title: polyA mRNA RNA-seq from liver (ENCLB555AZV)

description:
https://www.encodeproject.org/experiments/ENCSR000BZO/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from embryonic day 18 (E.18) liver 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: ENCSR000BZO
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-09-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AZV
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Mus musculus strain C57BL/6J liver tissue mixed sex embryo (18 days)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/e8b28471-0a35-4ebd-84f6-9bb61b8673b2/@@download/attachment/LID47149.pdf

value: liver

value: tissue

value: Liver

value: embryonic

value: pooled male and female

value: 18 day

value: ENCBS283ENC at ENCODE; https://www.encodeproject.org/ENCBS283ENC/


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

status: Public on Dec 07 2016

type: SRA

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

country: USA

institute: Penn State University

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_79
esc1_0h_79_rsem

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

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

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

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

tag: strain

tag: treatment

tag: cell type

value: ES-derived embryoid bodies with induced transcription factors


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_80
esc1_0h_80_rsem


title: polyA mRNA RNA-seq from limb (ENCLB555AYP)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR000BZN/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from embryonic day 14.5 (E.14.5) limb 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: ENCSR000BZN
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-09-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AYP
size range: >200
spikeins used: /references/ENCSR402QNO/

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

source_name: Mus musculus strain C57BL/6J limb tissue mixed sex embryo (14.5 days)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/fc375e72-321d-4803-b215-7ee5b1f56b7c/@@download/attachment/LID46986.pdf

value: limb

tag: description

value: Limb

tag: biosample encode accession

tag: dev stage

tag: Sex

tag: age

tag: health state

value: unknown

tag: lab

value: Thomas Gingeras, CSHL

tag: link

value: ENCBS277ENC at ENCODE; https://www.encodeproject.org/ENCBS277ENC/

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


title: polyA mRNA RNA-seq from limb (ENCLB555AYQ)

description:
https://www.encodeproject.org/experiments/ENCSR000BZN/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from embryonic day 14.5 (E.14.5) limb 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: ENCSR000BZN
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-09-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AYQ
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/cf398886-5e31-46c4-a68f-7607a85a5a6c/@@download/attachment/LID46985.pdf

value: ENCBS276ENC at ENCODE; https://www.encodeproject.org/ENCBS276ENC/


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_78
esc1_0h_78_rsem


title: polyA mRNA RNA-seq from cerebellum (ENCLB555AZN)

description:
https://www.encodeproject.org/experiments/ENCSR000BZM/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week cerebellum 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: ENCSR000BZM
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-09-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AZN
size range: >200
spikeins used: /references/ENCSR402QNO/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/4d7d85b1-3976-4cdd-bf9d-8f40ff4bcc06/@@download/attachment/LID47037.pdf

value: cerebellum

value: Cerebellum

value: adult

value: 8 week

value: ENCBS249ENC at ENCODE; https://www.encodeproject.org/ENCBS249ENC/


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_76
esc1_0h_76_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_75
esc1_0h_75_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_86
esc1_0h_86_rsem


title: polyA mRNA RNA-seq from central nervous system (ENCLB555BAC)

description:
https://www.encodeproject.org/experiments/ENCSR000BZL/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from  embryonic day 18 (E.18) central nervous system 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: ENCSR000BZL
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-09-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555BAC
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Mus musculus strain C57BL/6J central nervous system tissue mixed sex embryo (18 days)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/a0d29358-24ee-4ee8-bdee-78cb3b415848/@@download/attachment/LID46950.pdf

value: central nervous system

value: tissue

value: Central Nervous System

value: embryonic

value: ENCBS254ENC at ENCODE; https://www.encodeproject.org/ENCBS254ENC/


title: polyA mRNA RNA-seq from cerebellum (ENCLB555AZO)

description:
https://www.encodeproject.org/experiments/ENCSR000BZM/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from adult 8 week cerebellum 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: ENCSR000BZM
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-09-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AZO
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/3dbc7ac6-d64b-400e-9d5c-a73c61cefa7e/@@download/attachment/LID47036.pdf

value: pooled male and female

value: ENCBS248ENC at ENCODE; https://www.encodeproject.org/ENCBS248ENC/


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_73
esc1_0h_73_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: polyA mRNA RNA-seq from central nervous system (ENCLB555AZS)

description:
https://www.encodeproject.org/experiments/ENCSR000BZK/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from embryonic day 14 (E.14) central nervous system 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: ENCSR000BZK
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-09-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AZS
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Mus musculus strain C57BL/6J central nervous system tissue mixed sex embryo (14 days)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/86f4d6cd-2dbb-4e02-8cb6-a6c241e10234/@@download/attachment/LID46949.pdf

value: 14 day

value: unknown

value: Thomas Gingeras, CSHL

value: ENCBS253ENC at ENCODE; https://www.encodeproject.org/ENCBS253ENC/


title: polyA mRNA RNA-seq from central nervous system (ENCLB555AZR)

description:
https://www.encodeproject.org/experiments/ENCSR000BZK/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from embryonic day 14 (E.14) central nervous system 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: ENCSR000BZK
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-09-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AZR
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/2398632e-116e-4d4c-a711-45458d43e1bc/@@download/attachment/LID46948.pdf

value: ENCBS252ENC at ENCODE; https://www.encodeproject.org/ENCBS252ENC/

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


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_72
esc1_0h_72_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_71
esc1_0h_71_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_69
esc1_0h_69_rsem


title: polyA mRNA RNA-seq from placenta (ENCLB555AZL)

description:
https://www.encodeproject.org/experiments/ENCSR000BZP/
***************
biological replicate number: 1
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: ENCLB555AZL
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/5011c47c-bf1c-40bf-853e-41375e0a0931/@@download/attachment/LID46983.pdf

value: placenta

value: Placenta

value: adult

value: not collected

value: ENCBS352ENC at ENCODE; https://www.encodeproject.org/ENCBS352ENC/


title: polyA mRNA RNA-seq from brain (ENCLB555AZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000BZJ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from embryonic day 14.5 (E.14.5) whole 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: ENCSR000BZJ
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-09-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AZZ
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Mus musculus strain C57BL/6J brain tissue embryo (14.5 days)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/50234544-7073-4b63-b018-35b31f52146b/@@download/attachment/LID46987.pdf

value: brain

value: tissue

value: Whole Brain

value: ENCBS310ENC at ENCODE; https://www.encodeproject.org/ENCBS310ENC/

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


title: polyA mRNA RNA-seq from brain (ENCLB555AZY)

description:
https://www.encodeproject.org/experiments/ENCSR000BZJ/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from embryonic day 14.5 (E.14.5) whole 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: ENCSR000BZJ
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-09-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AZY
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/dc6d571d-52bf-4567-a9fe-346855d220bc/@@download/attachment/LID46988.pdf

value: embryonic

value: ENCBS311ENC at ENCODE; https://www.encodeproject.org/ENCBS311ENC/


title: polyA mRNA RNA-seq from liver (ENCLB555AZI)

description:
https://www.encodeproject.org/experiments/ENCSR000BZI/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from embryonic day 14.5 (E.14.5) liver 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: ENCSR000BZI
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-09-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AZI
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Mus musculus strain C57BL/6J liver tissue mixed sex embryo (14.5 days)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/9e3e53e9-24c7-4d8e-9d73-9b2699076f03/@@download/attachment/LID47147.pdf

value: liver

value: Liver

value: pooled male and female

value: unknown

value: ENCBS285ENC at ENCODE; https://www.encodeproject.org/ENCBS285ENC/


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_68
esc1_0h_68_rsem

value: ES-derived embryoid bodies with induced transcription factors


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_67
esc1_0h_67_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_66
esc1_0h_66_rsem


title: polyA mRNA RNA-seq from central nervous system (ENCLB555BAB)

description:
https://www.encodeproject.org/experiments/ENCSR000BZL/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from  embryonic day 18 (E.18) central nervous system 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: ENCSR000BZL
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-09-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555BAB
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/c6fe1ba7-b79b-416d-b2de-312044568263/@@download/attachment/LID46951.pdf

value: central nervous system

value: Central Nervous System

value: 18 day

value: Thomas Gingeras, CSHL

value: ENCBS255ENC at ENCODE; https://www.encodeproject.org/ENCBS255ENC/

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


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_77
esc1_0h_77_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_65
esc1_0h_65_rsem


title: polyA mRNA RNA-seq from central nervous system (ENCLB555AYN)

description:
https://www.encodeproject.org/experiments/ENCSR000BZG/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from embryonic day 11.5 (E11.5) central nervous system 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: ENCSR000BZG
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-09-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AYN
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Mus musculus strain C57BL/6J central nervous system tissue mixed sex embryo (11.5 days)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/b67ee5d4-bd65-4310-af9a-d2b45f503ad7/@@download/attachment/LID46947.pdf

value: tissue

value: ENCBS251ENC at ENCODE; https://www.encodeproject.org/ENCBS251ENC/


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_74
esc1_0h_74_rsem


title: polyA mRNA RNA-seq from central nervous system (ENCLB555AYM)

description:
https://www.encodeproject.org/experiments/ENCSR000BZG/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from embryonic day 11.5 (E11.5) central nervous system 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: ENCSR000BZG
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-09-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AYM
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/bfeec0fe-36cb-4481-8b67-03904b3ba81c/@@download/attachment/LID46946.pdf

value: ENCBS250ENC at ENCODE; https://www.encodeproject.org/ENCBS250ENC/


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_63
esc1_0h_63_rsem


title: NICD-Akt Sample 1

city: Palo Alto

first: Tanya

last: Stoyanova

state: California

address: 3155 Porter Drive, Palo Alto, CA 94304

department: Radiology

institute: Stanford University

data_processing:
Illumina CASAVA 1.8.2 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Reads were mapped to UCSC hg19 using MapSplice 2.1.8 software.
Gene expression was quantified using RSEM 1.2.25 and quantile normalized.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized RSEM quantification for each Sample

source_name: prostate

growth_protocol: Dissociated  mouse prostate cells were transduced with lentivirus for Notch1 or control, in addition to oncogenes Akt, Myc, or kRas. Cells were cultures with UGSM and grafted in mouse kidney capsule for regeneration

extract_protocol:
Total RNA was isolated from tumors generated from prostate regeneration using the RNeasy Mini kit (QIAGEN). Samples with a RNA integrity number (RIN) > 8 were used for construction of RNA-seq libraries.
RNA-seq libraries were constructed using the Ovation RNA-seq V2 (Nugen)

tag: tissue

value: tumor

tag: protocol

value: NICD-AKT


title: NICD-kRas Sample 2

value: NICD-kRas


title: NICD-Akt Sample 2


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_62
esc1_0h_62_rsem


title: NICD-kRas Sample 1


title: polyA mRNA RNA-seq from liver (ENCLB555AYB)

description:
https://www.encodeproject.org/experiments/ENCSR000BZH/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from embryonic day 14 (E.14) liver 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: ENCSR000BZH
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-09-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AYB
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Mus musculus strain C57BL/6J liver tissue mixed sex embryo (14 days)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/025ccaa5-5a46-485d-bd90-35fc1168e9f9/@@download/attachment/LID47144.pdf

value: liver

value: Liver

value: embryonic

value: 14 day

value: ENCBS280ENC at ENCODE; https://www.encodeproject.org/ENCBS280ENC/


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_61
esc1_0h_61_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 70

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_70
esc1_0h_70_rsem


title: polyA mRNA RNA-seq from liver (ENCLB555AZH)

description:
https://www.encodeproject.org/experiments/ENCSR000BZI/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from embryonic day 14.5 (E.14.5) liver 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: ENCSR000BZI
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-09-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AZH
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/dd5cc74f-39ab-442e-be55-6bb173e6e768/@@download/attachment/LID47146.pdf

value: pooled male and female

value: unknown

value: ENCBS284ENC at ENCODE; https://www.encodeproject.org/ENCBS284ENC/


title: NICD-Myc Sample 2

value: NICD-Myc


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_60
esc1_0h_60_rsem


title: NICD-Myc Sample 1


title: Prostate Control 2

description: Sample_Mouse Prostate2

value: normal

value: control


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_59
esc1_0h_59_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_58
esc1_0h_58_rsem


title: Prostate Control 1

description: Sample_Mouse Prostate1


title: PTBP2 CLIP IN Rosa-PTBP1; Emx1-cre

city: LOS ANGELES

first: Chia-ho

last: Lin

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

institute: UCLA

description: Crosslinked nuclear RNA.

data_processing:
Library strategy: iCLIP-Seq
PCR duplicates were removed by comparing random portions of the sequenced barcodes. Unique reads were mapped to the mouse genome (mm9/NCBI37) using Bowtie, allowing up to two nucleotide mismatches. Mapped reads were further mapped to the Known Gene table.
iCLIP data analyses were performed following the published paper (Konig J*, Zarnack K*, Curk T, Gregor R, Kayikci M, Zupan,B, Luscombe NM, Ule J (2010)).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *gff: The significant crosslink sites were selected based on the FDR <=0.01.

source_name: Neocortices, Rosa-PTBP1; Emx1-cre, PTBP2 IP

growth_protocol: Regular mouse husbandry.

extract_protocol:
Mouse neocortices are triturated in ice-cold HBSS solution and UV-irradiated at 400 mJ/cm2, 4 °C in Stratalinker. Nuclear fractions are prepared as in Damianov 2016.
Brain lysates were immunoprecipitated (IP) with specific antibodies. Crosslinked RNA was partially digested on the beads by micrococcal nucleases, dephosphorylated by alkaline phosphatase, ligated with a 3' linker and 5' labeled with P32-γ-ATP. The RNA-PTBP complexes were then resolved by SDS-PAGE and transferred to nitrocellulose membrane. FLAG-PTBP1 is 60 kDa and PTBP2 is 58 kDa. The nitrocellulose membrane between 80-110 kDa (i.e., the RNA-PTBP complexes) were cut and eluted the RNA with proteinase K treatment. The eluted RNA was reversed transcribed. The synthesized cDNA was circularized, linearized and amplified before sequencing on the Illumina Hi-Seq platform.

treatment_protocol: Genetically modified mice.

tag: strain/background

tag: genotype/variation

value: Rosa-PTBP1; Emx1-cre

value: Cerebral cortex

value: Postnatal day 1

tag: ip antibody

value: PTBP2 polyclonal (Black lab)


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_56
esc1_0h_56_rsem


title: PTBP2 CLIP IN WT

description: Crosslinked nuclear RNA.

source_name: Neocortices, WT, PTBP2 IP

value: WT


title: polyA mRNA RNA-seq from liver (ENCLB555AZU)

description:
https://www.encodeproject.org/experiments/ENCSR000BZO/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from embryonic day 18 (E.18) liver 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: ENCSR000BZO
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-09-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AZU
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/181e3cfb-0a38-4698-a238-1db2bf00603a/@@download/attachment/LID47148.pdf

value: liver

value: tissue

value: 18 day

value: Thomas Gingeras, CSHL

value: ENCBS282ENC at ENCODE; https://www.encodeproject.org/ENCBS282ENC/

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


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_55
esc1_0h_55_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: FLAG CLIP IN WT replicate #1

description: Crosslinked nuclear RNA.

source_name: Neocortices, WT, FLAG-PTBP1 IP

value: FLAG (Sigma-Aldrich, cat # F7425)


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_54
esc1_0h_54_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_53
esc1_0h_53_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_52
esc1_0h_52_rsem


title: FLAG CLIP IN Rosa-PTBP1; Emx1-cre

description: Crosslinked nuclear RNA.

source_name: Neocortices, Rosa-PTBP1; Emx1-cre, FLAG-PTBP1 IP


title: FLAG CLIP IN Rosa-PTBP1; PTBP2 loxp/loxp; Emx1-Cre

description: Crosslinked nuclear RNA.

source_name: Neocortices, Rosa-PTBP1; PTBP2 loxp/loxp; Emx1-Cre, FLAG-PTBP1 IP

value: Rosa-PTBP1; PTBP2 loxp/loxp; Emx1-Cre


title: FLAG CLIP IN WT replicate #2

description: Crosslinked nuclear RNA.


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_51
esc1_0h_51_rsem


title: Emx1-Ptbp2KO-Ptbp1KI

city: Riverside

first: Sikaz

last: Zheng

address: 201 School of Medicine Research Building, 900 University Avenue

department: Biomedical Sciences

institute: University of California Riverside

data_processing:
The libraries were mapped to mouse reference genome (GRCm38/mm10) and the indexed annotated junctions using the STAR aligner (Dobin et al., 2013). The parameters for STAR were specified as “--outFilterType BySJout --outFilterMultimapNmax 1 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000”.
Supplementary_files_format_and_content: SupTab1.xlsx: exon inclusion ratio
Supplementary_files_format_and_content: SupTab2.xlsx: gene abundance (RPKM)
Supplementary_files_format_and_content: SupTab3.xlsx: exon inclusion ratio
Supplementary_files_format_and_content: SupTab4.xlsx: exon inclusion ratio
Supplementary_files_format_and_content: SupTab5.xlsx: exon inclusion ratio
Supplementary_files_format_and_content: SupTab6.xlsx: exon inclusion ratio
Supplementary_files_format_and_content: SupTab7.xlsx: exon inclusion ratio
Supplementary_files_format_and_content: SupTab8.xlsx: exon inclusion ratio
Supplementary_files_format_and_content: SupTab9.xlsx: exon inclusion ratio
Supplementary_files_format_and_content: SupTab10.xlsx: exon inclusion ratio

source_name: Postnatal day 1 neocortices

growth_protocol: regular mouse husbandry

extract_protocol:
TRIZOL
Illumina True-Seq plus USER treatment to obtain strand-specific libraries. Refer Linares 2016 Elife

treatment_protocol: wildtype or genetically modified mice

value: Neocortices

tag: genotype


title: Emx1-Ptbp2KO

tag: strain


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_49
esc1_0h_49_rsem

tag: treatment


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_48
esc1_0h_48_rsem

tag: cell type


title: wildtype

value: wildtype


title: P2


title: P10


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_50
esc1_0h_50_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_47
esc1_0h_47_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_45
esc1_0h_45_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_46
esc1_0h_46_rsem


title: E17


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_57
esc1_0h_57_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_44
esc1_0h_44_rsem


title: Hippocampal CA1 GAMMA3 RNA-Seq

city: Cambridge

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

data_processing:
The raw fastq data of 50-bp single-end sequencing reads were aligned to the mouse mm9 reference genome using TopHat2.0. The mapped reads were processed by Cufflinks 2.2 with UCSC mm9 reference gene annotation to assemble aligned reads into transcripts, estimate transcript abundances, and test for differential expression. Relative abundance of transcript was measured by Fragments Per Kilobase of exon per Million fragments mapped (FPKM). Gene differential expression test between gamma and control groups was performed using Cuffdiff module with adjusted p-value <0.05 for statistical significance.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM statistics table format for RNA-Seq

source_name: Hippocampal CA1

growth_protocol: Hippocampal CA1 tissues from mouse strain 5xFAD (3-month old)

extract_protocol:
Total RNA was extracted using Rneasy Plus Kit (Qiagen).
RNASEQ library was constructed using BIOO NEXTflexTM mRNA-Seq Library Prep Kit.
Briefly, 1 micro gram of total mRNA was subject to a sequential workflow of poly-A purification, fragmentation,1st strand and 2nd strand synthesis, DNA end-adenylation, and adapter ligation. Finally, the libraries were enriched with 15 cycles of PCR reactions and cleaned with Agencourt AMPure XP magnetic beads (Beckman Coulter). The quality of prepared libraries was assessed using an Advanced Analytical-fragment Analyzer.  The bar-coded libraries were equally mixed for sequencing in a single lane on the Illumina HiSeq 2000 platform at the MIT BioMicro Center.

treatment_protocol: 1hr 40Hz stimulation of FS-PV+ interneurons with 473nm light, virus is ChR2 (GAMMA) or EYFP (CTRL)

value: FAD

value: 3 months

tag: tissue type

value: Hippocampal CA1


title: E14


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_43
esc1_0h_43_rsem


title: Hippocampal CA1 GAMMA1 RNA-Seq


title: Hippocampal CA1 GAMMA2 RNA-Seq


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_42
esc1_0h_42_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_41
esc1_0h_41_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_40
esc1_0h_40_rsem


title: Hippocampal CA1 CTRL3 RNA-Seq


title: Hippocampal CA1 CTRL1 RNA-Seq


title: Hippocampal CA1 CTRL2 RNA-Seq


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_37
esc1_0h_37_rsem


title: transgenic SRA mice infused with CGP, replicate 4

city: Iowa City

first: Henry

last: Keen

state: IA

department: Pharmacology

institute: University of Iowa

data_processing:
The quality of the sequence reads was assessed using the FastQC program.
Paired end reads (50-bp) were aligned to the mouse genome (build mm9) with the bowtie program using default parameters.
The GFOLD program was used to parse the BAM alignment files in order to calculate the total count of sequence reads per UCSC known gene transcript.
The resulting counts file was imported into edgeR (an R/Bioconductor package), which was used to normalize counts between samples and to generate pairwise comparisons between the different groups.
Expression of the UCP1 gene which was previously know to be signficantly induced in SRA mice and suppressed by CGP treatment was used as a positive control.
A p-value less than 0.001 was used to filter the list of candidate genes.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited file of normalized read counts per gene

source_name: inguinal adipose tissue

extract_protocol:
Total RNA from inguinal adipose tissue  was extracted using the Trizol method and purified using the Qiagen RNeasy column.  A DNase digestion was performed to remove genomic DNA.
Indexed sequencing libraries were generated from total RNA according to the manufacturer’s (Illumina) suggested protocol.

value: F

value: inguinal adipose tissue


title: transgenic SRA mice infused with CGP, replicate 3


title: polyA mRNA RNA-seq from liver (ENCLB555AYA)

description:
https://www.encodeproject.org/experiments/ENCSR000BZH/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from embryonic day 14 (E.14) liver 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: ENCSR000BZH
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-09-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AYA
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0c87a3ac-ec91-4222-983d-f4aed7b73e31/@@download/attachment/LID47145.pdf

tag: description

value: Liver

tag: biosample encode accession

value: embryonic

value: pooled male and female

value: 14 day

value: unknown

value: ENCBS281ENC at ENCODE; https://www.encodeproject.org/ENCBS281ENC/


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_36
esc1_0h_36_rsem


title: transgenic SRA mice infused with CGP, replicate 1

tag: Sex

value: M


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_64
esc1_0h_64_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: transgenic SRA mice infused with CGP, replicate 2


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_34
esc1_0h_34_rsem


title: non-transgenic mice infused with CGP, replicate 3


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_31
esc1_0h_31_rsem


title: non-transgenic mice infused with CGP, replicate 2


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_32
esc1_0h_32_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_33
esc1_0h_33_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_30
esc1_0h_30_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_29
esc1_0h_29_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_28
esc1_0h_28_rsem


title: transgenic SRA mice infused with saline, replicate 1


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_39
esc1_0h_39_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_27
esc1_0h_27_rsem


title: non-transgenic mice infused with saline, replicate 3


title: transgenic SRA mice infused with saline, replicate 3


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_38
esc1_0h_38_rsem


title: non-transgenic mice infused with saline, replicate 2


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_26
esc1_0h_26_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_35
esc1_0h_35_rsem


title: non-transgenic mice infused with saline, replicate 1


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_24
esc1_0h_24_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_25
esc1_0h_25_rsem


title: 80ug/ml SE+1:100 Conditioned Medium 24h rep2

city: San Marcos

first: Yuan

last: Lu

state: TX

address: university drive

institute: Xiphophorus Genetic Stock Center

description:
TC2_2_CM_su80_24h
TC2_24_GAGTGG_L003_R1_001.tar.gz

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing adaptor seuqence were trimmed off, then low qualtiy basecall was trimmed off, at last, low qualtiy sequence reads were filtered out.
Short sequencing reads were aligned to mus musculus genome mm9, gene expression value is quantified as raw read.
Differentially gene expression was analyzed using EdgeR
Genome_build: mm9
Supplementary_files_format_and_content: csv, raw gene expression read

molecule: polyA RNA

source_name: TRAMP-C2_80ug/ml SE+1:100 Conditioned Medium 24h

growth_protocol: TRAMPC2 cells were obtained from the American Type Culture Collection (ATCC). TRAMPC2 cells are cultured in RPMI1640 media with DHT and insulin(Invitrogen, Grand Island, NY) with 10% Fetal Bovine Serum (FBS) (GE Healthcare Life Sciences, Logan, Utah). 70% confluent TRAMPC2 cells were treated with indicated treatment.

extract_protocol:
Total RNA was extracted using Rneasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For sutherlandia and Hh-CM treatment, cells are plated in 60mm petri dishes until confluent; TRAMPC2 cells are treated with ethnol control, 8ug/ml suterlandia extrat, 80ug/ml sutherlandia extract, Hh-CM,  8ug/ml suterlandia extrat+Hh-CM, 80ug/ml sutherlandia extract+Hh-CM for 8hr or 24 hr.

tag: cell line

value: mouse prostate cancer cells

tag: passages

value: five to six

tag: treated with

value: 80ug/ml SE+1:100 Conditioned Medium for 24hrs


title: non-transgenic mice infused with CGP, replicate 4


title: 80ug/ml SE+1:100 Conditioned Medium 24h rep1

description:
TC2_1_CM_su80_24h
TC2_23_ATCACG_L003_R1_001.tar.gz


title: non-transgenic mice infused with CGP, replicate 1


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_22
esc1_0h_22_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_20
esc1_0h_20_rsem


title: 8ug/ml SE+1:100 Conditioned Medium 24h rep1

description:
TC2_1_CM_su8_24h
TC2_21_TAGCTT_L003_R1_001.tar.gz

source_name: TRAMP-C2_8ug/ml SE+1:100 Conditioned Medium 24h

value: 8ug/ml SE+1:100 Conditioned Medium for 24hrs


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_21
esc1_0h_21_rsem


title: 8ug/ml SE+1:100 Conditioned Medium 24h rep2

description:
TC2_2_CM_su8_24h
TC2_22_AGTCAA_L003_R1_001.tar.gz


title: control+1:100 Conditioned Medium 24h rep2

description:
TC2_2_CM_24h
TC2_20_GATCAG_L003_R1_001.tar.gz

source_name: TRAMP-C2_control+1:100 Conditioned Medium 24h

value: control+1:100 Conditioned Medium for 24hrs


title: control+1:100 Conditioned Medium 24h rep1

description:
TC2_1_CM_24h
TC2_19_CTTGTA_L003_R1_001.tar.gz


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_18
esc1_0h_18_rsem


title: transgenic SRA mice infused with saline, replicate 2


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_19
esc1_0h_19_rsem


title: 80 ug/ml SE 24h rep2

description:
TC2_2_su80_24h
TC2_18_GTCCGC_L003_R1_001.tar.gz

source_name: TRAMP-C2_80 ug/ml SE 24h

value: 80 ug/ml SE for 24hrs


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_17
esc1_0h_17_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_16
esc1_0h_16_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_15
esc1_0h_15_rsem


title: 8 ug/ml SE 24h rep1

description:
TC2_1_su8_24h
TC2_15_GGCTAC_L002_R1_001.tar.gz

source_name: TRAMP-C2_8 ug/ml SE 24h

value: 8 ug/ml SE for 24hrs


title: 8 ug/ml SE 24h rep2

description:
TC2_2_su8_24h
TC2_16_GTTTCG_L002_R1_001.tar.gz


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_14
esc1_0h_14_rsem


title: control 24h rep2

description:
TC2_2_ctrl_24h
TC2_14_CAGATC_L002_R1_001.tar.gz

source_name: TRAMP-C2_control 24h

value: solvent (ethanol control) for 24hrs


title: 80 ug/ml SE 24h rep1

description:
TC2_1_su80_24h
TC2_17_CCGTCC_L003_R1_001.tar.gz


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_12
esc1_0h_12_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_23
esc1_0h_23_rsem


title: 8ug/ml SE+1:100 Conditioned Medium 8h rep2

description:
TC2_2_CM_su8_8h
TC2_10_CGATGT_L002_R1_001.tar.gz

source_name: TRAMP-C2_8ug/ml SE+1:100 Conditioned Medium 8h

value: 8ug/ml SE+1:100 Conditioned Medium for 8hrs


title: 80ug/ml SE+1:100 Conditioned Medium 8h rep1

description:
TC2_1_CM_su80_8h
TC2_11_GTGAAA_L002_R1_001.tar.gz

source_name: TRAMP-C2_80ug/ml SE+1:100 Conditioned Medium 8h

value: 80ug/ml SE+1:100 Conditioned Medium for 8hrs


title: control+1:100 Conditioned Medium 8h rep1

description:
TC2_1_CM_8h
TC2_7_GTGGCC_L001_R1_001.tar.gz

source_name: TRAMP-C2_control+1:100 Conditioned Medium 8h

value: control+1:100 Conditioned Medium for 8hrs


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_6
esc1_0h_6_rsem


title: 8ug/ml SE+1:100 Conditioned Medium 8h rep1

description:
TC2_1_CM_su8_8h
TC2_9_ACTGAT_L002_R1_001.tar.gz


title: control+1:100 Conditioned Medium 8h rep2

description:
TC2_2_CM_8h
TC2_8_CGTACG_L001_R1_001.tar.gz


title: 80 ug/ml SE 8h rep2

description:
TC2_2_su80_8h
TC2_6_ACAGTG_L001_R1_001.tar.gz

source_name: TRAMP-C2_80 ug/ml SE 8h

value: 80 ug/ml SE for 8hrs


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_5
esc1_0h_5_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_10
esc1_0h_10_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_8
esc1_0h_8_rsem


title: 80 ug/ml SE 8h rep1

description:
TC2_1_su80_8h
TC2_5_ATTCCT_L001_R1_001.tar.gz


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_4
esc1_0h_4_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_3
esc1_0h_3_rsem


title: 8 ug/ml SE 8h rep2

description:
TC2_2_su8_8h
TC2_4_TTAGGC_L001_R1_001.tar.gz

source_name: TRAMP-C2_8 ug/ml SE 8h

value: 8 ug/ml SE for 8hrs


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_2
esc1_0h_2_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_7
esc1_0h_7_rsem


title: control 8h rep2

description:
TC2_2_ctrl_8h
TC2_2_ACTTGA_L001_R1_001.tar.gz

source_name: TRAMP-C2_control 8h

value: solvent (ethanol control) for 8hrs


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_1
esc1_0h_1_rsem


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_13
esc1_0h_13_rsem


title: 8 ug/ml SE 8h rep1

description:
TC2_1_su8_8h
TC2_3_TGACCA_L001_R1_001.tar.gz


title: control 24h rep1

description:
TC2_1_ctrl_24h
TC2_13_ATGTCA_L002_R1_001.tar.gz


title: control 8h rep1

description:
TC2_1_ctrl_8h
TC2_1_TAGCTT_L001_R1_001.tar.gz


title: 80ug/ml SE+1:100 Conditioned Medium 8h rep2

description:
TC2_2_CM_su80_8h
TC2_12_GCCAAT_L002_R1_001.tar.gz


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_11
esc1_0h_11_rsem


title: 36h RNA-Seq Replicate 2

data_processing:
Basecalling conversion to fastq files was performed using bcl2fastq
Expression was quantified from RNA-seq using the Gencode (Mudge and Harrow, 2015) mm10 transcriptome (vM3) and RSEM (parameters: --output-genome-bam –forward-prob=0 –calc-ci) (Li and Dewey, 2011). RSEM was set to use bowtie1  for read alignments (Langmead et al., 2009).
Genome_build: mm10
Supplementary_files_format_and_content: output files from RSEM including counts, FPKM and TPM values per gene (Gencode mm10 vM3 transcriptome)

source_name: ES-derived embryoid bodies with induced transcription factors

extract_protocol:
Cells were collected at different time points after NIL induction and RNA isolated using TRIzol LS (Life Technologies) followed by purification using Qiagen RNAeasy kit
RNA-Seq libraries were prepared using Illumina TruSeq RNA library preparation kit v2. Fifty base pair single-end sequencing was performed using Illumina HiSeq-2500 at the NYU Genome Core facility.

value: Embryoid Bodies


title: 48h RNA-Seq Replicate 2


title: 24h RNA-Seq Replicate 2


title: 12h RNA-Seq Replicate 2


title: polyA mRNA RNA-seq from CD14-positive monocyte (ENCLB555AWV)

description:
https://www.encodeproject.org/experiments/ENCSR000CUC/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent isolates of mobilized CD14+ monocytes. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CUC
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AWV
size range: >200
spikeins used: /references/ENCSR402QNO/

organism: Homo sapiens

source_name: Homo sapiens CD14-positive monocyte primary cell female

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/46fbb004-ef3f-4929-acb2-3327f3bc85a4/@@download/attachment/LID44594.pdf

value: CD14-positive monocyte

value: primary cell

value: Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2:not in 2011 analysis

tag: dev stage

value: unknown

value: female

tag: age

tag: health state

tag: lab

value: Thomas Gingeras, CSHL

tag: link

value: ENCBS627ENC at ENCODE; https://www.encodeproject.org/ENCBS627ENC/

value: Derived from ENCODE donor ENCDO266AAA; https://www.encodeproject.org/ENCDO266AAA/

value: Heimfeld sample source; http://labs.fhcrc.org/heimfeld/contact.html


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

description:
EB(iNgn2.Isl1.Lhx3.V5).single-cell-RNA-seq.cell_9
esc1_0h_9_rsem

value: ES-derived embryoid bodies with induced transcription factors


title: polyA mRNA RNA-seq from CD14-positive monocyte (ENCLB555AWY)

description:
https://www.encodeproject.org/experiments/ENCSR000CUC/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent isolates of mobilized CD14+ monocytes. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CUC
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AWY
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/7870b6db-c081-4c62-9090-380640bd60f1/@@download/attachment/LID44497.pdf

value: ENCBS626ENC at ENCODE; https://www.encodeproject.org/ENCBS626ENC/

value: Derived from ENCODE donor ENCDO265AAA; https://www.encodeproject.org/ENCDO265AAA/


title: polyA depleted RNA-seq from CD14-positive monocyte (ENCLB555ARX)

description:
https://www.encodeproject.org/experiments/ENCSR000CTY/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent isolates of mobilized CD14+ monocytes. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CTY
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ARX
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/9da83692-dddb-43fb-8567-a3a7dcdc7729/@@download/attachment/LID44658.pdf


title: 0h RNA-Seq Replicate 2


title: 36h RNA-Seq Replicate 1


title: 48h RNA-Seq Replicate 1


title: polyA depleted RNA-seq from B cell (ENCLB555AKT)

description:
https://www.encodeproject.org/experiments/ENCSR000CTW/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent isolates of CD20+ B cells. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CTW
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AKT
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens B primary cell female adult (27 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/7862f304-3daf-410b-9da2-19f95c73b1d1/@@download/attachment/LID44659.pdf

value: B cell

value: CD20+ B cells, African American, draw number 1

value: adult

value: 27 year

value: normal

tag: passage number

value: John Stamatoyannopoulos, UW

value: ENCBS484ENC at ENCODE; https://www.encodeproject.org/ENCBS484ENC/

value: Derived from ENCODE donor ENCDO115AAA; https://www.encodeproject.org/ENCDO115AAA/

value: ENCODE dbxrefs CD20+_RO01794; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=CD20+_RO01794

value: ENCODE dbxrefs CD20+; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=CD20+


title: polyA depleted RNA-seq from CD14-positive monocyte (ENCLB555ARY)

description:
https://www.encodeproject.org/experiments/ENCSR000CTY/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent isolates of mobilized CD14+ monocytes. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CTY
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ARY
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/2c9029e8-6c52-4546-9866-d78e04040593/@@download/attachment/LID44657.pdf

value: CD14-positive monocyte

value: primary cell

value: Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2:not in 2011 analysis

value: unknown

value: female

value: Thomas Gingeras, CSHL


title: 12h RNA-Seq Replicate 1

value: Embryoid Bodies


title: 24h RNA-Seq Replicate 1


title: polyA mRNA RNA-seq from B cell (ENCLB555AUP)

description:
https://www.encodeproject.org/experiments/ENCSR000CTV/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent isolates of CD20+ B cells. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CTV
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AUP
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6e4dacb7-e87d-4438-9e92-4e6a9b116502/@@download/attachment/LID44498.pdf

value: B cell


title: polyA mRNA RNA-seq from B cell (ENCLB555APR)

description:
https://www.encodeproject.org/experiments/ENCSR000CTV/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent isolates of CD20+ B cells. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CTV
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555APR
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens B primary cell female adult (43 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/8f00d99f-26c6-4c37-af3d-787432fa467b/@@download/attachment/LID44499.pdf

value: CD20+ B cells, caucasian, draw number 1

value: 43 year

value: ENCBS483ENC at ENCODE; https://www.encodeproject.org/ENCBS483ENC/

value: Derived from ENCODE donor ENCDO114AAA; https://www.encodeproject.org/ENCDO114AAA/

value: ENCODE dbxrefs CD20+_RO01778; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=CD20+_RO01778


title: polyA depleted RNA-seq from B cell (ENCLB555AKS)

description:
https://www.encodeproject.org/experiments/ENCSR000CTW/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent isolates of CD20+ B cells. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CTW
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AKS
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/9519845b-1217-454c-a6b5-a5afaa63d2fc/@@download/attachment/LID44660.pdf

value: adult

value: normal

value: John Stamatoyannopoulos, UW


title: EB+48hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K27ac. Rep3

description: ChIP-seq H3K27ac in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) replicate 3

library_source: genomic

data_processing:
Basecalling conversion to fastq files was performed using bcl2fastq for HiSeq runs and Picard for NextSeq runs
Alignment: All transcription factor ChIP-Seq fastq files were aligned to mouse genome (version mm10) using Bowtie (1.0.1) (Langmead et al., 2009) with options “-q --best --strata -m 1 --chunkmbs 1024”.  Only uniquely mapped reads were considered for further analysis.
All histone modification ChIP-Seq fastq files were aligned to mm10 genome build using bowtie2 (Ben Langmead & Salzberg, 2012) with default parameters. After filtering for uniquely-aligned reads that had 2 or less mismatches, potential PCR duplicates were removed using samtools rmdup (parameters: -s) (H. Li et al., 2009). Resulting BAM files were converted to BED format using bedtools bamtobed command when necessary (Quinlan & Hall, 2010). For H3K4me1, replicates files were concatenated for all further analysis. JAMM was used to obtain the average fragment length for each experiment (Ibrahim et al. 2015).
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-Seq replicate experiments were concatenated and converted to bigwig files using deepTools bamCoverage at 10bp resolution (parameters: --normalizeUsingRPKM)(Ramirez et al. 2014), using the average fragment length predicted by JAMM (Ibrahim et al. 2015).

molecule: genomic DNA

extract_protocol:
Cells were collected at different time points after NIL induction and fixed with 1 mM DSG (ProteoChem) followed by 1% formaldehyde (vol/vol) for 15 min at 20–25°C. Pellets containing ~25 × 10^6 cells were stored at −80 °C. Cells were thawed on ice, resuspended in 5 ml of Lysis Buffer  A (50 mM Hepes-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol (vol/vol), 0.5% Igepal (vol/vol), 0.25% Triton X-100 (vol/vol)) and incubated for 10 min at 4°C in a rotating platform. Samples were spun down for 5 min at 1,350 g, resuspended in 5 ml Lysis Buffer B (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0) and incubated for 10 min at 4 °C in a rotating platform. Samples were spun down for 5 min at 1,350 g, resuspended in 3 ml of Sonication Buffer (50 mM Hepes pH 7.5, 140 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% Trition X-100, 0.1% sodium deoxycholate (wt/vol), 0.1% SDS (wt/vol)). Nuclear extracts were sonicated on ice using a Branson 450 Sonifier (20% power amplitude; 18 cycles x 30 seconds pulses with 1 minute interval between each pulse) to sheer cross-linked DNA to an average fragment size of approximately 500 bp. Sonicated chromatin was incubated for 16 h at 4 °C with Dynabeads protein-G (Life Techologies) conjugated with either rabbit polyclonal antibody to V5 (ab15828, Abcam) to immunoprecipitate Lhx3 or a  combination of monoclonal antibodies (40.3A4, 39.3F7 and 40.206, DSHB) for Isl1. Ngn2 was immunoprecipitated by using a goat polyclonal antobody (sc-19233, Santa Cruz), whereas to immunoprecipitate Ebf2 and Onecut2, a rabbit polyclonal antibody (ab156999, Abcam) and a sheep polyclonal antibody (AF294, R&D Systems) were used, respectively. For histone modifications the following rabbit polyclonal antibodies were used: ab8895 (Abcam) for H3K4me1, ab7766 (Abcam) for H3K4me2, 39159 (Active Motif) for H3K4me3, ab4729 (Abcam) for H3K27ac and 39155 (Active Motif) for H3K27me3. After incubation, and with the aid of a magnetic device, beads were washed once with Sonication Buffer, than with Sonication buffer and 500 nM NaCl and once with LiCl Wash Buffer (20 mM Tris-HCl (pH 8.0), 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate) and 1 ml of TE (10 mM Tris, 1 mM EDTA, pH 8). Then, beads were centrifuged at 950 g for 3 min and the residual TE removed with a pipette. 210 µl of Elution Buffer (50 mM Tris-HCl (pH 8.0), 10 mM EDTA (pH 8.0), 1% SDS) was added to the beads followed by incubation at 65°C for 45 min with a brief pulse of vortex every 10 min. 200 µl of supernatant was removed after a 1 min centrifugation at 16,000 g. The crosslink was reversed by 16 h incubation at 65°C. RNA was digested by the addition of 200 µl of TE and RNAse A (Sigma) at a final concentration of 0.2 mg/ml and incubated for 2 h at 37°C. Protein was digested by the addition of Proteinase K (Invitrogen) at a final concentration of 0.2 mg/ml, supplemented with CaCl2 followed by a 30-min incubation at 55°C. DNA was extracted with phenol:chloroform:isoamyl alcohol (25:24:1; vol/vol) (Invitrogen) and then recovered with an ethanol precipitation with glycogens as carrier. The pellets were suspended in 70 µl of water.
One third (24ul) of ChIP DNA was used to prepare llumina DNA sequencing libraries. Briefly, after end repair and A-tailing, Illumina-compatible Bioo Scientific multiplexed adapters were ligated and the unligated adapters removed through purification using Agencourt AmpureXP beads (Beckman Coulter). Adapter-ligated DNA was amplified by PCR using TruSeq Fw primer (AATGATACGGCGACCACCGAGATCTACAC) and TruSeq Rev primer (CAAGCAGAAGACGGCATACGAGAT), both from Sigma. DNA libraries between 300 and 500 bp in size were gel purified. KAPA SYBR FAST Roche LightCycler 480 2X qPCR Master Mix (Kapa Biosystems) was used in 20 μl reactions that were analyzed in a Roche LightCycler. Fifty base pair single-end sequencing was performed using Illumina HiSeq-2500 at the NYU Genome Core facility.

tag: chip target

tag: chip antibody

value: Abcam ab4729


title: 0h RNA-Seq Replicate 1

tag: strain


title: polyA depleted RNA-seq from HepG2 (ENCLB555AWJ)

description:
https://www.encodeproject.org/experiments/ENCSR000CQU/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line HepG2. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQU
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AWJ
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens HepG2 immortalized cell line cytosolic fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/145b41a7-93dc-49d5-8230-8686c83710ca/@@download/attachment/LID18553.pdf

tag: line

value: immortalized cell line

value: hepatocellular carcinoma

value: child

value: male

value: 15 year

tag: subcellular fraction term name

value: cytosol

value: ENCBS744AAA at ENCODE; https://www.encodeproject.org/ENCBS744AAA/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027

value: ENCODE dbxrefs HepG2; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HepG2

value: ATCC sample source; http://www.atcc.org/products/all/HB-8065.aspx


title: EB+48hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K4me1.rep3

description: ChIP-seq H3K4me1 in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) replicate 3

value: Abcam ab8895

tag: treatment

tag: cell type

value: Embryoid Bodies


title: polyA depleted RNA-seq from H1-hESC (ENCLB555ATC)

description:
https://www.encodeproject.org/experiments/ENCSR000CQR/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the nuclear fraction of independent growths of the human embryonic stem cell line H1-hESC. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQR
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ATC
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens H1-hESC stem cell nuclear fraction male embryo

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ac30dca6-02e1-4823-93e5-125a0d6d3cfa/@@download/attachment/LID9199.pdf

value: stem cell

tag: description

value: embryonic stem cells

tag: biosample encode accession

value: embryonic

tag: Sex

value: unknown

value: healthy

value: Thomas Gingeras, CSHL

value: nucleus

value: ENCBS733AAA at ENCODE; https://www.encodeproject.org/ENCBS733AAA/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/

value: ENCODE dbxrefs Cellosaurus CVCL_9771; http://web.expasy.org/cellosaurus/CVCL_9771

value: ENCODE dbxrefs H1-hESC; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=H1-hESC


title: EB+48hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K27me3.rep2

description: ChIP-seq H3K27me3 in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2

value: Active motif 39155, 39157


title: polyA depleted RNA-seq from SK-N-SH (ENCLB555AXO)

description:
https://www.encodeproject.org/experiments/ENCSR000CQP/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line SK-N-SH that has been treated with retinoic acid. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQP
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AXO
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens SK-N-SH immortalized cell line treated with 6 ?M all-trans-retinoic acid for 48 hours

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/624a7763-9869-48a2-a16d-10b88dabbc20/@@download/attachment/LID9003.pdf

value: SK-N-SH

value: immortalized cell line

value: neuroblastoma cell line, treatment:differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)

value: child

tag: treatments

value: treatment_term_id:CHEBI:15367; treatment_term_name:all-trans-retinoic acid; treatment_type:chemical; duration:48; duration_units:hour;

value: female

value: 4 year

value: ENCBS366ENC at ENCODE; https://www.encodeproject.org/ENCBS366ENC/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/

value: ENCODE dbxrefs Cellosaurus CVCL_D044; http://web.expasy.org/cellosaurus/CVCL_D044

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

value: ATCC sample source; http://www.atcc.org/products/all/HTB-11.aspx


title: polyA depleted RNA-seq from endothelial cell of umbilical vein (ENCLB555AVC)

description:
https://www.encodeproject.org/experiments/ENCSR000CQS/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA-seq on human HUVEC cytosol long polyA- RNA
experiment encode accession: ENCSR000CQS
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AVC
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens endothelial of umbilical vein primary cell cytosolic fraction male newborn

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/eca1ff33-c921-4f74-ae63-2c8cc081bb5d/@@download/attachment/LID18556.pdf

value: endothelial cell of umbilical vein

value: primary cell

value: umbilical vein endothelial cells

value: unknown

tag: dev stage

value: newborn

value: male

value: Thomas Gingeras, CSHL

value: cytosol

value: ENCBS530ENC at ENCODE; https://www.encodeproject.org/ENCBS530ENC/

value: Derived from ENCODE donor ENCDO341AAA; https://www.encodeproject.org/ENCDO341AAA/

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


title: polyA depleted RNA-seq from HeLa-S3 (ENCLB555AOZ)

description:
https://www.encodeproject.org/experiments/ENCSR000CQT/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQT
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AOZ
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens HeLa-S3 immortalized cell line cytosolic fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/77de2ec5-de72-4198-90f2-2b4447962602/@@download/attachment/LID18551.pdf

value: immortalized cell line

value: Cervical adenocarcinoma

value: adult

value: female

tag: age

value: 31 year

value: cervical adenocarcinoma

value: ENCBS738AAA at ENCODE; https://www.encodeproject.org/ENCBS738AAA/

value: Derived from ENCODE donor ENCDO000AAB; https://www.encodeproject.org/ENCDO000AAB/

value: ENCODE dbxrefs Cellosaurus CVCL_0058; http://web.expasy.org/cellosaurus/CVCL_0058

value: ENCODE dbxrefs HeLa-S3; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HeLa-S3

value: ATCC sample source; http://www.atcc.org/products/all/CCL-2.2.aspx


title: EB+24hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K27me3.rep2

description: ChIP-seq H3K27me3 in EB+24hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2

value: Active motif 39155, 39157

value: Embryoid Bodies


title: EB+12hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K27me3.rep2

description: ChIP-seq H3K27me3 in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2


title: EB+48hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K27ac.rep2

description: ChIP-seq H3K27ac in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2

value: Abcam ab4729


title: EB+24hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K27ac.rep2

description: ChIP-seq H3K27ac in EB+24hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2


title: polyA depleted RNA-seq from K562 (ENCLB555ASK)

description:
https://www.encodeproject.org/experiments/ENCSR000CQM/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQM
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ASK
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens K562 immortalized cell line nuclear fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/57de8eb9-622f-4ab4-81c1-ecd8724b62e6/@@download/attachment/LID9195.pdf

value: leukemia, The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

value: 53 year

tag: health state

value: chronic myelogenous leukemia (CML)

value: Thomas Gingeras, CSHL

value: nucleus

value: ENCBS722AAA at ENCODE; https://www.encodeproject.org/ENCBS722AAA/

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

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

value: ENCODE dbxrefs K562; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=K562

value: ATCC sample source; http://www.atcc.org/products/all/CCL-243.aspx


title: polyA depleted RNA-seq from H1-hESC (ENCLB555AST)

description:
https://www.encodeproject.org/experiments/ENCSR000CQQ/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of the human embryonic stem cell line H1-hESC. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized  Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQQ
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AST
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens H1-hESC stem cell cytosolic fraction male embryo

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/f86b778b-4eb7-4745-b5ca-5bcd5157b62c/@@download/attachment/LID18549.pdf

value: stem cell

value: embryonic stem cells

value: embryonic

value: male

value: unknown

value: healthy

tag: lab

value: cytosol

value: ENCBS732AAA at ENCODE; https://www.encodeproject.org/ENCBS732AAA/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/

value: ENCODE dbxrefs Cellosaurus CVCL_9771; http://web.expasy.org/cellosaurus/CVCL_9771

value: ENCODE dbxrefs H1-hESC; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=H1-hESC


title: polyA depleted RNA-seq from SK-N-SH (ENCLB555AWU)

description:
https://www.encodeproject.org/experiments/ENCSR000CQP/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line SK-N-SH that has been treated with retinoic acid. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQP
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AWU
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/5ed32570-84c1-44d7-a173-cf5a1ce7d1d6/@@download/attachment/LID9011.pdf

value: SK-N-SH

value: immortalized cell line

value: neuroblastoma cell line, treatment:differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)

value: child

value: treatment_term_id:CHEBI:15367; treatment_term_name:all-trans-retinoic acid; treatment_type:chemical; duration:48; duration_units:hour;

value: female

value: 4 year

value: Thomas Gingeras, CSHL

tag: link

value: ENCBS367ENC at ENCODE; https://www.encodeproject.org/ENCBS367ENC/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/

value: ENCODE dbxrefs Cellosaurus CVCL_D044; http://web.expasy.org/cellosaurus/CVCL_D044

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

value: ATCC sample source; http://www.atcc.org/products/all/HTB-11.aspx


title: EB+0hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K27ac.rep2

description: ChIP-seq H3K27ac in EB+0hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2

value: Abcam ab4729

value: Embryoid Bodies


title: EB+12hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K27ac.rep2

description: ChIP-seq H3K27ac in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2


title: EB+48hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K4me3.rep2

description: ChIP-seq H3K4me3 in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2

value: Active motif 39159, 39160


title: EB+12hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K4me3.rep2

description: ChIP-seq H3K4me3 in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2


title: polyA depleted RNA-seq from K562 (ENCLB555ASL)

description:
https://www.encodeproject.org/experiments/ENCSR000CQM/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQM
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ASL
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/2f45ccd3-595e-420e-9426-6f3e6a6df77a/@@download/attachment/LID9196.pdf

value: leukemia, The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: nucleus

value: ENCBS725AAA at ENCODE; https://www.encodeproject.org/ENCBS725AAA/

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

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

value: ENCODE dbxrefs K562; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=K562

value: ATCC sample source; http://www.atcc.org/products/all/CCL-243.aspx


title: polyA depleted RNA-seq from HepG2 (ENCLB555APZ)

description:
https://www.encodeproject.org/experiments/ENCSR000CQU/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line HepG2. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQU
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555APZ
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/2d6d4283-96a7-430b-80be-c3ea48385d19/@@download/attachment/LID18552.pdf

value: immortalized cell line

value: hepatocellular carcinoma

value: child

value: male

value: 15 year

value: Thomas Gingeras, CSHL

value: cytosol

value: ENCBS741AAA at ENCODE; https://www.encodeproject.org/ENCBS741AAA/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027

value: ENCODE dbxrefs HepG2; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HepG2

value: ATCC sample source; http://www.atcc.org/products/all/HB-8065.aspx


title: EB+24hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K4me3.rep2

description: ChIP-seq H3K4me3 in EB+24hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2

value: Active motif 39159, 39160

value: Embryoid Bodies


title: polyA depleted RNA-seq from HepG2 (ENCLB555APO)

description:
https://www.encodeproject.org/experiments/ENCSR000CQK/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line HepG2. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQK
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555APO
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens HepG2 immortalized cell line nuclear fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/2567257d-2a2f-4b3d-ad07-9168ab0816db/@@download/attachment/LID9202.pdf

value: nucleus

value: ENCBS742AAA at ENCODE; https://www.encodeproject.org/ENCBS742AAA/


title: EB+0hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K27me3.rep2

description: ChIP-seq H3K27me3 in EB+0hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2

value: Active motif 39155, 39157


title: EB+0hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K4me3.rep2

description: ChIP-seq H3K4me3 in EB+0hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2


title: polyA depleted RNA-seq from HeLa-S3 (ENCLB555ASP)

description:
https://www.encodeproject.org/experiments/ENCSR000CQI/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQI
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ASP
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens HeLa-S3 immortalized cell line nuclear fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/4d882cfa-cd50-4e19-be9b-6216c8ba10d6/@@download/attachment/LID9200.pdf

value: immortalized cell line

value: Cervical adenocarcinoma

value: adult

value: female

value: 31 year

value: cervical adenocarcinoma

value: ENCBS736AAA at ENCODE; https://www.encodeproject.org/ENCBS736AAA/

value: Derived from ENCODE donor ENCDO000AAB; https://www.encodeproject.org/ENCDO000AAB/

value: ENCODE dbxrefs Cellosaurus CVCL_0058; http://web.expasy.org/cellosaurus/CVCL_0058

value: ENCODE dbxrefs HeLa-S3; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HeLa-S3

value: ATCC sample source; http://www.atcc.org/products/all/CCL-2.2.aspx


title: EB+48hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K4me2.rep2

description: ChIP-seq H3K4me2 in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2

value: Abcam ab7766


title: polyA depleted RNA-seq from HeLa-S3 (ENCLB555AOC)

description:
https://www.encodeproject.org/experiments/ENCSR000CQJ/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQJ
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AOC
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens HeLa-S3 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/c26cd47c-924f-4a71-9e60-cedbc85d6eef/@@download/attachment/LID8791.pdf

value: Thomas Gingeras, CSHL

value: ENCBS740AAA at ENCODE; https://www.encodeproject.org/ENCBS740AAA/


title: EB+24hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K4me2.rep2

description: ChIP-seq H3K4me2 in EB+24hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2

value: Embryoid Bodies


title: EB+12hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K4me2.rep2

description: ChIP-seq H3K4me2 in EB+12hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2


title: polyA depleted RNA-seq from HeLa-S3 (ENCLB555ASQ)

description:
https://www.encodeproject.org/experiments/ENCSR000CQI/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQI
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ASQ
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/3bfa07ad-e30a-407c-8c4e-91b58161505b/@@download/attachment/LID9201.pdf

value: nucleus

value: ENCBS739AAA at ENCODE; https://www.encodeproject.org/ENCBS739AAA/


title: EB+48hrDox(iNgn2.Isl1.Lhx3.V5).ChIP-seq_H3K4me1.rep2

description: ChIP-seq H3K4me1 in EB+48hrDox(iNgn2.Isl1.Lhx3.V5) replicate 2

value: Abcam ab8895


title: polyA depleted RNA-seq from K562 (ENCLB555AOF)

description:
https://www.encodeproject.org/experiments/ENCSR000CQL/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line K562. They are stranded PE76 Illumina GaIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQL
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AOF
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens K562 immortalized cell line cytosolic fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ede06b5d-6c5a-47ab-a825-ba02bff62416/@@download/attachment/LID18545.pdf

value: immortalized cell line

value: leukemia, The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

value: 53 year

value: chronic myelogenous leukemia (CML)

value: cytosol

value: ENCBS721AAA at ENCODE; https://www.encodeproject.org/ENCBS721AAA/

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

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

value: ENCODE dbxrefs K562; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=K562

value: ATCC sample source; http://www.atcc.org/products/all/CCL-243.aspx


title: polyA depleted RNA-seq from K562 (ENCLB555AOE)

description:
https://www.encodeproject.org/experiments/ENCSR000CQL/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line K562. They are stranded PE76 Illumina GaIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQL
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AOE
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0c6659e9-1ba2-457b-a18e-da4db43fe725/@@download/attachment/LID18546.pdf

value: adult

value: female

value: ENCBS724AAA at ENCODE; https://www.encodeproject.org/ENCBS724AAA/