title: ChIP-seq from K562 (ENCLB565EOJ)

description:
https://www.encodeproject.org/experiments/ENCSR350XWY/
***************
biological replicate number: 1
technical replicate number: 1
description: C11orf30 ChIP-seq on human K562
experiment encode accession: ENCSR350XWY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2016-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB565EOJ
size range: 450-650

tag: antibody

tag: line

value: immortalized cell line

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

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


title: ChIP-seq from kidney (ENCLB462RLJ)

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/ENCSR143WOK/
***************
biological replicate number: 1
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: ENCLB462RLJ

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

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

value: CTCF

value: kidney

value: tissue

tag: biosample encode accession

tag: dev stage

value: postnatal

tag: age

value: 0 day

tag: Sex

value: not collected

tag: lab

value: Richard Myers, HAIB

tag: link

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

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


title: ChIP-seq from MCF-7 (ENCLB170VAD)

description:
https://www.encodeproject.org/experiments/ENCSR468LUO/
***************
biological replicate number: 1
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: ENCLB170VAD
size range: 450-650

organism: Homo sapiens

source_name: Homo sapiens MCF-7 immortalized cell line

tag: description

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

value: female

value: 69 year

tag: health state

value: breast cancer (adenocarcinoma)

value: Michael Snyder, Stanford

value: ENCBS216AOQ at ENCODE; https://www.encodeproject.org/ENCBS216AOQ/

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

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

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


title: CR183_Neg

city: Chapel Hill

first: Bailey

last: Peck

state: NC

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

department: Genetics

institute: University of North Carolina at Chapel Hill

description: small RNA

library_source: transcriptomic

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)

molecule: total RNA

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.

tag: strain

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 Neg

tag: littermate pair

value: E

tag: sequence date

value: 29 weeks


title: ChIP-seq from stomach (ENCLB513QXP)

description:
https://www.encodeproject.org/experiments/ENCSR104QEN/
***************
biological replicate number: 1
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: ENCLB513QXP

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

tag: antibody

value: CTCF

value: stomach

value: tissue

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: CR243_Neg

description: small RNA

value: Sox9-EGFP on C57BL/6J background

value: G

value: 28 weeks


title: CR183_High

description: small RNA

value: Female

value: jejunum

value: Intestinal Epithelial Cells

value: Sox9-EGFP High


title: CR183_Low

description: small RNA

value: Conventionally-raised

value: Sox9-EGFP Low

value: E

value: 29 weeks


title: ChIP-seq from MCF-7 (ENCLB772BAJ)

description:
https://www.encodeproject.org/experiments/ENCSR465VLK/
***************
biological replicate number: 1
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: ENCLB772BAJ
size range: 450-650

tag: line

value: immortalized cell line

value: adult

value: 69 year

value: female

value: Michael Snyder, Stanford

value: breast cancer (adenocarcinoma)

value: ENCBS957OEW at ENCODE; https://www.encodeproject.org/ENCBS957OEW/

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: CR180_NS

description: small RNA

value: Sox9-EGFP on C57BL/6J background

value: Female

value: Sox9-EGFP Non-sorted IECs


title: ChIP-seq from K562 (ENCLB298MSG)

description:
https://www.encodeproject.org/experiments/ENCSR350XWY/
***************
biological replicate number: 2
technical replicate number: 1
description: C11orf30 ChIP-seq on human K562
experiment encode accession: ENCSR350XWY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2016-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB298MSG
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line

tag: biosample encode accession

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS906KIP at ENCODE; https://www.encodeproject.org/ENCBS906KIP/

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 (ENCLB990HZH)

description:
https://www.encodeproject.org/experiments/ENCSR360HRA/
***************
biological replicate number: 1
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: ENCLB990HZH
size range: 450-650

value: immortalized cell line

tag: dev stage

value: ENCBS357NWO at ENCODE; https://www.encodeproject.org/ENCBS357NWO/


title: CR242_Neg

description: small RNA

value: jejunum

value: Intestinal Epithelial Cells

value: Conventionally-raised

value: Sox9-EGFP Neg

value: F

tag: age

value: 28 weeks


title: CR180_Sublow

description: small RNA

tag: Sex

value: Sox9-EGFP Sublow

value: E

value: 29 weeks


title: ChIP-seq from HEK293 (ENCLB495HCN)

description:
https://www.encodeproject.org/experiments/ENCSR464KFG/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF140 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR464KFG
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: 2016-10-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB495HCN
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF140 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF140 under the control of a CMV promoter.

value: embryonic

value: female

value: unknown

tag: lab

value: Michael Snyder, Stanford

value: ENCBS212ZLO at ENCODE; https://www.encodeproject.org/ENCBS212ZLO/

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


title: ChIP-seq from HEK293 (ENCLB673UDE)

description:
https://www.encodeproject.org/experiments/ENCSR464KFG/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF140 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR464KFG
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: 2016-10-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB673UDE
size range: 450-650

value: immortalized cell line

tag: link

value: ENCBS627OXL at ENCODE; https://www.encodeproject.org/ENCBS627OXL/


title: eCLIP from K562 (ENCLB872GYN)

description:
https://www.encodeproject.org/experiments/ENCSR349KMG/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against UCHL5
experiment encode accession: ENCSR349KMG
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR751CSY
encode release date: 2016-08-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB872GYN
size range: 175-300

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

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

tag: passage number

value: Gene Yeo, UCSD

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

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

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

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


title: CR180_Neg

description: small RNA

value: Sox9-EGFP on C57BL/6J background

value: Female

value: jejunum

value: Intestinal Epithelial Cells

value: Conventionally-raised

value: Sox9-EGFP Neg

value: E

value: 29 weeks


title: CR180_High

description: small RNA

value: Sox9-EGFP High


title: ctr_hsc_l3 RNA-Seq

city: Houston

first: deqiang

last: sun

state: TX

address: 2121 W Holcombe Blvd

institute: Texas A&M University

description:
technical replicate of biological replicate 2
ctr_hsc_l3

data_processing:
RUM to make alignments; Customized script to count fragments on gene; DESEQ to do differential expression test;
Genome_build: mm9
Supplementary_files_format_and_content: XLSX file for two sample comparison testing if a gene is differentially expressed; includes average FPKM values for

source_name: Murine bone marrow derived primary HSCs

growth_protocol: Freshly sorted HSCs (SP KSL CD150+) from naïve or M. avium infected mice

extract_protocol:
Extract RNA using Qiagen Rneasy Micro kit
Tru-Seq RNA sample prep kit

value: bone marrow

value: Hematopoietic stem cells (HSCs)

tag: cell surface marker

value: SP KSL CD150+

tag: gender

value: 3-4 months

tag: treatment

value: Naïve


title: CR180_Low

description: small RNA

tag: strain

tag: tissue

tag: cell type

value: Sox9-EGFP Low


title: eCLIP from K562 (ENCLB574FHH)

description:
https://www.encodeproject.org/experiments/ENCSR347MVO/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against GEMIN5
experiment encode accession: ENCSR347MVO
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-09-21
lab: Gene Yeo, UCSD
library encode accession: ENCLB574FHH
size range: 175-300

value: Control

value: immortalized cell line

value: adult

value: female

value: 53 year

tag: health state

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

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

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

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


title: eCLIP from K562 (ENCLB901RWZ)

description:
https://www.encodeproject.org/experiments/ENCSR349KMG/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against UCHL5
experiment encode accession: ENCSR349KMG
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR751CSY
encode release date: 2016-08-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB901RWZ
size range: 175-300

value: ENCBS505ILK at ENCODE; https://www.encodeproject.org/ENCBS505ILK/

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


title: ctr_hsc_l1 RNA-Seq

description:
technical replicate of biological replicate 1
ctr_hsc_l1

value: bone marrow

value: Hematopoietic stem cells (HSCs)

value: Female

value: 5 months


title: eCLIP from K562 (ENCLB448DOH)

description:
https://www.encodeproject.org/experiments/ENCSR346IHS/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against PPIL4
experiment encode accession: ENCSR346IHS
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB448DOH
size range: 175-300

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


title: ChIP-seq from HEK293 (ENCLB914FJJ)

description:
https://www.encodeproject.org/experiments/ENCSR462FWS/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF101 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR462FWS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB914FJJ
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF101 fusion protein

tag: description

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF101 under the control of a CMV promoter.

value: embryonic

value: unknown

value: Michael Snyder, Stanford

value: ENCBS370DEV at ENCODE; https://www.encodeproject.org/ENCBS370DEV/

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


title: ctr_hsc_l2 RNA-Seq

description:
technical replicate of biological replicate 1
ctr_hsc_l2

value: SP KSL CD150+

value: Naïve


title: ChIP-seq from HEK293 (ENCLB760OCM) -2

description:
https://www.encodeproject.org/experiments/ENCSR342AGU/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq on eGFP-ZSCAN5A tagged human HEK293 cells.
experiment encode accession: ENCSR342AGU
assay title: ChIP-seq
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB760OCM
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZSCAN5A fusion protein

tag: antibody

value: Control

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZSCAN5A under the control of a CMV promoter.

value: female

value: ENCBS882KQI at ENCODE; https://www.encodeproject.org/ENCBS882KQI/


title: mav_hsc_l3 RNA-Seq

description:
technical replicate of biological replicate 2
mav_hsc_l3

value: bone marrow

value: Hematopoietic stem cells (HSCs)

value: 3-4 months

value: Mycobacterium avium infection


title: mav_hsc_l2 RNA-Seq

description:
technical replicate of biological replicate 1
mav_hsc_l2

value: Female

value: 5 months


title: mav_hsc_l1 RNA-Seq

description:
technical replicate of biological replicate 1
mav_hsc_l1


title: eCLIP from K562 (ENCLB186JKI)

description:
https://www.encodeproject.org/experiments/ENCSR456KXI/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against LARP7
experiment encode accession: ENCSR456KXI
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR863ZGZ
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB186JKI
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

tag: line

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

value: ENCBS079MXX at ENCODE; https://www.encodeproject.org/ENCBS079MXX/

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 HEK293 (ENCLB160EOD)

description:
https://www.encodeproject.org/experiments/ENCSR338DGO/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-SCRT2 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR338DGO
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: ENCLB160EOD
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-SCRT2 fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-SCRT2 under the control of a CMV promoter.

tag: biosample encode accession

value: embryonic

value: unknown

value: Michael Snyder, Stanford

value: ENCBS969EIC at ENCODE; https://www.encodeproject.org/ENCBS969EIC/

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


title: eCLIP from HepG2 (ENCLB651LPO)

description:
https://www.encodeproject.org/experiments/ENCSR459ONR/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against HNRNPM
experiment encode accession: ENCSR459ONR
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB651LPO
size range: 175-300

source_name: Homo sapiens HepG2 immortalized cell line

value: Control

tag: dev stage

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: ENCBS017VYZ at ENCODE; https://www.encodeproject.org/ENCBS017VYZ/

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 (ENCLB069IAV)

description:
https://www.encodeproject.org/experiments/ENCSR456KXI/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against LARP7
experiment encode accession: ENCSR456KXI
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR863ZGZ
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB069IAV
size range: 175-300

value: adult

value: female

tag: age

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

value: ENCBS024UMN at ENCODE; https://www.encodeproject.org/ENCBS024UMN/

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

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

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


title: ChIP-seq from MCF-7 (ENCLB057JGF)

description:
https://www.encodeproject.org/experiments/ENCSR389BLX/
***************
biological replicate number: 1
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: ENCLB057JGF
size range: 450-650

value: immortalized cell line

value: 69 year

tag: Sex

value: Michael Snyder, Stanford

value: breast cancer (adenocarcinoma)

value: ENCBS764AUT at ENCODE; https://www.encodeproject.org/ENCBS764AUT/

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


title: ChIP-seq from HEK293 (ENCLB896HDJ)

description:
https://www.encodeproject.org/experiments/ENCSR462FWS/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF101 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR462FWS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB896HDJ
size range: 450-650

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF101 under the control of a CMV promoter.

value: embryonic

value: unknown

tag: lab

value: ENCBS096IDY at ENCODE; https://www.encodeproject.org/ENCBS096IDY/

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


title: GF315_Low_mRNA

data_processing:
Seven bases were trimmed from the beginning of each read using Trimmomatic (v0.36) to eliminate remaining SMART adapter sequences
Reads were aligned to the GENCODE mouse transcriptome (vM10) using STAR (v2.4.2a) and SALMON (v0.6.0).
Transcript counts were then imported into R (v3.3.1), and were normalized and differential expression of genes quantified using DESeq2 (v1.12.4).
Genome_build: mm10
Supplementary_files_format_and_content: Comma separated file for all samples containing normalized count.

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
Libraries were created from 10 ng Total RNA using the the Clonetech SMARTer Ultra Low Input library preparation kit combined with Nextera XT DNA sample preparation kit (Illumina) by the UNC High Throughput Sequencing Core Facility (as per the Clonetech sample preparation guide). Four libraries randomly pooled per lane and sequenced 100 bp single-end on a HiSeq2000 platform at the UNC High Throughput Sequencing Core Facility.

value: Sox9-EGFP on C57BL/6J background

value: Female

value: jejunum

value: Intestinal Epithelial Cells

tag: condition

value: Germfree

tag: iec population

value: Sox9-EGFP Low

tag: littermate pair

value: D


title: GF305_Low_mRNA

value: C


title: eCLIP from HepG2 (ENCLB373DCN)

description:
https://www.encodeproject.org/experiments/ENCSR451HMR/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against GTF2F1
experiment encode accession: ENCSR451HMR
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB373DCN
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: Control

value: immortalized cell line

value: child

value: 15 year

value: male

tag: passage number

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

tag: link

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: GF244_Low_mRNA

tag: strain

value: Sox9-EGFP on C57BL/6J background

value: Female

value: jejunum

value: A


title: GF271_Low_mRNA

tag: tissue

value: Intestinal Epithelial Cells

value: Germfree

value: Sox9-EGFP Low

value: B


title: ChIP-seq from HEK293 (ENCLB884UKM)

description:
https://www.encodeproject.org/experiments/ENCSR338DGO/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-SCRT2 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR338DGO
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: ENCLB884UKM
size range: 450-650

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-SCRT2 under the control of a CMV promoter.

value: embryonic

value: unknown

value: female

value: Michael Snyder, Stanford

value: ENCBS843XAC at ENCODE; https://www.encodeproject.org/ENCBS843XAC/

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


title: CV304_Low_mRNA

tag: cell type

value: Conventionalized

value: C


title: CV314_Low_mRNA

value: Sox9-EGFP on C57BL/6J background

value: Female

value: D


title: ChIP-seq from HEK293 (ENCLB527VPB)

description:
https://www.encodeproject.org/experiments/ENCSR451CYX/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF280D ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR451CYX
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: 2016-10-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB527VPB
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF280D fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF280D under the control of a CMV promoter.

tag: health state

value: ENCBS214JNY at ENCODE; https://www.encodeproject.org/ENCBS214JNY/


title: eCLIP from HepG2 (ENCLB988JUB)

description:
https://www.encodeproject.org/experiments/ENCSR334OMC/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against DDX59
experiment encode accession: ENCSR334OMC
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-10-31
lab: Gene Yeo, UCSD
library encode accession: ENCLB988JUB
size range: 175-300

value: Control

value: child

value: 15 year

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS881CIF at ENCODE; https://www.encodeproject.org/ENCBS881CIF/

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 HEK293 (ENCLB398DTF)

description:
https://www.encodeproject.org/experiments/ENCSR451CYX/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF280D ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR451CYX
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: 2016-10-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB398DTF
size range: 450-650

value: immortalized cell line

tag: description

value: embryonic

value: female

value: unknown

value: Michael Snyder, Stanford

value: ENCBS107SDK at ENCODE; https://www.encodeproject.org/ENCBS107SDK/

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


title: ChIP-seq from K562 (ENCLB421OCV)

description:
https://www.encodeproject.org/experiments/ENCSR334HSW/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF318 ChIP-seq on human K562
experiment encode accession: ENCSR334HSW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2016-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB421OCV
size range: 450-650

tag: antibody

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: ENCBS207UAM at ENCODE; https://www.encodeproject.org/ENCBS207UAM/

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

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

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


title: ChIP-seq from MCF-7 (ENCLB834TZE)

description:
https://www.encodeproject.org/experiments/ENCSR449UFF/
***************
biological replicate number: 4
technical replicate number: 1
description: ZKSCAN1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR449UFF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB834TZE
size range: 450-650

tag: line

value: 69 year

value: breast cancer (adenocarcinoma)

value: ENCBS959SHH at ENCODE; https://www.encodeproject.org/ENCBS959SHH/

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

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


title: ChIP-seq from MCF-7 (ENCLB393KRV)

description:
https://www.encodeproject.org/experiments/ENCSR449UFF/
***************
biological replicate number: 3
technical replicate number: 1
description: ZKSCAN1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR449UFF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB393KRV
size range: 450-650

value: immortalized cell line

tag: biosample encode accession

value: female

value: ENCBS547AXB at ENCODE; https://www.encodeproject.org/ENCBS547AXB/


title: PolyA-RNA-GW3965

city: La Jolla

first: Nathanael

middle: Judge

last: Spann

address: 9500 Gilman Drive CMMW 219A

department: Cellular and Molecular Medicine

institute: UCSD

description: Sample 102

data_processing:
Libraries were sequenced for 36 or 50 cycles on an Illumina Genome Analyzer, Illumina Genome Analyzer II or HiSeq 2000, respectively, according to the manufacturer’s instructions.
For ChIP-Seq (single end reads), reads were aligned to the mm9 genome (NCBI37) using bowtie (v0.12.7), keeping only reads that mapped best to a single, unique location.
For RNA-Seq samples (single end reads), reads were aligned to the mm9 genome (NCBI37) using default parameter for RNA-Star. Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, then perform analyses as indicated in the study.
For ChIP-Seq, Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, and perform other analyses in the study. Each ChIP-Seq experiment was normalized to a total of 10^7 uniquely mapped tags by adjusting the number of tags at each position in the genome to the correct fractional amount given the total tags mapped. UCSC Genome Browser BigWig or BigWig hub text files were created by calculating ChIP-Fragment pileups given a fragment size of ~150 bp.
Genome_build: mm9
Supplementary_files_format_and_content: Processed files include BED-like files (ChIP-Seq peak positions), peak text files (ChIP-Seq peak data, using default HOMER parameters), and expression text files (RNA-Seq expression data, using default HOMER parameters).  All genomic coordinates are relative to mm9  (NCBI37) mouse assembly.

molecule: polyA RNA

growth_protocol:
Peritoneal thioglycollate-elicited macrophages (TGEMs): Primary cells were isolated from 6-8 week-old C57Bl/6 (Harlan Laboratories) male mice. Thioglycollate-elicited macrophages were isolated by peritoneal lavage 3-4 days following peritoneal injection of 2.5 ml thioglycollate. Cells were plated in RPMI medium 1640 and 10% fetal bovine serum, washed after adherence and again fed with fresh medium. The following day fresh medium containing 0.5% fetal bovine serum was added to the cells and serum starvation was carried overnight. After serum starvation the cells were treated with 100 ng/ml of Kdo2-Lipid A for 1 – 24 hours. For LXR experiments cells were treated with 1uM GW3965 or 20uM Desmosterol for 24 hours.
Bone marrow derived macrophages (BMDMs): Mouse bone marrow was harvested and washed once with PBS, seeded/cultured in DMEM containing 20 % FCS, 30 % L-cell conditioned media (as source of macrophage colony stimulating factor, M-CSF), and 100 U/ml penicillin/streptomycin in non-tissue culture-treated petri dishes. After 6-8 days of culture, non-adherent cells were washed off with room temperature PBS and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in RPMI-1640 containing 10% FCS, 100 U/ml penicillin/streptomycin, and 10ng/ml M-CSF. The following day fresh medium containing 0.5% fetal bovine serum was added to the cells and serum starvation was carried overnight. After serum starvation the cells were treated with 100 ng/ml of Kdo2-Lipid A for 1 – 24 hours. For LXR experiments cells were treated with 1uM GW3965 or 20uM Desmosterol for 24 hours.

extract_protocol:
ChIP-Seq: Sequencing libraries were prepared from collected DNA by blunting, A-tailing, adapter ligation as previously described (Heinz, S. et al. Molecular Cell 38, 576-589 (2010)) using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR-amplified for 12-15 cycles, size selected by gel extraction and sequenced on a Hi-Seq 2000 (Illumina) for 51 cycles.
RNA-Seq: Sequencing libraries were prepared from polyA enriched mRNA, either as previously described (Kaikkonen M.U. et al. Molecular Cell 51, 310-325 (2013)), or as follows. Poly A enriched mRNA was fragmented, in 2x Superscript III first-strand buffer with 10mM DTT (Invitrogen), by incubation at 94°C for 9 minutes, then immediately chilled on ice before the next step. The 10 µL of fragmented mRNA, 0.5 µL of Random primer (Invitrogen), 0.5 µL of Oligo dT primer (Invitrogen), 0.5 µL of SUPERase-In (Ambion), 1 µL of dNTPs (10 mM) and 1 µL of DTT (10 mM) were heated at 50°C for three minutes. At the end of incubation, 5.8 µL of water, 1 µL of DTT (100 mM), 0.1 µL Actinomycin D (2 µg/µL), 0.2 µL of 1% Tween-20 (Sigma) and 0.2 µL of Superscript III (Invitrogen) were added and incubated in a PCR machine using the following conditions: 25°C for 10 minutes, 50°C for 50 minutes, and a 4°C hold. The product was then purified with RNAClean XP beads according to manufacture’s instruction and eluted with 10 µL nuclease-free water. The RNA/cDNA double-stranded hybrid was then added to 1.5 µL of Blue Buffer (Enzymatics), 1.1 µL of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 µL of RNAse H (5 U/µL), 1.05 µL of water, 1 µL of DNA polymerase I (Enzymatics) and 0.15 µL of 1% Tween-20. The mixture was incubated at 16°C for 1 hour. The resulting dUTP-marked dsDNA was purified using 28 µL of Sera-Mag Speedbeads (Thermo Fisher Scientific), diluted with 20% PEG8000, 2.5M NaCl to final of 13% PEG, eluted with 40 µL EB buffer (10 mM Tris-Cl, pH 8.5) and frozen -80°C. The purified dsDNA (40 µL) underwent end repair by blunting, A-tailing and adapter ligation as previously described (Heinz, S. et al. Molecular Cell 38, 576-589 (2010)) using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR-amplified for 9-14 cycles, size selected by gel extraction, quantified Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and sequenced on either a Genome Analyzer II (Illumina) or Hi-Seq 2000 (Illumina) for 51 cycles.

tag: strain background

tag: treated with

value: GW3965 (1uM) for 24 hours


title: PolyA-RNA-notreatment

description: Sample 101

value: none (control)


title: PolyA-RNA-Desmosterol

description: Sample 103

value: desmosterol (20uM) for 24 hours


title: Input DNA BMDM DSG formaldehyde ChIP-Seq Srebp1 WT KLA24h

description:
formaldehyde cross-linked
Sample 100

source_name: bone marrow derived macrophages

tag: genotype/variation

value: Srebp1 WT

value: bone marrow derived macrophages

value: KLA for 24 hours


title: Input DNA BMDM DSG formaldehyde ChIP-Seq Srebp1 KO KLA24h

description:
formaldehyde cross-linked
Sample 99

value: Srebp1 -/-


title: ChIP-seq from MCF-7 (ENCLB170DGQ)

description:
https://www.encodeproject.org/experiments/ENCSR318LVG/
***************
biological replicate number: 2
technical replicate number: 1
description: ZBTB40 ChIP-seq on human MCF-7
experiment encode accession: ENCSR318LVG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR882IYK
encode release date: 2016-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB170DGQ
size range: 450-650

tag: dev stage

value: adult

tag: age

tag: Sex

tag: lab

value: Michael Snyder, Stanford

value: ENCBS705BBA at ENCODE; https://www.encodeproject.org/ENCBS705BBA/


title: CV270_Low_mRNA

value: Sox9-EGFP on C57BL/6J background

value: Female

value: jejunum

value: Intestinal Epithelial Cells

tag: condition

value: Conventionalized

tag: iec population

value: Sox9-EGFP Low

tag: littermate pair

value: B


title: CV246_Low_mRNA

tag: strain

tag: tissue

value: A


title: eCLIP from HepG2 (ENCLB921SNF)

description:
https://www.encodeproject.org/experiments/ENCSR317PWQ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against RBM15
experiment encode accession: ENCSR317PWQ
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB921SNF
size range: 175-300

value: Control

value: immortalized cell line

value: child

value: male

value: 15 year

tag: health state

value: hepatocellular carcinoma

tag: passage number

value: Gene Yeo, UCSD

tag: link

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: Input DNA BMDM formaldehyde ChIP-Seq Srebp1 WT KLA24h

description:
formaldehyde cross-linked
Sample 98

value: Srebp1 WT

tag: cell type

value: bone marrow derived macrophages

value: KLA for 24 hours


title: ChIP-seq from HEK293 (ENCLB892LYN)

description:
https://www.encodeproject.org/experiments/ENCSR447ZTA/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF558 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR447ZTA
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: ENCLB892LYN
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF558 fusion protein

tag: antibody

tag: line

tag: description

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF558 under the control of a CMV promoter.

tag: biosample encode accession

value: embryonic

value: female

value: unknown

value: Michael Snyder, Stanford

value: ENCBS079QRO at ENCODE; https://www.encodeproject.org/ENCBS079QRO/

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


title: Input DNA BMDM formaldehyde ChIP-Seq Srebp1 KO KLA6h

description:
formaldehyde cross-linked
Sample 95

tag: strain background

tag: genotype/variation

value: Srebp1 -/-

tag: treated with

value: KLA for 6 hours


title: Input DNA BMDM formaldehyde ChIP-Seq Srebp1 WT KLA6h

description:
formaldehyde cross-linked
Sample 96


title: eCLIP from K562 (ENCLB746THF)

description:
https://www.encodeproject.org/experiments/ENCSR316SZJ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against RPS5
experiment encode accession: ENCSR316SZJ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR486QAE
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB746THF
size range: 175-300

value: immortalized cell line

tag: dev stage

value: adult

tag: Sex

tag: age

value: 53 year

value: chronic myelogenous leukemia (CML)

tag: lab

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


title: ChIP-seq from K562 (ENCLB712CAM)

description:
https://www.encodeproject.org/experiments/ENCSR446LAV/
***************
biological replicate number: 2
technical replicate number: 1
description: DDX20 ChIP-seq on human K562
experiment encode accession: ENCSR446LAV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-04-22
lab: Michael Snyder, Stanford
library encode accession: ENCLB712CAM
size range: 450-650

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

value: ENCBS118YJZ at ENCODE; https://www.encodeproject.org/ENCBS118YJZ/

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


title: Input DNA BMDM formaldehyde ChIP-Seq Srebp1 KO KLA24h

description:
formaldehyde cross-linked
Sample 97

value: bone marrow derived macrophages

value: KLA for 24 hours


title: ChIP-seq from MCF-7 (ENCLB345ZOV)

description:
https://www.encodeproject.org/experiments/ENCSR318LVG/
***************
biological replicate number: 1
technical replicate number: 1
description: ZBTB40 ChIP-seq on human MCF-7
experiment encode accession: ENCSR318LVG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR882IYK
encode release date: 2016-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB345ZOV
size range: 450-650

value: 69 year

value: female

value: Michael Snyder, Stanford

value: breast cancer (adenocarcinoma)

value: ENCBS866ZXX at ENCODE; https://www.encodeproject.org/ENCBS866ZXX/

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: Input DNA BMDM formaldehyde ChIP-Seq Srebp1 WT KLA1h

description:
formaldehyde cross-linked
Sample 94

value: Srebp1 WT

value: KLA for 1 hours


title: Input DNA BMDM DSG formaldehyde ChIP-Seq Srebp1 WT No treatment

description:
formaldehyde cross-linked
Sample 92

value: none (control)


title: ChIP-seq from HEK293 (ENCLB592VSV)

description:
https://www.encodeproject.org/experiments/ENCSR447ZTA/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF558 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR447ZTA
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: ENCLB592VSV
size range: 450-650

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF558 under the control of a CMV promoter.

value: embryonic

value: unknown

value: ENCBS305FAK at ENCODE; https://www.encodeproject.org/ENCBS305FAK/

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


title: eCLIP from HepG2 (ENCLB747SFZ)

description:
https://www.encodeproject.org/experiments/ENCSR309GHK/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against CSTF2
experiment encode accession: ENCSR309GHK
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-08-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB747SFZ
size range: 175-300

value: Control

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: Input DNA BMDM DSG formaldehyde ChIP-Seq Srebp1 KO No treatment

description:
formaldehyde cross-linked
Sample 91

value: Srebp1 -/-

value: bone marrow derived macrophages

value: none (control)


title: ChIP-seq from K562 (ENCLB692OES)

description:
https://www.encodeproject.org/experiments/ENCSR446LAV/
***************
biological replicate number: 1
technical replicate number: 1
description: DDX20 ChIP-seq on human K562
experiment encode accession: ENCSR446LAV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-04-22
lab: Michael Snyder, Stanford
library encode accession: ENCLB692OES
size range: 450-650

value: immortalized cell line

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

value: adult

value: 53 year

value: female

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)

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

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: Input DNA BMDM formaldehyde ChIP-Seq Srebp1 KO KLA1h

description:
formaldehyde cross-linked
Sample 93

value: KLA for 1 hours


title: ChIP-seq from K562 (ENCLB294QSB)

description:
https://www.encodeproject.org/experiments/ENCSR334HSW/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF318 ChIP-seq on human K562
experiment encode accession: ENCSR334HSW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2016-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB294QSB
size range: 450-650

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


title: eCLIP from HepG2 (ENCLB595NXK)

description:
https://www.encodeproject.org/experiments/ENCSR307WAE/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against RPS5
experiment encode accession: ENCSR307WAE
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR828MEJ
encode release date: 2016-09-21
lab: Gene Yeo, UCSD
library encode accession: ENCLB595NXK
size range: 175-300

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: Gene Yeo, UCSD

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

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


title: ChIP-seq from HEK293 (ENCLB702VIC)

description:
https://www.encodeproject.org/experiments/ENCSR445PDR/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-GFI1B ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR445PDR
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: ENCLB702VIC
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-GFI1B fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-GFI1B under the control of a CMV promoter.

value: embryonic

value: female

value: unknown

value: Michael Snyder, Stanford

value: ENCBS321IHW at ENCODE; https://www.encodeproject.org/ENCBS321IHW/

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


title: Input DNA BMDM formaldehyde ChIP-Seq Srebp1 WT No Treatment

description:
formaldehyde cross-linked
Sample 90

value: Srebp1 WT

value: bone marrow derived macrophages

value: none (control)


title: input DNA TGEM Srebp1 ChIP-seq KLA24h

description:
disuccinimidyl glutarate-formaldehyde cross-linked
Sample 88

value: KLA for 24 hours


title: eCLIP from HepG2 (ENCLB977IOD)

description:
https://www.encodeproject.org/experiments/ENCSR307WAE/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against RPS5
experiment encode accession: ENCSR307WAE
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR828MEJ
encode release date: 2016-09-21
lab: Gene Yeo, UCSD
library encode accession: ENCLB977IOD
size range: 175-300

value: child

value: 15 year

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

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


title: Input DNA BMDM formaldehyde ChIP-Seq Srebp1 KO No treatment

description:
formaldehyde cross-linked
Sample 89

value: Srebp1 -/-


title: ChIP-seq from HEK293 (ENCLB967ZOP)

description:
https://www.encodeproject.org/experiments/ENCSR445PDR/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-GFI1B ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR445PDR
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: ENCLB967ZOP
size range: 450-650

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-GFI1B under the control of a CMV promoter.

value: embryonic

value: ENCBS320GSB at ENCODE; https://www.encodeproject.org/ENCBS320GSB/


title: input DNA TGEM Srebp1 ChIP-seq not treatment

description:
disuccinimidyl glutarate-formaldehyde cross-linked
Sample 87


title: input DNA TGEM LXR ChIP-seq no treatment

description:
disuccinimidyl glutarate-formaldehyde cross-linked
Sample 86


title: eCLIP from K562 (ENCLB305HZK)

description:
https://www.encodeproject.org/experiments/ENCSR305KNE/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against SF3B4
experiment encode accession: ENCSR305KNE
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB305HZK
size range: 175-300

value: Control

value: adult

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

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

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 (ENCLB688EAC)

description:
https://www.encodeproject.org/experiments/ENCSR316SZJ/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against RPS5
experiment encode accession: ENCSR316SZJ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR486QAE
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB688EAC
size range: 175-300

value: Gene Yeo, UCSD


title: PolyA RNA-seq siSrebf1 siRNA1 KLA24h

description: Sample 84

value: KLA for 24 hours


title: input DNA TGEM LXR ChIP-seq KLA24h

description:
disuccinimidyl glutarate-formaldehyde cross-linked
Sample 85


title: eCLIP from K562 (ENCLB575GHE)

description:
https://www.encodeproject.org/experiments/ENCSR303OQD/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against METAP2
experiment encode accession: ENCSR303OQD
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR750NTM
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB575GHE
size range: 175-300


title: ChIP-seq from HEK293 (ENCLB485KVU)

description:
https://www.encodeproject.org/experiments/ENCSR440COG/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF239 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR440COG
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: ENCLB485KVU
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF239 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF239 under the control of a CMV promoter.

value: unknown

value: Michael Snyder, Stanford

value: ENCBS169OUF at ENCODE; https://www.encodeproject.org/ENCBS169OUF/

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


title: PolyA RNA-seq siSrebf1 siRNA1 KLA6h

description: Sample 83

value: KLA for 6 hours


title: PolyA RNA-seq siSrebf1 siRNA1 KLA3h

description: Sample 82

value: KLA for 3 hours


title: ChIP-seq from HEK293 (ENCLB599OTW)

description:
https://www.encodeproject.org/experiments/ENCSR440COG/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF239 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR440COG
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: ENCLB599OTW
size range: 450-650

value: immortalized cell line

value: embryonic

value: ENCBS140ULK at ENCODE; https://www.encodeproject.org/ENCBS140ULK/


title: PolyA RNA-seq siSrebf1 siRNA1 noTx

description: Sample 81

value: none (control)


title: WT_4

first: Jin Billy

last: Li

state: California

address: 300 Pasteur Drive. Alway M303

institute: Stanford University

data_processing:
fastx_trimmer was used to trim the 76th base from reads.
Reads were mapped using TopHat and version 5.53 D. melanogaster Flybase gene annotations.
Read counts were obtained using featureCounts from the Subread package.
DESeq2 was used to obtain gene expression levels.
Genome_build: dm3 (BDGP release 5)
Supplementary_files_format_and_content: Normalized gene expression profiles for each sample in tab-delimited columns with a header in the first line.

organism: Drosophila melanogaster

source_name: head

growth_protocol: Heads were dissected from 3 day old male flies grown at 18C.

extract_protocol:
Total RNA was extracted using RNAdvance magnetic beads (Agencourt), treated using TURBO DNase (Thermo Fisher Scientific), depleted of ribosomal RNA, and treated again using TURBO DNase.
Libraries produced using the KAPA RNA-Seq Kit (Kapa Biosystems) were sequenced on an Illumina NextSeq 500 Sequencer using paired-end 75-bp cycles.

tag: strain

value: white Canton-S

value: head

value: 3 day


title: PolyA RNA-seq siControl siRNA1 KLA24h

description: Sample 80


title: eCLIP from HepG2 (ENCLB380NKX)

description:
https://www.encodeproject.org/experiments/ENCSR301TFY/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against DKC1
experiment encode accession: ENCSR301TFY
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR197LHH
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB380NKX
size range: 175-300

value: child

value: 15 year

value: male

value: hepatocellular carcinoma

value: ENCBS881CIF at ENCODE; https://www.encodeproject.org/ENCBS881CIF/

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: WT_3

tag: tissue


title: eCLIP from K562 (ENCLB952ANK)

description:
https://www.encodeproject.org/experiments/ENCSR303OQD/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against METAP2
experiment encode accession: ENCSR303OQD
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR750NTM
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB952ANK
size range: 175-300

value: adult

value: female

value: 53 year

tag: health state

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

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

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

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


title: PolyA RNA-seq siControl siRNA1 KLA6h

description: Sample 79

value: KLA for 6 hours


title: eCLIP from K562 (ENCLB925XPV)

description:
https://www.encodeproject.org/experiments/ENCSR438KWZ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against ILF3
experiment encode accession: ENCSR438KWZ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR760SFB
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB925XPV
size range: 175-300

value: immortalized cell line

tag: passage number

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


title: eCLIP from HepG2 (ENCLB199TOE)

description:
https://www.encodeproject.org/experiments/ENCSR301TFY/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against DKC1
experiment encode accession: ENCSR301TFY
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR197LHH
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB199TOE
size range: 175-300

value: child

value: male

value: 15 year

tag: link

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


title: eCLIP from K562 (ENCLB954REO)

description:
https://www.encodeproject.org/experiments/ENCSR438KWZ/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against ILF3
experiment encode accession: ENCSR438KWZ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR760SFB
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB954REO
size range: 175-300

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


title: ChIP-seq from GM12878 (ENCLB130QBB)

description:
https://www.encodeproject.org/experiments/ENCSR293QAR/
***************
biological replicate number: 1
technical replicate number: 1
description: MTA2 ChIP-seq on human GM12878
experiment encode accession: ENCSR293QAR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2016-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB130QBB
size range: 450-650

source_name: Homo sapiens GM12878 immortalized cell line

value: unknown

value: Michael Snyder, Stanford

value: ENCBS339VHO at ENCODE; https://www.encodeproject.org/ENCBS339VHO/

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

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526


title: eCLIP from K562 (ENCLB073FCW)

description:
https://www.encodeproject.org/experiments/ENCSR445FZX/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against PTBP1
experiment encode accession: ENCSR445FZX
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB073FCW
size range: 175-300

value: Control

value: adult

value: 53 year

value: female

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

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


title: WT_2

value: white Canton-S

value: head

value: 3 day


title: PolyA RNA-seq siControl siRNA1 KLA3h

description: Sample 78

tag: cell type

value: KLA for 3 hours


title: eCLIP from K562 (ENCLB504TND)

description:
https://www.encodeproject.org/experiments/ENCSR432XUP/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against SRSF1
experiment encode accession: ENCSR432XUP
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR925TYQ
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB504TND
size range: 175-300

tag: antibody

value: immortalized cell line

value: ENCBS081NLE at ENCODE; https://www.encodeproject.org/ENCBS081NLE/

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: eCLIP from K562 (ENCLB537AQC)

description:
https://www.encodeproject.org/experiments/ENCSR435EVK/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against SND1
experiment encode accession: ENCSR435EVK
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB537AQC
size range: 175-300

tag: line

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


title: WT_1


title: PolyA RNA-seq siControl siRNA1 noTx

description: Sample 77

value: none (control)


title: eCLIP from K562 (ENCLB361UOX)

description:
https://www.encodeproject.org/experiments/ENCSR432XUP/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against SRSF1
experiment encode accession: ENCSR432XUP
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR925TYQ
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB361UOX
size range: 175-300


title: eCLIP from K562 (ENCLB465NBM)

description:
https://www.encodeproject.org/experiments/ENCSR291XPT/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against PUS1
experiment encode accession: ENCSR291XPT
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR869TOB
encode release date: 2016-09-21
lab: Gene Yeo, UCSD
library encode accession: ENCLB465NBM
size range: 175-300

value: ENCBS505ILK at ENCODE; https://www.encodeproject.org/ENCBS505ILK/


title: ChIP-seq from GM12878 (ENCLB796OOU)

description:
https://www.encodeproject.org/experiments/ENCSR293QAR/
***************
biological replicate number: 2
technical replicate number: 1
description: MTA2 ChIP-seq on human GM12878
experiment encode accession: ENCSR293QAR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2016-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB796OOU
size range: 450-650

tag: description

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: adult

value: unknown

value: Michael Snyder, Stanford

value: ENCBS276RPG at ENCODE; https://www.encodeproject.org/ENCBS276RPG/

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

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878&PgId=166


title: PolyA RNA-seq siSrebf1 siRNA4 KLA24h

description: Sample 76

value: KLA for 24 hours


title: eCLIP from K562 (ENCLB686DSK)

description:
https://www.encodeproject.org/experiments/ENCSR291XPT/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against PUS1
experiment encode accession: ENCSR291XPT
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR869TOB
encode release date: 2016-09-21
lab: Gene Yeo, UCSD
library encode accession: ENCLB686DSK
size range: 175-300

tag: biosample encode accession

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

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

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


title: ChIP-seq from MCF-7 (ENCLB047FRN)

description:
https://www.encodeproject.org/experiments/ENCSR427BBI/
***************
biological replicate number: 2
technical replicate number: 1
description: MLLT1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR427BBI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR217LRF, ENCSR594UCI
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB047FRN
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: 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: AdarEA_2

value: y, sc, AdarE374A

value: head

value: 3 day


title: PolyA RNA-seq siSrebf1 siRNA4 noTx

description: Sample 74

tag: strain background

value: none (control)


title: ChIP-seq from MCF-7 (ENCLB082HVP)

description:
https://www.encodeproject.org/experiments/ENCSR427BBI/
***************
biological replicate number: 1
technical replicate number: 1
description: MLLT1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR427BBI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR217LRF, ENCSR594UCI
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB082HVP
size range: 450-650

value: adult

value: Michael Snyder, Stanford

value: ENCBS957OEW at ENCODE; https://www.encodeproject.org/ENCBS957OEW/


title: ChIP-seq from MCF-7 (ENCLB056CCS)

description:
https://www.encodeproject.org/experiments/ENCSR279IEM/
***************
biological replicate number: 2
technical replicate number: 1
description: SIX4 ChIP-seq on human MCF-7
experiment encode accession: ENCSR279IEM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR882IYK
encode release date: 2016-10-11
lab: Michael Snyder, Stanford
library encode accession: ENCLB056CCS
size range: 450-650

value: female

value: ENCBS253AAE at ENCODE; https://www.encodeproject.org/ENCBS253AAE/


title: ChIP-seq from K562 (ENCLB410LKO)

description:
https://www.encodeproject.org/experiments/ENCSR426MDV/
***************
biological replicate number: 1
technical replicate number: 1
description: MIER1 ChIP-seq on human K562
experiment encode accession: ENCSR426MDV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB410LKO
size range: 450-650

value: 53 year

value: chronic myelogenous leukemia (CML)

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

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: PolyA RNA-seq siSrebf1 siRNA3 noTx

description: Sample 73


title: AdarEA_1


title: ChIP-seq from MCF-7 (ENCLB966XCI)

description:
https://www.encodeproject.org/experiments/ENCSR279IEM/
***************
biological replicate number: 1
technical replicate number: 1
description: SIX4 ChIP-seq on human MCF-7
experiment encode accession: ENCSR279IEM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR882IYK
encode release date: 2016-10-11
lab: Michael Snyder, Stanford
library encode accession: ENCLB966XCI
size range: 450-650

value: immortalized cell line

value: 69 year

value: breast cancer (adenocarcinoma)

value: ENCBS868OVR at ENCODE; https://www.encodeproject.org/ENCBS868OVR/


title: eCLIP from HepG2 (ENCLB767GDI)

description:
https://www.encodeproject.org/experiments/ENCSR277DEO/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against NKRF
experiment encode accession: ENCSR277DEO
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR479XOI
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB767GDI
size range: 175-300

value: NKRF

value: child

value: 15 year

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS881CIF at ENCODE; https://www.encodeproject.org/ENCBS881CIF/

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 HEK293 (ENCLB691YKT)

description:
https://www.encodeproject.org/experiments/ENCSR418MKG/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF692 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR418MKG
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: 2016-10-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB691YKT
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF692 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF692 under the control of a CMV promoter.

value: embryonic

value: unknown

value: female

value: Michael Snyder, Stanford

value: ENCBS809DNX at ENCODE; https://www.encodeproject.org/ENCBS809DNX/

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


title: ChIP-seq from K562 (ENCLB381GMS)

description:
https://www.encodeproject.org/experiments/ENCSR426MDV/
***************
biological replicate number: 2
technical replicate number: 1
description: MIER1 ChIP-seq on human K562
experiment encode accession: ENCSR426MDV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB381GMS
size range: 450-650

value: immortalized cell line

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

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

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: T3-1

city: Townsville

first: Aurelie

last: Moya

state: QLD

address: James Cook drive

department: ARC Centre of Excellence for Coral Reefs Studies

country: Australia

institute: James Cook University

description: Pteropods exposed 3 days to pH 7.9

data_processing:
The reads from all the H. inflatus samples were trimmed from low quality regions and sequencing adaptors using libngs (https://github.com/sylvainforet/libngs) with a minimum quality of 20 and a minimum size of 75 bp.
The trimmed reads were then assembled using Trinity (Grabherr et al., 2011).
The sequences of the resulting assembly were clustered using cdhit-est (Fu et al., 2012) with a similarity threshold of 90% and a word size of 8 bp.
The multi-modal GC profile of this initial assembly is suggestive of contamination (Fig. S1a), probably originating from the Isochrysis galbana culture provided to the animals. In order to remove these potential contaminants, the transcripts were blasted against a database containing the NCBI refseq proteins augmented with sequences from the molluscs Biomphalaria glabrata (https://www.vectorbase.org/organisms/biomphalaria-glabrata) and Lymnea stagnalis (Sadamoto et al., 2012).
Sequences were then classified as putative H. inflatus sequences if they satisfied the following criteria: e-value less than 1e-10, a minimum bit-score of at least 100, and a delta bit-score of at least 100. Here delta bit-score refers to the difference between the best mollusc hit and the best non-mollusc hit.
Protein-coding sequences were predicted using Transdecoder (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3875132/) and annotated using Blast2GO (Conesa et al., 2005).
The reads were mapped back to the assembled transcripts using Bowtie2 (Langmead & Salzberg, 2012).
Differential gene expression was inferred using EdgeR (Robinson et al., 2010) using a FDR threshold of 5%.
Genome_build: Heliconoides_inflatus.fasta
Supplementary_files_format_and_content: Txt - edgeR results

organism: Heliconoides inflatus

source_name: Shelled pteropods_pH7.9

growth_protocol: Heliconoides inflatus individuals were collected in the Bay of Villefranche-sur-mer (43˚40’ N, 7˚18’ E) between 16th and 29th February 2012. Sampling was undertaken using very slow oblique tows of 2-4 min in duration at up to 100 m depth with a 57 cm diameter WP2 plankton net (200 µm mesh size). Plankton samples were immediately transported to the Laboratoire d’Océanographie de Villefranche. Using a tweezer, H. inflatus individuals where transferred to filtered seawater medium (pore size 0.2 µm).

extract_protocol:
Total RNA was extracted using RNeasy Plus Micro Kit (Qiagen) according to the manufacturer instructions. RNA quantity and quality were assessed using a NanoDrop ND-1000 spectrophotometer and denaturing gel electrophoresis using standard methods (Sambrook & Russel, 2001). Before being shipped on dry-ice to the Macrogen sequencing facilities in Seoul, South Korea, each RNA sample was precipitated in ethanol and sodium acetate (2x and 0.1x sample volume, respectively), and stored at -80 °C.
Library construction was performed by Macrogen (South Korea). The libraries were sequenced using the Illumina HiSeq2000 platform, producing an average of 63 million sequence reads (100 bp paired-end) per sample.

treatment_protocol: Individuals were exposed for 3 d to pH conditions maintained using a pH-stat system (IKS Karlsbard) that bubbled filtered seawater (pore size 0.2 µm) with either ambient air (control, pHT 8.1) or CO2 (treatment, pHT 7.9); pH was calibrated on the total scale using Tris/HCl and 2-aminopyridine/HCl buffer solutions with a salinity of 38.0. Three replicates were set up for each pH condition.Total alkalinity (AT), pHT, and dissolved inorganic carbon (CT) were measured at the start and end of the incubations. At the end of the 3-d incubations, the H. inflatus individuals from each of the three replicates were collected from the experimental jars by filtering the water over a 200 µm mesh. Specimens were rinsed with 0.45 µm filtered seawater, immediately snap-frozen in liquid nitrogen and stored at -80 °C until further treatment.

tag: exposed to

value: pH 7.9 for 3 days

value: whole pteropods


title: ChIP-seq from HEK293T (ENCLB063FMR)

description:
https://www.encodeproject.org/experiments/ENCSR272LXW/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human HEK293T
experiment encode accession: ENCSR272LXW
assay title: ChIP-seq
encode release date: 2016-11-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB063FMR
size range: 450-650

source_name: Homo sapiens HEK293T immortalized cell line

value: Control

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


title: PolyA RNA-seq siScap siRNA4 KLA24h

description: Sample 72

tag: treated with

value: KLA for 24 hours


title: PolyA RNA-seq siScap siRNA4 noTx

description: Sample 70

value: none (control)


title: eCLIP from HepG2 (ENCLB091DLX)

description:
https://www.encodeproject.org/experiments/ENCSR277DEO/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against NKRF
experiment encode accession: ENCSR277DEO
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR479XOI
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB091DLX
size range: 175-300

value: NKRF

tag: dev stage

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: T2-2

description: Pteropods exposed 3 days to pH 7.9


title: PolyA RNA-seq siSrebf1 siRNA3 KLA24h

description: Sample 75


title: AdarEA_4

value: y, sc, AdarE374A

value: head

value: 3 day


title: T2-1

description: Pteropods exposed 3 days to pH 7.9

value: pH 7.9 for 3 days

value: whole pteropods


title: ChIP-seq from HEK293 (ENCLB292XYX)

description:
https://www.encodeproject.org/experiments/ENCSR418MKG/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF692 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR418MKG
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: 2016-10-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB292XYX
size range: 450-650

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF692 under the control of a CMV promoter.

value: embryonic

value: unknown

tag: Sex

value: female

value: Michael Snyder, Stanford

value: ENCBS992CJC at ENCODE; https://www.encodeproject.org/ENCBS992CJC/

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


title: ChIP-seq from HEK293T (ENCLB044ISD)

description:
https://www.encodeproject.org/experiments/ENCSR272LXW/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on human HEK293T
experiment encode accession: ENCSR272LXW
assay title: ChIP-seq
encode release date: 2016-11-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB044ISD
size range: 450-650

value: Control

tag: age

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


title: T1-2

description: Pteropods exposed 3 days to pH 7.9


title: T1-1

description: Pteropods exposed 3 days to pH 7.9


title: AdarEA_3


title: eCLIP from K562 (ENCLB350FZY)

description:
https://www.encodeproject.org/experiments/ENCSR269AJF/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against RPS11
experiment encode accession: ENCSR269AJF
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR881RJL
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB350FZY
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

value: adult

value: 53 year

tag: lab

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

value: ENCBS505ILK at ENCODE; https://www.encodeproject.org/ENCBS505ILK/

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: C3-2

description: Pteropods exposed 3 days to pH 8.1

source_name: Shelled pteropods_pH8.1

value: pH 8.1 for 3 days

value: whole pteropods


title: PolyA RNA-seq siScap siRNA3 noTx

description: Sample 69

value: none (control)


title: C3-1

description: Pteropods exposed 3 days to pH 8.1


title: PolyA RNA-seq siScap siRNA3 KLA24h

description: Sample 71

value: KLA for 24 hours


title: PolyA RNA-seq siControl noTx

description: Sample 67


title: PolyA RNA-seq Srebf1-/- KLA24h

description: Sample 66

tag: genotype/variation

value: Srebp1 -/-

value: bone marrow derived macrophages


title: ChIP-seq from K562 (ENCLB181FUM)

description:
https://www.encodeproject.org/experiments/ENCSR416QLJ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-CEBPB ChIP-seq on human K562
experiment encode accession: ENCSR416QLJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889QUI
encode release date: 2016-01-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB181FUM
size range: 450-650

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

value: eGFP-CEBPB

value: immortalized cell line

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

value: female

value: Kevin White, UChicago

value: ENCBS378AAA at ENCODE; https://www.encodeproject.org/ENCBS378AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_AW15; http://web.expasy.org/cellosaurus/CVCL_AW15

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


title: eCLIP from K562 (ENCLB199EGB)

description:
https://www.encodeproject.org/experiments/ENCSR267OLV/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against SF3B4
experiment encode accession: ENCSR267OLV
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR305KNE
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB199EGB
size range: 175-300

value: adult

value: 53 year

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

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 (ENCLB589SOR)

description:
https://www.encodeproject.org/experiments/ENCSR269AJF/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against RPS11
experiment encode accession: ENCSR269AJF
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR881RJL
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB589SOR
size range: 175-300

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

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

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


title: C2-2

description: Pteropods exposed 3 days to pH 8.1

value: pH 8.1 for 3 days

tag: tissue

value: whole pteropods


title: ChIP-seq from K562 (ENCLB991KIJ)

description:
https://www.encodeproject.org/experiments/ENCSR414TYY/
***************
biological replicate number: 1
technical replicate number: 1
description: RUNX1 ChIP-seq on human K562
experiment encode accession: ENCSR414TYY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB991KIJ
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

tag: health state

value: Michael Snyder, Stanford

value: ENCBS207UAM at ENCODE; https://www.encodeproject.org/ENCBS207UAM/

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


title: eCLIP from K562 (ENCLB730UAZ)

description:
https://www.encodeproject.org/experiments/ENCSR266UVO/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against EFTUD2
experiment encode accession: ENCSR266UVO
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB730UAZ
size range: 175-300

value: Control

value: female

tag: passage number

value: ENCBS505ILK at ENCODE; https://www.encodeproject.org/ENCBS505ILK/


title: ChIP-seq from K562 (ENCLB764OUU)

description:
https://www.encodeproject.org/experiments/ENCSR416QLJ/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-CEBPB ChIP-seq on human K562
experiment encode accession: ENCSR416QLJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889QUI
encode release date: 2016-01-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB764OUU
size range: 450-650

value: eGFP-CEBPB

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

value: adult

value: 53 year

value: Kevin White, UChicago

tag: link

value: ENCBS406AAA at ENCODE; https://www.encodeproject.org/ENCBS406AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_AW15; http://web.expasy.org/cellosaurus/CVCL_AW15

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


title: eCLIP from K562 (ENCLB513QIG)

description:
https://www.encodeproject.org/experiments/ENCSR267OLV/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against SF3B4
experiment encode accession: ENCSR267OLV
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR305KNE
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB513QIG
size range: 175-300

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

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

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

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

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


title: ChIP-seq from K562 (ENCLB240LOR)

description:
https://www.encodeproject.org/experiments/ENCSR414TYY/
***************
biological replicate number: 2
technical replicate number: 1
description: RUNX1 ChIP-seq on human K562
experiment encode accession: ENCSR414TYY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB240LOR
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: Michael Snyder, Stanford

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

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


title: PolyA RNA-seq Srebf1-/-KLA6h

description: Sample 65

value: Srebp1 -/-

tag: cell type

value: bone marrow derived macrophages

value: KLA for 6 hours


title: PolyA RNA-seq Srebf1-/- KLA1h

description: Sample 64

value: KLA for 1 hours


title: C2-1

description: Pteropods exposed 3 days to pH 8.1

value: pH 8.1 for 3 days

value: whole pteropods


title: C1-2

description: Pteropods exposed 3 days to pH 8.1


title: ChIP-seq from HEK293 (ENCLB759APX)

description:
https://www.encodeproject.org/experiments/ENCSR417VWF/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZEB2 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR417VWF
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: ENCLB759APX
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZEB2 fusion protein

tag: antibody

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZEB2 under the control of a CMV promoter.

value: embryonic

value: unknown

value: female

value: ENCBS768DUW at ENCODE; https://www.encodeproject.org/ENCBS768DUW/

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


title: PolyA RNA-seq siControl KLA24

description: Sample 68

value: KLA for 24 hours


title: ChIP-seq from HEK293 (ENCLB649VIQ)

description:
https://www.encodeproject.org/experiments/ENCSR413ABE/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZFP2 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR413ABE
assay title: ChIP-seq
assembly: hg19, GRCh38
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: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB649VIQ
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZFP2 fusion protein

tag: line

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZFP2 under the control of a CMV promoter.

value: ENCBS441WOU at ENCODE; https://www.encodeproject.org/ENCBS441WOU/


title: eCLIP from K562 (ENCLB472AWB)

description:
https://www.encodeproject.org/experiments/ENCSR258QKO/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against XRCC6
experiment encode accession: ENCSR258QKO
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR687HHB
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB472AWB
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