title: ChIP-seq from K562 (ENCLB733EMZ)

description:
https://www.encodeproject.org/experiments/ENCSR924GXX/
***************
biological replicate number: 2
technical replicate number: 1
description: PHB2 ChIP-seq on human K562
experiment encode accession: ENCSR924GXX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2017-01-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB733EMZ
size range: 450-650

value: immortalized cell line

tag: dev stage

tag: age

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS406RFF at ENCODE; https://www.encodeproject.org/ENCBS406RFF/

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: Pre-immune repeat 1, Input DNA [13764X1]

status: Public on Oct 24 2017

type: SRA

city: Salt Lake City

first: Tim

last: Formosa

state: UT

address: 15 N Medical Dr East RM 4100

department: Biochemistry

country: USA

institute: University of Utah School of Medicine

library_source: genomic

data_processing:
Illumina sequencing reads for each biological replicate were sequentially aligned to both the S. cerevisiae genome (SGD release R64, UCSC SacCer3) and the Candida glabrata genome (Ensembl Fungi release 30, GCA_000002545.2) using Novoalign, allowing for one random assignment of multi-mapping reads. Alignments were assigned to the genome based on the best alignment metrics. Reads aligning to both genomes equally were considered orthologous and discarded.
Fragment coverage for S. cerevisiae was generated with BioToolBox bam2wig with an extension of 130 bp, a consensus fragment length as determined by peak cross-strand correlation, and depth-normalized by scaling to reads per million mapped (RPM).
The coverage tracks were further normalized for ChIP efficiency by dividing by the number of unique C. glabrata alignments (scaled to millions) in each sample (Orlando et al, 2014).
After normalization, a mean consensus track was generated by merging the replicates using bedtools and dividing by the number of replicates.
To generate fold enrichment tracks, genomic intervals with zero coverage in the Input samples were artificially set to a non-zero value of 1 (a value well below the genomic mean) and a fold enrichment calculated with macs2 bdgcmp. Coverage track manipulation was performed using the script manipulate_wig.
Genome_build: Saccharomyces cerevisiae: SGD release R64, UCSC SacCer3
Genome_build: Candida glabrata: Ensembl Fungi release 30, GCA_000002545.2
Supplementary_files_format_and_content: Calibrated BigWig files (ending in .cal.bw) represent individual replicate ChIP fragment coverage normalized for depth (RPM, Reads Per Million mapped) and calibrated for ChIP efficiency based on the number of Candida glabrata alignments.
Supplementary_files_format_and_content: Log2 fold enrichment BigWig files (ending in _log2FE.bw) represent ChIP fragment coverage normalized for depth, calibrated to Candida glabrata, averaged between all three biological replicates, divided by the Input coverage, and converted to a log2 scale. The Log2 fold enrichmnet BigWig files are available on the series record.

molecule: genomic DNA

organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus

source_name: Whole yeast cells

growth_protocol: Cultures were grown to logarithmic phase and harvested by centrigugation.

extract_protocol:
Cells were subjected to cross-linking with formaldehyde (1%) for 20 min at room temperature. Glycine (0.125 mM) was added to quench crosslinking and cells were washed with 1X phosphate-buffered saline. For the reference genome, Candida glabrata (ATCC® 36909) was grown at 25°C and cross-linked with formaldehyde as described above. Cross-linked S. cerevisiae (40 × 10^7) and C. glabrata (20 × 10^7) cells were mixed in FA140+SDS buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 140 mM NaCl, 0.1% SDS) and lysed by bead beating. Lysates from two sets of S. cerevisiae and C. glabrata mixture (120 × 10^7 cells) were pooled for sonication using a Diagenode Bioruptor™ (6 cycles of 5 min each, 30 sec ON and 30 sec OFF at high setting). Soluble chromatin was obtained by two sequential high-speed centrifugations. To remove SDS, soluble chromatin obtained from four batches of yeast cells were pooled and transferred to a 5 mL Float-A-Lyzer G2 dialysis device (3.5 - 5 kD MWCO) (Spectra/Por), dialyzed initially for 2 h in 1 L FA buffer (50 mM HEPES-KOH, pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate) with 140 mM NaCl followed by an overnight dialysis against 4 L of the same buffer.
The dialysate was centrifuged at 13,000 rpm for 15 min at 4°C. A 100 ml aliquot was set aside for isolating input DNA. The remaining dialysate was split equally into three tubes and pre-cleared using 50 ml of blocked Dynabeads® Protein A for 1h at 4°C with end-over-end rotation. Blocking of Dynabeads® Protein A beads was performed at 4°C with end-over-end rotation for 4h using FA buffer containing 140 mM NaCl, bovine serum albumin (BSA) (0.2 mg/mL, New England Biolabs) and fish skin gelatin (0.5%, Sigma). Pre-cleared dialysate was combined with the custom-made rabbit polyclonal a-Spt6 antibody (30 ml; McCullough 2015). Cross-reactivity of the antibody, which was raised against S. cerevisiae Spt6, for C. glabrata Spt6 was verified by western blot (Figure S6). For a background control, the additional set of pre-cleared dialysate prepared from the wild type control strain was combined with pre-immune serum (30 ml). 100 ml blocked Dynabeads® Protein A was then added and incubated overnight at 4°C with end-over-end rotation. Beads were sequentially washed 5 min each with end-over-end rotation at 4°C with FA buffer + 140 mM NaCl (three washes), FA buffer + 1000 mM NaCl (two washes), FA buffer + 500 mM NaCl (two washes), and one wash each with LiCl/NP40 buffer (10 mM Tris.Cl, pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% sodium deoxycholate) and TE (10 mM Tris.Cl, pH 8.0, 1 mM EDTA). Elution and reverse crosslinking of ChIP and input DNA followed by RNase A and Proteinase K digestion steps were performed as described previously (Chandrasekharan et al., 2011). ChIP and input DNA were purified using the Qiagen MinElute PCR Purification kit according to the manufacturer's instructions, except two washes each with buffer QG and PE were performed.
Sequencing libraries were constructed using NEBNext® Multiplex Oligos (Index Primers Set 1 and Set 2) and NEBNext® ChIP-seq Library Prep Reagent Set for Illumina, and subjected to 50 bp single-end sequencing in an Illumina Hiseq2000 sequencer.
HiSeq 50 Cycle Single-Read Sequencing version 4: Sequencing libraries (25 pM) were chemically denatured and applied to an Illumina HiSeq v4 single read flow cell using an Illumina cBot.  Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq SR Cluster Kit v4-cBot (GD-401-4001).  Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCSv2.2.38 and RTA v1.18.61), a 50 cycle single-read sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4002)

tag: reference control

value: Candida glabrata

tag: strain

tag: relevant genotype

value: WT


title: ChIP-seq from upper lobe of left lung (ENCLB225AOQ)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR970UZD/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human upper lobe of left lung
experiment encode accession: ENCSR970UZD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR492GDK
encode release date: 2016-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB225AOQ
size range: 450-650

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

organism: Homo sapiens

source_name: Homo sapiens upper lobe of left lung tissue female adult (53 years)

extract_protocol: not provided

tag: antibody

value: CTCF

value: upper lobe of left lung

value: tissue

tag: biosample encode accession

tag: Sex

tag: lab

value: Michael Snyder, Stanford

value: adult

tag: link

value: ENCBS218BVZ at ENCODE; https://www.encodeproject.org/ENCBS218BVZ/

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


title: rpb1-Y-A,FSP+KKR+, Input DNA [13764X18]

value: rpb1-Y1473A, LMFSPLV1490KMKRRRK


title: ChIP-seq from ascending aorta (ENCLB657XON)

description:
https://www.encodeproject.org/experiments/ENCSR960MDF/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human ascending aorta
experiment encode accession: ENCSR960MDF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR894EKG
encode release date: 2016-12-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB657XON
size range: 450-650

source_name: Homo sapiens ascending aorta tissue female adult (51 year)

value: ascending aorta

value: 51 year

value: ENCBS232BOV at ENCODE; https://www.encodeproject.org/ENCBS232BOV/

value: derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: ChIP-seq from HEK293T (ENCLB284DMO)

description:
https://www.encodeproject.org/experiments/ENCSR821YOI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human HEK293T
experiment encode accession: ENCSR821YOI
assay title: ChIP-seq
encode release date: 2017-02-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB284DMO
size range: 450-650

source_name: Homo sapiens HEK293T immortalized cell line

value: Control

tag: line

value: immortalized cell line

value: female

tag: health state

value: unknown

value: embryonic

value: ENCBS319KKV at ENCODE; https://www.encodeproject.org/ENCBS319KKV/

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


title: ChIP-seq from K562 (ENCLB795JQX)

description:
https://www.encodeproject.org/experiments/ENCSR822LBD/
***************
biological replicate number: 2
technical replicate number: 1
description: RBFOX2 ChIP-seq in K562
experiment encode accession: ENCSR822LBD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR932KYH
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB795JQX
size range: 200-400

source_name: Homo sapiens K562 immortalized cell line

tag: description

value: RBFOX2 ChIP-seq in K562

value: Xiang-Dong Fu, UCSD

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS705ZOS at ENCODE; https://www.encodeproject.org/ENCBS705ZOS/

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


title: rpb1-Y-A,FSP+KKR+, Input DNA [13764X6]

value: Candida glabrata

value: rpb1-Y1473A, LMFSPLV1490KMKRRRK


title: ChIP-seq from HEK293T (ENCLB485YOJ)

description:
https://www.encodeproject.org/experiments/ENCSR821YOI/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on human HEK293T
experiment encode accession: ENCSR821YOI
assay title: ChIP-seq
encode release date: 2017-02-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB485YOJ
size range: 450-650

value: Michael Snyder, Stanford

value: ENCBS986WKD at ENCODE; https://www.encodeproject.org/ENCBS986WKD/


title: rpb1-T-A,FSP+-KKR+, Input DNA [13764X5]

value: rpb1-T1471A, LMFSPLV1490KMKRRRK


title: ChIP-seq from spleen (ENCLB634NUX)

description:
https://www.encodeproject.org/experiments/ENCSR819SSW/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human spleen
experiment encode accession: ENCSR819SSW
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB634NUX
size range: 450-650

source_name: Homo sapiens spleen tissue female adult (53 years)

value: Control

value: spleen

value: tissue

value: adult

value: ENCBS440AZZ at ENCODE; https://www.encodeproject.org/ENCBS440AZZ/

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


title: ChIP-seq from thyroid gland (ENCLB684RNA)

description:
https://www.encodeproject.org/experiments/ENCSR955BIB/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human thyroid gland
experiment encode accession: ENCSR955BIB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR144QLB
encode release date: 2016-12-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB684RNA
size range: 450-650

source_name: Homo sapiens thyroid gland tissue female adult (51 year)

value: CTCF

value: thyroid gland

value: female

value: 51 year

value: ENCBS413MJK at ENCODE; https://www.encodeproject.org/ENCBS413MJK/

value: derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: ChIP-seq from testis (ENCLB399CET)

description:
https://www.encodeproject.org/experiments/ENCSR953MEE/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human testis
experiment encode accession: ENCSR953MEE
assay title: ChIP-seq
encode release date: 2017-01-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB399CET
size range: 450-650

source_name: Homo sapiens testis tissue male adult (54 years)

value: testis

value: male

value: 54 year

value: ENCBS746YNW at ENCODE; https://www.encodeproject.org/ENCBS746YNW/

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


title: spt6-R-H,KK-AA, Input DNA [13764X16]

value: Candida glabrata


title: spt6-R-H,KK-AA, Input DNA [13764X10]


title: ChIP-seq from K562 (ENCLB218JFX)

description:
https://www.encodeproject.org/experiments/ENCSR924GXX/
***************
biological replicate number: 1
technical replicate number: 1
description: PHB2 ChIP-seq on human K562
experiment encode accession: ENCSR924GXX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2017-01-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB218JFX
size range: 450-650

value: immortalized cell line

value: 53 year

value: Michael Snyder, Stanford

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: ChIP-seq from esophagus muscularis mucosa (ENCLB610GCX)

description:
https://www.encodeproject.org/experiments/ENCSR834ESZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human esophagus muscularis mucosa
experiment encode accession: ENCSR834ESZ
assay title: ChIP-seq
encode release date: 2017-03-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB610GCX
size range: 450-650

source_name: Homo sapiens esophagus muscularis mucosa tissue female adult (53 years)

value: Control

value: esophagus muscularis mucosa

value: tissue

value: female

value: adult

value: ENCBS643MHO at ENCODE; https://www.encodeproject.org/ENCBS643MHO/

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


title: spt6-R-H, Input DNA [13764X15]


title: spt6-R-H,KK-AA, Input DNA [13764X4]


title: ChIP-seq from HEK293 (ENCLB787DAO)

description:
https://www.encodeproject.org/experiments/ENCSR721QZV/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZSCAN18 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR721QZV
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: 2016-12-19
lab: Michael Snyder, Stanford
library encode accession: ENCLB787DAO
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZSCAN18 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZSCAN18 under the control of a CMV promoter.

value: unknown

value: embryonic

value: ENCBS763AYG at ENCODE; https://www.encodeproject.org/ENCBS763AYG/

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


title: microRNA-seq from midbrain (ENCLB127SHR)

description:
https://www.encodeproject.org/experiments/ENCSR835AJS/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on embryonic 10.5 day mouse midbrain
experiment encode accession: ENCSR835AJS
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-08-15
lab: Ali Mortazavi, UCI
library encode accession: ENCLB127SHR
size range: <30

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: Mus musculus strain B6NCrl midbrain tissue mixed sex embryo (10.5 days)

value: midbrain

value: Midbrain from 51 embryonic 10.5 day mice

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS613YYL at ENCODE; https://www.encodeproject.org/ENCBS613YYL/

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


title: ChIP-seq from GM12878 (ENCLB533DWH)

description:
https://www.encodeproject.org/experiments/ENCSR732PJX/
***************
biological replicate number: 2
technical replicate number: 1
description: NKRF ChIP-seq on human GM12878
experiment encode accession: ENCSR732PJX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB533DWH
size range: 450-650

source_name: Homo sapiens GM12878 immortalized cell line

value: NKRF

value: immortalized cell line

value: Michael Snyder, Stanford

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

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


title: rpb1-Y-A,FSP+KKR+, Input DNA [13764X12]

value: Candida glabrata

value: rpb1-Y1473A, LMFSPLV1490KMKRRRK


title: spt6-R-H, Input DNA [13764X9]


title: spt6-R-H, Input DNA [13764X3]


title: ChIP-seq from sigmoid colon (ENCLB445SQE)

description:
https://www.encodeproject.org/experiments/ENCSR923WJS/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on sigmoid colon
experiment encode accession: ENCSR923WJS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR190PGI
encode release date: 2017-06-15
lab: Richard Myers, HAIB
library encode accession: ENCLB445SQE

source_name: Homo sapiens sigmoid colon tissue male adult (54 years)

extract_protocol: extraction method: see document

value: sigmoid colon

value: tissue

value: male

value: Richard Myers, HAIB

value: 54 year

value: adult

value: ENCBS089VLX at ENCODE; https://www.encodeproject.org/ENCBS089VLX/

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

value: high resolution pathology slide image; https://www.encodeproject.org/documents/f08e09e8-d571-4a80-b574-da7e167668d5/@@download/attachment/82367.svs


title: ChIP-seq from HepG2 (ENCLB218YMG)

description:
https://www.encodeproject.org/experiments/ENCSR923UTX/
***************
biological replicate number: 2
technical replicate number: 1
description: NONO ChIP-seq in HepG2
experiment encode accession: ENCSR923UTX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR032EZQ
encode release date: 2017-08-17
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB218YMG
size range: 200-400

source_name: Homo sapiens HepG2 immortalized cell line

value: NONO

value: NONO ChIP-seq in HepG2

value: Xiang-Dong Fu, UCSD

value: hepatocellular carcinoma

value: 15 year

value: child

value: ENCBS719JYV at ENCODE; https://www.encodeproject.org/ENCBS719JYV/

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


title: ChIP-seq from GM12878 (ENCLB535PNP)

description:
https://www.encodeproject.org/experiments/ENCSR732PJX/
***************
biological replicate number: 1
technical replicate number: 1
description: NKRF ChIP-seq on human GM12878
experiment encode accession: ENCSR732PJX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB535PNP
size range: 450-650

value: NKRF

value: immortalized cell line

value: unknown

value: female

value: Michael Snyder, Stanford

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

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


title: microRNA-seq from midbrain (ENCLB426LIH)

description:
https://www.encodeproject.org/experiments/ENCSR835AJS/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on embryonic 10.5 day mouse midbrain
experiment encode accession: ENCSR835AJS
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-08-15
lab: Ali Mortazavi, UCI
library encode accession: ENCLB426LIH
size range: <30

value: midbrain

value: tissue

value: Midbrain from 69 embryonic 10.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS491CAX at ENCODE; https://www.encodeproject.org/ENCBS491CAX/

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


title: rpb1-T-A,FSP+-KKR+, Input DNA [13764X17]

value: Candida glabrata

value: rpb1-T1471A, LMFSPLV1490KMKRRRK


title: ChIP-seq from HepG2 (ENCLB426CCN)

description:
https://www.encodeproject.org/experiments/ENCSR923UTX/
***************
biological replicate number: 1
technical replicate number: 1
description: NONO ChIP-seq in HepG2
experiment encode accession: ENCSR923UTX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR032EZQ
encode release date: 2017-08-17
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB426CCN
size range: 200-400

value: NONO

value: immortalized cell line

value: NONO ChIP-seq in HepG2

value: male

value: Xiang-Dong Fu, UCSD

value: hepatocellular carcinoma

value: 15 year

value: child

value: ENCBS458WEZ at ENCODE; https://www.encodeproject.org/ENCBS458WEZ/

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


title: WT repeat 3, Input DNA [13764X14]

value: WT


title: microRNA-seq from heart (ENCLB008AQI)

description:
https://www.encodeproject.org/experiments/ENCSR832SAG/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on embryonic 12.5 day mouse heart
experiment encode accession: ENCSR832SAG
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-08-15
lab: Ali Mortazavi, UCI
library encode accession: ENCLB008AQI
size range: <30

source_name: Mus musculus strain B6NCrl heart tissue mixed sex embryo (12.5 days)

value: heart

value: tissue

value: embryonic

value: pooled male and female

value: ENCBS004ZLN at ENCODE; https://www.encodeproject.org/ENCBS004ZLN/


title: ChIP-seq from esophagus squamous epithelium (ENCLB204HFN)

description:
https://www.encodeproject.org/experiments/ENCSR734ZOZ/
***************
biological replicate number: 1
technical replicate number: 1
description: POLR2A ChIP-seq on human esophagus squamous epithelium
experiment encode accession: ENCSR734ZOZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR581RPO
encode release date: 2017-03-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB204HFN
size range: 450-650

source_name: Homo sapiens esophagus squamous epithelium tissue male adult (54 years)

value: esophagus squamous epithelium

value: Michael Snyder, Stanford

value: 54 year

value: adult

value: ENCBS278PSF at ENCODE; https://www.encodeproject.org/ENCBS278PSF/

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


title: ChIP-seq from transverse colon (ENCLB250JPO)

description:
https://www.encodeproject.org/experiments/ENCSR833FWC/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human transverse colon
experiment encode accession: ENCSR833FWC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR799YAO
encode release date: 2016-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB250JPO
size range: 450-650

source_name: Homo sapiens transverse colon tissue male adult (54 years)

value: CTCF

value: transverse colon

value: male

value: ENCBS866IBT at ENCODE; https://www.encodeproject.org/ENCBS866IBT/


title: rpb1-T-A,FSP+-KKR+, Input DNA [13764X11]

source_name: Whole yeast cells

value: Candida glabrata

value: rpb1-T1471A, LMFSPLV1490KMKRRRK


title: ChIP-seq from K562 (ENCLB658AYO)

description:
https://www.encodeproject.org/experiments/ENCSR920ASP/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZFX ChIP-seq on human K562
experiment encode accession: ENCSR920ASP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR420JAH
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB658AYO
size range: 200-800

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

value: eGFP-ZFX

value: immortalized cell line

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

value: female

value: Kevin White, UChicago

tag: passage number

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS205YAO at ENCODE; https://www.encodeproject.org/ENCBS205YAO/

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

value: ENCODE dbxrefs Cellosaurus CVCL_GZ97; http://web.expasy.org/cellosaurus/CVCL_GZ97


title: ChIP-seq from HEK293 (ENCLB716ACZ)

description:
https://www.encodeproject.org/experiments/ENCSR721QZV/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZSCAN18 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR721QZV
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: 2016-12-19
lab: Michael Snyder, Stanford
library encode accession: ENCLB716ACZ
size range: 450-650

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZSCAN18 under the control of a CMV promoter.

value: Michael Snyder, Stanford

value: unknown

value: embryonic

value: ENCBS534EOJ at ENCODE; https://www.encodeproject.org/ENCBS534EOJ/

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


title: ChIP-seq from suprapubic skin (ENCLB752TFG)

description:
https://www.encodeproject.org/experiments/ENCSR915TAF/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on -human (fragmentation date:Mon Sep 12 2016 00:00:00 GMT-0500 (CDT)
experiment encode accession: ENCSR915TAF
assay title: ChIP-seq
encode release date: 2017-02-02
lab: Richard Myers, HAIB
library encode accession: ENCLB752TFG

source_name: Homo sapiens suprapubic skin tissue female adult (51 year)

value: Control

value: suprapubic skin

value: tissue

value: Richard Myers, HAIB

value: 51 year

value: adult

value: ENCBS588FXB at ENCODE; https://www.encodeproject.org/ENCBS588FXB/

value: derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: high resolution pathology slide image; https://www.encodeproject.org/documents/c8b1c1d7-21b2-42ca-b898-8abf625ea8af/@@download/attachment/84266.svs


title: ChIP-seq from K562 (ENCLB287EPO)

description:
https://www.encodeproject.org/experiments/ENCSR920ASP/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZFX ChIP-seq on human K562
experiment encode accession: ENCSR920ASP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR420JAH
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB287EPO
size range: 200-800

value: eGFP-ZFX

value: immortalized cell line

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

value: female

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS675IUA at ENCODE; https://www.encodeproject.org/ENCBS675IUA/

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


title: WT repeat 2, Input DNA [13764X8]

value: Candida glabrata

value: WT


title: ChIP-seq from MCF-7 (ENCLB711UYU)

description:
https://www.encodeproject.org/experiments/ENCSR949IWY/
***************
biological replicate number: 1
technical replicate number: 1
description: PAX8 ChIP-seq on human MCF-7
experiment encode accession: ENCSR949IWY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR882IYK
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB711UYU
size range: 450-650

source_name: Homo sapiens MCF-7 immortalized cell line

value: 69 year

value: breast cancer (adenocarcinoma)

value: Michael Snyder, Stanford

value: ENCBS195LAY at ENCODE; https://www.encodeproject.org/ENCBS195LAY/

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


title: microRNA-seq from forebrain (ENCLB492PTO)

description:
https://www.encodeproject.org/experiments/ENCSR715QTV/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on embryonic 12.5 day mouse forebrain
experiment encode accession: ENCSR715QTV
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-08-15
lab: Ali Mortazavi, UCI
library encode accession: ENCLB492PTO
size range: <30

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (12.5 days)

value: forebrain

value: tissue

value: Forebrain from 68 embryonic 12.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS617DPG at ENCODE; https://www.encodeproject.org/ENCBS617DPG/

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


title: ChIP-seq from MCF-7 (ENCLB638PNT)

description:
https://www.encodeproject.org/experiments/ENCSR949IWY/
***************
biological replicate number: 2
technical replicate number: 1
description: PAX8 ChIP-seq on human MCF-7
experiment encode accession: ENCSR949IWY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR882IYK
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB638PNT
size range: 450-650

value: immortalized cell line

value: female

value: adult

value: ENCBS523HSQ at ENCODE; https://www.encodeproject.org/ENCBS523HSQ/

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


title: Pre-immune repeat 3, ChIP [13762X13]

description:
log2 fold-enrichment file:
PIa_log2FE.bw

value: Candida glabrata

value: WT


title: microRNA-seq from forebrain (ENCLB802OPG)

description:
https://www.encodeproject.org/experiments/ENCSR715QTV/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on embryonic 12.5 day mouse forebrain
experiment encode accession: ENCSR715QTV
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-08-15
lab: Ali Mortazavi, UCI
library encode accession: ENCLB802OPG
size range: <30

value: Forebrain from 120 embryonic 12.5 day mice

value: ENCBS974GPH at ENCODE; https://www.encodeproject.org/ENCBS974GPH/


title: ChIP-seq from HepG2 (ENCLB355XFO)

description:
https://www.encodeproject.org/experiments/ENCSR730TBC/
***************
biological replicate number: 1
technical replicate number: 1
description: MNT ChIP-seq on human HepG2
experiment encode accession: ENCSR730TBC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR399VVK
encode release date: 2017-06-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB355XFO
size range: 450-650

value: MNT

value: male

value: Michael Snyder, Stanford

value: hepatocellular carcinoma

value: 15 year

value: child

value: ENCBS717QJM at ENCODE; https://www.encodeproject.org/ENCBS717QJM/

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


title: Pre-immune repeat 2, ChIP [13762X7]


title: microRNA-seq from limb (ENCLB794GIJ)

description:
https://www.encodeproject.org/experiments/ENCSR715NEZ/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on embryonic 10.5 day mouse limb
experiment encode accession: ENCSR715NEZ
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-08-15
lab: Ali Mortazavi, UCI
library encode accession: ENCLB794GIJ
size range: <30

source_name: Mus musculus strain B6NCrl limb tissue mixed sex embryo (10.5 days)

value: limb

value: tissue

value: Limb from 51 embryonic 10.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS892NXC at ENCODE; https://www.encodeproject.org/ENCBS892NXC/

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


title: microRNA-seq from limb (ENCLB515LXI)

description:
https://www.encodeproject.org/experiments/ENCSR715NEZ/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on embryonic 10.5 day mouse limb
experiment encode accession: ENCSR715NEZ
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-08-15
lab: Ali Mortazavi, UCI
library encode accession: ENCLB515LXI
size range: <30

value: Limb from 69 embryonic 10.5 day mice

value: ENCBS844FSC at ENCODE; https://www.encodeproject.org/ENCBS844FSC/


title: Pre-immune repeat 1, ChIP [13762X1]

value: Candida glabrata

value: WT


title: ChIP-seq from transverse colon (ENCLB499RHQ)

description:
https://www.encodeproject.org/experiments/ENCSR717TBA/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on -human (fragmentation date:Wed Aug 24 2016 00:00:00 GMT-0500 (CDT)
experiment encode accession: ENCSR717TBA
assay title: ChIP-seq
encode release date: 2016-11-09
lab: Richard Myers, HAIB
library encode accession: ENCLB499RHQ

source_name: Homo sapiens transverse colon tissue female adult (53 years)

value: Control

value: transverse colon

value: female

value: Richard Myers, HAIB

value: 53 year

value: adult

value: ENCBS022PBN at ENCODE; https://www.encodeproject.org/ENCBS022PBN/

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

value: high resolution pathology slide image; https://www.encodeproject.org/documents/01a2c769-a3d7-421f-8905-77082e5a5a7a/@@download/attachment/83389.svs


title: ChIP-seq from HEK293T (ENCLB600OVW)

description:
https://www.encodeproject.org/experiments/ENCSR831EIW/
***************
biological replicate number: 1
technical replicate number: 1
description: FOXM1 ChIP-seq on human HEK293T
experiment encode accession: ENCSR831EIW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR272LXW
encode release date: 2017-04-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB600OVW
size range: 450-650

source_name: Homo sapiens HEK293T immortalized cell line

value: immortalized cell line

value: embryonic

value: unknown

value: Michael Snyder, Stanford

value: ENCBS276VDW at ENCODE; https://www.encodeproject.org/ENCBS276VDW/

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


title: ChIP-seq from K562 (ENCLB056KZR)

description:
https://www.encodeproject.org/experiments/ENCSR914NEI/
***************
biological replicate number: 2
technical replicate number: 1
description: MTA3 ChIP-seq on human K562
experiment encode accession: ENCSR914NEI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2017-06-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB056KZR
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line

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

value: chronic myelogenous leukemia (CML)

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

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: microRNA-seq from heart (ENCLB502ZUW)

description:
https://www.encodeproject.org/experiments/ENCSR832SAG/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on embryonic 12.5 day mouse heart
experiment encode accession: ENCSR832SAG
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-08-15
lab: Ali Mortazavi, UCI
library encode accession: ENCLB502ZUW
size range: <30

value: heart

value: tissue

value: Heart from 12.5 day mice

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS452TDN at ENCODE; https://www.encodeproject.org/ENCBS452TDN/

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


title: ChIP-seq from HepG2 (ENCLB958WUN)

description:
https://www.encodeproject.org/experiments/ENCSR730TBC/
***************
biological replicate number: 2
technical replicate number: 1
description: MNT ChIP-seq on human HepG2
experiment encode accession: ENCSR730TBC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR399VVK
encode release date: 2017-06-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB958WUN
size range: 450-650

value: MNT

value: immortalized cell line

value: male

value: Michael Snyder, Stanford

value: hepatocellular carcinoma

value: 15 year

value: child

value: ENCBS632SNG at ENCODE; https://www.encodeproject.org/ENCBS632SNG/

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


title: ChIP-seq from VCaP (ENCLB968FVP)

description:
https://www.encodeproject.org/experiments/ENCSR716BTZ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on human VCaP
experiment encode accession: ENCSR716BTZ
assay title: ChIP-seq
encode release date: 2017-04-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB968FVP
size range: 450-650

source_name: Homo sapiens VCaP immortalized cell line

value: Control

value: VCaP

value: prostate adenocarcinoma

value: 50 year

value: adult

value: ENCBS626UQL at ENCODE; https://www.encodeproject.org/ENCBS626UQL/

value: derived from ENCODE donor ENCDO000ACX; https://www.encodeproject.org/ENCDO000ACX/


title: ChIP-seq from HEK293T (ENCLB679RXW)

description:
https://www.encodeproject.org/experiments/ENCSR831EIW/
***************
biological replicate number: 2
technical replicate number: 1
description: FOXM1 ChIP-seq on human HEK293T
experiment encode accession: ENCSR831EIW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR272LXW
encode release date: 2017-04-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB679RXW
size range: 450-650

value: embryonic

value: unknown

value: female

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

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


title: rpb1-Y-A,FSP+KKR+, ChIP [13762X18]

description:
log2 fold-enrichment file:
YA_log2FE.bw

value: Candida glabrata

value: rpb1-Y1473A, LMFSPLV1490KMKRRRK


title: microRNA-seq from heart (ENCLB818LQZ)

description:
https://www.encodeproject.org/experiments/ENCSR912ATB/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on embryonic 10.5 day mouse heart
experiment encode accession: ENCSR912ATB
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-08-15
lab: Ali Mortazavi, UCI
library encode accession: ENCLB818LQZ
size range: <30

source_name: Mus musculus strain B6NCrl heart tissue mixed sex embryo (10.5 days)

value: heart

value: tissue

value: Heart from 69 embryonic 10.5 day mice

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS366XOW at ENCODE; https://www.encodeproject.org/ENCBS366XOW/

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


title: rpb1-Y-A,FSP+KKR+, ChIP [13762X12]

description:
log2 fold-enrichment file:
YA_log2FE.bw


title: ChIP-seq from uterus (ENCLB009XPV)

description:
https://www.encodeproject.org/experiments/ENCSR948PSS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human uterus
experiment encode accession: ENCSR948PSS
assay title: ChIP-seq
encode release date: 2016-11-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB009XPV
size range: 450-650

source_name: Homo sapiens uterus tissue female adult (53 years)

value: Control

value: uterus

value: Michael Snyder, Stanford

value: 53 year

value: adult

value: ENCBS201ZAR at ENCODE; https://www.encodeproject.org/ENCBS201ZAR/

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


title: rpb1-Y-A,FSP+KKR+, ChIP [13762X6]

description:
log2 fold-enrichment file:
YA_log2FE.bw

value: Candida glabrata


title: ChIP-seq from MCF-7 (ENCLB342WII)

description:
https://www.encodeproject.org/experiments/ENCSR814KDE/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-GABPA tagged MCF7 cell line.
experiment encode accession: ENCSR814KDE
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Kevin White, UChicago
library encode accession: ENCLB342WII
size range: 200-800

source_name: Homo sapiens MCF-7 immortalized cell line stably expressing C-terminal eGFP-GABPA fusion protein

value: immortalized cell line

value: MCF7 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to GABPA

value: female

value: Kevin White, UChicago

value: breast cancer (adenocarcinoma)

value: 69 year

value: ENCBS274OZJ at ENCODE; https://www.encodeproject.org/ENCBS274OZJ/

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

value: ENCODE dbxrefs Cellosaurus CVCL_HA14; http://web.expasy.org/cellosaurus/CVCL_HA14


title: SMA mouse brain, polysomal RNA, late symptomatic, rep 1

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

country: Italy

institute: University of Trento

description:
sma_poly_late_1
polysomal RNA extracted from a SMA mouse brain at late-symptomatic stage

data_processing:
Reads generated from each sample were aligned to the mouse genome (GRCm38.p4) with Tophat (version 2.0.14), using the Gencode M6 transcript annotation as transcriptome guide. All programs were used with default settings unless otherwise specified. Mapped reads were subsequently assembled into transcripts guided by reference annotation (Gencode M6) with Cufflinks (version 2.2.1). Expression levels were quantified by Cufflinks with normalized FPKM (fragments per kilobase of exon per million mapped fragments).
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: tab-delimited text files including a brief annotation and gene-specific RPKM values, calculated by Cufflinks

source_name: SMA mouse brain_polysomal RNA_late symptomatic

growth_protocol: The ‘Taiwanese’ mouse model of severe SMA was used in this study (Hsieh-Li et al., 2000; Riessland et al., 2010; Somers et al., 2015). All mice were on a congenic FVB background, with colonies at the University of Edinburgh established from breeding pairs purchased from Jackson Labs. ‘Taiwanese’ SMA mice (Smn-/-; SMN2tg/0) carry two copies of SMN2 on one allele and are on a null murine Smn background. Litters were retrospectively genotyped using standard PCR protocols. All mice were housed within the animal care facilities in Edinburgh under standard SPF conditions. All animal procedures and breeding were performed in accordance with University of Edinburgh institutional guidelines and under appropriate project and personal licenses granted by the UK Home Office.

extract_protocol:
Cytoplasmic lysates from frozen mouse tissues and polysomal profiling were performed as described previously (Lunelli et al., 2016).RNA was extracted from control and SMA brains (at early and late symptomatic stage). Sucrose fractions from all fractions (total RNA) or polysomal fractions only (polysomal RNA) were pooled. The fractions were first digested with proteinase K (100 mg/mL, Euroclone) for 90 minutes at 37°C and then RNA was extracted with acid-phenol:chloroform:isoamylalcohol, pH 4.5 (Sigma Aldrich) and isopropanol precipitation.
RNA libraries were prepared for sequencing using standard Illumina protocols, using the TruSeq® Stranded Total RNA (Illumina) kit

treatment_protocol: Early symptomatic brains were P5 and late symptomatic brains were P7. Neonatal mice were euthanized by overdose of anaesthetic, before decapitation to allow the brain to be removed. Following isolation, all tissues were immediately snap-frozen on dry ice and then transferred to -80 °C for storage.

tag: strain background

value: congenic FVB background

tag: genotype/variation

value: Taiwanese mouse model of severe Spinal muscular atrophy (SMA)

tag: Stage

value: late-symtomatic

tag: tissue

value: brain

tag: rna fraction

value: polysomal RNA

tag: replicate


title: rpb1-T-A,FSP+-KKR+, ChIP [13762X11]

description:
log2 fold-enrichment file:
TA_log2FE.bw

tag: reference control

tag: strain

value: rpb1-T1471A, LMFSPLV1490KMKRRRK


title: rpb1-T-A,FSP+-KKR+, ChIP [13762X17]

description:
log2 fold-enrichment file:
TA_log2FE.bw

tag: relevant genotype


title: SMA mouse brain, polysomal RNA, late symptomatic, rep 3

description:
sma_poly_late_3
polysomal RNA extracted from a SMA mouse brain at late-symptomatic stage


title: ChIP-seq from spleen (ENCLB460XJC)

description:
https://www.encodeproject.org/experiments/ENCSR729GXE/
***************
biological replicate number: 1
technical replicate number: 1
description: POLR2A ChIP-seq on human spleen
experiment encode accession: ENCSR729GXE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR895OZW
encode release date: 2017-03-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB460XJC
size range: 450-650

source_name: Homo sapiens spleen tissue male adult (37 years)

tag: antibody

value: spleen

value: tissue

tag: biosample encode accession

value: male

value: Michael Snyder, Stanford

tag: age

value: 37 year

tag: dev stage

value: adult

value: ENCBS148ECB at ENCODE; https://www.encodeproject.org/ENCBS148ECB/

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


title: ChIP-seq from tibial nerve (ENCLB746SDR)

description:
https://www.encodeproject.org/experiments/ENCSR935XOT/
***************
biological replicate number: 1
technical replicate number: 1
description: POLR2A ChIP-seq on human tibial nerve
experiment encode accession: ENCSR935XOT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR522PLW
encode release date: 2017-04-04
lab: Michael Snyder, Stanford
library encode accession: ENCLB746SDR
size range: 450-650

source_name: Homo sapiens tibial nerve tissue female adult (53 years)

value: tibial nerve

tag: Sex

value: female

tag: lab

value: 53 year

tag: link

value: ENCBS316JCG at ENCODE; https://www.encodeproject.org/ENCBS316JCG/

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


title: ChIP-seq from K562 (ENCLB143OZQ)

description:
https://www.encodeproject.org/experiments/ENCSR914NEI/
***************
biological replicate number: 3
technical replicate number: 1
description: MTA3 ChIP-seq on human K562
experiment encode accession: ENCSR914NEI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2017-06-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB143OZQ
size range: 450-650

tag: line

value: immortalized cell line

tag: health state

value: chronic myelogenous leukemia (CML)

value: ENCBS626VGF at ENCODE; https://www.encodeproject.org/ENCBS626VGF/

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


title: ChIP-seq from prostate gland (ENCLB856XDC)

description:
https://www.encodeproject.org/experiments/ENCSR829HTO/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human prostate gland
experiment encode accession: ENCSR829HTO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR109IEL
encode release date: 2016-11-29
lab: Michael Snyder, Stanford
library encode accession: ENCLB856XDC
size range: 450-650

source_name: Homo sapiens prostate gland tissue male adult (54 years)

value: CTCF

value: prostate gland

value: 54 year

value: ENCBS282GPE at ENCODE; https://www.encodeproject.org/ENCBS282GPE/

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


title: SMA mouse brain, polysomal RNA, late symptomatic, rep 2

description:
sma_poly_late_2
polysomal RNA extracted from a SMA mouse brain at late-symptomatic stage

tag: strain background

value: congenic FVB background

tag: genotype/variation

value: Taiwanese mouse model of severe Spinal muscular atrophy (SMA)

value: late-symtomatic

value: brain

value: polysomal RNA


title: control mouse brain, polysomal RNA, late symptomatic, rep 3

description:
ctrl_poly_late_3
polysomal RNA extracted from a control mouse brain at late-symptomatic stage

source_name: control mouse brain_polysomal RNA_late symptomatic

value: control

tag: Stage

tag: tissue


title: ChIP-seq from VCaP (ENCLB244AHP)

description:
https://www.encodeproject.org/experiments/ENCSR716BTZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human VCaP
experiment encode accession: ENCSR716BTZ
assay title: ChIP-seq
encode release date: 2017-04-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB244AHP
size range: 450-650

value: Control

value: VCaP

value: male

value: Michael Snyder, Stanford

value: prostate adenocarcinoma

value: 50 year

value: adult

value: ENCBS316RCQ at ENCODE; https://www.encodeproject.org/ENCBS316RCQ/

value: derived from ENCODE donor ENCDO000ACX; https://www.encodeproject.org/ENCDO000ACX/


title: control mouse brain, polysomal RNA, late symptomatic, rep 2

description:
ctrl_poly_late_2
polysomal RNA extracted from a control mouse brain at late-symptomatic stage

tag: rna fraction

tag: replicate


title: microRNA-seq from heart (ENCLB772OFF)

description:
https://www.encodeproject.org/experiments/ENCSR912ATB/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on embryonic 10.5 day mouse heart
experiment encode accession: ENCSR912ATB
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-08-15
lab: Ali Mortazavi, UCI
library encode accession: ENCLB772OFF
size range: <30

value: heart

value: tissue

tag: description

value: Heart from 51 embryonic 10.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS510GHM at ENCODE; https://www.encodeproject.org/ENCBS510GHM/

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


title: spt6-R-H,KK-AA, ChIP [13762X16]

description:
log2 fold-enrichment file:
RKK_log2FE.bw

source_name: Whole yeast cells

tag: reference control

value: Candida glabrata

tag: strain

tag: relevant genotype


title: rpb1-T-A,FSP+-KKR+, ChIP [13762X5]

description:
log2 fold-enrichment file:
TA_log2FE.bw

value: rpb1-T1471A, LMFSPLV1490KMKRRRK


title: ChIP-seq from HEK293 (ENCLB116ZVJ)

description:
https://www.encodeproject.org/experiments/ENCSR811JJM/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF19 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR811JJM
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: 2016-12-19
lab: Michael Snyder, Stanford
library encode accession: ENCLB116ZVJ
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZNF19 fusion protein

tag: antibody

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF19 under the control of a CMV promoter.

tag: biosample encode accession

value: female

value: Michael Snyder, Stanford

value: unknown

tag: age

value: ENCBS620EBJ at ENCODE; https://www.encodeproject.org/ENCBS620EBJ/

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


title: control mouse brain, polysomal RNA, late symptomatic, rep 1

description:
ctrl_poly_late_1
polysomal RNA extracted from a control mouse brain at late-symptomatic stage

value: congenic FVB background

value: control

value: late-symtomatic

value: brain

value: polysomal RNA


title: ChIP-seq from HEK293 (ENCLB311XZG)

description:
https://www.encodeproject.org/experiments/ENCSR811JJM/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF19 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR811JJM
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: 2016-12-19
lab: Michael Snyder, Stanford
library encode accession: ENCLB311XZG
size range: 450-650

tag: Sex

tag: lab

tag: dev stage

value: embryonic

value: ENCBS761ZMR at ENCODE; https://www.encodeproject.org/ENCBS761ZMR/


title: ChIP-seq from GM12878 (ENCLB501GUQ)

description:
https://www.encodeproject.org/experiments/ENCSR828NCB/
***************
biological replicate number: 2
technical replicate number: 1
description: GATAD2B ChIP-seq on human GM12878
experiment encode accession: ENCSR828NCB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB501GUQ
size range: 450-650

source_name: Homo sapiens GM12878 immortalized cell line

tag: line

value: adult

tag: health state

tag: link

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

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


title: ChIP-seq from MCF-7 (ENCLB400YZY)

description:
https://www.encodeproject.org/experiments/ENCSR713NUS/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-E2F4 tagged MCF7 cell line.
experiment encode accession: ENCSR713NUS
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Kevin White, UChicago
library encode accession: ENCLB400YZY
size range: 200-800
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens MCF-7 immortalized cell line stably expressing C-terminal eGFP-E2F4 fusion protein

value: Control

value: immortalized cell line

value: MCF7 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to E2F4

value: Kevin White, UChicago

tag: passage number

value: breast cancer (adenocarcinoma)

value: 69 year

value: ENCBS660MSK at ENCODE; https://www.encodeproject.org/ENCBS660MSK/

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

value: ENCODE dbxrefs Cellosaurus CVCL_HA12; http://web.expasy.org/cellosaurus/CVCL_HA12


title: ChIP-seq from GM12878 (ENCLB122YZP)

description:
https://www.encodeproject.org/experiments/ENCSR828NCB/
***************
biological replicate number: 1
technical replicate number: 1
description: GATAD2B ChIP-seq on human GM12878
experiment encode accession: ENCSR828NCB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB122YZP
size range: 450-650

value: unknown

value: female

value: Michael Snyder, Stanford

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


title: ChIP-seq from sigmoid colon (ENCLB115OMI)

description:
https://www.encodeproject.org/experiments/ENCSR925GDS/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human sigmoid colon
experiment encode accession: ENCSR925GDS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR747VNS
encode release date: 2016-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB115OMI
size range: 450-650

source_name: Homo sapiens sigmoid colon tissue female adult (53 years)

value: CTCF

value: sigmoid colon

value: tissue

value: 53 year

value: ENCBS835BNK at ENCODE; https://www.encodeproject.org/ENCBS835BNK/

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


title: spt6-R-H,KK-AA, ChIP [13762X10]

value: Candida glabrata


title: spt6-R-H,KK-AA, ChIP [13762X4]


title: ChIP-seq from suprapubic skin (ENCLB819DPO)

description:
https://www.encodeproject.org/experiments/ENCSR825RBI/
***************
biological replicate number: 1
technical replicate number: 1
description: POLR2A ChIP-seq on human suprapubic skin
experiment encode accession: ENCSR825RBI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR312YGL
encode release date: 2017-04-04
lab: Michael Snyder, Stanford
library encode accession: ENCLB819DPO
size range: 450-650

source_name: Homo sapiens suprapubic skin tissue female adult (53 years)

value: suprapubic skin

value: adult

value: ENCBS296VML at ENCODE; https://www.encodeproject.org/ENCBS296VML/


title: ChIP-seq from stomach (ENCLB363MBK)

description:
https://www.encodeproject.org/experiments/ENCSR714JRB/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on stomach
experiment encode accession: ENCSR714JRB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR864PNP
encode release date: 2016-11-09
lab: Richard Myers, HAIB
library encode accession: ENCLB363MBK

source_name: Homo sapiens stomach tissue female adult (51 year)

value: stomach

value: Richard Myers, HAIB

value: 51 year

value: ENCBS066DAE at ENCODE; https://www.encodeproject.org/ENCBS066DAE/

value: derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: high resolution pathology slide image; https://www.encodeproject.org/documents/30eab777-0f1f-4412-807d-a20ab5c6589d/@@download/attachment/84279.svs


title: SMA mouse brain, total RNA, late symptomatic, rep 2

description:
sma_tot_late_2
total cytoplasmic RNA extracted from a SMA mouse brain at late-symptomatic stage

source_name: SMA mouse brain_total RNA_late symptomatic

tag: strain background

value: congenic FVB background

tag: genotype/variation

value: Taiwanese mouse model of severe Spinal muscular atrophy (SMA)

tag: Stage

value: late-symtomatic

tag: tissue

value: brain

value: total RNA


title: spt6-R-H, ChIP [13762X15]

description:
log2 fold-enrichment file:
RH_log2FE.bw

tag: reference control


title: ChIP-seq from K562 (ENCLB836ZKZ)

description:
https://www.encodeproject.org/experiments/ENCSR711VWL/
***************
biological replicate number: 2
technical replicate number: 1
description: HDAC1 ChIP-seq on human K562
experiment encode accession: ENCSR711VWL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2017-09-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB836ZKZ
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line

value: immortalized cell line

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Michael Snyder, Stanford

value: ENCBS352MRW at ENCODE; https://www.encodeproject.org/ENCBS352MRW/

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


title: spt6-R-H, ChIP [13762X9]

description:
log2 fold-enrichment file:
RH_log2FE.bw

value: Candida glabrata

tag: strain


title: ChIP-seq from HEK293 (ENCLB977BDE)

description:
https://www.encodeproject.org/experiments/ENCSR727PIC/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF34 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR727PIC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR429LAP, ENCSR274OGE, ENCSR342AGU, ENCSR688NWK, ENCSR354FNX, ENCSR157LMX, 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: 2017-03-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB977BDE
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZNF34 fusion protein

tag: description

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF34 under the control of a CMV promoter.

value: unknown

value: embryonic

value: ENCBS916VDS at ENCODE; https://www.encodeproject.org/ENCBS916VDS/

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


title: control mouse brain, total RNA, late symptomatic, rep 3

description:
ctrl_tot_late_3
total cytoplasmic RNA extracted from a control mouse brain at late-symptomatic stage

source_name: control mouse brain_total RNA_late symptomatic

value: congenic FVB background

value: control

tag: rna fraction

tag: replicate


title: microRNA-seq from vagina (ENCLB238ULW)

description:
https://www.encodeproject.org/experiments/ENCSR913DCT/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human vagina
experiment encode accession: ENCSR913DCT
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB238ULW
size range: <30

source_name: Homo sapiens vagina tissue female adult (51 year)

value: vagina

value: tissue

value: Vagina 4-1

tag: biosample encode accession

value: Barbara Wold, Caltech

tag: age

value: 51 year

value: adult

value: ENCBS402XXG at ENCODE; https://www.encodeproject.org/ENCBS402XXG/

value: derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: ChIP-seq from K562 (ENCLB440DSO)

description:
https://www.encodeproject.org/experiments/ENCSR711VWL/
***************
biological replicate number: 1
technical replicate number: 1
description: HDAC1 ChIP-seq on human K562
experiment encode accession: ENCSR711VWL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2017-09-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB440DSO
size range: 450-650

tag: antibody

value: immortalized cell line

tag: Sex

value: female

tag: lab

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS185MQS at ENCODE; https://www.encodeproject.org/ENCBS185MQS/

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


title: ChIP-seq from HEK293 (ENCLB702XMI)

description:
https://www.encodeproject.org/experiments/ENCSR727PIC/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF34 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR727PIC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR429LAP, ENCSR274OGE, ENCSR342AGU, ENCSR688NWK, ENCSR354FNX, ENCSR157LMX, 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: 2017-03-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB702XMI
size range: 450-650

tag: line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF34 under the control of a CMV promoter.

tag: health state

value: unknown

tag: dev stage

value: embryonic

value: ENCBS463NTZ at ENCODE; https://www.encodeproject.org/ENCBS463NTZ/

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


title: control mouse brain, total RNA, late symptomatic, rep 2

description:
ctrl_tot_late_2
total cytoplasmic RNA extracted from a control mouse brain at late-symptomatic stage

tag: strain background

value: congenic FVB background

value: control

value: late-symtomatic

value: brain

value: total RNA


title: spt6-R-H, ChIP [13762X3]

description:
log2 fold-enrichment file:
RH_log2FE.bw

value: Candida glabrata

tag: relevant genotype


title: SMA mouse brain, total RNA, late symptomatic, rep 3

description:
sma_tot_late_3
total cytoplasmic RNA extracted from a SMA mouse brain at late-symptomatic stage

tag: genotype/variation

value: Taiwanese mouse model of severe Spinal muscular atrophy (SMA)

tag: Stage


title: ChIP-seq from transverse colon (ENCLB938BDD)

description:
https://www.encodeproject.org/experiments/ENCSR714EQS/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on transverse colon
experiment encode accession: ENCSR714EQS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR170BPY
encode release date: 2016-11-09
lab: Richard Myers, HAIB
library encode accession: ENCLB938BDD

source_name: Homo sapiens transverse colon tissue female adult (53 years)

value: transverse colon

value: tissue

value: female

value: Richard Myers, HAIB

value: adult

tag: link

value: ENCBS022PBN at ENCODE; https://www.encodeproject.org/ENCBS022PBN/

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

value: high resolution pathology slide image; https://www.encodeproject.org/documents/01a2c769-a3d7-421f-8905-77082e5a5a7a/@@download/attachment/83389.svs


title: control mouse brain, total RNA, late symptomatic, rep 1

description:
ctrl_tot_late_1
total cytoplasmic RNA extracted from a control mouse brain at late-symptomatic stage

tag: tissue


title: microRNA-seq from vagina (ENCLB303ZFX)

description:
https://www.encodeproject.org/experiments/ENCSR913DCT/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human vagina
experiment encode accession: ENCSR913DCT
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB303ZFX
size range: <30

value: vagina

tag: description

value: Vagina 4-2

value: Barbara Wold, Caltech

value: 51 year

value: ENCBS738IGW at ENCODE; https://www.encodeproject.org/ENCBS738IGW/

value: derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: ChIP-seq from lower leg skin (ENCLB633XGW)

description:
https://www.encodeproject.org/experiments/ENCSR727HME/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human lower leg skin
experiment encode accession: ENCSR727HME
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR287HAL
encode release date: 2016-11-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB633XGW
size range: 450-650

source_name: Homo sapiens lower leg skin tissue female adult (51 year)

value: CTCF

value: lower leg skin

value: Michael Snyder, Stanford

value: ENCBS207AJN at ENCODE; https://www.encodeproject.org/ENCBS207AJN/


title: ChIP-seq from GM12878 (ENCLB984OVA)

description:
https://www.encodeproject.org/experiments/ENCSR725VFL/
***************
biological replicate number: 1
technical replicate number: 1
description: TCF12 ChIP-seq on human GM12878
experiment encode accession: ENCSR725VFL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2017-06-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB984OVA
size range: 450-650

value: immortalized cell line

value: unknown

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

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


title: ChIP-seq from tibial nerve (ENCLB111TTL)

description:
https://www.encodeproject.org/experiments/ENCSR822PJT/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human tibial nerve
experiment encode accession: ENCSR822PJT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR396WMW
encode release date: 2016-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB111TTL
size range: 450-650

source_name: Homo sapiens tibial nerve tissue female adult (51 year)

value: tibial nerve

value: tissue

value: female

value: adult

value: ENCBS689AWK at ENCODE; https://www.encodeproject.org/ENCBS689AWK/


title: SMA mouse brain, polysomal RNA, early symptomatic, rep 2

description:
sma_poly_early_2
polysomal RNA extracted from a SMA mouse brain at early-symptomatic stage

source_name: SMA mouse brain_polysomal RNA_early symptomatic

value: congenic FVB background

value: Taiwanese mouse model of severe Spinal muscular atrophy (SMA)

value: early-symptomatic

value: brain

tag: rna fraction

value: polysomal RNA


title: WT repeat 2, ChIP [13762X8]

description:
log2 fold-enrichment file:
WTa_log2FE.bw

tag: reference control

value: Candida glabrata

tag: strain

value: WT


title: WT repeat 1, ChIP [13762X2]


title: WT repeat 3, ChIP [13762X14]


title: WT repeat 1, Input DNA [13764X2]


title: SMA mouse brain, total RNA, late symptomatic, rep 1

description:
sma_tot_late_1
total cytoplasmic RNA extracted from a SMA mouse brain at late-symptomatic stage

value: late-symtomatic

value: total RNA

tag: replicate


title: ChIP-seq from epithelial cell of prostate (ENCLB588PFU)

description:
https://www.encodeproject.org/experiments/ENCSR910PDW/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on human epithelial cell of prostate
experiment encode accession: ENCSR910PDW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR131SEB
encode release date: 2017-03-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB588PFU
size range: 450-650

source_name: Homo sapiens epithelial of prostate primary cell male

tag: antibody

value: epithelial cell of prostate

value: primary cell

tag: biosample encode accession

value: male

value: Michael Snyder, Stanford

tag: age

value: unknown

value: ENCBS706NVS at ENCODE; https://www.encodeproject.org/ENCBS706NVS/

value: derived from ENCODE donor ENCDO569WSJ; https://www.encodeproject.org/ENCDO569WSJ/


title: ChIP-seq from GM12878 (ENCLB797QGH)

description:
https://www.encodeproject.org/experiments/ENCSR725VFL/
***************
biological replicate number: 2
technical replicate number: 1
description: TCF12 ChIP-seq on human GM12878
experiment encode accession: ENCSR725VFL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2017-06-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB797QGH
size range: 450-650

tag: line

value: immortalized cell line

value: adult

tag: Sex

value: female

tag: lab

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

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


title: ChIP-seq from epithelial cell of prostate (ENCLB910GSC)

description:
https://www.encodeproject.org/experiments/ENCSR910PDW/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on human epithelial cell of prostate
experiment encode accession: ENCSR910PDW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR131SEB
encode release date: 2017-03-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB910GSC
size range: 450-650

tag: dev stage

value: ENCBS143IKI at ENCODE; https://www.encodeproject.org/ENCBS143IKI/


title: ChIP-seq from prostate gland (ENCLB866TLS)

description:
https://www.encodeproject.org/experiments/ENCSR912ZIY/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on prostate
experiment encode accession: ENCSR912ZIY
assay title: ChIP-seq
assembly: hg19
possible controls: ENCSR689LFI
encode release date: 2017-06-15
lab: Richard Myers, HAIB
library encode accession: ENCLB866TLS

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

value: prostate gland

value: tissue

value: Richard Myers, HAIB

value: 37 year

value: ENCBS720KJI at ENCODE; https://www.encodeproject.org/ENCBS720KJI/

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


title: ChIP-seq from GM12878 (ENCLB077FFN)

description:
https://www.encodeproject.org/experiments/ENCSR822AHX/
***************
biological replicate number: 1
technical replicate number: 1
description: IKZF2 ChIP-seq on human GM12878
experiment encode accession: ENCSR822AHX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2017-06-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB077FFN
size range: 450-650

tag: health state

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

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


title: Pre-immune repeat 3, Input DNA [12410X9]

source_name: Whole yeast cells

value: Candida glabrata

tag: relevant genotype

value: WT


title: Pre-immune repeat 2, Input DNA [12410X8]


title: control mouse brain, polysomal RNA, early symptomatic, rep 2

description:
ctrl_poly_early_2
polysomal RNA extracted from a control mouse brain at early-symptomatic stage

source_name: control mouse brain_polysomal RNA_early symptomatic

tag: strain background

value: congenic FVB background

tag: genotype/variation

value: control

tag: Stage

value: early-symptomatic

value: brain

value: polysomal RNA


title: SMA mouse brain, polysomal RNA, early symptomatic, rep 1

description:
sma_poly_early_1
polysomal RNA extracted from a SMA mouse brain at early-symptomatic stage

value: Taiwanese mouse model of severe Spinal muscular atrophy (SMA)

tag: tissue


title: ChIP-seq from K562 (ENCLB512SXK)

description:
https://www.encodeproject.org/experiments/ENCSR709DRM/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-E2F5 ChIP-seq on human K562
experiment encode accession: ENCSR709DRM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR362FFL
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB512SXK
size range: 200-800
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-E2F5 fusion protein

value: immortalized cell line

tag: description

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to E2F5

value: female

value: Kevin White, UChicago

tag: passage number

value: chronic myelogenous leukemia (CML)

value: 53 year

value: adult

tag: link

value: ENCBS165WTA at ENCODE; https://www.encodeproject.org/ENCBS165WTA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_GZ80; http://web.expasy.org/cellosaurus/CVCL_GZ80


title: ChIP-seq from GM12878 (ENCLB824DJX)

description:
https://www.encodeproject.org/experiments/ENCSR822AHX/
***************
biological replicate number: 2
technical replicate number: 1
description: IKZF2 ChIP-seq on human GM12878
experiment encode accession: ENCSR822AHX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2017-06-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB824DJX
size range: 450-650

source_name: Homo sapiens GM12878 immortalized cell line

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

value: Michael Snyder, Stanford

value: unknown

value: ENCBS519VWT at ENCODE; https://www.encodeproject.org/ENCBS519VWT/

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

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


title: Pre-immune repeat 1, Input DNA [12410X7]

tag: reference control

value: Candida glabrata

tag: strain

value: WT


title: SMA mouse brain, total RNA, early symptomatic, rep 2

description:
sma_tot_early_2
total cytoplasmic RNA extracted from a SMA mouse brain at early-symptomatic stage

source_name: SMA mouse brain_total RNA_early symptomatic

value: congenic FVB background

value: Taiwanese mouse model of severe Spinal muscular atrophy (SMA)

value: early-symptomatic

value: brain

tag: rna fraction

value: total RNA

tag: replicate


title: control mouse brain, polysomal RNA, early symptomatic, rep 1

description:
ctrl_poly_early_1
polysomal RNA extracted from a control mouse brain at early-symptomatic stage

value: control

value: polysomal RNA


title: ChIP-seq from MCF-7 (ENCLB143FKD)

description:
https://www.encodeproject.org/experiments/ENCSR725ELR/
***************
biological replicate number: 2
technical replicate number: 1
description: LARP7 ChIP-seq on human MCF-7
experiment encode accession: ENCSR725ELR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR882IYK
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB143FKD
size range: 450-650

source_name: Homo sapiens MCF-7 immortalized cell line

tag: antibody

tag: line

value: immortalized cell line

tag: biosample encode accession

value: female

value: breast cancer (adenocarcinoma)

tag: age

value: 69 year

value: adult

value: ENCBS028FSB at ENCODE; https://www.encodeproject.org/ENCBS028FSB/

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


title: SMA mouse brain, total RNA, early symptomatic, rep 1

description:
sma_tot_early_1
total cytoplasmic RNA extracted from a SMA mouse brain at early-symptomatic stage


title: ChIP-seq from K562 (ENCLB573EWI)

description:
https://www.encodeproject.org/experiments/ENCSR807BGP/
***************
biological replicate number: 2
technical replicate number: 1
description: MTA1 ChIP-seq on human K562
experiment encode accession: ENCSR807BGP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB573EWI
size range: 450-650

tag: dev stage

value: 53 year

tag: Sex

tag: lab

value: Michael Snyder, Stanford

tag: health state

value: chronic myelogenous leukemia (CML)

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

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: spt6-KK,AA repeat 2, Input DNA [12412X11]

value: Candida glabrata

tag: relevant genotype


title: ChIP-seq from K562 (ENCLB732NWZ)

description:
https://www.encodeproject.org/experiments/ENCSR807BGP/
***************
biological replicate number: 1
technical replicate number: 1
description: MTA1 ChIP-seq on human K562
experiment encode accession: ENCSR807BGP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB732NWZ
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: ENCBS207UAM at ENCODE; https://www.encodeproject.org/ENCBS207UAM/

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


title: ChIP-seq from lower leg skin (ENCLB586PXF)

description:
https://www.encodeproject.org/experiments/ENCSR821NQM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human lower leg skin
experiment encode accession: ENCSR821NQM
assay title: ChIP-seq
encode release date: 2017-03-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB586PXF
size range: 450-650

value: Control

value: lower leg skin

value: tissue

value: 51 year

value: ENCBS207AJN at ENCODE; https://www.encodeproject.org/ENCBS207AJN/

value: derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: ChIP-seq from MCF-7 (ENCLB649CZS)

description:
https://www.encodeproject.org/experiments/ENCSR725ELR/
***************
biological replicate number: 1
technical replicate number: 1
description: LARP7 ChIP-seq on human MCF-7
experiment encode accession: ENCSR725ELR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR882IYK
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB649CZS
size range: 450-650

value: immortalized cell line

value: female

value: breast cancer (adenocarcinoma)

value: 69 year

value: adult

value: ENCBS726ASX at ENCODE; https://www.encodeproject.org/ENCBS726ASX/

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


title: spt6-KK,AA repeat 1, Input DNA [12412X10]

value: Candida glabrata


title: control mouse brain, total RNA, early symptomatic, rep 1

description:
ctrl_tot_early_1
total cytoplasmic RNA extracted from a control mouse brain at early-symptomatic stage

source_name: control mouse brain_total RNA_early symptomatic

tag: strain background

value: congenic FVB background

tag: genotype/variation

value: control

tag: Stage

value: early-symptomatic

tag: tissue

value: brain

value: total RNA


title: ChIP-seq from sigmoid colon (ENCLB584MNM)

description:
https://www.encodeproject.org/experiments/ENCSR724FCJ/
***************
biological replicate number: 1
technical replicate number: 1
description: POLR2A ChIP-seq on human sigmoid colon
experiment encode accession: ENCSR724FCJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR439EEV
encode release date: 2016-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB584MNM
size range: 450-650

source_name: Homo sapiens sigmoid colon tissue female adult (51 year)

value: sigmoid colon

value: tissue

value: Michael Snyder, Stanford

tag: link

value: ENCBS214RWK at ENCODE; https://www.encodeproject.org/ENCBS214RWK/


title: spt6-KK,AA repeat 3, Input DNA [12412X12]

tag: reference control

tag: strain


title: control mouse brain, total RNA, early symptomatic, rep 2

description:
ctrl_tot_early_2
total cytoplasmic RNA extracted from a control mouse brain at early-symptomatic stage

tag: rna fraction

tag: replicate


title: ChIP-seq from stomach (ENCLB611MQG)

description:
https://www.encodeproject.org/experiments/ENCSR804FRO/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on -human (fragmentation date:Tue Aug 30 2016 00:00:00 GMT-0500 (CDT)
experiment encode accession: ENCSR804FRO
assay title: ChIP-seq
encode release date: 2016-11-09
lab: Richard Myers, HAIB
library encode accession: ENCLB611MQG

source_name: Homo sapiens stomach tissue male adult (54 years)

tag: antibody

value: Control

value: stomach

value: male

value: Richard Myers, HAIB

value: 54 year

value: ENCBS721EEQ at ENCODE; https://www.encodeproject.org/ENCBS721EEQ/

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

value: high resolution pathology slide image; https://www.encodeproject.org/documents/cb208506-a0a3-4020-8d0c-f673d114f2d8/@@download/attachment/82354.svs


title: ChIP-seq from K562 (ENCLB766EJE)

description:
https://www.encodeproject.org/experiments/ENCSR805ITZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-NR2C1 tagged K562 cell line.
experiment encode accession: ENCSR805ITZ
assay title: ChIP-seq
encode release date: 2016-02-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB766EJE
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-NR2C1 fusion protein

tag: line

value: immortalized cell line

tag: description

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to NR2C1-L

tag: biosample encode accession

value: female

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: 53 year

value: adult

value: ENCBS936SUX at ENCODE; https://www.encodeproject.org/ENCBS936SUX/

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

value: ENCODE dbxrefs Cellosaurus CVCL_AW36; http://web.expasy.org/cellosaurus/CVCL_AW36


title: ChIP-seq from K562 (ENCLB312GNT)

description:
https://www.encodeproject.org/experiments/ENCSR817QKV/
***************
biological replicate number: 1
technical replicate number: 1
description: EP400 ChIP-seq on human K562
experiment encode accession: ENCSR817QKV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2017-06-29
lab: Michael Snyder, Stanford
library encode accession: ENCLB312GNT
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line

tag: dev stage

tag: Sex

tag: age

value: Michael Snyder, Stanford

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

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

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


title: ChIP-seq from sigmoid colon (ENCLB411HCE)

description:
https://www.encodeproject.org/experiments/ENCSR906UPC/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on sigmoid colon
experiment encode accession: ENCSR906UPC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR185GDB
encode release date: 2017-06-15
lab: Richard Myers, HAIB
library encode accession: ENCLB411HCE

source_name: Homo sapiens sigmoid colon tissue male adult (37 years)

value: sigmoid colon

value: tissue

value: male

tag: lab

value: Richard Myers, HAIB

value: 37 year

value: ENCBS806WZK at ENCODE; https://www.encodeproject.org/ENCBS806WZK/

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


title: rpb1-FSP+,KRR+ repeat 3, Input DNA [12412X9]

value: Candida glabrata

tag: relevant genotype


title: rpb1-FSP+,KRR+ repeat 2, Input DNA [12412X8]


title: rpb1-FSP+,KRR+ repeat 1, Input DNA [12412X7]


title: ChIP-seq from K562 (ENCLB410LRX)

description:
https://www.encodeproject.org/experiments/ENCSR817QKV/
***************
biological replicate number: 2
technical replicate number: 1
description: EP400 ChIP-seq on human K562
experiment encode accession: ENCSR817QKV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2017-06-29
lab: Michael Snyder, Stanford
library encode accession: ENCLB410LRX
size range: 450-650

value: immortalized cell line

value: 53 year

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

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


title: ChIP-seq from K562 (ENCLB731CDH)

description:
https://www.encodeproject.org/experiments/ENCSR709DRM/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-E2F5 ChIP-seq on human K562
experiment encode accession: ENCSR709DRM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR362FFL
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB731CDH
size range: 200-800
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to E2F5

value: Kevin White, UChicago

tag: passage number

value: adult

value: ENCBS925NOW at ENCODE; https://www.encodeproject.org/ENCBS925NOW/

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

value: ENCODE dbxrefs Cellosaurus CVCL_GZ80; http://web.expasy.org/cellosaurus/CVCL_GZ80


title: 6mA.IP.Stressed.3

city: Atlanta

first: Bing

last: Yao

state: GA

address: 615 Michael St. Rm 323

department: Human Genetics

institute: Emory University

data_processing:
Library strategy: 6mA-IP-seq
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to mm9 using tophat v2.0.13 and differential RPKM expression values were extracted using cuffdiff v2.2.1
6mA-IP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.9 with the standard parameters.
Differential regions (Loss.of.N6mA.xlsx and Gain.of.N6mA.xlsx) were identified by edgeR v3.4
Genome_build: mm9
Supplementary_files_format_and_content: RPKM, N6mA gain or loss

source_name: Mice prefrontal cortex

growth_protocol: All of the wild type mice that we used were on the C57BL/6 genetic background.All animal were hosted in Emory mice facility and procedures were performed according to protocols approved by Emory University Institutional Animal Care and Use Committee.

extract_protocol:
Mouse prefrontal cortex were dissected from the brain. Genomic DNAs were isolated by different brain tissues in 600 μl digestion buffer (100 mM Tris-HCl, pH 8.5, 5 mM EDTA, 0.2% SDS, 200 mM NaCl), Proteinase K (Thermo) treatment at 55°C for overnight. The second day, 600 μl of Phenol:Chloroform:Isoamyl Alcohol (25:24:1 Saturated with 10 mM Tris, pH 8.0, 1 mM EDTA) (P-3803, Sigma) was added to samples, mixed completely, and centrifuged for 10 min at 12,000 rpm. The aqueous layer solution was transferred into a new Eppendorf tube and precipitated with 600 μl isopropanol. The pellet was washed with 75% ethanol, air-dried, and eluted with Nuclease-Free Water (Ambion). PFC samples were homogenized in Trizol (Invitrogen) and processed according to the manufacturer’s instructions. RNA was then reverse transcribed using a SuperScript® III First-Strand Synthesis System (Invitrogen).
Genomic DNA was sonicated to 200-300bp fragments for IP-based 6mA enrichment using rabbit polyclonal antibody raised against 6mA (Synaptic Systems) at 1:100 in 1X IP buffer containing 100Mm Tris-HCl pH7.4, 150Mm NaCl, 0.05% Triton X-100. The IP was conducted with overnight platform rotation at 4°C without beads. Dynabeads Protein G (Novex by life technologies, REF 10009D 30mg/ml) were added and the mixture was rotated at 4°C for 2hr. The IPed beads were washed six times at room temperature with 1X ice-cold IP buffer, 5min each with rotation. After the wash, the IPed DNA fragments were eluted by either protease K digestion or 6mA competition. For protease K digestion-based elution, the IPed beads were treated with digestion buffer containing 1x TE, 0.25% SDS, and 0.25% Proteinase K (2.5mg/ml) at 55°C and 1400rpm for 2hr. The eluted DNA fragments were extracted once with phenol: chloroform: isoamyl alchohol =25:24:1 followed by extraction with chloroform alone, and then precipitation with glycogen, NaAc pH5.2, and 100% ethanol at -20C for at least 2hr or overnight. For 6mA base competition based elution, the IPed beads were treated with 1X IP buffer plus 2.6mM 6mA three times for 30 min each at room temperature. The eluted DNA fragments were precipitated without extraction with phenol and chloroform. 25ng of input genomic DNA or experimental enriched DNA were utilized for each library construction. 150-300 bp DNA fragments were selected by AMPure XP Beads (Beckman Coulter) after the adapter ligation. An Agilent 2100 BioAnalyzer was used to quantify the amplified DNA, qPCR was applied to accurately quantify the library concentration. 20 pM diluted libraries were used for sequencing. 50-cycle single-end sequencings were performed using Illumina HISeq 2000. Image processing and sequence extraction were done using the standard Illumina Pipeline. RNA-seq libraries were generated from duplicated samples per condition using the Illumina TruSeq RNA Sample Preparation Kit v2 following manufacturer’s protocol. The RNA-seq libraries were sequenced as 50-cycle pair-end runs using Illumina HiSeq 2000.

treatment_protocol: Mice were individually placed into a modified well-ventilated 50-ml centrifuge tube (Corning Inc., Corning, NY) daily from 10am to 12pm for 2 hours in their home cages during one or two whole weeks. The restrained mice could change from supine to prone position, but were not able to move forward or backward in tubes. The non-restrained control mice remained undisturbed in their home cages. After restraint stress, mice were released from the tube and returned to their home cages.

tag: stressed

value: yes

value: Synaptic Systems N6-methyladenosine (Cat. No. 202 003)


title: 6mA.IP.Stressed.2


title: ChIP-seq from esophagus muscularis mucosa (ENCLB166EIB)

description:
https://www.encodeproject.org/experiments/ENCSR922GUA/
***************
biological replicate number: 1
technical replicate number: 1
description: POLR2A ChIP-seq on human esophagus muscularis mucosa
experiment encode accession: ENCSR922GUA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR834ESZ
encode release date: 2017-03-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB166EIB
size range: 450-650

source_name: Homo sapiens esophagus muscularis mucosa tissue female adult (53 years)

value: esophagus muscularis mucosa

value: tissue

value: Michael Snyder, Stanford

tag: link

value: ENCBS643MHO at ENCODE; https://www.encodeproject.org/ENCBS643MHO/

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


title: 6mA.IP.Stressed.1


title: ChIP-seq from Peyer's patch (ENCLB676SXR)

description:
https://www.encodeproject.org/experiments/ENCSR921JFJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human Peyer's patch
experiment encode accession: ENCSR921JFJ
assay title: ChIP-seq
encode release date: 2017-01-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB676SXR
size range: 450-650

source_name: Homo sapiens Peyer's patch tissue male adult (54 years)

value: Control

value: Peyer's patch

value: male

value: 54 year

value: ENCBS404OGY at ENCODE; https://www.encodeproject.org/ENCBS404OGY/

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


title: ChIP-seq from HEK293T (ENCLB132SEO)

description:
https://www.encodeproject.org/experiments/ENCSR906PEI/
***************
biological replicate number: 1
technical replicate number: 1
description: SP1 ChIP-seq on human HEK293T
experiment encode accession: ENCSR906PEI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR386FAB
encode release date: 2017-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB132SEO
size range: 450-650

source_name: Homo sapiens HEK293T immortalized cell line

value: immortalized cell line

value: embryonic

value: unknown

value: female

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

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


title: WT repeat 3, Input DNA [12410X12]

tag: reference control

value: Candida glabrata

value: WT


title: 6mA.IP.Ctrl.3

tag: strain

value: no

value: Synaptic Systems N6-methyladenosine (Cat. No. 202 003)


title: ChIP-seq from HEK293T (ENCLB082WSX)

description:
https://www.encodeproject.org/experiments/ENCSR906PEI/
***************
biological replicate number: 2
technical replicate number: 1
description: SP1 ChIP-seq on human HEK293T
experiment encode accession: ENCSR906PEI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR386FAB
encode release date: 2017-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB082WSX
size range: 450-650

value: Michael Snyder, Stanford

value: ENCBS276VDW at ENCODE; https://www.encodeproject.org/ENCBS276VDW/


title: WT repeat 2, Input DNA [12410X11]


title: ChIP-seq from sigmoid colon (ENCLB933FIX)

description:
https://www.encodeproject.org/experiments/ENCSR721AHD/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human sigmoid colon
experiment encode accession: ENCSR721AHD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR983XKG
encode release date: 2016-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB933FIX
size range: 450-650

value: CTCF

value: sigmoid colon

value: tissue

value: 37 year

value: adult

value: ENCBS919RQL at ENCODE; https://www.encodeproject.org/ENCBS919RQL/

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


title: 6mA.IP.Ctrl.2