title: eCLIP from K562 (ENCLB812WPR)

description:
https://www.encodeproject.org/experiments/ENCSR486QAE/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against RPS5
experiment encode accession: ENCSR486QAE
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB812WPR
size range: 175-300

value: Control

value: immortalized cell line

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS318IMK at ENCODE; https://www.encodeproject.org/ENCBS318IMK/

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 (ENCLB183AFP)

status: Public on Jan 04 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/ENCSR502OEK/
***************
biological replicate number: 1
technical replicate number: 1
description: ELF1 ChIP-seq on human K562
experiment encode accession: ENCSR502OEK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB183AFP
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 K562 immortalized cell line

tag: antibody

tag: line

tag: description

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

tag: dev stage

tag: age

tag: Sex

value: female

tag: lab

value: Michael Snyder, Stanford

tag: health state

tag: link

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

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


title: eCLIP from K562 (ENCLB075CXB)

description:
https://www.encodeproject.org/experiments/ENCSR484LTQ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against NCBP2
experiment encode accession: ENCSR484LTQ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR921SHJ
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB075CXB
size range: 175-300

library_source: transcriptomic

molecule: total RNA

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

tag: passage number

value: Gene Yeo, UCSD

value: ENCBS517UIR at ENCODE; https://www.encodeproject.org/ENCBS517UIR/

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


title: eCLIP from K562 (ENCLB411ZVM)

description:
https://www.encodeproject.org/experiments/ENCSR484LTQ/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against NCBP2
experiment encode accession: ENCSR484LTQ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR921SHJ
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB411ZVM
size range: 175-300

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


title: ChIP-seq from K562 (ENCLB181VJH)

description:
https://www.encodeproject.org/experiments/ENCSR502OEK/
***************
biological replicate number: 2
technical replicate number: 1
description: ELF1 ChIP-seq on human K562
experiment encode accession: ENCSR502OEK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB181VJH
size range: 450-650

value: ENCBS734NZL at ENCODE; https://www.encodeproject.org/ENCBS734NZL/


title: eCLIP from K562 (ENCLB283UYZ)

description:
https://www.encodeproject.org/experiments/ENCSR502NKG/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against HLTF
experiment encode accession: ENCSR502NKG
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB283UYZ
size range: 175-300

value: Control

value: immortalized cell line


title: D. yak male 2

first: Jin Billy

last: Li

state: California

address: 300 Pasteur Drive. Alway M303

department: Genetics

institute: Stanford University

data_processing:
Primer sequences were trimmed off paired or single-end sequencing reads before mapping using Tophat.
RNA editing levels were calculated as the fraction of G reads at each site. Only sites covered by 50 reads were used
Genome_build: dm3/droSim1/droYak2/droAna2/dp3/droVir3
Supplementary_files_format_and_content: Processed data files are tab-delineated with a header line and include editing levels of different Drosophila strains and species.

organism: Drosophila yakuba

source_name: male whole body

growth_protocol: Whole bodies of adult male and female flies aged 5 days old were collected.

extract_protocol:
Total RNA was extracted using the Rneasy Kit (Qiagen). After DNase I treatment, 3 ug of total RNA was used to synthesize the cDNA using iScript Advanced cDNA Synthesis Kit (Bio-Rad). cDNA was purified using the MinElute PCR Purification Kit (Qiagen)
Libraries were prepared by pooling all of the PCR products for a particular sample and barcoding them uniquely using a 15 cycle PCR reaction.
microfluidic multiplex PCR (mmPCR-seq) or targeted sequencing

tag: developmental stage

value: 5 day old adult

tag: replicate

tag: library strategy

value: mmPCR-seq

tag: strain


title: ChIP-seq from HEK293 (ENCLB315SEM)

description:
https://www.encodeproject.org/experiments/ENCSR499QIO/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq on eGFP-ZSCAN4 tagged human HEK293 cells.
experiment encode accession: ENCSR499QIO
assay title: ChIP-seq
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB315SEM
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZSCAN4 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZSCAN4 under the control of a CMV promoter.

value: embryonic

value: unknown

value: ENCBS401QNO at ENCODE; https://www.encodeproject.org/ENCBS401QNO/

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


title: eCLIP from HepG2 (ENCLB578WMP)

description:
https://www.encodeproject.org/experiments/ENCSR479XOI/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against NKRF
experiment encode accession: ENCSR479XOI
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB578WMP
size range: 175-300

source_name: Homo sapiens HepG2 immortalized cell line

value: child

value: male

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: eCLIP from HepG2 (ENCLB078PCR)

description:
https://www.encodeproject.org/experiments/ENCSR499ZCU/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against SRSF1
experiment encode accession: ENCSR499ZCU
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB078PCR
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: Gene Yeo, UCSD

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

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


title: ChIP-seq from GM12878 (ENCLB675VMV)

description:
https://www.encodeproject.org/experiments/ENCSR469WII/
***************
biological replicate number: 2
technical replicate number: 1
description: BMI1 ChIP-seq on human GM12878
experiment encode accession: ENCSR469WII
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2016-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB675VMV
size range: 450-650

source_name: Homo sapiens GM12878 immortalized cell line

value: immortalized cell line

value: adult

value: female

value: Michael Snyder, Stanford

value: ENCBS607NAA at ENCODE; https://www.encodeproject.org/ENCBS607NAA/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: ChIP-seq from GM12878 (ENCLB194CMR)

description:
https://www.encodeproject.org/experiments/ENCSR469WII/
***************
biological replicate number: 1
technical replicate number: 1
description: BMI1 ChIP-seq on human GM12878
experiment encode accession: ENCSR469WII
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2016-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB194CMR
size range: 450-650

value: unknown

value: ENCBS436SAI at ENCODE; https://www.encodeproject.org/ENCBS436SAI/


title: eCLIP from HepG2 (ENCLB104YKZ)

description:
https://www.encodeproject.org/experiments/ENCSR497ANA/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against HNRNPC
experiment encode accession: ENCSR497ANA
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB104YKZ
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
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: child

value: male

value: ENCBS626BOT at ENCODE; https://www.encodeproject.org/ENCBS626BOT/


title: eCLIP from K562 (ENCLB413HWU)

description:
https://www.encodeproject.org/experiments/ENCSR496UBM/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against SF3B1
experiment encode accession: ENCSR496UBM
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-10-31
lab: Gene Yeo, UCSD
library encode accession: ENCLB413HWU
size range: 175-300

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS318IMK at ENCODE; https://www.encodeproject.org/ENCBS318IMK/

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 HEK293 (ENCLB446HCO)

description:
https://www.encodeproject.org/experiments/ENCSR461ZJT/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF501 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR461ZJT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR157LMX, ENCSR274OGE, ENCSR342AGU, ENCSR354FNX, ENCSR429LAP, ENCSR688NWK
encode release date: 2016-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB446HCO
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF501 fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF501 under the control of a CMV promoter.

value: embryonic

value: ENCBS207QGV at ENCODE; https://www.encodeproject.org/ENCBS207QGV/

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


title: D. yak female 2

source_name: female whole body

value: 5 day old adult

value: mmPCR-seq


title: ChIP-seq from HEK293 (ENCLB698DAK)

description:
https://www.encodeproject.org/experiments/ENCSR461ZJT/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF501 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR461ZJT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR157LMX, ENCSR274OGE, ENCSR342AGU, ENCSR354FNX, ENCSR429LAP, ENCSR688NWK
encode release date: 2016-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB698DAK
size range: 450-650

value: female

value: unknown

value: Michael Snyder, Stanford

value: ENCBS152WBM at ENCODE; https://www.encodeproject.org/ENCBS152WBM/


title: D. yak male 1


title: ChIP-seq from liver (ENCLB326KQI)

description:
https://www.encodeproject.org/experiments/ENCSR999LAC/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on e14.5 liver-mouse (fragmentation date:Tue Sep 30 2014 00:00:00 GMT-0500 (CDT)
experiment encode accession: ENCSR999LAC
assay title: ChIP-seq
encode release date: 2016-02-05
lab: Richard Myers, HAIB
library encode accession: ENCLB326KQI

organism: Mus musculus

source_name: Mus musculus strain B6NCrl liver tissue mixed sex embryo (14.5 days)

value: Control

value: liver

value: tissue

value: pulverized livers pooled from multiple dissections of embryonic 14.5 day mice

value: pooled male and female

value: Richard Myers, HAIB

value: ENCBS464EKT at ENCODE; https://www.encodeproject.org/ENCBS464EKT/

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


title: D. yak female 1


title: ChIP-seq from K562 (ENCLB047HZO)

description:
https://www.encodeproject.org/experiments/ENCSR494TDU/
***************
biological replicate number: 1
technical replicate number: 1
description: NRF1 ChIP-seq on human K562
experiment encode accession: ENCSR494TDU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB047HZO
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: ENCBS232KKV at ENCODE; https://www.encodeproject.org/ENCBS232KKV/

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 stomach (ENCLB578VSU)

description:
https://www.encodeproject.org/experiments/ENCSR993MMD/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on P0 stomach-mouse (fragmentation date:2015-08-26
experiment encode accession: ENCSR993MMD
assay title: ChIP-seq
encode release date: 2016-01-14
lab: Richard Myers, HAIB
library encode accession: ENCLB578VSU

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

value: Control

value: stomach

value: postnatal

value: 0 day

value: not collected

value: ENCBS551QZH at ENCODE; https://www.encodeproject.org/ENCBS551QZH/


title: ChIP-seq from K562 (ENCLB116QWY)

description:
https://www.encodeproject.org/experiments/ENCSR494TDU/
***************
biological replicate number: 2
technical replicate number: 1
description: NRF1 ChIP-seq on human K562
experiment encode accession: ENCSR494TDU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB116QWY
size range: 450-650

value: female

value: Michael Snyder, Stanford

value: ENCBS293ZDP at ENCODE; https://www.encodeproject.org/ENCBS293ZDP/


title: ChIP-seq from midbrain (ENCLB712BYF)

description:
https://www.encodeproject.org/experiments/ENCSR985ZTV/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on CTCF-mouse
experiment encode accession: ENCSR985ZTV
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR601HSS
encode release date: 2016-05-18
lab: Richard Myers, HAIB
library encode accession: ENCLB712BYF

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

value: CTCF

value: midbrain

value: tissue

value: Richard Myers, HAIB

value: ENCBS848MFZ at ENCODE; https://www.encodeproject.org/ENCBS848MFZ/

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


title: eCLIP from HepG2 (ENCLB019FNY)

description:
https://www.encodeproject.org/experiments/ENCSR456JJQ/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against RBM22
experiment encode accession: ENCSR456JJQ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR775UPS
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB019FNY
size range: 175-300

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: 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 (ENCLB371PGL)

description:
https://www.encodeproject.org/experiments/ENCSR456JJQ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against RBM22
experiment encode accession: ENCSR456JJQ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR775UPS
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB371PGL
size range: 175-300

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


title: ChIP-seq from K562 (ENCLB705OSO)

description:
https://www.encodeproject.org/experiments/ENCSR494PWZ/
***************
biological replicate number: 2
technical replicate number: 1
description: ZC3H8 ChIP-seq on human K562
experiment encode accession: ENCSR494PWZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB705OSO
size range: 450-650

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Michael Snyder, Stanford

value: ENCBS320BUL at ENCODE; https://www.encodeproject.org/ENCBS320BUL/

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 liver (ENCLB728FIQ)

description:
https://www.encodeproject.org/experiments/ENCSR982LJQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on e14.5 liver
experiment encode accession: ENCSR982LJQ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR982SZZ, ENCSR321TTR
encode release date: 2016-05-17
lab: Richard Myers, HAIB
library encode accession: ENCLB728FIQ

value: liver

value: tissue

value: pulverized livers pooled from multiple dissections of embryonic 14.5 day mice

value: embryonic

value: pooled male and female

value: Richard Myers, HAIB

value: ENCBS464EKT at ENCODE; https://www.encodeproject.org/ENCBS464EKT/

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


title: ChIP-seq from heart (ENCLB997HEJ)

description:
https://www.encodeproject.org/experiments/ENCSR890SJI/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on P0 heart-mouse (fragmentation date:2015-08-26)
experiment encode accession: ENCSR890SJI
assay title: ChIP-seq
encode release date: 2016-01-14
lab: Richard Myers, HAIB
library encode accession: ENCLB997HEJ

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

value: Control

value: heart

value: postnatal

value: 0 day

value: not collected

value: ENCBS345FLN at ENCODE; https://www.encodeproject.org/ENCBS345FLN/


title: ChIP-seq from liver (ENCLB188IIF)

description:
https://www.encodeproject.org/experiments/ENCSR982LJQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on e14.5 liver
experiment encode accession: ENCSR982LJQ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR982SZZ, ENCSR321TTR
encode release date: 2016-05-17
lab: Richard Myers, HAIB
library encode accession: ENCLB188IIF


title: eCLIP from K562 (ENCLB817HIH)

description:
https://www.encodeproject.org/experiments/ENCSR454EER/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against RBM15
experiment encode accession: ENCSR454EER
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB817HIH
size range: 175-300

value: immortalized cell line

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

value: ENCBS318IMK at ENCODE; https://www.encodeproject.org/ENCBS318IMK/

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


title: eCLIP from HepG2 (ENCLB588AJF)

description:
https://www.encodeproject.org/experiments/ENCSR454OFD/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against DDX55
experiment encode accession: ENCSR454OFD
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB588AJF
size range: 175-300

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: ChIP-seq from intestine (ENCLB926YIO)

description:
https://www.encodeproject.org/experiments/ENCSR862ZBY/
***************
biological replicate number: 1
technical replicate number: 1
description: Reverse Crosslink Control ChIP-seq on postnatal 0 day mouse intestine (fragmentation date 09-30-14)
experiment encode accession: ENCSR862ZBY
assay title: ChIP-seq
encode release date: 2016-01-14
lab: Richard Myers, HAIB
library encode accession: ENCLB926YIO

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

value: Control

value: intestine

value: tissue

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: ChIP-seq from K562 (ENCLB126ABP)

description:
https://www.encodeproject.org/experiments/ENCSR492SGS/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-GTF2A2 tagged K562 cell ine.
experiment encode accession: ENCSR492SGS
assay title: ChIP-seq
encode release date: 2016-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB126ABP

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-GTF2A2 fusion protein

value: immortalized cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to GTF2A2

value: adult

value: 53 year

value: female

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: ENCBS725FFW at ENCODE; https://www.encodeproject.org/ENCBS725FFW/

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

value: ENCODE dbxrefs Cellosaurus CVCL_GZ87; http://web.expasy.org/cellosaurus/CVCL_GZ87


title: ChIP-seq from K562 (ENCLB189DCJ)

description:
https://www.encodeproject.org/experiments/ENCSR489RLS/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-ILK tagged K562 cell line.
experiment encode accession: ENCSR489RLS
assay title: ChIP-seq
encode release date: 2016-02-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB189DCJ
size range: 450-650

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

value: Control

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

value: ENCBS002PZY at ENCODE; https://www.encodeproject.org/ENCBS002PZY/

value: ENCODE dbxrefs Cellosaurus CVCL_AW27; http://web.expasy.org/cellosaurus/CVCL_AW27


title: ChIP-seq from heart (ENCLB326ESZ)

description:
https://www.encodeproject.org/experiments/ENCSR777VNA/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on P0 heart
experiment encode accession: ENCSR777VNA
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR890SJI, ENCSR431KAV
encode release date: 2016-05-17
lab: Richard Myers, HAIB
library encode accession: ENCLB326ESZ

value: heart

value: tissue

value: postnatal

value: 0 day

value: not collected

value: Richard Myers, HAIB

value: ENCBS345FLN at ENCODE; https://www.encodeproject.org/ENCBS345FLN/


title: eCLIP from K562 (ENCLB030EVI)

description:
https://www.encodeproject.org/experiments/ENCSR489RJI/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against RBM27
experiment encode accession: ENCSR489RJI
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR194AVW
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB030EVI
size range: 175-300

value: immortalized cell line

value: adult

value: female

value: 53 year

value: Gene Yeo, UCSD

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

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 heart (ENCLB547CGW)

description:
https://www.encodeproject.org/experiments/ENCSR777VNA/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on P0 heart
experiment encode accession: ENCSR777VNA
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR890SJI, ENCSR431KAV
encode release date: 2016-05-17
lab: Richard Myers, HAIB
library encode accession: ENCLB547CGW

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


title: eCLIP from HepG2 (ENCLB234DPJ)

description:
https://www.encodeproject.org/experiments/ENCSR438NCK/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against PTBP1
experiment encode accession: ENCSR438NCK
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-09-21
lab: Gene Yeo, UCSD
library encode accession: ENCLB234DPJ
size range: 175-300

value: Control

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

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

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 K562 (ENCLB382GVE)

description:
https://www.encodeproject.org/experiments/ENCSR489RJI/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against RBM27
experiment encode accession: ENCSR489RJI
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR194AVW
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB382GVE
size range: 175-300

value: immortalized cell line

value: chronic myelogenous leukemia (CML)

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

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


title: ChIP-seq from liver (ENCLB153SAF)

description:
https://www.encodeproject.org/experiments/ENCSR765RPR/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on P0 liver
experiment encode accession: ENCSR765RPR
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR236UIQ
encode release date: 2016-05-17
lab: Richard Myers, HAIB
library encode accession: ENCLB153SAF

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

value: liver

value: tissue

value: postnatal

value: 0 day

value: not collected

value: Richard Myers, HAIB

value: ENCBS504NHW at ENCODE; https://www.encodeproject.org/ENCBS504NHW/


title: ChIP-seq from HEK293 (ENCLB100XVY)

description:
https://www.encodeproject.org/experiments/ENCSR429LAP/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq on eGFP-SP7 tagged human HEK293 cells.
experiment encode accession: ENCSR429LAP
assay title: ChIP-seq
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB100XVY
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-SP7 fusion protein

value: Control

value: HEK293 cell line stably expressing N-terminal tagged eGFP-SP7 under the control of a CMV promoter.

value: embryonic

value: unknown

value: female

value: Michael Snyder, Stanford

value: ENCBS387JTD at ENCODE; https://www.encodeproject.org/ENCBS387JTD/

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


title: ChIP-seq from liver (ENCLB952RKL)

description:
https://www.encodeproject.org/experiments/ENCSR765RPR/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on P0 liver
experiment encode accession: ENCSR765RPR
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR236UIQ
encode release date: 2016-05-17
lab: Richard Myers, HAIB
library encode accession: ENCLB952RKL

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


title: ChIP-seq from lung (ENCLB094BJD)

description:
https://www.encodeproject.org/experiments/ENCSR718KRA/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on e14.5 lung-mouse (fragmentation date:2014-09-30)
experiment encode accession: ENCSR718KRA
assay title: ChIP-seq
encode release date: 2016-01-29
lab: Richard Myers, HAIB
library encode accession: ENCLB094BJD

source_name: Mus musculus strain B6NCrl lung tissue mixed sex embryo (14.5 days)

value: lung

value: pulverized lungs pooled from multiple dissections of embryonic 14.5 day mice

value: pooled male and female

value: ENCBS999OEH at ENCODE; https://www.encodeproject.org/ENCBS999OEH/


title: ChIP-seq from lung (ENCLB690PRV)

description:
https://www.encodeproject.org/experiments/ENCSR677SIH/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on CTCF-mouse
experiment encode accession: ENCSR677SIH
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR718KRA
encode release date: 2016-05-18
lab: Richard Myers, HAIB
library encode accession: ENCLB690PRV

value: CTCF

value: tissue


title: ChIP-seq from lung (ENCLB757BVO)

description:
https://www.encodeproject.org/experiments/ENCSR677SIH/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on CTCF-mouse
experiment encode accession: ENCSR677SIH
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR718KRA
encode release date: 2016-05-18
lab: Richard Myers, HAIB
library encode accession: ENCLB757BVO

value: Richard Myers, HAIB


title: eCLIP from HepG2 (ENCLB287CLY)

description:
https://www.encodeproject.org/experiments/ENCSR406OOZ/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against SUB1
experiment encode accession: ENCSR406OOZ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR641PRC
encode release date: 2016-08-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB287CLY
size range: 175-300

value: immortalized cell line

value: child

value: 15 year

value: male

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 (ENCLB742PBR)

description:
https://www.encodeproject.org/experiments/ENCSR487EUV/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against NONO
experiment encode accession: ENCSR487EUV
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB742PBR
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

value: Control

value: adult

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

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

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 liver (ENCLB023ASA)

description:
https://www.encodeproject.org/experiments/ENCSR982SZZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on e14.5 liver-mouse (fragmentation date:2015-01-08)
experiment encode accession: ENCSR982SZZ
assay title: ChIP-seq
encode release date: 2016-01-14
lab: Richard Myers, HAIB
library encode accession: ENCLB023ASA

value: liver

value: tissue

value: pulverized livers pooled from multiple dissections of embryonic 14.5 day mice

value: embryonic

value: pooled male and female

value: Richard Myers, HAIB

value: ENCBS464EKT at ENCODE; https://www.encodeproject.org/ENCBS464EKT/

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


title: ChIP-seq from midbrain (ENCLB723LQR)

description:
https://www.encodeproject.org/experiments/ENCSR985ZTV/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on CTCF-mouse
experiment encode accession: ENCSR985ZTV
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR601HSS
encode release date: 2016-05-18
lab: Richard Myers, HAIB
library encode accession: ENCLB723LQR

value: CTCF

value: midbrain

value: postnatal

value: 0 day

value: not collected

value: ENCBS848MFZ at ENCODE; https://www.encodeproject.org/ENCBS848MFZ/


title: ChIP-seq from forebrain (ENCLB757QCH)

description:
https://www.encodeproject.org/experiments/ENCSR677HXC/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on postnatal 0 day mouse forebrain
experiment encode accession: ENCSR677HXC
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR264HIK
encode release date: 2016-05-18
lab: Richard Myers, HAIB
library encode accession: ENCLB757QCH

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

value: forebrain

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

value: ENCBS900GJR at ENCODE; https://www.encodeproject.org/ENCBS900GJR/


title: eCLIP from HepG2 (ENCLB635SAQ)

description:
https://www.encodeproject.org/experiments/ENCSR445LJH/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against PPIG
experiment encode accession: ENCSR445LJH
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB635SAQ
size range: 175-300

value: Control

value: immortalized cell line

value: child

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 (ENCLB648CVW)

description:
https://www.encodeproject.org/experiments/ENCSR406OOZ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against SUB1
experiment encode accession: ENCSR406OOZ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR641PRC
encode release date: 2016-08-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB648CVW
size range: 175-300

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


title: ChIP-seq from hindbrain (ENCLB393DON)

description:
https://www.encodeproject.org/experiments/ENCSR655SYB/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on P0 brain, hindbrain-mouse (fragmentation date:Tue Sep 30 2014 00:00:00 GMT-0500 (CDT)
experiment encode accession: ENCSR655SYB
assay title: ChIP-seq
encode release date: 2016-02-05
lab: Richard Myers, HAIB
library encode accession: ENCLB393DON

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

value: hindbrain

value: tissue

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

value: postnatal

value: 0 day

value: not collected

value: Richard Myers, HAIB

value: ENCBS399IKT at ENCODE; https://www.encodeproject.org/ENCBS399IKT/

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


title: ChIP-seq from forebrain (ENCLB783TWE)

description:
https://www.encodeproject.org/experiments/ENCSR677HXC/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIP-seq on postnatal 0 day mouse forebrain
experiment encode accession: ENCSR677HXC
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR264HIK
encode release date: 2016-05-18
lab: Richard Myers, HAIB
library encode accession: ENCLB783TWE

value: CTCF

value: forebrain

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

value: ENCBS900GJR at ENCODE; https://www.encodeproject.org/ENCBS900GJR/


title: ChIP-seq from kidney (ENCLB220BYM)

description:
https://www.encodeproject.org/experiments/ENCSR655KFC/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on P0 kidney-mouse (fragmentation date: 2015-02-05)
experiment encode accession: ENCSR655KFC
assay title: ChIP-seq
encode release date: 2016-01-29
lab: Richard Myers, HAIB
library encode accession: ENCLB220BYM

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

value: Control

value: kidney

value: ENCBS591PKP at ENCODE; https://www.encodeproject.org/ENCBS591PKP/


title: ChIP-seq from midbrain (ENCLB224NKT)

description:
https://www.encodeproject.org/experiments/ENCSR601HSS/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on P0 brain, midbrain-mouse (fragmentation date:Thu Feb 05 2015 00:00:00 GMT-0600 (CST)
experiment encode accession: ENCSR601HSS
assay title: ChIP-seq
encode release date: 2016-01-29
lab: Richard Myers, HAIB
library encode accession: ENCLB224NKT

value: midbrain

value: ENCBS848MFZ at ENCODE; https://www.encodeproject.org/ENCBS848MFZ/


title: ChIP-seq from K562 (ENCLB922NZS)

description:
https://www.encodeproject.org/experiments/ENCSR402XII/
***************
biological replicate number: 1
technical replicate number: 1
description: CSDE1 ChIP-seq on human K562
experiment encode accession: ENCSR402XII
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2016-10-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB922NZS
size range: 450-650

value: immortalized cell line

value: adult

value: 53 year

value: female

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)

value: ENCBS520IYS at ENCODE; https://www.encodeproject.org/ENCBS520IYS/

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


title: ChIP-seq from K562 (ENCLB527HRB)

description:
https://www.encodeproject.org/experiments/ENCSR557SDQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-HINFP tagged K562 cell line.
experiment encode accession: ENCSR557SDQ
assay title: ChIP-seq
encode release date: 2016-02-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB527HRB
size range: 450-650

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

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

value: Kevin White, UChicago

value: ENCBS422ZTW at ENCODE; https://www.encodeproject.org/ENCBS422ZTW/

value: ENCODE dbxrefs Cellosaurus CVCL_AW24; http://web.expasy.org/cellosaurus/CVCL_AW24


title: ChIP-seq from lung (ENCLB070WBC)

description:
https://www.encodeproject.org/experiments/ENCSR527DME/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on P0 lung
experiment encode accession: ENCSR527DME
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR227UFB
encode release date: 2016-05-17
lab: Richard Myers, HAIB
library encode accession: ENCLB070WBC

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

value: lung

value: tissue

value: postnatal

value: 0 day

value: not collected

value: Richard Myers, HAIB

value: ENCBS506ZRP at ENCODE; https://www.encodeproject.org/ENCBS506ZRP/

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


title: ChIP-seq from K562 (ENCLB650BRJ)

description:
https://www.encodeproject.org/experiments/ENCSR486IFJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ESRRA ChIP-seq on human K562
experiment encode accession: ENCSR486IFJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB650BRJ
size range: 450-650

value: ESRRA

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: female

value: 53 year

value: ENCBS293ZDP at ENCODE; https://www.encodeproject.org/ENCBS293ZDP/

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 HepG2 (ENCLB473MOT)

description:
https://www.encodeproject.org/experiments/ENCSR485QCG/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against BCCIP
experiment encode accession: ENCSR485QCG
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR655BRZ
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB473MOT
size range: 175-300

source_name: Homo sapiens HepG2 immortalized cell line

value: BCCIP

value: child

value: 15 year

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS447JNO at ENCODE; https://www.encodeproject.org/ENCBS447JNO/

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 K562 (ENCLB279IWB)

description:
https://www.encodeproject.org/experiments/ENCSR402XII/
***************
biological replicate number: 2
technical replicate number: 1
description: CSDE1 ChIP-seq on human K562
experiment encode accession: ENCSR402XII
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2016-10-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB279IWB
size range: 450-650

value: immortalized cell line

value: chronic myelogenous leukemia (CML)

value: Michael Snyder, Stanford

value: ENCBS101QRF at ENCODE; https://www.encodeproject.org/ENCBS101QRF/

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


title: ChIP-seq from lung (ENCLB910PQR)

description:
https://www.encodeproject.org/experiments/ENCSR527DME/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on P0 lung
experiment encode accession: ENCSR527DME
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR227UFB
encode release date: 2016-05-17
lab: Richard Myers, HAIB
library encode accession: ENCLB910PQR

value: lung

value: tissue

value: postnatal

value: 0 day

value: not collected

value: Richard Myers, HAIB

value: ENCBS506ZRP at ENCODE; https://www.encodeproject.org/ENCBS506ZRP/

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


title: ChIP-seq from HepG2 (ENCLB466SQH)

description:
https://www.encodeproject.org/experiments/ENCSR399VVK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human HepG2
experiment encode accession: ENCSR399VVK
assay title: ChIP-seq
encode release date: 2016-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB466SQH
size range: 450-650

value: Control

value: child

value: 15 year

value: male

value: hepatocellular carcinoma

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


title: ChIP-seq from HepG2 (ENCLB735WME)

description:
https://www.encodeproject.org/experiments/ENCSR399VVK/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on human HepG2
experiment encode accession: ENCSR399VVK
assay title: ChIP-seq
encode release date: 2016-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB735WME
size range: 450-650

value: immortalized cell line

value: Michael Snyder, Stanford

value: ENCBS667BFL at ENCODE; https://www.encodeproject.org/ENCBS667BFL/

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


title: ChIP-seq from embryonic facial prominence (ENCLB062SRL)

description:
https://www.encodeproject.org/experiments/ENCSR526JRI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on embryonic 11.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR526JRI
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR068AQC
encode release date: 2016-10-14
lab: Bing Ren, UCSD
library encode accession: ENCLB062SRL
size range: 300-500

source_name: Mus musculus strain B6NCrl embryonic facial prominence tissue mixed sex embryo (11.5 days)

value: embryonic facial prominence

value: tissue

value: Craniofacial prominence from 109 embyronic 11.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS141GPQ at ENCODE; https://www.encodeproject.org/ENCBS141GPQ/


title: ChIP-seq from embryonic facial prominence (ENCLB112EBV)

description:
https://www.encodeproject.org/experiments/ENCSR526JRI/
***************
biological replicate number: 2
technical replicate number: 1,2
description: H3K9me3 ChIP-seq on embryonic 11.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR526JRI
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR068AQC
encode release date: 2016-10-14
lab: Bing Ren, UCSD
library encode accession: ENCLB112EBV
size range: 300-500
instrument models: Illumina HiSeq 2000,Illumina HiSeq 4000

value: Craniofacial prominence from 88 embyronic 11.5 day mice

value: ENCBS468NAL at ENCODE; https://www.encodeproject.org/ENCBS468NAL/

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


title: eCLIP from HepG2 (ENCLB896QXF)

description:
https://www.encodeproject.org/experiments/ENCSR485QCG/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against BCCIP
experiment encode accession: ENCSR485QCG
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR655BRZ
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB896QXF
size range: 175-300

value: BCCIP

value: child

value: 15 year

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS847PBZ at ENCODE; https://www.encodeproject.org/ENCBS847PBZ/

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 heart (ENCLB661GKS)

description:
https://www.encodeproject.org/experiments/ENCSR491NUM/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on CTCF-mouse
experiment encode accession: ENCSR491NUM
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR109LQX
encode release date: 2016-05-18
lab: Richard Myers, HAIB
library encode accession: ENCLB661GKS

value: CTCF

value: heart

value: tissue

value: postnatal

value: 0 day

value: not collected

value: Richard Myers, HAIB

value: ENCBS345FLN at ENCODE; https://www.encodeproject.org/ENCBS345FLN/


title: eCLIP from K562 (ENCLB733FAO)

description:
https://www.encodeproject.org/experiments/ENCSR483NOP/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against SLBP
experiment encode accession: ENCSR483NOP
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR950WBG
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB733FAO
size range: 175-300

value: SLBP

value: immortalized cell line

value: adult

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS540UNM at ENCODE; https://www.encodeproject.org/ENCBS540UNM/

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 K562 (ENCLB180ZTB)

description:
https://www.encodeproject.org/experiments/ENCSR486IFJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ESRRA ChIP-seq on human K562
experiment encode accession: ENCSR486IFJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB180ZTB
size range: 450-650

value: ESRRA

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: Michael Snyder, Stanford

value: ENCBS351GWD at ENCODE; https://www.encodeproject.org/ENCBS351GWD/


title: ChIP-seq from heart (ENCLB062WBN)

description:
https://www.encodeproject.org/experiments/ENCSR491NUM/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on CTCF-mouse
experiment encode accession: ENCSR491NUM
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR109LQX
encode release date: 2016-05-18
lab: Richard Myers, HAIB
library encode accession: ENCLB062WBN

value: CTCF

value: heart

value: tissue

value: postnatal

value: 0 day

value: not collected

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


title: ChIP-seq from K562 (ENCLB085EWN)

description:
https://www.encodeproject.org/experiments/ENCSR494PWZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ZC3H8 ChIP-seq on human K562
experiment encode accession: ENCSR494PWZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB085EWN
size range: 450-650

value: immortalized cell line

value: adult

value: 53 year

value: female

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


title: ChIP-seq from heart (ENCLB115VAM)

description:
https://www.encodeproject.org/experiments/ENCSR431KAV/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on P0 heart-mouse (fragmentation date:2015-08-26)
experiment encode accession: ENCSR431KAV
assay title: ChIP-seq
encode release date: 2016-01-14
lab: Richard Myers, HAIB
library encode accession: ENCLB115VAM

value: Control

value: Richard Myers, HAIB

value: ENCBS345FLN at ENCODE; https://www.encodeproject.org/ENCBS345FLN/


title: ChIP-seq from stomach (ENCLB346PPO)

description:
https://www.encodeproject.org/experiments/ENCSR450KVW/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on P0 stomach
experiment encode accession: ENCSR450KVW
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR993MMD, ENCSR281FZS
encode release date: 2016-05-17
lab: Richard Myers, HAIB
library encode accession: ENCLB346PPO

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

value: stomach

value: ENCBS551QZH at ENCODE; https://www.encodeproject.org/ENCBS551QZH/


title: eCLIP from K562 (ENCLB014GQG)

description:
https://www.encodeproject.org/experiments/ENCSR482ZSE/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against U2AF1
experiment encode accession: ENCSR482ZSE
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB014GQG
size range: 175-300

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

value: ENCBS152EMG at ENCODE; https://www.encodeproject.org/ENCBS152EMG/

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 stomach (ENCLB618WJC)

description:
https://www.encodeproject.org/experiments/ENCSR450KVW/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on P0 stomach
experiment encode accession: ENCSR450KVW
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR993MMD, ENCSR281FZS
encode release date: 2016-05-17
lab: Richard Myers, HAIB
library encode accession: ENCLB618WJC

value: tissue

value: postnatal

value: 0 day

value: not collected

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


title: ChIP-seq from HEK293 (ENCLB334XGU)

description:
https://www.encodeproject.org/experiments/ENCSR482BBZ/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-GLIS1 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR482BBZ
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: ENCLB334XGU
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-GLIS1 fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-GLIS1 under the control of a CMV promoter.

value: embryonic

value: unknown

value: female

value: Michael Snyder, Stanford

value: ENCBS695XFP at ENCODE; https://www.encodeproject.org/ENCBS695XFP/

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


title: ChIP-seq from liver (ENCLB118VWC)

description:
https://www.encodeproject.org/experiments/ENCSR397RHW/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on CTCF-mouse
experiment encode accession: ENCSR397RHW
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR999LAC
encode release date: 2016-05-18
lab: Richard Myers, HAIB
library encode accession: ENCLB118VWC

source_name: Mus musculus strain B6NCrl liver tissue mixed sex embryo (14.5 days)

value: CTCF

value: liver

value: pulverized livers pooled from multiple dissections of embryonic 14.5 day mice

value: pooled male and female

value: Richard Myers, HAIB

value: ENCBS464EKT at ENCODE; https://www.encodeproject.org/ENCBS464EKT/


title: ChIP-seq from liver (ENCLB245OTQ)

description:
https://www.encodeproject.org/experiments/ENCSR397RHW/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on CTCF-mouse
experiment encode accession: ENCSR397RHW
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR999LAC
encode release date: 2016-05-18
lab: Richard Myers, HAIB
library encode accession: ENCLB245OTQ

value: tissue


title: ChIP-seq from lung (ENCLB452UJZ)

description:
https://www.encodeproject.org/experiments/ENCSR418SBY/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on CTCF-mouse
experiment encode accession: ENCSR418SBY
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR275BEG
encode release date: 2016-05-18
lab: Richard Myers, HAIB
library encode accession: ENCLB452UJZ

value: lung

value: postnatal

value: 0 day

value: not collected

value: ENCBS506ZRP at ENCODE; https://www.encodeproject.org/ENCBS506ZRP/


title: eCLIP from HepG2 (ENCLB711ANS)

description:
https://www.encodeproject.org/experiments/ENCSR384MWO/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against CSTF2
experiment encode accession: ENCSR384MWO
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR309GHK
encode release date: 2016-08-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB711ANS
size range: 175-300

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: eCLIP from HepG2 (ENCLB459KPV)

description:
https://www.encodeproject.org/experiments/ENCSR384MWO/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against CSTF2
experiment encode accession: ENCSR384MWO
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR309GHK
encode release date: 2016-08-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB459KPV
size range: 175-300

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


title: eCLIP from HepG2 (ENCLB279NMT)

description:
https://www.encodeproject.org/experiments/ENCSR384KAN/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against PTBP1
experiment encode accession: ENCSR384KAN
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR438NCK
encode release date: 2016-09-21
lab: Gene Yeo, UCSD
library encode accession: ENCLB279NMT
size range: 175-300

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


title: ChIP-seq from stomach (ENCLB265AIA)

description:
https://www.encodeproject.org/experiments/ENCSR389SQZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on P0 stomach-mouse (fragmentation date: 2015-02-05)
experiment encode accession: ENCSR389SQZ
assay title: ChIP-seq
encode release date: 2016-01-29
lab: Richard Myers, HAIB
library encode accession: ENCLB265AIA

value: Control

value: stomach

value: tissue

value: Richard Myers, HAIB

value: ENCBS551QZH at ENCODE; https://www.encodeproject.org/ENCBS551QZH/

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


title: ChIP-seq from lung (ENCLB533GEV)

description:
https://www.encodeproject.org/experiments/ENCSR418SBY/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on CTCF-mouse
experiment encode accession: ENCSR418SBY
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR275BEG
encode release date: 2016-05-18
lab: Richard Myers, HAIB
library encode accession: ENCLB533GEV

value: CTCF

value: lung

value: postnatal

value: 0 day

value: not collected

value: ENCBS506ZRP at ENCODE; https://www.encodeproject.org/ENCBS506ZRP/


title: ChIP-seq from HEK293 (ENCLB498HLU)

description:
https://www.encodeproject.org/experiments/ENCSR482BBZ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-GLIS1 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR482BBZ
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: ENCLB498HLU
size range: 450-650

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-GLIS1 under the control of a CMV promoter.

value: embryonic

value: female

value: unknown

value: Michael Snyder, Stanford

value: ENCBS300BBW at ENCODE; https://www.encodeproject.org/ENCBS300BBW/

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


title: eCLIP from HepG2 (ENCLB875HIL)

description:
https://www.encodeproject.org/experiments/ENCSR384KAN/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against PTBP1
experiment encode accession: ENCSR384KAN
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR438NCK
encode release date: 2016-09-21
lab: Gene Yeo, UCSD
library encode accession: ENCLB875HIL
size range: 175-300

value: child

value: 15 year

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS575NGC at ENCODE; https://www.encodeproject.org/ENCBS575NGC/

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

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


title: ChIP-seq from limb (ENCLB642CLW)

description:
https://www.encodeproject.org/experiments/ENCSR295PZC/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on CTCF-mouse
experiment encode accession: ENCSR295PZC
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR164BWS
encode release date: 2016-05-18
lab: Richard Myers, HAIB
library encode accession: ENCLB642CLW

source_name: Mus musculus strain B6NCrl limb tissue mixed sex embryo (14.5 days)

value: CTCF

value: limb

value: tissue

value: pulverized limbs pooled from multiple dissections of embryonic 14.5 day mice

value: pooled male and female

value: Richard Myers, HAIB

value: ENCBS282TXV at ENCODE; https://www.encodeproject.org/ENCBS282TXV/

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


title: ChIP-seq from limb (ENCLB694FNQ)

description:
https://www.encodeproject.org/experiments/ENCSR295PZC/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on CTCF-mouse
experiment encode accession: ENCSR295PZC
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR164BWS
encode release date: 2016-05-18
lab: Richard Myers, HAIB
library encode accession: ENCLB694FNQ

value: embryonic


title: eCLIP from HepG2 (ENCLB584FIB)

description:
https://www.encodeproject.org/experiments/ENCSR376KLZ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against SUPV3L1
experiment encode accession: ENCSR376KLZ
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-08-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB584FIB
size range: 175-300

value: Control

value: immortalized cell line

value: child

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

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


title: ChIP-seq from HEK293 (ENCLB755IEY)

description:
https://www.encodeproject.org/experiments/ENCSR481FEC/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZBTB8A ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR481FEC
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: ENCLB755IEY
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZBTB8A fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZBTB8A under the control of a CMV promoter.

value: female

value: unknown

value: Michael Snyder, Stanford

value: ENCBS218CJM at ENCODE; https://www.encodeproject.org/ENCBS218CJM/

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


title: eCLIP from K562 (ENCLB441BNG)

description:
https://www.encodeproject.org/experiments/ENCSR483NOP/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against SLBP
experiment encode accession: ENCSR483NOP
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR950WBG
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB441BNG
size range: 175-300

value: SLBP

value: adult

value: 53 year

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

value: ENCBS943ICN at ENCODE; https://www.encodeproject.org/ENCBS943ICN/

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 (ENCLB329YDM)

description:
https://www.encodeproject.org/experiments/ENCSR482AWB/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against HNRNPUL1
experiment encode accession: ENCSR482AWB
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB329YDM
size range: 175-300

value: Control

value: immortalized cell line

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

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


title: ChIP-seq from HEK293 (ENCLB143MYU)

description:
https://www.encodeproject.org/experiments/ENCSR481FEC/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZBTB8A ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR481FEC
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: ENCLB143MYU
size range: 450-650

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZBTB8A under the control of a CMV promoter.

value: embryonic

value: female

value: unknown

value: ENCBS078UYW at ENCODE; https://www.encodeproject.org/ENCBS078UYW/


title: eCLIP from adrenal gland (ENCLB754IRC)

description:
https://www.encodeproject.org/experiments/ENCSR368GER/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on adrenal gland tissue from the GTEx collection against HNRNPU
experiment encode accession: ENCSR368GER
assay title: eCLIP
possible controls: ENCSR096YAP
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB754IRC
size range: 175-300

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

value: HNRNPU

value: adrenal gland

value: tissue

value: Adrenal Gland GTEx tissue aliquot

value: adult

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 MCF-7 (ENCLB955XMX)

description:
https://www.encodeproject.org/experiments/ENCSR389BLX/
***************
biological replicate number: 2
technical replicate number: 1
description: GATAD2B ChIP-seq on human MCF-7
experiment encode accession: ENCSR389BLX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR882IYK
encode release date: 2016-10-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB955XMX
size range: 450-650

source_name: Homo sapiens MCF-7 immortalized cell line

value: immortalized cell line

value: 69 year

value: breast cancer (adenocarcinoma)

value: Michael Snyder, Stanford

value: ENCBS110CZN at ENCODE; https://www.encodeproject.org/ENCBS110CZN/

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


title: eCLIP from adrenal gland (ENCLB364TED)

description:
https://www.encodeproject.org/experiments/ENCSR368GER/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on adrenal gland tissue from the GTEx collection against HNRNPU
experiment encode accession: ENCSR368GER
assay title: eCLIP
possible controls: ENCSR096YAP
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB364TED
size range: 175-300

value: Gene Yeo, UCSD


title: ChIP-seq from stomach (ENCLB683URD)

description:
https://www.encodeproject.org/experiments/ENCSR281FZS/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on P0 stomach-mouse (fragmentation date:2015-08-26
experiment encode accession: ENCSR281FZS
assay title: ChIP-seq
encode release date: 2016-01-14
lab: Richard Myers, HAIB
library encode accession: ENCLB683URD

value: Control

value: stomach

value: postnatal

value: 0 day

value: not collected

value: Richard Myers, HAIB

value: ENCBS551QZH at ENCODE; https://www.encodeproject.org/ENCBS551QZH/

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


title: ChIP-seq from lung (ENCLB995OWX)

description:
https://www.encodeproject.org/experiments/ENCSR275BEG/
***************
biological replicate number: 1
technical replicate number: 1
description: Reverse Crosslink Control ChIP-seq on postnatal 0 day mouse lung (fragmentation date 08-13-14)
experiment encode accession: ENCSR275BEG
assay title: ChIP-seq
encode release date: 2016-01-14
lab: Richard Myers, HAIB
library encode accession: ENCLB995OWX

value: lung

value: tissue

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

value: ENCBS307DXQ at ENCODE; https://www.encodeproject.org/ENCBS307DXQ/


title: ChIP-seq from forebrain (ENCLB550LBB)

description:
https://www.encodeproject.org/experiments/ENCSR264HIK/
***************
biological replicate number: 1
technical replicate number: 1
description: Reverse Crosslink Control ChIP-seq on postnatal 0 day mouse forebrain (fragmentation date 09-30-14)
experiment encode accession: ENCSR264HIK
assay title: ChIP-seq
encode release date: 2016-01-14
lab: Richard Myers, HAIB
library encode accession: ENCLB550LBB

value: forebrain

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

value: ENCBS900GJR at ENCODE; https://www.encodeproject.org/ENCBS900GJR/


title: ChIP-seq from HEK293 (ENCLB442DRR)

description:
https://www.encodeproject.org/experiments/ENCSR477OJI/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF423 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR477OJI
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: ENCLB442DRR
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF423 fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF423 under the control of a CMV promoter.

value: embryonic

value: unknown

value: female

value: Michael Snyder, Stanford

value: ENCBS992HKQ at ENCODE; https://www.encodeproject.org/ENCBS992HKQ/

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


title: ChIP-seq from liver (ENCLB413CSZ)

description:
https://www.encodeproject.org/experiments/ENCSR321TTR/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on e14.5 liver-mouse (fragmentation date:2015-01-08)
experiment encode accession: ENCSR321TTR
assay title: ChIP-seq
encode release date: 2016-01-14
lab: Richard Myers, HAIB
library encode accession: ENCLB413CSZ

value: Control

value: liver

value: pulverized livers pooled from multiple dissections of embryonic 14.5 day mice

value: pooled male and female

value: Richard Myers, HAIB

value: ENCBS464EKT at ENCODE; https://www.encodeproject.org/ENCBS464EKT/


title: ChIP-seq from liver (ENCLB252MOH)

description:
https://www.encodeproject.org/experiments/ENCSR236UIQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on P0 liver-mouse (fragmentation date:2015-01-13)
experiment encode accession: ENCSR236UIQ
assay title: ChIP-seq
encode release date: 2016-01-14
lab: Richard Myers, HAIB
library encode accession: ENCLB252MOH

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

value: tissue

value: postnatal

value: 0 day

value: not collected

value: ENCBS504NHW at ENCODE; https://www.encodeproject.org/ENCBS504NHW/

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


title: ChIP-seq from lung (ENCLB269PDT)

description:
https://www.encodeproject.org/experiments/ENCSR227UFB/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on P0 lung-mouse (fragmentation date:2015-01-13)
experiment encode accession: ENCSR227UFB
assay title: ChIP-seq
encode release date: 2016-02-02
lab: Richard Myers, HAIB
library encode accession: ENCLB269PDT

value: lung

value: ENCBS506ZRP at ENCODE; https://www.encodeproject.org/ENCBS506ZRP/


title: ChIP-seq from HEK293 (ENCLB623NON)

description:
https://www.encodeproject.org/experiments/ENCSR477OJI/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF423 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR477OJI
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: ENCLB623NON
size range: 450-650

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF423 under the control of a CMV promoter.

value: embryonic

value: unknown

value: female

value: Michael Snyder, Stanford

value: ENCBS519RHO at ENCODE; https://www.encodeproject.org/ENCBS519RHO/


title: ChIP-seq from limb (ENCLB614ZHA)

description:
https://www.encodeproject.org/experiments/ENCSR164BWS/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on e14.5 limb-mouse (fragmentation date: 2014-09-30)
experiment encode accession: ENCSR164BWS
assay title: ChIP-seq
encode release date: 2016-01-29
lab: Richard Myers, HAIB
library encode accession: ENCLB614ZHA

value: Control

value: limb

value: pulverized limbs pooled from multiple dissections of embryonic 14.5 day mice

value: pooled male and female

value: Richard Myers, HAIB

value: ENCBS282TXV at ENCODE; https://www.encodeproject.org/ENCBS282TXV/


title: eCLIP from K562 (ENCLB395CQN)

description:
https://www.encodeproject.org/experiments/ENCSR468ZQA/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against NPM1
experiment encode accession: ENCSR468ZQA
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB395CQN
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

value: adult

value: 53 year

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: 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: eCLIP from K562 (ENCLB423YJJ)

description:
https://www.encodeproject.org/experiments/ENCSR366YOG/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against QKI
experiment encode accession: ENCSR366YOG
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR615AAW
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB423YJJ
size range: 175-300

value: QKI

value: immortalized cell line

value: female

value: ENCBS517UIR at ENCODE; https://www.encodeproject.org/ENCBS517UIR/


title: ChIP-seq from hindbrain (ENCLB656PGG)

description:
https://www.encodeproject.org/experiments/ENCSR150RGT/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on CTCF-mouse
experiment encode accession: ENCSR150RGT
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR655SYB
encode release date: 2016-05-18
lab: Richard Myers, HAIB
library encode accession: ENCLB656PGG

value: CTCF

value: hindbrain

value: tissue

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

value: postnatal

value: 0 day

value: not collected

value: ENCBS399IKT at ENCODE; https://www.encodeproject.org/ENCBS399IKT/

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


title: ChIP-seq from hindbrain (ENCLB177OBS)

description:
https://www.encodeproject.org/experiments/ENCSR150RGT/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on CTCF-mouse
experiment encode accession: ENCSR150RGT
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR655SYB
encode release date: 2016-05-18
lab: Richard Myers, HAIB
library encode accession: ENCLB177OBS

value: Richard Myers, HAIB


title: ChIP-seq from kidney (ENCLB710JGJ)

description:
https://www.encodeproject.org/experiments/ENCSR143WOK/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on CTCF-mouse
experiment encode accession: ENCSR143WOK
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR655KFC
encode release date: 2016-05-18
lab: Richard Myers, HAIB
library encode accession: ENCLB710JGJ

value: kidney

value: ENCBS591PKP at ENCODE; https://www.encodeproject.org/ENCBS591PKP/


title: eCLIP from K562 (ENCLB419TPX)

description:
https://www.encodeproject.org/experiments/ENCSR366YOG/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against QKI
experiment encode accession: ENCSR366YOG
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR615AAW
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB419TPX
size range: 175-300

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

value: ENCBS318IMK at ENCODE; https://www.encodeproject.org/ENCBS318IMK/

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 HEK293 (ENCLB755UDB)

description:
https://www.encodeproject.org/experiments/ENCSR365GRX/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZFP37 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR365GRX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR157LMX, ENCSR274OGE, ENCSR342AGU, ENCSR354FNX, ENCSR429LAP, ENCSR688NWK
encode release date: 2016-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB755UDB
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZFP37 fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZFP37 under the control of a CMV promoter.

value: embryonic

value: unknown

value: female

value: Michael Snyder, Stanford

value: ENCBS841DEH at ENCODE; https://www.encodeproject.org/ENCBS841DEH/

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


title: ChIP-seq from heart (ENCLB960KIF)

description:
https://www.encodeproject.org/experiments/ENCSR109LQX/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on P0 heart-mouse (fragmentation date: 2015-02-05)
experiment encode accession: ENCSR109LQX
assay title: ChIP-seq
encode release date: 2016-02-02
lab: Richard Myers, HAIB
library encode accession: ENCLB960KIF

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

value: Control

value: heart

value: tissue

value: postnatal

value: 0 day

value: not collected

value: Richard Myers, HAIB

value: ENCBS345FLN at ENCODE; https://www.encodeproject.org/ENCBS345FLN/

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


title: ChIP-seq from HEK293 (ENCLB754PWX)

description:
https://www.encodeproject.org/experiments/ENCSR365GRX/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZFP37 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR365GRX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR157LMX, ENCSR274OGE, ENCSR342AGU, ENCSR354FNX, ENCSR429LAP, ENCSR688NWK
encode release date: 2016-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB754PWX
size range: 450-650

value: immortalized cell line

value: ENCBS853DEI at ENCODE; https://www.encodeproject.org/ENCBS853DEI/


title: ChIP-seq from stomach (ENCLB576XEH)

description:
https://www.encodeproject.org/experiments/ENCSR104QEN/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on CTCF-mouse
experiment encode accession: ENCSR104QEN
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR389SQZ
encode release date: 2016-05-18
lab: Richard Myers, HAIB
library encode accession: ENCLB576XEH

value: CTCF

value: stomach

value: ENCBS551QZH at ENCODE; https://www.encodeproject.org/ENCBS551QZH/


title: CR243_Low

city: Chapel Hill

first: Bailey

last: Peck

state: NC

address: 120 Mason Farm Rd, 5100H Genetic Medicine Bldg

institute: University of North Carolina at Chapel Hill

description: small RNA

data_processing:
Small RNA-seq data was aligned using methodology described in Baran-Gale et al. (PLOS ONE, 2012), with the following modification: only contigs with greater than one read alignment were passed into the to Shrimp alignment pipeline.
Reads were trimmed by cutAdapt to remove adaptor remnants. Trimmed reads of 14-41 nt are first mapped exactly (no mismatches) using Bowtie. Windows are determined using these mapped reads, and the unmapped reads, are realigned to these windows using SHRiMP2 with mismatches allowed (See Baran-Gale et al, 2012), these would be considered edits & isomiRs, and are named based on the canonical miRNA (miRbase).
Reads were normalized using Reads per Million Mapped to miRNAs (RPMMM). We pulled out miRNAs and isomiRs with at least 400 RPMMM in at least 1 sample for downstream analyses.
Genome_build: mm9
Supplementary_files_format_and_content: Multiple sample Tab-delimited file with RPMMMs of all miRNAs & isomiRs (no expression threshold)

source_name: Intestinal Epithelial Cells

growth_protocol: Germfree animals were raised at the University of North Carolina's Gnotobiotic Core Facility. At 8-10 weeks of age, one littermate was transferred to the UNC MBRB Animal facility and conventionalized by oral gavage with fecal slurry prepared from fecal pellets collected from the conventionally raised Sox9-EGFP mouse colony. Following 2-week conventionalization, both animals were harvested for their jejunal IECs, and samples sorted using previously described methods (Van Landeghem et al., 2012). Animal studies were approved my our institutions IACUC (protocol 13-162).

extract_protocol:
Sorted cells were lysed and RNA was extracted using Norgen Single cell and Total RNA isolation kits as per the manufacturer's instructions
Small RNA libraries were prepared at the University of Texas Health Sciences Center at San Antonio Genome Sequencing Facility. Libraries were prepared using an average of 50 ng of total RNA using the TriLink CleanTag Small RNA Ligation kit (TriLink Biotechnologies, San Diego, CA) and suggested library preparation method. Six to seven libraries were pooled per lane, and the small RNA sequencing was conducted at the Genome Sequencing Facility of Greehey Children's Cancer Research Institute at University of Texas Health Science Center at San Antonio single-end 50x on the HiSeq2000 platform.

treatment_protocol: Jejunal IECs were stained for Annexin-V, CD31, CD45, and by Sytox-blue. FACS was used to gete these populations out during sorting.

value: Sox9-EGFP on C57BL/6J background

value: Female

tag: tissue

value: jejunum

tag: cell type

value: Intestinal Epithelial Cells

tag: condition

value: Conventionally-raised

tag: iec population

value: Sox9-EGFP Low

tag: littermate pair

value: G

tag: sequence date

value: 28 weeks


title: ChIP-seq from HEK293 (ENCLB419BYD)

description:
https://www.encodeproject.org/experiments/ENCSR468IJT/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-SP7 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR468IJT
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: ENCLB419BYD
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-SP7 fusion protein

tag: antibody

tag: line

tag: description

value: HEK293 cell line stably expressing N-terminal tagged eGFP-SP7 under the control of a CMV promoter.

tag: biosample encode accession

tag: dev stage

value: embryonic

value: unknown

value: female

value: Michael Snyder, Stanford

value: ENCBS983QBQ at ENCODE; https://www.encodeproject.org/ENCBS983QBQ/

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


title: CR243_High

description: small RNA

tag: Sex

value: Sox9-EGFP High

tag: age


title: ChIP-seq from MCF-7 (ENCLB362YTD)

description:
https://www.encodeproject.org/experiments/ENCSR468LUO/
***************
biological replicate number: 3
technical replicate number: 1
description: SIN3A ChIP-seq on human MCF-7
experiment encode accession: ENCSR468LUO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2016-02-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB362YTD
size range: 450-650

value: immortalized cell line

value: adult

value: 69 year

tag: lab

tag: health state

value: breast cancer (adenocarcinoma)

tag: link

value: ENCBS616MBU at ENCODE; https://www.encodeproject.org/ENCBS616MBU/

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: CR242_NS

description: small RNA

tag: strain

value: Sox9-EGFP on C57BL/6J background

value: Female

value: jejunum

value: Intestinal Epithelial Cells

value: Conventionally-raised

value: Sox9-EGFP Non-sorted IECs

value: F


title: ChIP-seq from K562 (ENCLB491YHQ)

description:
https://www.encodeproject.org/experiments/ENCSR468BNS/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-NR4A1 tagged K562 cell line.
experiment encode accession: ENCSR468BNS
assay title: ChIP-seq
encode release date: 2016-09-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB491YHQ
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-NR4A1 fusion protein

value: Control

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to NR4A1

value: 53 year

value: female

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: ENCBS862GKZ at ENCODE; https://www.encodeproject.org/ENCBS862GKZ/

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

value: ENCODE dbxrefs Cellosaurus CVCL_AW37; http://web.expasy.org/cellosaurus/CVCL_AW37


title: CR242_Sublow

description: small RNA

tag: tissue

value: Sox9-EGFP Sublow

value: 28 weeks


title: CR242_Low

description: small RNA

value: Sox9-EGFP on C57BL/6J background

value: Female

tag: cell type

value: Sox9-EGFP Low


title: CR242_High

description: small RNA

value: jejunum

value: Intestinal Epithelial Cells

tag: condition

value: Conventionally-raised

value: Sox9-EGFP High


title: ChIP-seq from HEK293 (ENCLB544MOG)

description:
https://www.encodeproject.org/experiments/ENCSR468IJT/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-SP7 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR468IJT
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: ENCLB544MOG
size range: 450-650

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-SP7 under the control of a CMV promoter.

value: embryonic

value: unknown

value: Michael Snyder, Stanford

value: ENCBS516AIH at ENCODE; https://www.encodeproject.org/ENCBS516AIH/

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


title: CR183_NS

description: small RNA

tag: iec population

value: Sox9-EGFP Non-sorted IECs

value: E

value: 29 weeks


title: ChIP-seq from HEK293 (ENCLB794UMJ)

description:
https://www.encodeproject.org/experiments/ENCSR468NLK/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq on eGFP-ZNF165 tagged human HEK293 cells.
experiment encode accession: ENCSR468NLK
assay title: ChIP-seq
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB794UMJ
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF165 fusion protein

value: Control

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF165 under the control of a CMV promoter.

value: female

value: ENCBS519XFO at ENCODE; https://www.encodeproject.org/ENCBS519XFO/


title: ChIP-seq from HEK293 (ENCLB529UQM)

description:
https://www.encodeproject.org/experiments/ENCSR354FNX/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq on eGFP-ZNF18 tagged human HEK293 cells.
experiment encode accession: ENCSR354FNX
assay title: ChIP-seq
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB529UQM
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF18 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF18 under the control of a CMV promoter.

value: ENCBS867IQP at ENCODE; https://www.encodeproject.org/ENCBS867IQP/


title: ChIP-seq from MCF-7 (ENCLB400SMX)

description:
https://www.encodeproject.org/experiments/ENCSR465VLK/
***************
biological replicate number: 2
technical replicate number: 1
description: FOXK2 ChIP-seq on human MCF-7
experiment encode accession: ENCSR465VLK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR217LRF, ENCSR594UCI
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB400SMX
size range: 450-650

value: adult

value: 69 year

value: breast cancer (adenocarcinoma)

value: ENCBS308QKF at ENCODE; https://www.encodeproject.org/ENCBS308QKF/

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: eCLIP from K562 (ENCLB748FLS)

description:
https://www.encodeproject.org/experiments/ENCSR356GCJ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against TIA1
experiment encode accession: ENCSR356GCJ
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-08-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB748FLS
size range: 175-300

value: immortalized cell line

value: 53 year

value: chronic myelogenous leukemia (CML)

tag: passage number

value: Gene Yeo, UCSD

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

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 (ENCLB498HDN)

description:
https://www.encodeproject.org/experiments/ENCSR360HRA/
***************
biological replicate number: 2
technical replicate number: 1
description: KDM1A ChIP-seq on human K562
experiment encode accession: ENCSR360HRA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB498HDN
size range: 450-650

value: female

value: Michael Snyder, Stanford

value: ENCBS538DYC at ENCODE; https://www.encodeproject.org/ENCBS538DYC/


title: CR183_Sublow

description: small RNA

value: Sox9-EGFP on C57BL/6J background

value: Female

value: jejunum

value: Intestinal Epithelial Cells

value: Conventionally-raised

value: Sox9-EGFP Sublow

tag: littermate pair

value: E

tag: sequence date

value: 29 weeks