title: ChIP-seq from IMR-90 (ENCLB850EBA)

description:
https://www.encodeproject.org/experiments/ENCSR000HPG/
***************
biological replicate number: 3
technical replicate number: 1
description: SMC3 ChIP-seq on human IMR90
experiment encode accession: ENCSR000HPG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR970FKL
encode release date: 2016-10-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB850EBA
size range: 150-350

value: primary cell

value: Fetal lung fibroblasts

value: ENCBS048GPK at ENCODE; https://www.encodeproject.org/ENCBS048GPK/


title: ChIP-seq from MCF-7 (ENCLB462SZP)

status: Public on Jan 03 2017

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR066TET/
***************
biological replicate number: 1
technical replicate number: 1
description: RFX1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR066TET
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR217LRF
encode release date: 2016-06-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB462SZP
size range: 450-650

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens MCF-7 immortalized cell line

tag: antibody

tag: line

value: immortalized cell line

tag: description

value: Mammary gland, adenocarcinoma. (PMID:4357757)

tag: biosample encode accession

tag: dev stage

value: adult

tag: age

value: 69 year

tag: Sex

value: female

tag: lab

value: Michael Snyder, Stanford

tag: health state

value: breast cancer (adenocarcinoma)

tag: link

value: ENCBS536NWC at ENCODE; https://www.encodeproject.org/ENCBS536NWC/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031

value: ATCC sample source; http://www.atcc.org/Products/All/HTB-22.aspx


title: ChIP-seq from HEK293 (ENCLB430LNO)

description:
https://www.encodeproject.org/experiments/ENCSR065WUF/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-KLF17 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR065WUF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB430LNO
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-KLF17 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-KLF17 under the control of a CMV promoter.

value: embryonic

value: unknown

value: ENCBS485LHG at ENCODE; https://www.encodeproject.org/ENCBS485LHG/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: ChIP-seq from MCF-7 (ENCLB452EKC)

description:
https://www.encodeproject.org/experiments/ENCSR062HDL/
***************
biological replicate number: 1
technical replicate number: 1
description: HSF1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR062HDL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB452EKC
size range: 450-650

value: ENCBS168ISE at ENCODE; https://www.encodeproject.org/ENCBS168ISE/


title: ChIP-seq from HEK293 (ENCLB721PXQ)

description:
https://www.encodeproject.org/experiments/ENCSR065WUF/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-KLF17 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR065WUF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB721PXQ
size range: 450-650

value: immortalized cell line

value: ENCBS328EZX at ENCODE; https://www.encodeproject.org/ENCBS328EZX/


title: eCLIP from K562 (ENCLB806OUQ)

description:
https://www.encodeproject.org/experiments/ENCSR062NNB/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against IGF2BP2
experiment encode accession: ENCSR062NNB
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR387RGT
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB806OUQ
size range: 175-300

library_source: transcriptomic

molecule: total RNA

source_name: Homo sapiens K562 immortalized cell line

extract_protocol:
pipeline protocol: https://www.encodeproject.org/documents/dde0b669-0909-4f8b-946d-3cb9f35a6c52/@@download/attachment/eCLIP_analysisSOP_v1.P.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/fa2a3246-6039-46ba-b960-17fe06e7876a/@@download/attachment/CLIP_SOP_v1.0.pdf

value: adult

value: 53 year

tag: passage number

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

value: ENCBS978JIM at ENCODE; https://www.encodeproject.org/ENCBS978JIM/

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: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: ChIP-seq from MCF-7 (ENCLB724CXF)

description:
https://www.encodeproject.org/experiments/ENCSR062HDL/
***************
biological replicate number: 2
technical replicate number: 1
description: HSF1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR062HDL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB724CXF
size range: 450-650

value: Mammary gland, adenocarcinoma. (PMID:4357757)

value: female

value: 69 year

value: breast cancer (adenocarcinoma)

value: Michael Snyder, Stanford

value: ENCBS034XKZ at ENCODE; https://www.encodeproject.org/ENCBS034XKZ/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031

value: ATCC sample source; http://www.atcc.org/Products/All/HTB-22.aspx


title: eCLIP from K562 (ENCLB968PKX)

description:
https://www.encodeproject.org/experiments/ENCSR062NNB/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against IGF2BP2
experiment encode accession: ENCSR062NNB
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR387RGT
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB968PKX
size range: 175-300

value: immortalized cell line

value: adult

value: ENCBS283QAE at ENCODE; https://www.encodeproject.org/ENCBS283QAE/


title: eCLIP from HepG2 (ENCLB797ADQ)

description:
https://www.encodeproject.org/experiments/ENCSR060VZF/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against SRSF9
experiment encode accession: ENCSR060VZF
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB797ADQ
size range: 175-300

source_name: Homo sapiens HepG2 immortalized cell line

value: Control

value: child

value: 15 year

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS470TSC at ENCODE; https://www.encodeproject.org/ENCBS470TSC/

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: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: eCLIP from HepG2 (ENCLB004YEU)

description:
https://www.encodeproject.org/experiments/ENCSR061EVO/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against SND1
experiment encode accession: ENCSR061EVO
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR167OYL
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB004YEU
size range: 175-300

extract_protocol:
pipeline protocol: https://www.encodeproject.org/documents/dde0b669-0909-4f8b-946d-3cb9f35a6c52/@@download/attachment/eCLIP_analysisSOP_v1.P.pdf
general protocol: https://www.encodeproject.org/documents/842f7424-5396-424a-a1a3-3f18707c3222/@@download/attachment/eCLIP_SOP_v1.P_110915.pdf
extraction method: see document

value: ENCBS859FFE at ENCODE; https://www.encodeproject.org/ENCBS859FFE/


title: eCLIP from HepG2 (ENCLB201FCW)

description:
https://www.encodeproject.org/experiments/ENCSR061EVO/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against SND1
experiment encode accession: ENCSR061EVO
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR167OYL
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB201FCW
size range: 175-300

value: ENCBS861HMN at ENCODE; https://www.encodeproject.org/ENCBS861HMN/


title: siRNA RNA-seq from K562 (ENCLB753ZMK)

description:
https://www.encodeproject.org/experiments/ENCSR047MQO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting VEZF1.
experiment encode accession: ENCSR047MQO
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR942MUW, ENCSR109YDL, ENCSR074DIJ
encode release date: 2016-11-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB753ZMK
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line transiently expressing siRNA targeting VEZF1

value: K562 cells treated with a siRNA knockdown against VEZF1, used in RNA-seq experiments.

value: 53 year

value: female

value: Sherman Weissman, Yale

value: chronic myelogenous leukemia (CML)

value: ENCBS418DST at ENCODE; https://www.encodeproject.org/ENCBS418DST/

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


title: eCLIP from K562 (ENCLB193BWY)

description:
https://www.encodeproject.org/experiments/ENCSR059CWF/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against SBDS
experiment encode accession: ENCSR059CWF
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR038TMA
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB193BWY
size range: 175-300

value: SBDS

value: immortalized cell line

value: adult

value: ENCBS489LOC at ENCODE; https://www.encodeproject.org/ENCBS489LOC/

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


title: eCLIP from HepG2 (ENCLB872UTJ)

description:
https://www.encodeproject.org/experiments/ENCSR049GND/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against U2AF2
experiment encode accession: ENCSR049GND
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB872UTJ
size range: 175-300

value: Control

value: child

value: 15 year

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS836LJE at ENCODE; https://www.encodeproject.org/ENCBS836LJE/

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


title: eCLIP from K562 (ENCLB786EUD)

description:
https://www.encodeproject.org/experiments/ENCSR059CWF/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against SBDS
experiment encode accession: ENCSR059CWF
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR038TMA
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB786EUD
size range: 175-300

value: 53 year

value: female

value: ENCBS931MQO at ENCODE; https://www.encodeproject.org/ENCBS931MQO/

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


title: siRNA RNA-seq from K562 (ENCLB675TPO)

description:
https://www.encodeproject.org/experiments/ENCSR047MQO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting VEZF1.
experiment encode accession: ENCSR047MQO
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR942MUW, ENCSR109YDL, ENCSR074DIJ
encode release date: 2016-11-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB675TPO
size range: >200
spikeins used: /references/ENCSR866KGS/

value: K562 cells treated with a siRNA knockdown against VEZF1, used in RNA-seq experiments.

value: Sherman Weissman, Yale

value: chronic myelogenous leukemia (CML)

value: ENCBS552WRL at ENCODE; https://www.encodeproject.org/ENCBS552WRL/

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


title: ChIP-seq from HepG2 (ENCLB555ADE)

description:
https://www.encodeproject.org/experiments/ENCSR101FJT/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF143 ChIP-seq on human HepG2
experiment encode accession: ENCSR101FJT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR613TDP
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB555ADE
size range: 150-350

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/7e85e27a-1b03-493d-b73f-db4ce2246318/@@download/attachment/wgEncodeSydhHistone.release3.html.pdf, general protocol: https://www.encodeproject.org/documents/0612f0bf-3665-47f8-af5d-09aab3d4ca24/@@download/attachment/wgEncodeSydhTfbs.release3.html.pdf

value: immortalized cell line

value: Hepatocellular carcinoma

value: Michael Snyder, Stanford

value: ENCBS522AAA at ENCODE; https://www.encodeproject.org/ENCBS522AAA/

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


title: siRNA RNA-seq from K562 (ENCLB445OOS)

description:
https://www.encodeproject.org/experiments/ENCSR047MQO/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting VEZF1.
experiment encode accession: ENCSR047MQO
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR942MUW, ENCSR109YDL, ENCSR074DIJ
encode release date: 2016-11-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB445OOS
size range: >200
spikeins used: /references/ENCSR866KGS/

value: adult

value: ENCBS768HCT at ENCODE; https://www.encodeproject.org/ENCBS768HCT/


title: eCLIP from HepG2 (ENCLB150JWV)

description:
https://www.encodeproject.org/experiments/ENCSR044NGV/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against XRCC6
experiment encode accession: ENCSR044NGV
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-09-21
lab: Gene Yeo, UCSD
library encode accession: ENCLB150JWV
size range: 175-300

value: Control

value: child

value: 15 year

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS859FFE at ENCODE; https://www.encodeproject.org/ENCBS859FFE/

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


title: ChIP-seq from K562 (ENCLB627UNC)

description:
https://www.encodeproject.org/experiments/ENCSR041AXL/
***************
biological replicate number: 2
technical replicate number: 1
description: RFX1 ChIP-seq on human K562
experiment encode accession: ENCSR041AXL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-06-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB627UNC
size range: 450-650

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS288EEL at ENCODE; https://www.encodeproject.org/ENCBS288EEL/

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


title: eCLIP from K562 (ENCLB297AJH)

description:
https://www.encodeproject.org/experiments/ENCSR038TMA/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against SBDS
experiment encode accession: ENCSR038TMA
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB297AJH
size range: 175-300

value: immortalized cell line

value: ENCBS489LOC at ENCODE; https://www.encodeproject.org/ENCBS489LOC/

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

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


title: ChIP-seq from K562 (ENCLB424ZPB)

description:
https://www.encodeproject.org/experiments/ENCSR041AXL/
***************
biological replicate number: 1
technical replicate number: 1
description: RFX1 ChIP-seq on human K562
experiment encode accession: ENCSR041AXL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-06-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB424ZPB
size range: 450-650

value: adult

value: Michael Snyder, Stanford

value: ENCBS697XFI at ENCODE; https://www.encodeproject.org/ENCBS697XFI/


title: ChIP-seq from K562 (ENCLB956UEP)

description:
https://www.encodeproject.org/experiments/ENCSR038RGL/
***************
biological replicate number: 1
technical replicate number: 1
description: MCM7 ChIP-seq on human K562
experiment encode accession: ENCSR038RGL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB956UEP
size range: 450-650

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: ENCBS576ESJ at ENCODE; https://www.encodeproject.org/ENCBS576ESJ/

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


title: ChIP-seq from K562 (ENCLB712EEZ)

description:
https://www.encodeproject.org/experiments/ENCSR038RGL/
***************
biological replicate number: 2
technical replicate number: 1
description: MCM7 ChIP-seq on human K562
experiment encode accession: ENCSR038RGL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB712EEZ
size range: 450-650

value: ENCBS837GDT at ENCODE; https://www.encodeproject.org/ENCBS837GDT/


title: ChIP-seq from K562 (ENCLB166HWY)

description:
https://www.encodeproject.org/experiments/ENCSR033VAZ/
***************
biological replicate number: 3
technical replicate number: 1
description: TARDBP ChIP-seq on human K562
experiment encode accession: ENCSR033VAZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-04-22
lab: Michael Snyder, Stanford
library encode accession: ENCLB166HWY
size range: 450-650

value: TARDBP

value: ENCBS994WPS at ENCODE; https://www.encodeproject.org/ENCBS994WPS/


title: ChIP-seq from K562 (ENCLB610CGS)

description:
https://www.encodeproject.org/experiments/ENCSR031TFS/
***************
biological replicate number: 2
technical replicate number: 1
description: POLR2A ChIP-seq on human K562
experiment encode accession: ENCSR031TFS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB610CGS
size range: 450-650

value: 53 year

value: female

value: ENCBS783WYV at ENCODE; https://www.encodeproject.org/ENCBS783WYV/


title: ChIP-seq from K562 (ENCLB224WPQ)

description:
https://www.encodeproject.org/experiments/ENCSR033VAZ/
***************
biological replicate number: 2
technical replicate number: 1
description: TARDBP ChIP-seq on human K562
experiment encode accession: ENCSR033VAZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-04-22
lab: Michael Snyder, Stanford
library encode accession: ENCLB224WPQ
size range: 450-650

value: chronic myelogenous leukemia (CML)

value: ENCBS232KKV at ENCODE; https://www.encodeproject.org/ENCBS232KKV/

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


title: ChIP-seq from MCF-7 (ENCLB375OHG)

description:
https://www.encodeproject.org/experiments/ENCSR028NUR/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF592 ChIP-seq on human MCF-7
experiment encode accession: ENCSR028NUR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB375OHG
size range: 450-650

value: immortalized cell line

value: 69 year

value: breast cancer (adenocarcinoma)

value: ENCBS158RRU at ENCODE; https://www.encodeproject.org/ENCBS158RRU/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031


title: ChIP-seq from MCF-7 (ENCLB882HUK)

description:
https://www.encodeproject.org/experiments/ENCSR028NUR/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF592 ChIP-seq on human MCF-7
experiment encode accession: ENCSR028NUR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB882HUK
size range: 450-650

value: adult

value: Michael Snyder, Stanford

value: ENCBS488MMM at ENCODE; https://www.encodeproject.org/ENCBS488MMM/


title: ChIP-seq from HEK293 (ENCLB278GJK)

description:
https://www.encodeproject.org/experiments/ENCSR049NDP/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq on eGFP-ZNF572 tagged human HEK293 cells.
experiment encode accession: ENCSR049NDP
assay title: ChIP-seq
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB278GJK
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF572 fusion protein

value: Control

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF572 under the control of a CMV promoter.

value: embryonic

value: unknown

value: ENCBS882KSU at ENCODE; https://www.encodeproject.org/ENCBS882KSU/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: eCLIP from K562 (ENCLB515OJU)

description:
https://www.encodeproject.org/experiments/ENCSR028CRL/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against DDX3X
experiment encode accession: ENCSR028CRL
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB515OJU
size range: 175-300

value: 53 year

value: female

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

value: ENCBS831COV at ENCODE; https://www.encodeproject.org/ENCBS831COV/

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

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


title: ChIP-seq from HepG2 (ENCLB548MBI)

description:
https://www.encodeproject.org/experiments/ENCSR019KPC/
***************
biological replicate number: 1
technical replicate number: 1
description: PLRG1 ChIP-seq on human HepG2
experiment encode accession: ENCSR019KPC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR121CWV
encode release date: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB548MBI
size range: 450-650

value: immortalized cell line

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: ENCBS157PJQ at ENCODE; https://www.encodeproject.org/ENCBS157PJQ/

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


title: ChIP-seq from HEK293 (ENCLB652XZN)

description:
https://www.encodeproject.org/experiments/ENCSR022IZK/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF623 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR022IZK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB652XZN
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF623 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF623 under the control of a CMV promoter.

value: embryonic

value: unknown

value: Michael Snyder, Stanford

value: ENCBS644JET at ENCODE; https://www.encodeproject.org/ENCBS644JET/


title: ChIP-seq from HEK293 (ENCLB817TDH)

description:
https://www.encodeproject.org/experiments/ENCSR021DJC/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-BCL11A ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR021DJC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB817TDH
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-BCL11A fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-BCL11A under the control of a CMV promoter.

value: female

value: ENCBS941THM at ENCODE; https://www.encodeproject.org/ENCBS941THM/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: eCLIP from HepG2 (ENCLB635HXC)

description:
https://www.encodeproject.org/experiments/ENCSR018ZUE/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against FKBP4
experiment encode accession: ENCSR018ZUE
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR704LTK
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB635HXC
size range: 175-300

value: Gene Yeo, UCSD

value: ENCBS035IIS at ENCODE; https://www.encodeproject.org/ENCBS035IIS/

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

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


title: ChIP-seq from HEK293 (ENCLB212HQB)

description:
https://www.encodeproject.org/experiments/ENCSR021DJC/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-BCL11A ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR021DJC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB212HQB
size range: 450-650

value: immortalized cell line

value: ENCBS541ZKU at ENCODE; https://www.encodeproject.org/ENCBS541ZKU/


title: ChIP-seq from HEK293 (ENCLB321XJI)

description:
https://www.encodeproject.org/experiments/ENCSR017QBI/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF600 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR017QBI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB321XJI
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF600 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF600 under the control of a CMV promoter.

value: ENCBS172MXQ at ENCODE; https://www.encodeproject.org/ENCBS172MXQ/


title: ChIP-seq from HepG2 (ENCLB489LUV)

description:
https://www.encodeproject.org/experiments/ENCSR019KPC/
***************
biological replicate number: 2
technical replicate number: 1
description: PLRG1 ChIP-seq on human HepG2
experiment encode accession: ENCSR019KPC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR121CWV
encode release date: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB489LUV
size range: 450-650

value: child

value: 15 year

value: male

value: hepatocellular carcinoma

value: ENCBS787RAZ at ENCODE; https://www.encodeproject.org/ENCBS787RAZ/

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


title: ChIP-seq from HEK293 (ENCLB883JER)

description:
https://www.encodeproject.org/experiments/ENCSR017QBI/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF600 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR017QBI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB883JER
size range: 450-650

value: embryonic

value: unknown

value: female

value: Michael Snyder, Stanford

value: ENCBS629GNX at ENCODE; https://www.encodeproject.org/ENCBS629GNX/


title: ChIP-seq from HEK293 (ENCLB115CML)

description:
https://www.encodeproject.org/experiments/ENCSR022IZK/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF623 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR022IZK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB115CML
size range: 450-650

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF623 under the control of a CMV promoter.

value: ENCBS163UGH at ENCODE; https://www.encodeproject.org/ENCBS163UGH/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: ChIP-seq from HEK293 (ENCLB850YXH)

description:
https://www.encodeproject.org/experiments/ENCSR011XCI/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF585B ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR011XCI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB850YXH
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF585B fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF585B under the control of a CMV promoter.

value: ENCBS284GFM at ENCODE; https://www.encodeproject.org/ENCBS284GFM/


title: eCLIP from HepG2 (ENCLB522ATB)

description:
https://www.encodeproject.org/experiments/ENCSR018ZUE/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against FKBP4
experiment encode accession: ENCSR018ZUE
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR704LTK
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB522ATB
size range: 175-300

value: child

value: Gene Yeo, UCSD

value: ENCBS885JQS at ENCODE; https://www.encodeproject.org/ENCBS885JQS/

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

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


title: ChIP-seq from MCF-7 (ENCLB924UKO)

description:
https://www.encodeproject.org/experiments/ENCSR017CEO/
***************
biological replicate number: 3
technical replicate number: 1
description: CUX1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR017CEO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR217LRF
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB924UKO
size range: 450-650

value: adult

value: 69 year

value: breast cancer (adenocarcinoma)

value: ENCBS123ZGI at ENCODE; https://www.encodeproject.org/ENCBS123ZGI/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031


title: VM_8w

city: Lund

first: Per

last: Brattas

address: Sölvegatan 17

country: Sweden

institute: Lund University

description: Processed data in Embryo.Repeats.uniqID.UniqueReads.NOT.IN.EXON.final.txt

data_processing:
RNA-seq reads were mapped to the human genome assembly hg38 using STAR aligner v4.1. For mRNA analysis, default parameters were used. For analysis of retrotransposons we used the --outFilterMultimapNmax 1 to only report uniquely mapping reads
ChIP-seq reads were mapped to the human genome assembly hg38 using Bowtie2 with --very-sensitive. All alignments with MAPQ < 10 were discarded.
ChIP-seq peaks were called with MACS2 normalizing against IN. H3K9me3 peaks were called using --broad, TRIM28 peaks were called with default parameters. A cutoff of -q 0.05 was used for both data sets.
mRNA and non-coding RNAs were quantified using the subread package FeatureCounts (--primary) and iGenome NCBI annotation. Retrotransposons were quantified using the RepeatMasker track from UCSC.
Genome_build: hg38
Supplementary_files_format_and_content: RNA-Seq: Matrix of quantification of non-exonic retroelements using featureCounts.
Supplementary_files_format_and_content: ChIP-Seq: Bed files with called peaks.

molecule: polyA RNA

source_name: human fetus

extract_protocol:
miRNeasy Micro Kit (Qiagen)
KAPA stranded RNA-seq with RiboErase kit.

tag: cell type

tag: fetal region

value: Ventral Mesencephalon

tag: embryonic age

value: 8 weeks


title: ChIP-seq from HEK293 (ENCLB357BRZ)

description:
https://www.encodeproject.org/experiments/ENCSR011XCI/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF585B ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR011XCI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB357BRZ
size range: 450-650

value: embryonic

value: unknown

value: female

value: Michael Snyder, Stanford

value: ENCBS472HLI at ENCODE; https://www.encodeproject.org/ENCBS472HLI/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: VM_7.5w

value: 7 weeks, 5 days


title: VM_6.5w

value: 6 weeks, 5 days


title: VM_7w

value: 7 weeks


title: VM_4.5w

value: 4 weeks, 5 days


title: ChIP-seq from K562 (ENCLB559BCO)

description:
https://www.encodeproject.org/experiments/ENCSR011NOZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF407 ChIP-seq on human K562
experiment encode accession: ENCSR011NOZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-11-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB559BCO
size range: 450-650

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: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS576ESJ at ENCODE; https://www.encodeproject.org/ENCBS576ESJ/

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

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


title: ChIP-seq from K562 (ENCLB020AEM)

description:
https://www.encodeproject.org/experiments/ENCSR011NOZ/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF407 ChIP-seq on human K562
experiment encode accession: ENCSR011NOZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-11-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB020AEM
size range: 450-650

value: ENCBS839CNN at ENCODE; https://www.encodeproject.org/ENCBS839CNN/

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


title: ChIP-seq from MCF-7 (ENCLB656YGH)

description:
https://www.encodeproject.org/experiments/ENCSR017CEO/
***************
biological replicate number: 2
technical replicate number: 1
description: CUX1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR017CEO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR217LRF
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB656YGH
size range: 450-650

value: Mammary gland, adenocarcinoma. (PMID:4357757)

value: female

value: 69 year

value: breast cancer (adenocarcinoma)

value: Michael Snyder, Stanford

value: ENCBS168ISE at ENCODE; https://www.encodeproject.org/ENCBS168ISE/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031

value: ATCC sample source; http://www.atcc.org/Products/All/HTB-22.aspx


title: ChIP-seq from K562 (ENCLB623DFV)

description:
https://www.encodeproject.org/experiments/ENCSR031TFS/
***************
biological replicate number: 1
technical replicate number: 1
description: POLR2A ChIP-seq on human K562
experiment encode accession: ENCSR031TFS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB623DFV
size range: 450-650

value: immortalized cell line

value: adult

value: ENCBS465MWC at ENCODE; https://www.encodeproject.org/ENCBS465MWC/


title: VM_11w

value: Ventral Mesencephalon

value: 11 weeks


title: ChIP-seq from HEK293 (ENCLB581JXH)

description:
https://www.encodeproject.org/experiments/ENCSR007GUS/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq on eGFP-CTCF tagged human HEK293 cells.
experiment encode accession: ENCSR007GUS
assay title: ChIP-seq
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB581JXH
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-CTCF fusion protein

value: Control

value: HEK293 cell line stably expressing N-terminal tagged eGFP-CTCF under the control of a CMV promoter.

value: embryonic

value: unknown

value: ENCBS454VNJ at ENCODE; https://www.encodeproject.org/ENCBS454VNJ/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: ChIP-seq from HEK293 (ENCLB685MAE)

description:
https://www.encodeproject.org/experiments/ENCSR011CKE/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF2 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR011CKE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB685MAE
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF2 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF2 under the control of a CMV promoter.

value: female

value: ENCBS158KCV at ENCODE; https://www.encodeproject.org/ENCBS158KCV/


title: eCLIP from K562 (ENCLB453XQN)

description:
https://www.encodeproject.org/experiments/ENCSR006OEQ/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against FAM120A
experiment encode accession: ENCSR006OEQ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR811FFO
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB453XQN
size range: 175-300

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

value: ENCBS230JWL at ENCODE; https://www.encodeproject.org/ENCBS230JWL/

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: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: eCLIP from K562 (ENCLB229UZS)

description:
https://www.encodeproject.org/experiments/ENCSR006OEQ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against FAM120A
experiment encode accession: ENCSR006OEQ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR811FFO
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB229UZS
size range: 175-300

value: immortalized cell line

value: adult

value: ENCBS736PRC at ENCODE; https://www.encodeproject.org/ENCBS736PRC/


title: VM_7.5w-b2.2

value: Ventral Mesencephalon

value: 7 weeks, 5 days


title: VM_7.5w-b2.1


title: ChIP-seq from HEK293 (ENCLB838GRG)

description:
https://www.encodeproject.org/experiments/ENCSR011CKE/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF2 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR011CKE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB838GRG
size range: 450-650

value: embryonic

value: unknown

value: Michael Snyder, Stanford

value: ENCBS824HHH at ENCODE; https://www.encodeproject.org/ENCBS824HHH/


title: ChIP-seq from K562 (ENCLB842NPF)

description:
https://www.encodeproject.org/experiments/ENCSR005NMT/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ID3 ChIP-seq on human K562
experiment encode accession: ENCSR005NMT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR781GAA
encode release date: 2016-02-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB842NPF
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-ID3 fusion protein

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ID3

value: female

value: Kevin White, UChicago

value: ENCBS384AAA at ENCODE; https://www.encodeproject.org/ENCBS384AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_AW26; http://web.expasy.org/cellosaurus/CVCL_AW26

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


title: HB-post-basal plate

value: Posterior basal plate

value: 8 weeks, 6 days


title: HB-basal plate

value: Basal plate


title: eCLIP from HepG2 (ENCLB844OXM)

description:
https://www.encodeproject.org/experiments/ENCSR099KAK/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against DDX6
experiment encode accession: ENCSR099KAK
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB844OXM
size range: 175-300

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/fa2a3246-6039-46ba-b960-17fe06e7876a/@@download/attachment/CLIP_SOP_v1.0.pdf

value: Control

value: immortalized cell line

value: child

value: 15 year

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS621TAB at ENCODE; https://www.encodeproject.org/ENCBS621TAB/

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: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: ChIP-seq from liver (ENCLB695QKX)

description:
https://www.encodeproject.org/experiments/ENCSR041SMK/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on postnatal 0 day mouse liver
experiment encode accession: ENCSR041SMK
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR014GMV
encode release date: 2016-05-18
lab: Richard Myers, HAIB
library encode accession: ENCLB695QKX

organism: Mus musculus

source_name: Mus musculus strain B6NCrl liver tissue postnatal (0 days)

value: CTCF

value: liver

value: tissue

value: pulverized livers pooled from multiple dissections of postnatal 0 day mice

value: postnatal

value: 0 day

value: not collected

value: Richard Myers, HAIB

value: ENCBS152FNH at ENCODE; https://www.encodeproject.org/ENCBS152FNH/

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


title: Diencephalon

value: Diencephalon

value: 8 weeks, 6 days


title: ChIP-seq from K562 (ENCLB334VFQ)

description:
https://www.encodeproject.org/experiments/ENCSR004GKA/
***************
biological replicate number: 1
technical replicate number: 1
description: ZEB2 ChIP-seq on human K562
experiment encode accession: ENCSR004GKA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB334VFQ
size range: 450-650

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: adult

value: 53 year

value: female

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)

value: ENCBS994WPS at ENCODE; https://www.encodeproject.org/ENCBS994WPS/

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: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: eCLIP from K562 (ENCLB313FIH)

description:
https://www.encodeproject.org/experiments/ENCSR000SSH/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against SLTM
experiment encode accession: ENCSR000SSH
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR820GBM
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB313FIH
size range: 175-300

value: SLTM

value: Gene Yeo, UCSD

value: ENCBS831COV at ENCODE; https://www.encodeproject.org/ENCBS831COV/

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


title: eCLIP from adrenal gland (ENCLB963NCC)

description:
https://www.encodeproject.org/experiments/ENCSR096YAP/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on adrenal gland against HNRNPU
experiment encode accession: ENCSR096YAP
assay title: eCLIP
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB963NCC
size range: 175-300

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

value: Control

value: adrenal gland

value: tissue

value: Adrenal Gland GTEx tissue aliquot

value: male

value: 37 year

value: ENCBS168TDE at ENCODE; https://www.encodeproject.org/ENCBS168TDE/

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


title: eCLIP from HepG2 (ENCLB483UDN)

description:
https://www.encodeproject.org/experiments/ENCSR097NEE/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against PPIG
experiment encode accession: ENCSR097NEE
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR445LJH
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB483UDN
size range: 175-300

value: PPIG

value: immortalized cell line

value: child

value: 15 year

value: hepatocellular carcinoma

value: ENCBS308ZPA at ENCODE; https://www.encodeproject.org/ENCBS308ZPA/

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

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


title: Ctx

description: Processed data in Embryo.Repeats.uniqID.UniqueReads.NOT.IN.EXON.final.txt

value: Cortex

value: 8 weeks, 6 days


title: eCLIP from K562 (ENCLB211JXD)

description:
https://www.encodeproject.org/experiments/ENCSR000SSH/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against SLTM
experiment encode accession: ENCSR000SSH
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR820GBM
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB211JXD
size range: 175-300

value: SLTM

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

value: ENCBS253VOZ at ENCODE; https://www.encodeproject.org/ENCBS253VOZ/

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: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: ChIP-seq from K562 (ENCLB314DMO)

description:
https://www.encodeproject.org/experiments/ENCSR005NMT/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ID3 ChIP-seq on human K562
experiment encode accession: ENCSR005NMT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR781GAA
encode release date: 2016-02-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB314DMO
size range: 450-650

value: immortalized cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ID3

value: Kevin White, UChicago

value: ENCBS425AAA at ENCODE; https://www.encodeproject.org/ENCBS425AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_AW26; http://web.expasy.org/cellosaurus/CVCL_AW26


title: eCLIP from adrenal gland (ENCLB784TYD)

description:
https://www.encodeproject.org/experiments/ENCSR096YAP/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP control experiment on adrenal gland against HNRNPU
experiment encode accession: ENCSR096YAP
assay title: eCLIP
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB784TYD
size range: 175-300

value: Control

value: adrenal gland

value: tissue

value: Adrenal Gland GTEx tissue aliquot

value: male

value: 37 year

value: ENCBS168TDE at ENCODE; https://www.encodeproject.org/ENCBS168TDE/

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


title: ChIP-seq from intestine (ENCLB232JXB)

description:
https://www.encodeproject.org/experiments/ENCSR002ZAG/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on postnatal 0 day mouse intestine
experiment encode accession: ENCSR002ZAG
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR862ZBY
encode release date: 2016-05-18
lab: Richard Myers, HAIB
library encode accession: ENCLB232JXB

source_name: Mus musculus strain B6NCrl intestine tissue postnatal (0 days)

value: CTCF

value: intestine

value: pulverized intestines pooled from multiple dissections of postnatal 0 day mice

value: postnatal

value: 0 day

value: not collected

value: Richard Myers, HAIB

value: ENCBS271FHW at ENCODE; https://www.encodeproject.org/ENCBS271FHW/

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


title: hiPSCd neuron-only treated with Bic/4AP for 4 h Hs_Bic-4AP_4h_2

city: Heidelberg

first: Priit

last: Pruunsild

address: INF 364

department: Neurobiology

country: Germany

institute: University of Heidelberg

description: polyA purified

data_processing:
Illumina Casava1.7 software used for basecalling.
hiPSCd neuron/mouse primary neuron co-culture sample reads were filtered for human reads as follows. Paired-end reads were aligned independently, without pairing, to the mouse genome assembly GRCm38/mm10 with Bowtie2 version 2.1.0. Unaligned read pairs were joined and split again to eliminate pairs with one aligned read. Then, genome-unaligned paired-end reads were aligned to GRCm38/mm10 transcriptomes (UCSC Genes/knownGene), respectively, with Bowtie2 (2.1.0). The reads not aligned to the mouse genome and transcriptome were handled as reads obtained from hiPSCd neuron-only samples.
Processed mixed-species sample reads and human-cells-only sample reads were aligned to gene model annotations of the human genome assembly GRCh37/hg19 with TopHat version v2.0.9.
Mapped reads per gene were counted strand-specifically with HTSeq-count (HTSeq version 0.6.0 or 0.6.1) in the union overlap resolution mode.
Differentially expressed genes were determined with the DESeq2 package version 1.8.1.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: HTSeq-count read counts per gene.

source_name: hiPSC-derived neurons

growth_protocol: We differentiated iPSCs to NPCs using a slightly modified spin embryoid body protocol (Kim et al., 2011) with dual SMAD inhibition (Chambers et al., 2009). Differentiation of NPCs was initiated by plating 50,000 cells/cm2 on PO/Lam dishes without EGF and FGF2.  Neuronal differentiation was allowed to proceed for 7 (co-cultures) or 10 (hiPSCd neuron-only cultures) weeks.

extract_protocol:
Total RNA was purified from cultured cells (3.5 cm dish) with RNeasy Mini (hiPSCd neuron/mouse primary neuron co-cultures) or Micro (hiPSCd neuron-only cultures) Kit (Qiagen) along with on-column RNase-Free DNase (Qiagen) digestion of DNA
Poly(A)+ RNA was isolated from total RNA with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). cDNA libraries were prepared with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs). NEBNext Multiplex Oligos for Illumina (New England Biolabs) were used.

treatment_protocol: Bicuculline (50 µM) applied together with 4-aminopyridine (250 µM) (Bic/4AP)

value: forebrain neuron-like, heterogenous

tag: passages

value: from iPSC passages 30-40

tag: iPSc line

value: iPS D1

tag: developmental stage

value: postmitotic


title: SC-8

value: Spinal Cord

value: 11 weeks

tag: antibody


title: ChIP-seq from intestine (ENCLB410BSQ)

description:
https://www.encodeproject.org/experiments/ENCSR002ZAG/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIP-seq on postnatal 0 day mouse intestine
experiment encode accession: ENCSR002ZAG
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR862ZBY
encode release date: 2016-05-18
lab: Richard Myers, HAIB
library encode accession: ENCLB410BSQ

value: tissue


title: ChIP-seq from HEK293T (ENCLB013ZSX)

description:
https://www.encodeproject.org/experiments/ENCSR090ZDO/
***************
biological replicate number: 2
technical replicate number: 1
description: SUZ12 ChIP-seq on human HEK293T
experiment encode accession: ENCSR090ZDO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR272LXW
encode release date: 2016-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB013ZSX
size range: 450-650

source_name: Homo sapiens HEK293T immortalized cell line

tag: line

value: immortalized cell line

value: embryonic

value: unknown

value: female

value: Michael Snyder, Stanford

value: ENCBS582KZL at ENCODE; https://www.encodeproject.org/ENCBS582KZL/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: hiPSCd neuron-only treated with Bic/4AP for 4 h Hs_Bic-4AP_4h_1

description: polyA purified


title: hiPSCd neuron-only treated with Bic/4AP for 4 h Hs_Bic-4AP_4h_4

description: polyA purified


title: SC-6


title: SC-4


title: hiPSCd neuron-only treated with Bic/4AP for 1 h Hs_Bic-4AP_1h_4

description: polyA purified


title: ChIP-seq from liver (ENCLB312QXP)

description:
https://www.encodeproject.org/experiments/ENCSR041SMK/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIP-seq on postnatal 0 day mouse liver
experiment encode accession: ENCSR041SMK
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR014GMV
encode release date: 2016-05-18
lab: Richard Myers, HAIB
library encode accession: ENCLB312QXP

value: CTCF

value: liver

tag: description

value: pulverized livers pooled from multiple dissections of postnatal 0 day mice

value: postnatal

value: 0 day

value: not collected

value: Richard Myers, HAIB

value: ENCBS152FNH at ENCODE; https://www.encodeproject.org/ENCBS152FNH/


title: ChIP-seq from K562 (ENCLB687SDX)

description:
https://www.encodeproject.org/experiments/ENCSR004GKA/
***************
biological replicate number: 2
technical replicate number: 1
description: ZEB2 ChIP-seq on human K562
experiment encode accession: ENCSR004GKA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB687SDX
size range: 450-650

source_name: Homo sapiens K562 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

tag: biosample encode accession

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS603CUX at ENCODE; https://www.encodeproject.org/ENCBS603CUX/

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: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: ChIP-seq from HEK293T (ENCLB924BZQ)

description:
https://www.encodeproject.org/experiments/ENCSR090ZDO/
***************
biological replicate number: 1
technical replicate number: 1
description: SUZ12 ChIP-seq on human HEK293T
experiment encode accession: ENCSR090ZDO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR272LXW
encode release date: 2016-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB924BZQ
size range: 450-650

value: immortalized cell line

tag: dev stage

value: embryonic

value: female

value: unknown

value: Michael Snyder, Stanford

value: ENCBS323RYE at ENCODE; https://www.encodeproject.org/ENCBS323RYE/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: Ganglionic Eminence

value: Ganglionic Eminence

value: 8 weeks, 6 days


title: eCLIP from HepG2 (ENCLB086ERJ)

description:
https://www.encodeproject.org/experiments/ENCSR090VXV/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against DDX3X
experiment encode accession: ENCSR090VXV
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB086ERJ
size range: 175-300

source_name: Homo sapiens HepG2 immortalized cell line

value: Control

value: child

tag: age

value: 15 year

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS362ASG at ENCODE; https://www.encodeproject.org/ENCBS362ASG/

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: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: eCLIP from HepG2 (ENCLB238HOU)

description:
https://www.encodeproject.org/experiments/ENCSR097NEE/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against PPIG
experiment encode accession: ENCSR097NEE
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR445LJH
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB238HOU
size range: 175-300

value: PPIG

value: immortalized cell line

tag: Sex


title: hiPSCd neuron-only treated with Bic/4AP for 1 h Hs_Bic-4AP_1h_3

description: polyA purified

value: forebrain neuron-like, heterogenous

value: from iPSC passages 30-40

value: iPS D1

value: postmitotic


title: hiPSCd neuron-only treated with Bic/4AP for 1 h Hs_Bic-4AP_1h_2

description: polyA purified


title: SC-2

value: Spinal Cord

value: 11 weeks


title: eCLIP from HepG2 (ENCLB696VPE)

description:
https://www.encodeproject.org/experiments/ENCSR081WUU/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against TBRG4
experiment encode accession: ENCSR081WUU
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB696VPE
size range: 175-300

value: Control

value: child

tag: lab

value: ENCBS621TAB at ENCODE; https://www.encodeproject.org/ENCBS621TAB/


title: SC-10


title: eCLIP from HepG2 (ENCLB139UVG)

description:
https://www.encodeproject.org/experiments/ENCSR080OLK/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against ILF3
experiment encode accession: ENCSR080OLK
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-08-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB139UVG
size range: 175-300

value: 15 year

value: male

value: Gene Yeo, UCSD

tag: health state


title: hiPSCd neuron-only untreated control Hs_CNTR_3

description: polyA purified


title: hiPSCd neuron-only untreated control Hs_CNTR_4

description: polyA purified


title: HB-4

value: Hindbrain


title: hiPSCd neuron-only treated with Bic/4AP for 1 h Hs_Bic-4AP_1h_1

description: polyA purified


title: hNES-WT-3

description: Processed data in hg38.d10.Repeats.uniqID.UniqueReads.NOT.IN.EXON.final.txt

source_name: hNES cell culture

growth_protocol: AF22 (iPS-derived, hNES) were cultured in DMEM/F12 (Thermo Fisher Scientific) supplemented with Glutamine (2mM, Sigma), Penicillin/Streptomycin (1x, Gibco), N2 supplement (1x, Thermo Fisher Scientific), B27 (0.05x, Invitrogen) , EGF and FGF2 (both 10ng/ml, Thermo Fisher Scientific). Cells were grown on NuncTM T25 or T75 flasks pre-coated with Poly L-Ornithine (15µg/ml, Sigma) and Laminin (2mg/ml, Sigma).  Cells were passaged every 2-3 days using TryplLETM Express enzyme (Life Technologies) and Defined Trypsin Inhibitor (Life Technologies) and plated at a density of 6x104 per cm2.

treatment_protocol: Cells were transduced with an MOI 1 and allowed to expand 10days prior to FACS (FACSAria, BD sciences). GFP+ cells were snap frozen before isolation of RNA.

value: iPS-derived neural progenitor cells

tag: genotype

value: WT


title: hNES-WT-2


title: ChIP-seq from K562 (ENCLB140LPS)

description:
https://www.encodeproject.org/experiments/ENCSR065XVO/
***************
biological replicate number: 2
technical replicate number: 1
description: CHAMP1 ChIP-seq on human K562
experiment encode accession: ENCSR065XVO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2016-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB140LPS
size range: 450-650

value: adult

value: 53 year

value: female

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)

tag: link

value: ENCBS719UQU at ENCODE; https://www.encodeproject.org/ENCBS719UQU/

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

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


title: ChIP-seq from K562 (ENCLB935DOS)

description:
https://www.encodeproject.org/experiments/ENCSR065XVO/
***************
biological replicate number: 1
technical replicate number: 1
description: CHAMP1 ChIP-seq on human K562
experiment encode accession: ENCSR065XVO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2016-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB935DOS
size range: 450-650

value: immortalized cell line

value: ENCBS125ACM at ENCODE; https://www.encodeproject.org/ENCBS125ACM/


title: hNES-WT-1

tag: cell type


title: Sai-WT-2

source_name: Sai cell culture

growth_protocol: Sai2 (fetal-derived) were cultured in DMEM/F12 (Thermo Fisher Scientific) supplemented with Glutamine (2mM, Sigma), Penicillin/Streptomycin (1x, Gibco), N2 supplement (1x, Thermo Fisher Scientific), B27 (0.05x, Invitrogen) , EGF and FGF2 (both 10ng/ml, Thermo Fisher Scientific). Cells were grown on NuncTM T25 or T75 flasks pre-coated with Poly L-Ornithine (15µg/ml, Sigma) and Laminin (2mg/ml, Sigma).  Cells were passaged every 2-3 days using TryplLETM Express enzyme (Life Technologies) and Defined Trypsin Inhibitor (Life Technologies) and plated at a density of 6x104 per cm2.

value: fetal-derived neural progenitor cells


title: hiPSCd neuron-only untreated control Hs_CNTR_1

description: polyA purified

value: forebrain neuron-like, heterogenous

value: from iPSC passages 30-40

value: iPS D1

value: postmitotic


title: eCLIP from HepG2 (ENCLB370HZY)

description:
https://www.encodeproject.org/experiments/ENCSR056RZV/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against FUBP3
experiment encode accession: ENCSR056RZV
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-09-21
lab: Gene Yeo, UCSD
library encode accession: ENCLB370HZY
size range: 175-300

value: Control

value: child

value: 15 year

value: male

tag: passage number

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS492SDY at ENCODE; https://www.encodeproject.org/ENCBS492SDY/

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: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: eCLIP from K562 (ENCLB640UDS)

description:
https://www.encodeproject.org/experiments/ENCSR051IXX/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against RBFOX2
experiment encode accession: ENCSR051IXX
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-09-21
lab: Gene Yeo, UCSD
library encode accession: ENCLB640UDS
size range: 175-300

value: immortalized cell line

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS175JIH at ENCODE; https://www.encodeproject.org/ENCBS175JIH/

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

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


title: Sai-WT-3

value: fetal-derived neural progenitor cells

value: WT


title: hiPSCd neuron-only untreated control Hs_CNTR_2

description: polyA purified

value: forebrain neuron-like, heterogenous

value: from iPSC passages 30-40

value: iPS D1

value: postmitotic


title: Sai-WT-1


title: TRIM28-KD_hNES-3

value: iPS-derived neural progenitor cells

value: TRIM-28 KD


title: TRIM28-KD_Sai-3


title: eCLIP from K562 (ENCLB274AUW)

description:
https://www.encodeproject.org/experiments/ENCSR057DWB/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against TIA1
experiment encode accession: ENCSR057DWB
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR356GCJ
encode release date: 2016-08-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB274AUW
size range: 175-300

value: Gene Yeo, UCSD

value: ENCBS126AJR at ENCODE; https://www.encodeproject.org/ENCBS126AJR/

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


title: TRIM28-KD_hNES-1


title: TRIM28-KD_Sai-2


title: eCLIP from HepG2 (ENCLB334YPG)

description:
https://www.encodeproject.org/experiments/ENCSR041NUV/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against EIF3D
experiment encode accession: ENCSR041NUV
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR755PSW
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB334YPG
size range: 175-300

value: immortalized cell line

value: child

value: 15 year

value: male

value: hepatocellular carcinoma

value: ENCBS621TAB at ENCODE; https://www.encodeproject.org/ENCBS621TAB/

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

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


title: eCLIP from HepG2 (ENCLB100IZV)

description:
https://www.encodeproject.org/experiments/ENCSR041NUV/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against EIF3D
experiment encode accession: ENCSR041NUV
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR755PSW
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB100IZV
size range: 175-300

value: ENCBS492SDY at ENCODE; https://www.encodeproject.org/ENCBS492SDY/


title: TRIM28-KD_hNES-2


title: TRIM28-KD_Sai-1

value: fetal-derived neural progenitor cells


title: eCLIP from HepG2 (ENCLB725YBH)

description:
https://www.encodeproject.org/experiments/ENCSR023UHL/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against FASTKD2
experiment encode accession: ENCSR023UHL
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR671FKF
encode release date: 2016-08-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB725YBH
size range: 175-300

value: ENCBS074YUC at ENCODE; https://www.encodeproject.org/ENCBS074YUC/


title: eCLIP from HepG2 (ENCLB560DJG)

description:
https://www.encodeproject.org/experiments/ENCSR023UHL/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against FASTKD2
experiment encode accession: ENCSR023UHL
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR671FKF
encode release date: 2016-08-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB560DJG
size range: 175-300


title: eCLIP from HepG2 (ENCLB004PMM)

description:
https://www.encodeproject.org/experiments/ENCSR018RVZ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against NCBP2
experiment encode accession: ENCSR018RVZ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR257OYO
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB004PMM
size range: 175-300

value: ENCBS362ASG at ENCODE; https://www.encodeproject.org/ENCBS362ASG/


title: eCLIP from K562 (ENCLB868TFN)

description:
https://www.encodeproject.org/experiments/ENCSR057DWB/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against TIA1
experiment encode accession: ENCSR057DWB
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR356GCJ
encode release date: 2016-08-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB868TFN
size range: 175-300

value: adult

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS549CIX at ENCODE; https://www.encodeproject.org/ENCBS549CIX/

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

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


title: tRNA E18.5 WT4

status: Public on Jan 02 2017

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

description: transfer RNA

data_processing:
For tRNA-seq data, reads were quality-trimmed (removing bases from read ends with Q > 20) and adapters were trimmed. Reads were aligned to the mouse reference genome (UCSC mm10) with options '-m 1 -v 2'.
For tRNA-seq data, processed data files generated by bedtools 'featureCounts' (subread package) from bowtie alignments.
Genome_build: GRCm28/UCSC mm10
Supplementary_files_format_and_content: [.txt] FeatureCounts output files

source_name: tRNA E18.5 WT

extract_protocol:
Total RNA was extracted using Trizol reagents (Thermo Fisher Scientific) from snap‐frozen material and treated with DNase (Turbo DNase, Thermo Fisher Scientific). Ribosomal RNA was removed using Ribo‐zero (Epicentre, Illumina). And tRNA was isolated by using MirVana kit (Thermo Fisher Scientific).
tRNA sequencing library preparation: size‐selected or with the MirVana Isolation Kit (Thermo Fisher Scientific) for 20‐ to 200‐base‐paired RNAs. tRNAs were then de‐aminoacylated in 0.1 M Tris–HCl pH 9.0 and 1 mM EDTA for 30 min at 37°C. tRNA libraries were performed according to TruSeq Small RNA Preparation Kit (Illumina) instructions. Briefly, 3′ adenylated and 5′ phosphorylated adapters suitable for Illumina RNA sequencing were ligated to 300 ng of RNA obtained after de‐aminoacylation. RNA was reverse‐transcribed at 50°C for 1 h (SuperScript III cDNA synthesis kit,Thermo Fisher Scientific), followed by 16‐cycle PCR amplification with Phusion DNA polymerase (Thermo Fisher Scientific) and size‐selected (140–210 base pairs) before sequencing.
Small RNA Illumina library preparation protocols were used.

tag: strain

value: embryo

tag: tissue

value: brain frontal lobe

tag: genotype/variation

value: WT


title: tRNA E18.5 WT3

description: transfer RNA

tag: developmental stage


title: eCLIP from HepG2 (ENCLB278TOU)

description:
https://www.encodeproject.org/experiments/ENCSR018RVZ/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against NCBP2
experiment encode accession: ENCSR018RVZ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR257OYO
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB278TOU
size range: 175-300

tag: antibody

value: immortalized cell line

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: Gene Yeo, UCSD

value: ENCBS308ZPA at ENCODE; https://www.encodeproject.org/ENCBS308ZPA/

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


title: tRNA E18.5 WT2

description: transfer RNA


title: tRNA E18.5 WT1

description: transfer RNA


title: tRNA E18.5 NSun2 -/- 4

description: transfer RNA

source_name: tRNA E18.5 NSun2 -/-

value: NSun2 -/-


title: tRNA E18.5 NSun2 -/- 2

description: transfer RNA


title: tRNA E18.5 NSun2 -/- 1

description: transfer RNA


title: tRNA E13.5 WT1

description: transfer RNA

source_name: tRNA E13.5 WT


title: bye1 deletion NET-seq

city: Boston

first: Stirling

last: Churchman

state: MA

address: NRB Rm 356, 77 Ave Loius Pasteur

department: Genetics

institute: Harvard Medical School

description: nascent RNA isolated by IP against Rpb3-3x FLAG affinity label

data_processing:
Libraries were sequened in 76 base pair reads for all NextSeq libraires. For reads shorter than 75 basepairs respectively the adapter sequenice  (ATCTCGTATGCCGTCTTCTGCTTG) was trimmed from the fastq files and files were filtered using PrinSeq version prinseq-lite-0.20.2 (http://prinseq.sourceforge.net).
The linker contained a molecular barcode with a random hexamer sequence. These random hexamers were removed using custom python scripts.
Data were then aligned to the SacCer3 genome using the TopHat2 aligner v2.0.5 and reverse transcription mispriming events are identified and removed where molecular barcode sequences correspond exactly to the genomic sequence adjacent to the aligned read.
For NET-seq only the position corresponding to the 5’ end of the sequencing read (after removal of the barcode), which corresponds to the 3’ end of the nascent RNA fragment, is recorded with a custom python script using HTSeq package in python .
NET-seq coverage files in bedgraph format are normalized by the number of uniquely mapping 10^6 reads.
Genome_build: sacCer3
Supplementary_files_format_and_content: bedgraph: Chromosome, Start, End, Score

organism: Saccharomyces cerevisiae

source_name: yeast BY4741, mid-exponential phase

growth_protocol: Yeast strains were grown in YPD at 30°C with shaking from an initial OD of 0.05 to mid-log phase with an OD of 0.6-0.8.

extract_protocol:
For NET-seq frozen cells were cryogenically pulverized for lysis and nascent RNA was isolated via an immunoprecipitation at 4°C of Rpb3-3xFLAG and purified using the miRNeasy kit (Qiagen, 217004).
For NET-seq a preadenylated RNA linker was ligated onto the 3’ end of the immunoprecipitated RNA. Fragmentation of the ligated samples by alkaline hydrolysis followed by a size selection after electrophoresis on a polyacrylamide gel allowed for the final DNA library to contain inserts of a narrow range. cDNA synthesis by reverse transcription (SuperScriptsIII (Invitrogen)) was performed with a long 5’ phosohorylated primer split by two 18 carbon spacers. Circularization of the RT product was performed with CircLigase (Epicentre) according to the manufacturer’s directions. The PCR was performed directly on the circularized product resulting in DNA with Illumina cluster generation sequences on each end and a sequencing primer binding site positioned so that sequencing would start at the 3’ end. DNA was purified from a PCR reaction that had not reached saturation (~8-10 cycles) by band extraction from a polyacrylamide gel. DNA was sequenced on the Illumina NextSeq 500 according to the manufacturer’s instructions in 75 base pair reads.

value: BY4741, rpb3::rpb3-3xFLAG NAT, bye1::HIS3

tag: library strategy

value: NET-seq


title: bre1 deletion NET-seq

value: BY4741, rpb3::rpb3-3xFLAG NAT, bre1::HIS3


title: paf1 deletion NET-seq

value: BY4741, rpb3::rpb3-3xFLAG NAT, paf1::HIS3


title: node

status: Public on Jan 01 2017

city: Shanghai

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

country: China

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

data_processing:
The rna-seq data was monitored by the Fast-QC software
The rna-seq reads were alignment by the TopHat software
The rna-seq reads were assembled by the Cufflink software. The expression levels were estimated by Cufflink software.
Genome_build: MSU Rice Genome Annotation, Release 7
Supplementary_files_format_and_content: The processed data contained the FPKM calculated by TopHat

organism: Oryza sativa

source_name: node

growth_protocol: Rice was grown at 29ºC with a 12-h light (~ 80000 Lux) and 12-h dark photoperiod in the greenhouse or plant chamber.

extract_protocol:
RNA extraction using Trizol protocols
paired-end library

value: nodes I and II


title: stem

source_name: stem

value: stem


title: leaf blade

source_name: leaf blade

value: leaf blade


title: ChIP-seq from HEK293 (ENCLB485LCK)

description:
https://www.encodeproject.org/experiments/ENCSR072LQF/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF76 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR072LQF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB485LCK
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF76 fusion protein

tag: line

tag: description

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF76 under the control of a CMV promoter.

value: embryonic

value: unknown

value: female

value: Michael Snyder, Stanford

value: ENCBS889BJN at ENCODE; https://www.encodeproject.org/ENCBS889BJN/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: tRNA E18.5 NSun2 -/- 3

description: transfer RNA

value: embryo

value: brain frontal lobe


title: Wt – 120 min

city: Marburg

first: Patrick

last: Sobetzko

address: Hans-Meerwein-Straße

department: Department of Chromosome Biology

institute: Philipps-Universität Marburg LOEWE-Zentrum für Synthetische Mikrobiologie

description:
temporal gene expression wildtype 120 min
sample grown in LB in a fermenter @ 37°C, constant pH 7.5 and air saturated partial oxygen pressure

data_processing:
GATC software for read mapping on MG1655
verified with in-house pipeline
Gene wise natural spline interpolation of temporal data from initial time points to a dataset of 10 minutes steps (see processed data files). Expression values at the time points of the raw data are not affected by the interpolation.
gene expression sum normalized to 1 at each time point
Supplementary_files_format_and_content: expression of genes in time, rows = genes, cols = time points

organism: Escherichia coli

source_name: Escherichia coli CSH50

growth_protocol: LB medium, 37°C, airated, constant pH 7.5

extract_protocol:
RNA extraction Kit
GATC

value: wildtype

tag: time

value: 120 minutes


title: Wt – 300 min

description:
temporal gene expression wildtype 300 min
sample grown in LB in a fermenter @ 37°C, constant pH 7.5 and air saturated partial oxygen pressure

value: 300 minutes


title: Wt – 60 min

description:
temporal gene expression wildtype 60 min
sample grown in LB in a fermenter @ 37°C, constant pH 7.5 and air saturated partial oxygen pressure

value: 60 minutes


title: Wt – 180 min

description:
temporal gene expression wildtype 180 min
sample grown in LB in a fermenter @ 37°C, constant pH 7.5 and air saturated partial oxygen pressure

value: 180 minutes


title: Hns -180 min

description:
temporal gene expression hns mutant 180 min
sample grown in LB in a fermenter @ 37°C, constant pH 7.5 and air saturated partial oxygen pressure

source_name: Escherichia coli CSH50 Δhns

value: delta-hns


title: Hns – 60 min

description:
temporal gene expression hns mutant 60 min
sample grown in LB in a fermenter @ 37°C, constant pH 7.5 and air saturated partial oxygen pressure


title: Fis – 180 min

description:
temporal gene expression fis mutant 180 min
sample grown in LB in a fermenter @ 37°C, constant pH 7.5 and air saturated partial oxygen pressure

source_name: Escherichia coli CSH50 Δfis

value: delta-fis


title: Fis – 420 min

description:
temporal gene expression fis mutant 420 min
sample grown in LB in a fermenter @ 37°C, constant pH 7.5 and air saturated partial oxygen pressure

value: 420 minutes


title: Wt – 420 min

description:
temporal gene expression wildtype 420 min
sample grown in LB in a fermenter @ 37°C, constant pH 7.5 and air saturated partial oxygen pressure


title: Hns – 420 min

description:
temporal gene expression hns mutant 420 min
sample grown in LB in a fermenter @ 37°C, constant pH 7.5 and air saturated partial oxygen pressure


title: Fis – 60 min

description:
temporal gene expression fis mutant 60 min
sample grown in LB in a fermenter @ 37°C, constant pH 7.5 and air saturated partial oxygen pressure


title: Fis – 120 min

description:
temporal gene expression fis mutant 120 min
sample grown in LB in a fermenter @ 37°C, constant pH 7.5 and air saturated partial oxygen pressure


title: Hns – 120 min

description:
temporal gene expression hns mutant 120 min
sample grown in LB in a fermenter @ 37°C, constant pH 7.5 and air saturated partial oxygen pressure


title: 455

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

country: Canada

institute: University of Alberta

data_processing:
All the reads were demultiplexed according to their index sequences using CASAVA version 1.8 (Illumina)
Paired end fastq files were mapped to refenrence genome by using Tophat 2.0.10 with default parameters.
The output mapping files from the TopHat2 alignment, along with the GTF file from ENSEMBL (http://uswest.ensembl.org/) rat gene annotation v75.30, were used in the htseq-count (http://www-huber.embl.de/users/anders/HTSeq/) to count the total number of reads mapped to each gene.
The expression level of mRNAs in each library was obtained by normalizing reads number to counts per million reads (CPM): CPM = (gene reads number / total mapped reads number per library) × 1,000,000.
Genome_build: UMD3.1
Supplementary_files_format_and_content: Tab-delimited text files include CPM values for each Sample

organism: Bos taurus

source_name: Rumen

extract_protocol:
rumen tissue samples were frozen on liquid nitrogen, and RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-200-0012) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: residual feed intake

value: Low RFI

value: rumen epithelial tissue


title: 451


title: tRNA E13.5 NSun2 -/- 1

description: transfer RNA

source_name: tRNA E13.5 NSun2 -/-

tag: age

value: NSun2 -/-


title: rtf1 deletion NET-seq

value: BY4741, rpb3::rpb3-3xFLAG NAT, rtf1::HIS3

value: NET-seq


title: 409


title: tRNA E13.5 NSun2 -/- 2

description: transfer RNA


title: 317


title: 299


title: 281


title: 271


title: 219


title: 205

value: High RFI


title: 201


title: Rbp4_L5_500cell_rep3

city: Seattle

first: Lucas

middle: T

last: Gray

state: WA

address: 615 Westlake Ave N

department: Molecular Genetics

institute: Allen Institute for Brain Science

data_processing:
library strategy: ATAC-seq
Reads in FASTQ format were aligned to GRCm38 (mm10) using Bowtie v1.1.0 (Langmead et al., 2009) with settings –m 1 –X 2000 –chunkmbs 256 in paired-end mode.
Unaligned reads were processed with the Trim galore wrapper for Cutadapt (Martin, 2011) to remove Nextera primer sequences (settings: --nextera –paired –three_prime_clip_R1 1 –three_prime_clip_R2 1), and were then aligned again using Bowtie (settings –m 1 –X 2000 -3 1 –chunkmbs 256).
The Samtools collection (Li et al., 2009) was used to sort, remove PCR duplicates (rmdup), index BAM files, and calculate library statistics (flagstat). We used CollectInsertSizeMetrics.jar from Picard v1.110 (Broad Institute 2015) to analyze fragment size statistics, and preseq v0.1.0 (Daley and Smith, 2013) to analyze library sequencing saturation.
To downsample BAM files to 3.2M reads, the data were sorted by name instead of location using Samtools sort in SAM format, then R sample() was used to select random read pairs, and a custom Perl script then filtered the selected reads. Samtools view was then used to convert files back to BAM format.
After downsampling, aligned reads were analyzed for peak and region enrichment of open chromatin using HotSpot v4.1 (John et al., 2011) with default settings (FDR < 0.01).
DiffBind v1.16.3 (Stark and Brown, 2011,Ross-Innes et al., 2012) was used to calculate merged peak locations, based on the outer boundaries of overlapping peaks from all cell lines analyzed, and peak accessibility scores for each replicate were calculated using DiffBind with the default setting DBA_SCORE_TMM_MINUS_EFFECTIVE, which uses trimmed mean of M-values (TMM) normalization (Robinson and Oshlack, 2010) built into the edgeR package (Robinson et al., 2010) using read counts minus control (genomic) read counts and full library size.
For overall views of aligned data from each cell class, we built merged BAM files using samtools merge and sort.
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak: chr, start, and end coordinates from HotSpot peak results
Supplementary_files_format_and_content: broadPeak: chr, start, and end coordinates form HotSpot region results
Supplementary_files_format_and_content: bed: merged peak locations in BED format as calculated by DiffBind
Supplementary_files_format_and_content: tmmScores: A matrix of TMM scores for each merged peak in each sample as calculated by DiffBind

growth_protocol: Animals were provided food and water ad libitum and were maintained at a regular 12 h day/night cycle at no more than 5 adult animals per cage. Animals were maintained on the C57BL/6J background.

extract_protocol:
We used an isoflurane chamber to anesthetize adult male mice (P56 ± 3), decapitated them, removed the brains, and transferred them immediately to freshly prepared, ice-cold artificial cerebrospinal fluid (ACSF: 126 mM NaCl, 20 mM NaHCO3, 20 mM dextrose, 3 mM KCl, 1.25 mM NaH2PO4, 2 mM CaCl2, 2 mM mgCL2, 50 μM DL-AP5 sodium salt, 20 μM DNQX, and 0.1 μM tetrodotoxin, mixed then bubbled with 95% O2/5% CO2 carbogen gas). We sectioned the brains to generate 400 μm–thick sections using a Leica VT1000S vibratome with a chilled chamber, and immediately transferred the slices to a bubbled ACSF-containing chamberat room temperature. Individual slices of interest were microdissected in a Petri dish while submerged in ACSF under a fluorescence dissecting microscope. Dissected tissue was transferred to a microcentrifuge tube containing ACSF with 1 mg/mL pronase (Sigma, Cat#P6911) for 70 min at room temperature. After incubation, with tissue pieces settled at the bottom of the tubes, ACSF with pronase was exchanged twice with ACSF containing 1% fetal bovine serum (FBS). We next dissociated the tissue into a single-cell suspension by trituration through Pasteur pipettes with polished openings of 600 μm-, 300 μm-, and 150 μm-diameter. 500 cells were sorted into a well of an 8-well PCR strip containing 2 μL ACSF on a BD FACSAriaII SORP with a 130 μm nozzle at 10 psi sheath pressure, and in the single-cell sorting mode. We excluded dead cells by labelling with DAPI (DAPI*2HCl, Life Technologies Cat#D1306) added to the single-cell suspension at 2 ng/mL. We retained only cells that had high tdTomato fluorescence and low DAPI labeling.
Immediately after FACS collection, cells were lysed with 25 µL Lysis Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1 % IGEPAL CA-630). Nuclei were pelleted by centrifugation at 500 x g for 30 minutes at 4 °C in a refrigerated microcentrifuge. After pelleting, the supernatant was removed and cells were resuspended by repeated pipetting in 25 µL Reaction Mix (12.5 µL Nextera TD Buffer, 2 µL Nextera TD Enzyme, and 10.5 µL water). Samples were then tagmented by incubation at 37 °C for 1 hour on a heat block. After tagmentation, the reactions were stopped with addition of 5 µL Cleanup Buffer (900 mM NaCl, 300 mM EDTA), 2 µL 5% SDS, and 2 µL Proteinase K and incubation at 40 °C for 30 min. Tagmented DNA was purified using AMPure XP beads at a ratio of 1.8:1 beads to reaction volume, with a final resuspension volume of 11 µL. For indexing and amplification, we added 15 µL KAPA HotStart Ready mix (Kapa Biosystems, Cat# KK2602) and 2 µL each of Nextera i5 and i7 indexed amplification primers. These samples were incubated at 72 °C for 3 minutes, then PCR amplified as follows: 95 °C for 3 min; 9 cycles of 98 °C for 20 sec, 65 °C for 15 sec, and 72 °C for 15 sec; 72 °C final extension for 1 min. Samples were then purified using AMPure XP as above, re-amplified for additional 9 cycles under the same conditions, and then purified once more as before using Ampure XP beads to produce 11 µL final volume. Library quality and quantity were assessed using 1 µL of the final, purified DNA on a BioAnalyzer High Sensitivity DNA chip. For mES cell populations, ES cells grown on mouse embryonic fibroblast (MEF) feeders were passaged onto gelatin plates to dilute/remove feeder cells, and they were made into single-cell suspensions by treatment with Trypsin-EDTA (Thermo Fisher Scientific, Cat#25300054). Cells were washed twice in PBS with 1% FBS, then were resuspended in PBS with 1% FBS and 2 ng/mL DAPI. 500-cell populations of DAPI-negative ES cells were sorted into individual wells of an 8-well PCR strip containing 2 uL of PBS.

tag: strain background

tag: age (days)

tag: cre driver

tag: reporter

tag: broad class

value: Glutamatergic

tag: cortical layer

tag: tissue/cell type

value: Visual cortex


title: 155

tag: tissue


title: 115


title: 55


title: 51


title: 345


title: 33


title: 11


title: MPH12_Kit-K5-

city: Bethesda

first: Matthew

middle: P

last: Hoffman

state: MD

address: 30 Convent Dr MSC4370

institute: NIDCR

data_processing:
Read QC analysis: FastQC
read mapping, STAR v2.4.2a with the following options:  --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None  --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 5 --alignSJDBoverhangMin 3 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 21 –alignIntronMax 0 --alignMatesGapMax 0
bam grooming: Sorting, Readgroup addition and duplicate marking using Picard Tools v1.129
Gene quantification. Per gene raw read counts were generated using Subread's featureCounts software v1.4.6-p3. Settings: -p -t exon -g gene_name
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: gene quantifications (raw read counts) in tab-delimited .txt format

source_name: Submandibular gland epithelal cells E15 (Ecad+;Kit-;K5-venus-)

extract_protocol:
RNA was isloated using Ambions RNAqueous-4PCR kit and were treated with DNase (DNA-free Kit, Ambion).
Total RNA was extracted from epithelial cells sorted by FACS analysis and RNAseq performed by Cofactor Genomics (www.cofactorgenomics.com). Single-ended reads (50 nt in length) were produced using Illumina sequencer (Illumina). Reads were mapped to the GRCm38/mm10 using the STAR 2.4.2a aligner and gene counts generated with Subread's featureCounts tool.

treatment_protocol: Fluorescence-activated cell sorting: SMGs were prepared for FACS analysis as previously described (Knox SM, et al,. Parasympathetic innervation maintains epithelial progenitor cells during salivary organogenesis. Science 329, 1645-1647 (2010). Anti-E-cadherin APC (FAB7481A, R&D Systems) and anti-Kit PE (BD Biosciences) were also used. Fluorescence levels were analyzed using FlowJo (Tree Star).

tag: strain

value: embryonic day 15

value: submandibular salivary glands

tag: cell type

value: FACs sorted epithelial cells

tag: cell subtype


title: MPH11_Kit-K5+

source_name: Submandibular gland epithelal cells E15 (Ecad+;Kit-;K5-venus+)

tag: developmental stage


title: MPH10_Kit+K5-

source_name: Submandibular gland epithelal cells E15 (Ecad+;Kit+;K5-venus-)


title: MPH7_Kit-K5+


title: 47


title: MPH6_Kit+K5-


title: MPH4_Kit-K5-