madison, Wisconsin, USA). The DNA was fragmented with a Covaris S2 (Covaris,Woburn, Massachusetts, USA) to 150–200 bp, followed by end repair and addition of a 3’ adenine base. Cytosine-methylated adapters provided by Illumina (Illumina, San Diego, California, USA) were ligated to the sonicated DNA at 16 0C for 16 h with T4 DNA ligase (New England Biolabs). Adaptor-ligated DNA was isolated by two rounds of purification with AMPure XP beads (Beckman Coulter Genomics, Danvers, Massachusetts, USA). Adaptor-ligated DNA (<= 450 ng) was subjected to sodium bisulphite conversion using the MethylCode kit (Life Technologies, Carlsbad, California, USA) as per the manufacturer’s instructions. The bisulphite-converted, adaptor-ligated DNA molecules were enriched by eight cycles of PCR with the following reaction composition: 25 ul of Kapa HiFi Hotstart Uracil1 Readymix (Kapa Biosystems, Woburn, Massachusetts,USA) and 5 ul TruSeq PCR Primer Mix (Illumina) (50 ul final). The thermocycling parameters were: 95 0C 2 min, 98 0C 30 s, then four cycles of 98 0C 15 s, 60 0C 30 s and 72 0C 4 min, ending with one 72 0C 10-min step. The reaction products were purified using AMPure XP beads.
Two separate PCR reactions were performed on subsets of the adaptor-ligated, bisulphite-converted DNA, yielding up to two independent libraries from the same biological sample.

value: pluripotent


title: hESO-14 rep2


title: PBNT1


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 23

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_23
esc1_6h_23_rsem


title: total RNA-seq from MEL cell line (ENCLB796NEB)

description:
https://www.encodeproject.org/experiments/ENCSR000CWF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on mouse MEL treated by dimethyl sulfoxide at 2.0%
experiment encode accession: ENCSR000CWF
assay title: total RNA-seq
assembly: mm10
encode release date: 2012-06-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB796NEB
size range: 300-350

source_name: Mus musculus strain MEL MEL immortalized cell line treated with 2% dimethyl sulfoxide for 5 days

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6f6a5d8c-0b06-4457-bfbb-ee4944eab1d6/@@download/attachment/wgEncodeSydhRnaSeq.release2.html.pdf

tag: description

value: Leukemia (K562 analog)

value: treatment_term_id:CHEBI:28262; treatment_term_name:dimethyl sulfoxide; treatment_type:chemical; duration:5; duration_units:day; UCSC-ENCODE-cv:DMSO_2.0pct;

tag: health state

value: Michael Snyder, Stanford

value: ENCBS050ENC at ENCODE; https://www.encodeproject.org/ENCBS050ENC/

value: ENCODE dbxrefs MEL; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=MEL


title: total RNA-seq from MEL cell line (ENCLB762QZB)

description:
https://www.encodeproject.org/experiments/ENCSR000CWF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on mouse MEL treated by dimethyl sulfoxide at 2.0%
experiment encode accession: ENCSR000CWF
assay title: total RNA-seq
assembly: mm10
encode release date: 2012-06-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB762QZB
size range: 300-350

value: MEL cell line

value: immortalized cell line

value: unknown


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 22

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_22
esc1_6h_22_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: DNase-seq from MEL cell line (ENCLB933EUN)

description:
https://www.encodeproject.org/experiments/ENCSR372SMH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR372SMH
assay title: DNase-seq
assembly: mm10
encode release date: 2015-10-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB933EUN

value: treatment_term_id:CHEBI:49976; treatment_term_name:zinc dichloride; treatment_type:chemical; duration:24; duration_units:hour;

value: not collected

value: John Stamatoyannopoulos, UW

value: ENCBS588DZE at ENCODE; https://www.encodeproject.org/ENCBS588DZE/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 21

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_21
esc1_6h_21_rsem


title: total RNA-seq from MEL cell line (ENCLB766WYO)

description:
https://www.encodeproject.org/experiments/ENCSR000CWE/
***************
biological replicate number: 2
technical replicate number: 1
description: Stanford mouse MEL RNA-seq
experiment encode accession: ENCSR000CWE
assay title: total RNA-seq
assembly: mm10
encode release date: 2012-06-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB766WYO
size range: 300-350

value: Bing Ren, UCSD

value: ENCBS049ENC at ENCODE; https://www.encodeproject.org/ENCBS049ENC/

value: Derived from ENCODE donor ENCDO073AAA; https://www.encodeproject.org/ENCDO073AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_2111; http://web.expasy.org/cellosaurus/CVCL_2111


title: total RNA-seq from MEL cell line (ENCLB191ZSN)

description:
https://www.encodeproject.org/experiments/ENCSR000CWE/
***************
biological replicate number: 1
technical replicate number: 1
description: Stanford mouse MEL RNA-seq
experiment encode accession: ENCSR000CWE
assay title: total RNA-seq
assembly: mm10
encode release date: 2012-06-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB191ZSN
size range: 300-350

value: Leukemia (K562 analog)


title: Clone 12 hF Replicate 1

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
Human fibroblast RNA-seq reads were aliged to the Human genome (hg19) using Tophat v2.0.8 using Ensembl gene v72 as gene model.
RNA-Seq reads from hF x mESC fusion were aligned independently to Human (hg19, Ensembl v72) and Mouse (mm9, Ensembl v67) using Tophat v2.0.8. Reads aligned to both Human and Mouse were excluded from the further anlaysis.
Reads overlapping with each gene was counted using  HTSeq and differentially expressed genes were identified using edgeR
FPKM values were estimated using R script
Genome_build: hg19; mm9
Supplementary_files_format_and_content: hg19 FPKM values

source_name: Limiting dilution of TERT-immortalised NHDF17914 fibroblast

growth_protocol: Human fibroblast (hF) clones were maintainedat 3% O2  in DMEM supplemented with 10% FCS, 1% non-essential amminoacids, 2mM L-glutammine and antibiotics (10 µg/ml penicillin and streptomycin). After hF x mESC fusion, heterokaryons and hybrids were cultured in mouse ESC medium (KO-DMEM supplemented with 10% FCS, 1% non-essential amminoacids, 2mM L-glutammine, 50μM β-mercaptoethanol, antibiotics (10 µg/ml penicillin and streptomycin) and LIF) and selected 12hrs after by adding puromycin (1.5 μg/ml) and HAT (20μM hypoxantine, 0.08 mM aminopterin, and 3.2 mM thymidine; Sigma).

extract_protocol:
Total RNA was exacted by RNABee (Amsbio) accordingly to manifacturer instructions
RNA-seq libraries were prepared from 0.6μg total RNA accordingly to Illumina True-seq RNA sample preparation v2 guide (Illumina). Libraries were amplified 14 cycles before deep-sequencing.

treatment_protocol: hF clones were fused with mESC by PEG (Roche)

value: human fibroblast clones derived from TERT-immortalised NHDF17914 (Lonza)

tag: time point

value: before fusion with mouse ESC


title: Clone 34 hF Replicate 1


title: Clone 12 hF Replicate 2


title: total RNA-seq from ES-E14 (ENCLB118KZE)

description:
https://www.encodeproject.org/experiments/ENCSR000CWC/
***************
biological replicate number: 2
technical replicate number: 1
description: Stanford mouse ES-E14 RNA-seq
experiment encode accession: ENCSR000CWC
assay title: total RNA-seq
assembly: mm10
encode release date: 2012-06-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB118KZE
size range: 300-350

source_name: Mus musculus strain 129/Ola ES-E14 stem cell male embryo

value: stem cell

value: mouse embryonic stem cell line E14

value: embryonic

value: male

value: Michael Snyder, Stanford

value: ENCBS043ENC at ENCODE; https://www.encodeproject.org/ENCBS043ENC/

value: Derived from ENCODE donor ENCDO015AAA; https://www.encodeproject.org/ENCDO015AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_C320; http://web.expasy.org/cellosaurus/CVCL_C320

value: ENCODE dbxrefs ES-E14; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=ES-E14


title: Clone 34 hF Replicate 2


title: xeno_OS-2_37

city: Minneapolis

first: Milcah

last: Scott

state: MN

address: 2101 6th Street Se

department: Department of Microbiology and Immunology

institute: University of Minnesota

description: xenograft tumor OS-2 replicate

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to a HISAT2 index for mapping which was built from a multi-sequence fasta file containing both the canine (canFam3) and murine (mm10) genomes with the HISAT2 aligner (2.0.2-beta) using default parameters.
Rsubread featureCounts (1.4.6) was used to estimate transcript abundance using default parameters.
Genome_build: mm10 and canFam3
Supplementary_files_format_and_content: tab-delimited text file include count values for each sample and includes data for both dog and mouse genes.

organism:
Canis lupus familiaris
Mus musculus

source_name: xenograft (athymic nude mice strain strain NCr nu/nu) of canine osteosarcoma cells OS-2

extract_protocol:
Total RNA was extracted from primary intratibial tumors and from cell lines using Qiagen miRNeasy Mini Kit.
Sequencing libaries were prepared using Illumina TruSeq Library Preparation Kits

tag: host mouse strain

tag: cell line

tag: tissue

value: xenograft canine osteosarcoma cells OS-2


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 19

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_19
esc1_6h_19_rsem

tag: strain

value: ES-derived embryoid bodies with induced transcription factors


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 20

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_20
esc1_6h_20_rsem

tag: treatment


title: xeno_OS-2_43

description: xenograft tumor OS-2 replicate

value: athymic nude mice strain strain NCr nu/nu


title: LD

city: Fuzhou

first: Chen

last: Lisong

address: Shangdian street NO.15

institute: Fujian Agriculture and Forestry University

data_processing:
Basecalls performed
Get rid of some contaminant reads from the fq file and get the final clean reads.
The clear reads were mapped to Citrus clementina genome (JGI version 1.1, http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Csinensis) using SOAP, only perfectly mapped sequences were retained and analyzed further. rRNAs, tRNAs, snRNAs and snoRNAs were removed from the sRNAs sequences through BLASTn search using NCBI Genebank database (http://www.ncbi.nlm.nih.gov/blast/Blast.cgi/) and Rfam (12.0) database (http://www.sanger.ac.uk/resources/databases/rfam.html) (e = 0.01). The remaining sequences were aligned with known plant miRNAs from miRBase 21 (http://www.mirbase.org/).
Reads that were not annotated were used to predict novel miRNAs using a prediction software Mireap (http://sourceforge.net/projects/mireap/), which was developed by the BGI
Genome_build: Citrus clementina genome, mirBase 21
Supplementary_files_format_and_content: fasta file with read counts of sequences and text files of read counts and statistics of identified miRNAs.

organism: Citrus sinensis

source_name: magnesium-deficient leaves

growth_protocol: 5-week-old seedlings of ‘Xuegan’ [Citrus sinensis (L.) Osbeck] were transplanted into 6 L pots containing fine river sand. Ten weeks after transplanting, each pot was supplied every other day with Mg-deficient (0 mM MgSO4) or Mg-sufficient (1 mM MgSO4, control) nutrient solution for 16 weeks. There were 10 replications per Mg treatment with 2 pots in a completely randomized design.

extract_protocol:
About 0.1 g mixed frozen Mg -sufficient and Mg -deficient leaves from five replictations were used to extract RNA. Total RNA was extracted from frozen roots using TRIzol reagent (Invitrogen, Carlsbad, CA)
Small RNA samples were sequenced by Beijing Genomics Institute (BGI) (Shenzhen, Guangdong, China) using the high throughput pyrosequencing technology developed by Illumina. Two sRNA libraries were constructed, sRNAs were isolated from the total RNA by size fractionation with 15% Tris-borate-EDTA urea polyacrylamide gel (TBU). Then the sRNAs were ligated with 5' and 3' adaptor by T4 RNA ligase after being dephosphorylatd by alkaline phosphatase. The adaptor-ligated sRNAs were transcribed to single-stranded cDNA using Superscript II reverse transcriptase (Invitrogen). Thereafter, the single-stranded cDNA was used as templates for double-stranded synthesis by PCR amplification using the primer designed according to the adapter sequence. The obtained PCR products were sequenced on a Solexa sequencer (Illumina) at the Beijing Genomics Institute (BGI), Shenzhen, China.

treatment_protocol: LD(0 mM MgSO4，Mg-deficient，LD) , LS (Mg-sufficient,control, LS)

value: Fully expanded Citrus sinensis leaves were excised from the seedlings

tag: cultivar

value: Xuegan


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 18

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_18
esc1_6h_18_rsem

tag: cell type


title: LS

source_name: magnesium-sufficient leaves


title: xeno_OS-2_34

description: xenograft tumor OS-2 replicate


title: total RNA-seq from ES-E14 (ENCLB212CDP)

description:
https://www.encodeproject.org/experiments/ENCSR000CWC/
***************
biological replicate number: 1
technical replicate number: 1
description: Stanford mouse ES-E14 RNA-seq
experiment encode accession: ENCSR000CWC
assay title: total RNA-seq
assembly: mm10
encode release date: 2012-06-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB212CDP
size range: 300-350

tag: biosample encode accession

value: unknown


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 17

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_17
esc1_6h_17_rsem


title: polyA mRNA RNA-seq from megakaryocyte-erythroid progenitor cell (ENCLB501DBY)

description:
https://www.encodeproject.org/experiments/ENCSR000CIF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on mouse megakaryocyte-erythroid progenitor cells (paired end)
experiment encode accession: ENCSR000CIF
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB501DBY
size range: >175

source_name: Mus musculus strain C57BL/6J megakaryocyte-erythroid progenitor primary cell female adult (5 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/d6ec08a9-8b45-424d-aad9-55cbc02d527f/@@download/attachment/wgEncodePsuRnaSeq.html.pdf

value: megakaryocyte-erythroid progenitor cell

value: primary cell

value: mouse megakaryocyte erythroid progenitor cells with lineages CD16/32 and CD34-

tag: dev stage

value: adult

value: female

value: 5 week

value: Ross Hardison, PennState

value: ENCBS176ENC at ENCODE; https://www.encodeproject.org/ENCBS176ENC/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/

value: ENCODE dbxrefs MEP; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=MEP


title: xeno_OS-2_30

description: xenograft tumor OS-2 replicate


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 16

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_16
esc1_6h_16_rsem


title: polyA mRNA RNA-seq from megakaryocyte-erythroid progenitor cell (ENCLB295XLR)

description:
https://www.encodeproject.org/experiments/ENCSR000CIF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on mouse megakaryocyte-erythroid progenitor cells (paired end)
experiment encode accession: ENCSR000CIF
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB295XLR
size range: >175

tag: Sex

value: ENCBS190OUH at ENCODE; https://www.encodeproject.org/ENCBS190OUH/


title: xeno_OS-1_23

description: xenograft tumor OS-1 replicate

source_name: xenograft (athymic nude mice strain strain NCr nu/nu) of canine osteosarcoma cells OS-1

value: xenograft canine osteosarcoma cells OS-1


title: polyA mRNA RNA-seq from megakaryocyte (ENCLB824EGV)

description:
https://www.encodeproject.org/experiments/ENCSR000CIC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on mouse megakaryote (paired end)
experiment encode accession: ENCSR000CIC
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB824EGV
size range: >175

source_name: Mus musculus megakaryocyte primary cell mixed sex embryo (14.5 days)

value: megakaryocyte

value: Megakaryocyte

value: embryonic

value: pooled male and female

tag: age

value: ENCBS351ENC at ENCODE; https://www.encodeproject.org/ENCBS351ENC/

value: Derived from ENCODE donor ENCDO083AAA; https://www.encodeproject.org/ENCDO083AAA/

value: ENCODE dbxrefs MEGAKARYO; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=MEGAKARYO


title: hESO-14 rep3

tag: genotype

value: pluripotent


title: xeno_OS-1_1

description: xenograft tumor OS-1 replicate

value: athymic nude mice strain strain NCr nu/nu


title: xeno_OS-1_15

description: xenograft tumor OS-1 replicate


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 14

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_14
esc1_6h_14_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: polyA mRNA RNA-seq from megakaryocyte (ENCLB392IAT)

description:
https://www.encodeproject.org/experiments/ENCSR000CIC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on mouse megakaryote (paired end)
experiment encode accession: ENCSR000CIC
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB392IAT
size range: >175

value: primary cell

value: unknown

tag: lab


title: polyA mRNA RNA-seq from G1E-ER4 (ENCLB309KMX)

description:
https://www.encodeproject.org/experiments/ENCSR000CIB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on mouse G1E-ER4 (paired end) differentiated for 30 hours
experiment encode accession: ENCSR000CIB
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB309KMX
size range: >175

source_name: Mus musculus G1E-ER4 immortalized cell line treated with 10 nM 17beta-estradiol for 30 hours

tag: line

value: immortalized cell line

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)

value: postnatal

tag: treatments

value: treatment_term_id:CHEBI:16469; treatment_term_name:17beta-estradiol; treatment_type:chemical; duration:30; duration_units:hour; UCSC-ENCODE-cv:diffProtD_30hr;

value: male

value: 0 day

value: Ross Hardison, PennState

tag: link

value: ENCBS328ENC at ENCODE; https://www.encodeproject.org/ENCBS328ENC/

value: Derived from ENCODE donor ENCDO089AAA; https://www.encodeproject.org/ENCDO089AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_D047; http://web.expasy.org/cellosaurus/CVCL_D047


title: polyA mRNA RNA-seq from G1E-ER4 (ENCLB929LXJ)

description:
https://www.encodeproject.org/experiments/ENCSR000CIB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on mouse G1E-ER4 (paired end) differentiated for 30 hours
experiment encode accession: ENCSR000CIB
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB929LXJ
size range: >175

tag: description

tag: health state


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

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_12
esc1_6h_12_rsem


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 13

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_13
esc1_6h_13_rsem


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 11

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_11
esc1_6h_11_rsem


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 10

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_10
esc1_6h_10_rsem


title: polyA mRNA RNA-seq from G1E-ER4 (ENCLB181WZL)

description:
https://www.encodeproject.org/experiments/ENCSR000CIA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on mouse G1E-ER4 (paired end) differentiated for 24 hours
experiment encode accession: ENCSR000CIA
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB181WZL
size range: >175

source_name: Mus musculus G1E-ER4 immortalized cell line treated with 10 nM 17beta-estradiol for 24 hours

value: treatment_term_id:CHEBI:16469; treatment_term_name:17beta-estradiol; treatment_type:chemical; duration:24; duration_units:hour; UCSC-ENCODE-cv:diffProtD_24hr;

value: ENCBS327ENC at ENCODE; https://www.encodeproject.org/ENCBS327ENC/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 8

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_8
esc1_6h_8_rsem


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 7

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_7
esc1_6h_7_rsem


title: polyA mRNA RNA-seq from G1E-ER4 (ENCLB974HGK)

description:
https://www.encodeproject.org/experiments/ENCSR000CHZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on mouse G1E-ER4 (paired end) differentiated for 3 hours
experiment encode accession: ENCSR000CHZ
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB974HGK
size range: >175

source_name: Mus musculus G1E-ER4 immortalized cell line treated with 10 nM 17beta-estradiol for 3 hours

value: treatment_term_id:CHEBI:16469; treatment_term_name:17beta-estradiol; treatment_type:chemical; duration:3; duration_units:hour; UCSC-ENCODE-cv:diffProtD_3hr;

value: ENCBS329ENC at ENCODE; https://www.encodeproject.org/ENCBS329ENC/


title: polyA mRNA RNA-seq from G1E-ER4 (ENCLB391HUK)

description:
https://www.encodeproject.org/experiments/ENCSR000CHZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on mouse G1E-ER4 (paired end) differentiated for 3 hours
experiment encode accession: ENCSR000CHZ
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB391HUK
size range: >175


title: polyA mRNA RNA-seq from G1E-ER4 (ENCLB780LOT)

description:
https://www.encodeproject.org/experiments/ENCSR000CHY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on mouse G1E-ER4 (paired end)
experiment encode accession: ENCSR000CHY
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB780LOT
size range: >175

source_name: Mus musculus G1E-ER4 immortalized cell line

value: ENCBS325ENC at ENCODE; https://www.encodeproject.org/ENCBS325ENC/


title: polyA mRNA RNA-seq from G1E-ER4 (ENCLB626OVH)

description:
https://www.encodeproject.org/experiments/ENCSR000CHY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on mouse G1E-ER4 (paired end)
experiment encode accession: ENCSR000CHY
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB626OVH
size range: >175


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 15

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_15
esc1_6h_15_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: polyA mRNA RNA-seq from G1E-ER4 (ENCLB442NRS)

description:
https://www.encodeproject.org/experiments/ENCSR000CHX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on mouse G1E-ER4 (paired end) differentiated for 7 hours
experiment encode accession: ENCSR000CHX
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB442NRS
size range: >175

source_name: Mus musculus G1E-ER4 immortalized cell line treated with 10 nM 17beta-estradiol for 7 hours

value: treatment_term_id:CHEBI:16469; treatment_term_name:17beta-estradiol; treatment_type:chemical; duration:7; duration_units:hour; UCSC-ENCODE-cv:diffProtD_7hr;

value: unknown

value: ENCBS330ENC at ENCODE; https://www.encodeproject.org/ENCBS330ENC/


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 5

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_5
esc1_6h_5_rsem


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

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_6
esc1_6h_6_rsem


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 4

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_4
esc1_6h_4_rsem


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 3

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_3
esc1_6h_3_rsem


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 2

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_2
esc1_6h_2_rsem


title: polyA mRNA RNA-seq from G1E-ER4 (ENCLB958POH)

description:
https://www.encodeproject.org/experiments/ENCSR000CHW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on mouse G1E-ER4 (paired end) differentiated for 14 hours
experiment encode accession: ENCSR000CHW
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB958POH
size range: >175

source_name: Mus musculus G1E-ER4 immortalized cell line treated with 10 nM 17beta-estradiol for 14 hours

value: immortalized cell line

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)

value: postnatal

value: treatment_term_id:CHEBI:16469; treatment_term_name:17beta-estradiol; treatment_type:chemical; duration:14; duration_units:hour; UCSC-ENCODE-cv:diffProtD_14hr;

value: ENCBS326ENC at ENCODE; https://www.encodeproject.org/ENCBS326ENC/


title: polyA mRNA RNA-seq from G1E-ER4 (ENCLB112FKJ)

description:
https://www.encodeproject.org/experiments/ENCSR000CHW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on mouse G1E-ER4 (paired end) differentiated for 14 hours
experiment encode accession: ENCSR000CHW
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB112FKJ
size range: >175

value: male

value: 0 day

value: Ross Hardison, PennState


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 1

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_1
esc1_6h_1_rsem


title: polyA mRNA RNA-seq from G1E-ER4 (ENCLB318QDM)

description:
https://www.encodeproject.org/experiments/ENCSR000CHX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on mouse G1E-ER4 (paired end) differentiated for 7 hours
experiment encode accession: ENCSR000CHX
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB318QDM
size range: >175

value: Derived from ENCODE donor ENCDO089AAA; https://www.encodeproject.org/ENCDO089AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_D047; http://web.expasy.org/cellosaurus/CVCL_D047


title: xeno_OS-1_11

description: xenograft tumor OS-1 replicate

tag: host mouse strain

value: athymic nude mice strain strain NCr nu/nu

tag: cell line

value: xenograft canine osteosarcoma cells OS-1


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_96
esc1_0h_96_rsem

tag: strain


title: polyA mRNA RNA-seq from G1E (ENCLB521PWE)

description:
https://www.encodeproject.org/experiments/ENCSR000CHV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on mouse G1E (paired end)
experiment encode accession: ENCSR000CHV
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB521PWE
size range: >175

source_name: Mus musculus G1E immortalized cell line

value: Gata1- erythroid progenitor

value: ENCBS324ENC at ENCODE; https://www.encodeproject.org/ENCBS324ENC/

value: ENCODE dbxrefs Cellosaurus CVCL_D046; http://web.expasy.org/cellosaurus/CVCL_D046

value: ENCODE dbxrefs G1E; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=G1E


title: polyA mRNA RNA-seq from G1E-ER4 (ENCLB590TOQ)

description:
https://www.encodeproject.org/experiments/ENCSR000CIA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on mouse G1E-ER4 (paired end) differentiated for 24 hours
experiment encode accession: ENCSR000CIA
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB590TOQ
size range: >175

value: treatment_term_id:CHEBI:16469; treatment_term_name:17beta-estradiol; treatment_type:chemical; duration:24; duration_units:hour; UCSC-ENCODE-cv:diffProtD_24hr;

value: unknown

value: ENCBS327ENC at ENCODE; https://www.encodeproject.org/ENCBS327ENC/


title: polyA mRNA RNA-seq from hematopoietic multipotent progenitor cell (ENCLB242BHC)

description:
https://www.encodeproject.org/experiments/ENCSR000CHU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on mouse FV progenitor (paired end)
experiment encode accession: ENCSR000CHU
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB242BHC
size range: >175

source_name: Mus musculus hematopoietic multipotent progenitor primary cell mixed sex adult (10-12 weeks)

value: primary cell

value: Friend virus infected murine CD34-,CD133-,Kit+,Sca1+ progenitor cells. Strains which can be used to generate the cells must carry the Fv2 sensitive allele (Fv2s).

value: adult

value: pooled male and female

value: ENCBS041RGJ at ENCODE; https://www.encodeproject.org/ENCBS041RGJ/

value: Derived from ENCODE donor ENCDO005AAA; https://www.encodeproject.org/ENCDO005AAA/

value: ENCODE dbxrefs FVprogenitor_2; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=FVprogenitor_2


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_94
esc1_0h_94_rsem

tag: treatment

value: ES-derived embryoid bodies with induced transcription factors


title: polyA mRNA RNA-seq from hematopoietic multipotent progenitor cell (ENCLB256JII)

description:
https://www.encodeproject.org/experiments/ENCSR000CHU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on mouse FV progenitor (paired end)
experiment encode accession: ENCSR000CHU
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB256JII
size range: >175

value: Ross Hardison, PennState

value: ENCBS242ENC at ENCODE; https://www.encodeproject.org/ENCBS242ENC/

value: ENCODE dbxrefs FVprogenitor; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=FVprogenitor


title: Single-cell RNA-seq in EB+6hrDox(iNgn2.Isl1.Lhx3.V5) cell 9

description:
EB+6hrDox(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_9
esc1_6h_9_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_92
esc1_0h_92_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_95
esc1_0h_95_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_93
esc1_0h_93_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_90
esc1_0h_90_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_91
esc1_0h_91_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_89
esc1_0h_89_rsem


title: polyA mRNA RNA-seq from frontal cortex (ENCLB555BAE)

description:
https://www.encodeproject.org/experiments/ENCSR000BZS/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week frontal cortex tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BZS
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-09-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555BAE
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Mus musculus strain C57BL/6J frontal cortex tissue mixed sex adult (8 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/a567f9d8-bd41-4abb-bd35-39a5fd27e646/@@download/attachment/LID47082.pdf

value: frontal cortex

value: tissue

value: Frontal Lobe

value: 8 week

value: Thomas Gingeras, CSHL

value: ENCBS263ENC at ENCODE; https://www.encodeproject.org/ENCBS263ENC/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/

value: ENCODE dbxrefs FrontalLobe; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=FrontalLobe


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_88
esc1_0h_88_rsem


title: polyA mRNA RNA-seq from erythroblast (ENCLB655XTP)

description:
https://www.encodeproject.org/experiments/ENCSR000CHS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on mouse erythroblast (paired end)
experiment encode accession: ENCSR000CHS
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB655XTP
size range: >175

source_name: Mus musculus erythroblast primary cell mixed sex embryo (14.5 days)

value: erythroblast

value: primary cell

value: Erythroblast, ter119+ cells from liver

value: embryonic

value: unknown

value: ENCBS240ENC at ENCODE; https://www.encodeproject.org/ENCBS240ENC/

value: Derived from ENCODE donor ENCDO083AAA; https://www.encodeproject.org/ENCDO083AAA/

value: ENCODE dbxrefs ERYTHROBL; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=ERYTHROBL


title: polyA mRNA RNA-seq from leukemia stem cell (ENCLB130OTK)

description:
https://www.encodeproject.org/experiments/ENCSR000CHT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on mouse FVL stem (paired end)
experiment encode accession: ENCSR000CHT
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB130OTK
size range: >175

source_name: Mus musculus leukemia stem cell mixed sex adult (10-12 weeks)

value: leukemia stem cell

value: stem cell

value: Friend virus infected murine CD34+,CD133+,Kit+,Sca1+ Leukemia stem cells. Strains which can be used to generate the cells must carry the Fv2 sensitive allele (Fv2s).

value: adult

value: pooled male and female

value: Ross Hardison, PennState

value: ENCBS791VAM at ENCODE; https://www.encodeproject.org/ENCBS791VAM/

value: Derived from ENCODE donor ENCDO005AAA; https://www.encodeproject.org/ENCDO005AAA/

value: ENCODE dbxrefs FVLstem; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=FVLstem


title: polyA mRNA RNA-seq from leukemia stem cell (ENCLB358YQP)

description:
https://www.encodeproject.org/experiments/ENCSR000CHT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on mouse FVL stem (paired end)
experiment encode accession: ENCSR000CHT
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB358YQP
size range: >175

value: ENCBS241ENC at ENCODE; https://www.encodeproject.org/ENCBS241ENC/


title: polyA mRNA RNA-seq from erythroblast (ENCLB050AEZ)

description:
https://www.encodeproject.org/experiments/ENCSR000CHS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on mouse erythroblast (paired end)
experiment encode accession: ENCSR000CHS
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB050AEZ
size range: >175

value: erythroblast

value: primary cell

value: ENCBS794XFM at ENCODE; https://www.encodeproject.org/ENCBS794XFM/


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_87
esc1_0h_87_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: polyA mRNA RNA-seq from cortical plate (ENCLB555AYF)

description:
https://www.encodeproject.org/experiments/ENCSR000BZR/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week cortical brain tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BZR
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-09-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AYF
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Mus musculus strain C57BL/6J cortical plate tissue mixed sex adult (8 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/25d46c22-af6d-4922-aaed-f2eeb7cbfb8a/@@download/attachment/LID47032.pdf

value: cortical plate

value: tissue

value: Cortex

value: 8 week

value: unknown

value: Thomas Gingeras, CSHL

value: ENCBS258ENC at ENCODE; https://www.encodeproject.org/ENCBS258ENC/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: polyA mRNA RNA-seq from frontal cortex (ENCLB555BAD)

description:
https://www.encodeproject.org/experiments/ENCSR000BZS/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week frontal cortex tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BZS
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-09-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555BAD
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/b0fca54b-9424-4b58-82b0-58d6a060dc6c/@@download/attachment/LID47081.pdf

value: frontal cortex

value: Frontal Lobe

value: adult

value: pooled male and female

value: ENCBS262ENC at ENCODE; https://www.encodeproject.org/ENCBS262ENC/

value: ENCODE dbxrefs FrontalLobe; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=FrontalLobe


title: polyA mRNA RNA-seq from G1E (ENCLB817UEY)

description:
https://www.encodeproject.org/experiments/ENCSR000CHV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on mouse G1E (paired end)
experiment encode accession: ENCSR000CHV
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB817UEY
size range: >175

value: immortalized cell line

value: Gata1- erythroid progenitor

value: postnatal

value: male

value: 0 day

value: Ross Hardison, PennState

value: ENCBS324ENC at ENCODE; https://www.encodeproject.org/ENCBS324ENC/

value: Derived from ENCODE donor ENCDO089AAA; https://www.encodeproject.org/ENCDO089AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_D046; http://web.expasy.org/cellosaurus/CVCL_D046

value: ENCODE dbxrefs G1E; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=G1E


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_85
esc1_0h_85_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: polyA mRNA RNA-seq from cortical plate (ENCLB555AYE)

description:
https://www.encodeproject.org/experiments/ENCSR000BZR/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week cortical brain tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BZR
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-09-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AYE
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/f38ce4f0-7d75-4d68-97d7-d4ab5a8d2ee5/@@download/attachment/LID47033.pdf

value: cortical plate

value: tissue

value: Cortex

value: 8 week

value: unknown

value: Thomas Gingeras, CSHL

value: ENCBS259ENC at ENCODE; https://www.encodeproject.org/ENCBS259ENC/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_84
esc1_0h_84_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_83
esc1_0h_83_rsem


title: polyA mRNA RNA-seq from urinary bladder (ENCLB555AYW)

description:
https://www.encodeproject.org/experiments/ENCSR000BZQ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week bladder tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BZQ
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-09-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AYW
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Mus musculus strain C57BL/6J urinary bladder tissue adult (8 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6ea5cb23-1aea-4f8b-9efb-490492d313b9/@@download/attachment/LID47030.pdf

value: urinary bladder

value: Urinary Bladder

value: adult

value: not collected

value: ENCBS246ENC at ENCODE; https://www.encodeproject.org/ENCBS246ENC/


title: polyA mRNA RNA-seq from placenta (ENCLB555AZM)

description:
https://www.encodeproject.org/experiments/ENCSR000BZP/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week placental tissue from staged pregnant females in mouse strain C57BL/6J. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BZP
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-09-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AZM
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Mus musculus strain C57BL/6J placenta tissue adult (8 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/53d9f491-d9de-4d38-92b0-a9d74893d3d0/@@download/attachment/LID46984.pdf

value: placenta

value: Placenta

value: ENCBS353ENC at ENCODE; https://www.encodeproject.org/ENCBS353ENC/


title: polyA mRNA RNA-seq from urinary bladder (ENCLB555AYC)

description:
https://www.encodeproject.org/experiments/ENCSR000BZQ/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week bladder tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000BZQ
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-09-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AYC
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/69c71486-f4cb-4a5d-ab95-99bab74f4bae/@@download/attachment/LID47031.pdf

value: ENCBS247ENC at ENCODE; https://www.encodeproject.org/ENCBS247ENC/


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_82
esc1_0h_82_rsem

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.

value: ES-derived embryoid bodies with induced transcription factors


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_81
esc1_0h_81_rsem