title: ChIP-seq from HEK293 (ENCLB259AER)

description:
https://www.encodeproject.org/experiments/ENCSR159GFL/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF518A ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR159GFL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB259AER
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF518A fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF518A under the control of a CMV promoter.

value: ENCBS562OGG at ENCODE; https://www.encodeproject.org/ENCBS562OGG/


title: eCLIP from K562 (ENCLB039AEI)

status: Public on Jan 04 2017

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR658IQB/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against SMNDC1
experiment encode accession: ENCSR658IQB
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR631CJA
encode release date: 2015-12-16
lab: Gene Yeo, UCSD
library encode accession: ENCLB039AEI
size range: 175-300

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens K562 immortalized cell line

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

tag: antibody

tag: line

tag: biosample encode accession

tag: dev stage

value: adult

tag: Sex

value: female

tag: age

value: 53 year

tag: health state

value: chronic myelogenous leukemia (CML)

tag: passage number

tag: lab

value: Gene Yeo, UCSD

tag: link

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

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

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

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


title: ChIP-seq from HEK293 (ENCLB741SRO)

description:
https://www.encodeproject.org/experiments/ENCSR159GFL/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF518A ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR159GFL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB741SRO
size range: 450-650

library_source: genomic

molecule: genomic DNA

tag: description

value: embryonic

value: unknown

value: Michael Snyder, Stanford

value: ENCBS033LOT at ENCODE; https://www.encodeproject.org/ENCBS033LOT/

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


title: eCLIP from K562 (ENCLB650JTP)

description:
https://www.encodeproject.org/experiments/ENCSR661ICQ/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against PUM2
experiment encode accession: ENCSR661ICQ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR439GXW
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB650JTP
size range: 175-300

value: immortalized cell line

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


title: CCTO46-ORSI-07Apr2011

city: Corvallis

first: Richard

middle: C

last: Cronn

state: Oregon

address: 3200 SW Jefferson Way

department: Pacific Northwest Research Station

institute: USDA Forest Service

description: Douglas-fir annual transcriptome analysis

data_processing:
Base-calling and demultiplexing was performed using Casava v1.8 (Illumina Inc.).
Transcript read mapping: To quantify transcript abundance in diurnal and RNA-Seq samples, we mapped reads to the pan-transcriptome reference with bowtie2.2.3 (Langmead and Salzberg, 2012) using the following call:  bowtie2 --end-to-end -D 15 -R 2 -L 22 -i S,1,1.15. This allows 15 consecutive seed extension attempts before the aligner moved on (-D 15), a maximum of 2 attempts to re-seed reads with repetitive seeds (-R 2), and a 22 bp seed (-L 22) with zero allowed mismatches in this seed. The function to determine the interval between seed substrings during multi-seed alignment was set to f(x) = 1 + 1.15 * sqrt(x), where x is the read length (-i S,1,1.15) (based on the 101 bp read lengths this resulted in an interval of 13 bp).  Output from this step is provided as processed data file "filename2.gz"
Transcript filtering and normalization: Since many transcripts showed near-zero counts, we excluded transcripts showing median counts at or below 5 from analyses because they were essentially indistinguishable from background transcription. For transcripts meeting the median cut-off, counts were normalized using DESeq normalization (Anders and Huber, 2010; Bullard et al., 2010; Dillies et al., 2012).
Transcript count interpolation: For the Annual Expression study, five trees from two families were sampled at 16 time points (80 total samples). Thirteen samples were too low-quality and had to be dropped from the analysis. To obtain full coverage over the 16 sample time points-- two trees from family A (CCTO44, CCCTO90) and three from family B (CCTO43, CCTO46, CCTO89) were used.  Counts were median filtered by gene (retained if median>5 counts), and then normalized for library size using DESeq normalization. For cyclic expression analysis, normalized values were averaged and then analyzed by family. The 16 sample time points  were not quite evenly spaced, so new values at equally spaced time intervals were inferred using linear interpolation on the the family averages.  This was done individually for every gene in the table.
Genome_build: Douglas-fir pan-transcriptome reference v2.03 (TSA in submission)
Supplementary_files_format_and_content: tab-separated text files were generated using  bowtie 2.2.3; Counts represent the number of reads mapping to each transcript model
Supplementary_files_format_and_content: tab-separated text files were generated using DESeq; Counts represent the number of reads mapping to each transcript model, after the application of a normalization factor to correct for library size
Supplementary_files_format_and_content: tab-separated text files were generated using a custom R-script; Counts represent the interpolated DESeq-adjusted counts for each transcript model, where interpolations correct for uneven sample intervals.

molecule: polyA RNA

organism: Pseudotsuga menziesii

growth_protocol: Trees used for annual transcriptome analysis are a sample from a reciprocal translocation study (Harrington et al., 2010) that includes families from multiple geographic sources in the Pacific Northwestern region of North America. Sources were chosen to maximize climatic differences in geographic origin (temperature, precipitation), and differences in growth phenology determined for the same seed lots. Three source climate zones are represented: a cold/wet region (Washington Cascades high elevation; 47.3° N, -121.6° W, 950 m elevation); a cool/wet region (Washington Coast low elevation; 47.2° N, -123.9° W, 111 m elevation); and a warm/dry region (Oregon Siskiyou low elevation; 43.3° N, -123.1° W, 429 m elevation). Two-year old trees were planted in a warm/dry region similar to Oregon Siskiyou sources (J. Herbert Stone Nursery , Central Point, Oregon, USA; 42.3° N, -122.9° W, 390 m elevation) in November, 2009, and sampling of the 2010 cohort of needles was initiated on October 27, 2010 at approximately three week intervals until November, 2011 (16 samples points).  Needles were collected at approximately 12:00 pm (ZT = 04:20 to 06:30). Annual precipitation at the Central Point, OR garden site during our experiment was 460 mm, minimum air temperature was -8.0°C, and maximum air temperature was 37.5°C. Environmental data (sunrise; sunset; day length; cumulative weekly precipitation; mean minimum and maximum weekly temperature) was collected for this experiment.

extract_protocol:
Needles (8 – 12 per sample) were collected 2.5 - 5 cm basipetal of dormant branch apical buds from branches representing four cardinal directions. Needles were flash-frozen in liquid N2, followed by homogenization on dry ice (FastPrep-24 mill, matrix A; MP Biomedical, Solon, OH., USA). Ice-cold extraction buffer (1.5 mL of 3M LiCl/8M urea; 1% PVP K-60; 0.1M dithiothreitol; Tai et al., 2004) was added to ground tissue, homogenized, then centrifuged at 200g x 10 min., 4°C. The supernatant was incubated overnight at 4°C, and crude RNA was pelleted (20,000g x 30 min., 4°C) and cleaned using the ZR Plant RNA MiniPrep kit (Zymo Research, Irvine, CA., USA) and DNAse treatment (Turbo DNAse; New England Biolabs, Ipswich, MA., USA). RNA concentration was estimated using a Qubit fluorometer (Invitrogen, Carlsbad, CA., USA), and total RNA yield averaged 0.3 µg/mg tissue.
Indexed Illumina RNA-Seq libraries used 2 µg total RNA and TruSeq chemistry (Illumina Inc., San Diego, CA), modified for strand-specific sampling (Parkhomchuk et al., 2009). In this protocol, the first-strand synthesis reaction was desalted to remove unincorporated dNTPs using Sephadex G-25 (Sigma-Aldrich, St. Louis, MO., USA) filtration. Desalted products were reconstituted in dNTP-free second-strand synthesis buffer, second strand enzyme mix (New England Biolabs, Ipswich, MA., USA), and a dUTP/dNTP mixture (ThermoScientific, Waltham, MA., USA) to incorporate dUTP into the second strand. All other steps follow Illumina protocols, except that uracil-containing strands were degraded using a uracil-specific excision reagent mixture (37°C for 15 minutes; New England Biolabs) prior to PCR. Amplified libraries were quantified by fluorometry and pooled at equimolar 6-plex representation at 10 nM. Sequencing was performed at Oregon State University's Center for Genome Research and Biocomputing (Corvallis, OR., USA) using a HiSeq 2000 (Illumina Inc.) with version 3.0 chemistry.

tag: family-tag

value: Oregon Siskiyou low elevation


title: eCLIP from K562 (ENCLB288CKF)

description:
https://www.encodeproject.org/experiments/ENCSR647CLF/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against GPKOW
experiment encode accession: ENCSR647CLF
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR393STP
encode release date: 2016-10-31
lab: Gene Yeo, UCSD
library encode accession: ENCLB288CKF
size range: 175-300

value: GPKOW

value: adult


title: CCTO46-ORSI-10Mar2011


title: CCTO46-ORSI-07Jul2011


title: ChIP-seq from K562 (ENCLB611UDM)

description:
https://www.encodeproject.org/experiments/ENCSR157TCS/
***************
biological replicate number: 1
technical replicate number: 1
description: SMARCE1 ChIP-seq on human K562
experiment encode accession: ENCSR157TCS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB611UDM
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: female

value: 53 year

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

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


title: CCTO46-ORSI-23Feb2011


title: eCLIP from K562 (ENCLB194PVV)

description:
https://www.encodeproject.org/experiments/ENCSR631CJA/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against SMNDC1
experiment encode accession: ENCSR631CJA
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-12-16
lab: Gene Yeo, UCSD
library encode accession: ENCLB194PVV
size range: 175-300

value: Control

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

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

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

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


title: eCLIP from K562 (ENCLB850EER)

description:
https://www.encodeproject.org/experiments/ENCSR647CLF/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against GPKOW
experiment encode accession: ENCSR647CLF
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR393STP
encode release date: 2016-10-31
lab: Gene Yeo, UCSD
library encode accession: ENCLB850EER
size range: 175-300

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

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


title: RAMPAGE from stomach (ENCLB433IYQ)

description:
https://www.encodeproject.org/experiments/ENCSR686VRS/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human stomach tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR686VRS
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR752UNJ
encode release date: 2016-10-31
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB433IYQ
size range: >200

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

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/304d5e1c-0e5f-49b1-bbf9-2e545b03c688/@@download/attachment/296879.pdf

value: stomach

value: tissue

value: Stomach aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: Thomas Gingeras, CSHL

value: ENCBS607DWD at ENCODE; https://www.encodeproject.org/ENCBS607DWD/

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


title: ChIP-seq from K562 (ENCLB465TLL)

description:
https://www.encodeproject.org/experiments/ENCSR155KHM/
***************
biological replicate number: 1
technical replicate number: 1
description: ARNT ChIP-seq on human K562
experiment encode accession: ENCSR155KHM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-04-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB465TLL
size range: 450-650

value: ARNT

value: immortalized cell line

value: adult

value: 53 year

value: female

value: Michael Snyder, Stanford

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


title: ChIP-seq from K562 (ENCLB108AIV)

description:
https://www.encodeproject.org/experiments/ENCSR157TCS/
***************
biological replicate number: 2
technical replicate number: 1
description: SMARCE1 ChIP-seq on human K562
experiment encode accession: ENCSR157TCS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB108AIV
size range: 450-650

value: chronic myelogenous leukemia (CML)

value: ENCBS344LIE at ENCODE; https://www.encodeproject.org/ENCBS344LIE/

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


title: CCTO46-ORSI-06Jan2011

value: Oregon Siskiyou low elevation


title: eCLIP from K562 (ENCLB044YKX)

description:
https://www.encodeproject.org/experiments/ENCSR595PFU/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against NSUN2
experiment encode accession: ENCSR595PFU
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-09-21
lab: Gene Yeo, UCSD
library encode accession: ENCLB044YKX
size range: 175-300

value: Control

value: Gene Yeo, UCSD

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

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

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


title: ChIP-seq from K562 (ENCLB945YAD)

description:
https://www.encodeproject.org/experiments/ENCSR155KHM/
***************
biological replicate number: 2
technical replicate number: 1
description: ARNT ChIP-seq on human K562
experiment encode accession: ENCSR155KHM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-04-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB945YAD
size range: 450-650

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


title: RAMPAGE from omental fat pad (ENCLB311XXT)

description:
https://www.encodeproject.org/experiments/ENCSR544IYF/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human omentum tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR544IYF
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR080HPT
encode release date: 2016-10-31
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB311XXT
size range: >200

source_name: Homo sapiens omental fat pad tissue male adult (54 years)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/9696ae21-0b63-466a-84ce-a13f93f1647d/@@download/attachment/296887.pdf

value: omental fat pad

value: tissue

value: Visceral adipose tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: male

value: 54 year

value: Thomas Gingeras, CSHL

value: ENCBS889JOH at ENCODE; https://www.encodeproject.org/ENCBS889JOH/

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


title: ibm11_Ler_1st

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

description: ibm1-1 mutant 1st generation

data_processing:
The raw reads were trimmed using Trimmomatic (Bolger et al, 2014 Bioinformatics) in order to remove adapter sequences. Reads with an average quality value of at least 15 in a window of 4 nucleotides were trimmed from both ends. After trimming, reads shorter than 16 bases were discarded.
The remaining sequences were aligned using Bismark (Krueger et al. 2011, Bioinformatics) against the Arabidopsis thaliana genome TAIR10 version or the PacBio Ler-0 genome assembly (http://www.pacb.com/uncategorized/new-data-release-arabidopsis-assembly/) for Col-0 ibm1 or Ler-0 ibm1 mutant, respectively. Duplicated reads were collapsed into one read.
Chloroplast sequences were used to estimate the bisulfite conversion.
Genome_build: Arabidopsis thaliana Col-0: TAIR10; Ler-0: PacBio assembly (http://www.pacb.com/uncategorized/new-data-release-arabidopsis-assembly/)
Supplementary_files_format_and_content: For each genotype, the CX_Report generated by Bismark is reported (Krueger et al. 2011, Bioinformatics).

organism: Arabidopsis thaliana

source_name: rosette leaves

growth_protocol: Plants were grown in plates under long-day conditions (21°C, 16 h light, 8 h dark)

extract_protocol:
Genomic DNA was extracted using the Plant DNeasy kit (Qiagen) following the manufacturer's instructions.
Libraries were constructed starting from 150 ng of genomic DNA, using the EZ-DNA Methylation-Gold Kit (Zymo Research), following by DNA library preparation with the TruSeq DNA methylation kit (Illumina), according to manufacturer's instructions.

tag: ecotype

tag: tissue

value: rosette leaves

value: 3 weeks


title: CCTO46-ORSI-09Nov2010

value: Oregon Siskiyou low elevation


title: eCLIP from K562 (ENCLB989WTG)

description:
https://www.encodeproject.org/experiments/ENCSR154HRN/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against HNRNPA1
experiment encode accession: ENCSR154HRN
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR898ZCL
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB989WTG
size range: 175-300

value: immortalized cell line

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS205QYW at ENCODE; https://www.encodeproject.org/ENCBS205QYW/

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

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


title: eCLIP from K562 (ENCLB061NQW)

description:
https://www.encodeproject.org/experiments/ENCSR539ZTS/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against TROVE2
experiment encode accession: ENCSR539ZTS
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR687GJH
encode release date: 2015-12-16
lab: Gene Yeo, UCSD
library encode accession: ENCLB061NQW
size range: 175-300

value: Gene Yeo, UCSD

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

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

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


title: CCTO46-ORSI-27Oct2010


title: eCLIP from K562 (ENCLB996FJM)

description:
https://www.encodeproject.org/experiments/ENCSR539ZTS/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against TROVE2
experiment encode accession: ENCSR539ZTS
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR687GJH
encode release date: 2015-12-16
lab: Gene Yeo, UCSD
library encode accession: ENCLB996FJM
size range: 175-300

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


title: CCTO44-ORSI-07Oct2011


title: ChIP-seq from GM12878 (ENCLB722AKA)

description:
https://www.encodeproject.org/experiments/ENCSR145XQO/
***************
biological replicate number: 1
technical replicate number: 1
description: HDGF ChIP-seq on human GM12878
experiment encode accession: ENCSR145XQO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR398JTO
encode release date: 2016-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB722AKA
size range: 450-650

source_name: Homo sapiens GM12878 immortalized cell line

value: HDGF

value: unknown

value: Michael Snyder, Stanford

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

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

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


title: ChIP-seq from HEK293 (ENCLB526QAW)

description:
https://www.encodeproject.org/experiments/ENCSR141PZA/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-SP3 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR141PZA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB526QAW
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-SP3 fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-SP3 under the control of a CMV promoter.

value: embryonic

value: female

value: ENCBS227SEC at ENCODE; https://www.encodeproject.org/ENCBS227SEC/

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


title: eCLIP from K562 (ENCLB084BHO)

description:
https://www.encodeproject.org/experiments/ENCSR575DKE/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against FTO
experiment encode accession: ENCSR575DKE
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-10-31
lab: Gene Yeo, UCSD
library encode accession: ENCLB084BHO
size range: 175-300

value: Control

value: adult

value: 53 year

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

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

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


title: RAMPAGE from Peyer's patch (ENCLB217WHE)

description:
https://www.encodeproject.org/experiments/ENCSR514XCC/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human ileum tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR514XCC
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR450BNZ
encode release date: 2016-10-31
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB217WHE
size range: >200

source_name: Homo sapiens Peyer's patch tissue female adult (51 year)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/88a8316f-e609-44fe-bc52-189aa5625c63/@@download/attachment/296892.pdf

value: Peyer's patch

value: tissue

value: Small intestine aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 51 year

value: Thomas Gingeras, CSHL

value: ENCBS168WDM at ENCODE; https://www.encodeproject.org/ENCBS168WDM/

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


title: ChIP-seq from HEK293 (ENCLB797TMH)

description:
https://www.encodeproject.org/experiments/ENCSR141PZA/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-SP3 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR141PZA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB797TMH
size range: 450-650

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-SP3 under the control of a CMV promoter.

value: embryonic

value: unknown

value: female

value: Michael Snyder, Stanford

value: ENCBS451MRF at ENCODE; https://www.encodeproject.org/ENCBS451MRF/


title: eCLIP from K562 (ENCLB779GIU)

description:
https://www.encodeproject.org/experiments/ENCSR157BRV/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against GTF2F1
experiment encode accession: ENCSR157BRV
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB779GIU
size range: 175-300

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

value: Control

value: adult

value: 53 year

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

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

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

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


title: eCLIP from K562 (ENCLB090ZQT)

description:
https://www.encodeproject.org/experiments/ENCSR468FSW/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against SRSF7
experiment encode accession: ENCSR468FSW
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR145PHJ
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB090ZQT
size range: 175-300

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

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

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


title: eCLIP from K562 (ENCLB401OEL)

description:
https://www.encodeproject.org/experiments/ENCSR468FSW/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against SRSF7
experiment encode accession: ENCSR468FSW
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR145PHJ
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB401OEL
size range: 175-300

value: immortalized cell line


title: CCTO44-ORSI-07Sep2011

description: Douglas-fir annual transcriptome analysis

value: Oregon Siskiyou low elevation


title: RAMPAGE from suprapubic skin (ENCLB221ZPR)

description:
https://www.encodeproject.org/experiments/ENCSR480WCN/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human suprapubic skin tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR480WCN
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR450ENK
encode release date: 2016-10-31
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB221ZPR
size range: >200

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

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/76e4104a-3479-4b41-ae4e-16b670c889ba/@@download/attachment/296888.pdf

value: suprapubic skin

value: tissue

value: Suprapubic skin (not sun exposed) aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: Thomas Gingeras, CSHL

value: ENCBS586YKG at ENCODE; https://www.encodeproject.org/ENCBS586YKG/

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


title: CCTO44-ORSI-28Jul2011


title: eCLIP from K562 (ENCLB424DBJ)

description:
https://www.encodeproject.org/experiments/ENCSR461LGW/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against UPF1
experiment encode accession: ENCSR461LGW
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB424DBJ
size range: 175-300

value: Control

value: adult

value: female

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


title: ChIP-seq from K562 (ENCLB693QTZ)

description:
https://www.encodeproject.org/experiments/ENCSR137ZMQ/
***************
biological replicate number: 1
technical replicate number: 1
description: REST ChIP-seq on human K562
experiment encode accession: ENCSR137ZMQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB693QTZ
size range: 450-650

value: REST

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

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Michael Snyder, Stanford

value: ENCBS048GNZ at ENCODE; https://www.encodeproject.org/ENCBS048GNZ/

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


title: CCTO44-ORSI-17Aug2011

value: Oregon Siskiyou low elevation


title: CCTO46-ORSI-30Nov2010


title: ChIP-seq from K562 (ENCLB077NGB)

description:
https://www.encodeproject.org/experiments/ENCSR137ZMQ/
***************
biological replicate number: 2
technical replicate number: 1
description: REST ChIP-seq on human K562
experiment encode accession: ENCSR137ZMQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB077NGB
size range: 450-650

value: immortalized cell line

value: ENCBS044UVO at ENCODE; https://www.encodeproject.org/ENCBS044UVO/

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

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


title: eCLIP from K562 (ENCLB932JNU)

description:
https://www.encodeproject.org/experiments/ENCSR154HRN/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against HNRNPA1
experiment encode accession: ENCSR154HRN
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR898ZCL
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB932JNU
size range: 175-300

value: Gene Yeo, UCSD

value: ENCBS328LML at ENCODE; https://www.encodeproject.org/ENCBS328LML/


title: CCTO44-ORSI-26Oct2011


title: ChIP-seq from GM12878 (ENCLB434KMC)

description:
https://www.encodeproject.org/experiments/ENCSR145XQO/
***************
biological replicate number: 2
technical replicate number: 1
description: HDGF ChIP-seq on human GM12878
experiment encode accession: ENCSR145XQO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR398JTO
encode release date: 2016-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB434KMC
size range: 450-650

value: HDGF

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

value: adult

value: unknown

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

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

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

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


title: eCLIP from K562 (ENCLB022FVI)

description:
https://www.encodeproject.org/experiments/ENCSR456ASB/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against UPF1
experiment encode accession: ENCSR456ASB
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR461LGW
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB022FVI
size range: 175-300

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

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

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


title: CCTO44-ORSI-07Jul2011

value: Oregon Siskiyou low elevation


title: CCTO46-ORSI-07Feb2011


title: eCLIP from K562 (ENCLB235NQC)

description:
https://www.encodeproject.org/experiments/ENCSR456ASB/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against UPF1
experiment encode accession: ENCSR456ASB
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR461LGW
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB235NQC
size range: 175-300

value: immortalized cell line

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

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

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


title: CCTO44-ORSI-17Jun2011


title: ChIP-seq from MCF-7 (ENCLB139AGY)

description:
https://www.encodeproject.org/experiments/ENCSR135ANT/
***************
biological replicate number: 1
technical replicate number: 1
description: NRF1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR135ANT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB139AGY
size range: 450-650

source_name: Homo sapiens MCF-7 immortalized cell line

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

value: 69 year

value: breast cancer (adenocarcinoma)

value: Michael Snyder, Stanford

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

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

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

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


title: eCLIP from K562 (ENCLB809FVC)

description:
https://www.encodeproject.org/experiments/ENCSR439GXW/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against PUM2
experiment encode accession: ENCSR439GXW
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB809FVC
size range: 175-300

value: Control

value: adult

value: female

value: 53 year

value: Gene Yeo, UCSD


title: CCTO44-ORSI-06May2011

value: Oregon Siskiyou low elevation


title: CCTO44-ORSI-07Apr2011


title: ChIP-seq from HEK293 (ENCLB966JSO)

description:
https://www.encodeproject.org/experiments/ENCSR134QIE/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZFP3 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR134QIE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB966JSO
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZFP3 fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZFP3 under the control of a CMV promoter.

value: embryonic

value: unknown

value: ENCBS543JVF at ENCODE; https://www.encodeproject.org/ENCBS543JVF/

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


title: eCLIP from K562 (ENCLB149CTU)

description:
https://www.encodeproject.org/experiments/ENCSR438GZQ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against KHSRP
experiment encode accession: ENCSR438GZQ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR305IPT
encode release date: 2015-12-16
lab: Gene Yeo, UCSD
library encode accession: ENCLB149CTU
size range: 175-300

value: KHSRP

value: chronic myelogenous leukemia (CML)

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

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

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

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


title: CCTO44-ORSI-10Mar2011


title: CCTO44-ORSI-23Feb2011


title: eCLIP from K562 (ENCLB852JGH)

description:
https://www.encodeproject.org/experiments/ENCSR305IPT/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against KHSRP
experiment encode accession: ENCSR305IPT
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-12-16
lab: Gene Yeo, UCSD
library encode accession: ENCLB852JGH
size range: 175-300

value: Control

value: adult


title: eCLIP from K562 (ENCLB057VON)

description:
https://www.encodeproject.org/experiments/ENCSR438GZQ/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against KHSRP
experiment encode accession: ENCSR438GZQ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR305IPT
encode release date: 2015-12-16
lab: Gene Yeo, UCSD
library encode accession: ENCLB057VON
size range: 175-300

value: 53 year

value: female

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


title: ChIP-seq from K562 (ENCLB336CSQ)

description:
https://www.encodeproject.org/experiments/ENCSR130PDE/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-NR4A1 ChIP-seq on human K562
experiment encode accession: ENCSR130PDE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR468BNS
encode release date: 2016-09-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB336CSQ
size range: 450-650

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

value: immortalized cell line

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

value: Kevin White, UChicago

value: ENCBS445AAA at ENCODE; https://www.encodeproject.org/ENCBS445AAA/

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

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


title: CCTO44-ORSI-07Feb2011

value: Oregon Siskiyou low elevation


title: eCLIP from K562 (ENCLB105SXR)

description:
https://www.encodeproject.org/experiments/ENCSR393STP/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against GPKOW
experiment encode accession: ENCSR393STP
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-10-31
lab: Gene Yeo, UCSD
library encode accession: ENCLB105SXR
size range: 175-300

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

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


title: eCLIP from K562 (ENCLB025TEX)

description:
https://www.encodeproject.org/experiments/ENCSR128VXC/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against SND1
experiment encode accession: ENCSR128VXC
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR435EVK
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB025TEX
size range: 175-300

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

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

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


title: ChIP-seq from MCF-7 (ENCLB212AIR)

description:
https://www.encodeproject.org/experiments/ENCSR135ANT/
***************
biological replicate number: 3
technical replicate number: 1
description: NRF1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR135ANT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB212AIR
size range: 450-650

value: adult

value: 69 year

value: Michael Snyder, Stanford

value: breast cancer (adenocarcinoma)

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

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

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


title: ChIP-seq from K562 (ENCLB952VTX)

description:
https://www.encodeproject.org/experiments/ENCSR130PDE/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-NR4A1 ChIP-seq on human K562
experiment encode accession: ENCSR130PDE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR468BNS
encode release date: 2016-09-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB952VTX
size range: 450-650

value: immortalized cell line

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

value: 53 year

value: female

value: Kevin White, UChicago

value: ENCBS392AAA at ENCODE; https://www.encodeproject.org/ENCBS392AAA/


title: CCTO44-ORSI-06Jan2011

description: Douglas-fir annual transcriptome analysis

value: Oregon Siskiyou low elevation


title: eCLIP from K562 (ENCLB179WTX)

description:
https://www.encodeproject.org/experiments/ENCSR145PHJ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against SRSF7
experiment encode accession: ENCSR145PHJ
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB179WTX
size range: 175-300

value: Control

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

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

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


title: T4P mNET-Seq  siCPSF73 rep2

city: Oxford

first: Monika

last: Gullerova

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

data_processing:
library strategy: mNET-Seq
Adapter trimming with Cutadapt v. 1.8.3 in paired end mode with the following parameters: -A GATCGTCGGACTGTAGAACTCTGAAC -a TGGAATTCTCGGGTGCCAAGG --minimum-length 10
Alignment with Tophat v. 2.0.13 and the parameters -g 1 -r 3000 --no-coverage-search to hg19
Extraction of properly paired, properly mapped reads (samflags 0x63, 0x93, 0x53, 0xA3) with SAMtools v. 1.2
For mNET-Seq profiles only the most 3’ nucleotide of the second read was used with the strandedness of the first read
BigWig files were generated from the above bedgraph files through the bedGraphToBigWig tool (Kent et al., 2002).
Data was visualized with Bedtools v. 2.23.0 (genomeCoverageBed).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

source_name: T4P mNET-Seq  siCPSF73

growth_protocol: HeLa cells were maintained in DMEM with 10% fetal bovine serum.

extract_protocol:
Nascent RNAs were prufied from Pol II IP products of solubilized chromatin.
Libraries were prepared acooding to the protocols of Trueseq small RNA sequencing preparation kit (Illumina) for mNET-seq; Ultra directional RNA sequencing preparation kit (NEB) for chrRNA and Np RNA-seq.

treatment_protocol:
1% Empigen was aded IP buffer and IP washing buffer.
siRNAs were transfected for 60-72 hrs accroding to RNAiMAX reagent protocol.

tag: cell line

value: HeLa

tag: genotype/variation

value: CPSF73 KD, Thr4 phospho

tag: molecule subtype

value: Polymerase bound RNA


title: eCLIP from K562 (ENCLB524SNO)

description:
https://www.encodeproject.org/experiments/ENCSR128VXC/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against SND1
experiment encode accession: ENCSR128VXC
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR435EVK
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB524SNO
size range: 175-300

tag: antibody

value: adult

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

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

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


title: siRNA RNA-seq from K562 (ENCLB606EKO)

description:
https://www.encodeproject.org/experiments/ENCSR128HAQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control siRNA against no target in K562 cells followed by RNA-seq.
experiment encode accession: ENCSR128HAQ
assay title: siRNA RNA-seq
assembly: GRCh38
encode release date: 2016-10-11
lab: Michael Snyder, Stanford
library encode accession: ENCLB606EKO
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line transiently expressing siRNA targeting Non-specific target control

tag: line

value: immortalized cell line

value: K562 cells treated with siRNA knockdown using a human non-targeting control.

value: 53 year

value: Sherman Weissman, Yale

value: ENCBS309YBN at ENCODE; https://www.encodeproject.org/ENCBS309YBN/


title: CCTO44-ORSI-09Nov2010

value: Oregon Siskiyou low elevation


title: CCTO44-ORSI-30Nov2010


title: S5P mNET-Seq pla-B rep2

source_name: S5P mNET-Seq pla-B

value: pla-B treatment, Ser5 phospho


title: S5P mNET-Seq DMSO rep2

source_name: S5P mNET-Seq DMSO

value: DMSO control for pla-B, Ser5 phospho


title: eCLIP from K562 (ENCLB947OFZ)

description:
https://www.encodeproject.org/experiments/ENCSR125CLF/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against IGF2BP1
experiment encode accession: ENCSR125CLF
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB947OFZ
size range: 175-300

value: Control

tag: biosample encode accession

value: female

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

value: ENCBS476AUA at ENCODE; https://www.encodeproject.org/ENCBS476AUA/

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


title: CCTO43-ORSI-26Oct2011


title: ChIP-seq from HEK293 (ENCLB453PDK)

description:
https://www.encodeproject.org/experiments/ENCSR123TVS/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq on eGFP-ZFP62 tagged human HEK293 cells.
experiment encode accession: ENCSR123TVS
assay title: ChIP-seq
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB453PDK
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZFP62 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZFP62 under the control of a CMV promoter.

tag: dev stage

value: embryonic

value: unknown

value: Michael Snyder, Stanford

value: ENCBS584YDT at ENCODE; https://www.encodeproject.org/ENCBS584YDT/

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


title: Total mNET-Seq

source_name: Total mNET-Seq

value: HeLa

value: Total polymerase, replicate of Total mNET-Seq (first rep in Nojima et al. 2015, Cell)

value: Polymerase bound RNA


title: ChIP-seq from K562 (ENCLB557YKO)

description:
https://www.encodeproject.org/experiments/ENCSR121PFY/
***************
biological replicate number: 2
technical replicate number: 1
description: CDC5L ChIP-seq on human K562
experiment encode accession: ENCSR121PFY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB557YKO
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line

value: immortalized cell line

value: adult

value: 53 year

tag: Sex

value: ENCBS824PND at ENCODE; https://www.encodeproject.org/ENCBS824PND/

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

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


title: ChIP-seq from HEK293 (ENCLB968JSK)

description:
https://www.encodeproject.org/experiments/ENCSR134QIE/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZFP3 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR134QIE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB968JSK
size range: 450-650

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZFP3 under the control of a CMV promoter.

value: female

tag: age

value: ENCBS232OEE at ENCODE; https://www.encodeproject.org/ENCBS232OEE/


title: CCTO43-ORSI-23Feb2011

value: Oregon Siskiyou low elevation


title: S7P mNET-Seq rep2

source_name: S7P mNET-Seq

value: Ser7 phospho


title: CCTO43-ORSI-07Feb2011


title: ChIP-seq from K562 (ENCLB576AXT)

description:
https://www.encodeproject.org/experiments/ENCSR126FZN/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-PTRF ChIP-seq on human K562
experiment encode accession: ENCSR126FZN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR369LPC
encode release date: 2016-01-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB576AXT
size range: 450-650

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

value: eGFP-PTRF

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

value: Kevin White, UChicago

tag: health state

value: chronic myelogenous leukemia (CML)

value: ENCBS931QBF at ENCODE; https://www.encodeproject.org/ENCBS931QBF/

value: ENCODE dbxrefs Cellosaurus CVCL_AW38; http://web.expasy.org/cellosaurus/CVCL_AW38


title: ChIP-seq from K562 (ENCLB834VOO)

description:
https://www.encodeproject.org/experiments/ENCSR126FZN/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-PTRF ChIP-seq on human K562
experiment encode accession: ENCSR126FZN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR369LPC
encode release date: 2016-01-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB834VOO
size range: 450-650

value: immortalized cell line

tag: passage number

value: ENCBS258BIP at ENCODE; https://www.encodeproject.org/ENCBS258BIP/


title: CCTO43-ORSI-10Mar2011


title: CCTO43-ORSI-06Jan2011


title: ChIP-seq from K562 (ENCLB691DTZ)

description:
https://www.encodeproject.org/experiments/ENCSR121PFY/
***************
biological replicate number: 1
technical replicate number: 1
description: CDC5L ChIP-seq on human K562
experiment encode accession: ENCSR121PFY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB691DTZ
size range: 450-650

value: adult

value: 53 year

tag: lab

value: Michael Snyder, Stanford

value: ENCBS140MLH at ENCODE; https://www.encodeproject.org/ENCBS140MLH/


title: RAMPAGE from transverse colon (ENCLB720FTV)

description:
https://www.encodeproject.org/experiments/ENCSR297QGC/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human transverse colon tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR297QGC
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR403SZN
encode release date: 2016-10-31
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB720FTV
size range: >200

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

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/8234c22a-26dc-4827-97ce-91079687818d/@@download/attachment/296882.pdf

value: transverse colon

value: tissue

value: Transverse colon tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 51 year

value: Thomas Gingeras, CSHL

tag: link

value: ENCBS999VTF at ENCODE; https://www.encodeproject.org/ENCBS999VTF/

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


title: CCTO44-ORSI-27Oct2010

value: Oregon Siskiyou low elevation


title: ChIP-seq from HepG2 (ENCLB915FZX)

description:
https://www.encodeproject.org/experiments/ENCSR121CWV/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on human HepG2
experiment encode accession: ENCSR121CWV
assay title: ChIP-seq
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB915FZX
size range: 450-650

source_name: Homo sapiens HepG2 immortalized cell line

value: Control

tag: description

value: Hepatocellular carcinoma

value: child

value: 15 year

value: male

value: hepatocellular carcinoma

value: ENCBS716YFX at ENCODE; https://www.encodeproject.org/ENCBS716YFX/

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

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

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


title: CCTO43-ORSI-09Nov2010

tag: family-tag


title: CCTO43-ORSI-30Nov2010


title: ChIP-seq from HepG2 (ENCLB407FJZ)

description:
https://www.encodeproject.org/experiments/ENCSR121CWV/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on human HepG2
experiment encode accession: ENCSR121CWV
assay title: ChIP-seq
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB407FJZ
size range: 450-650

value: immortalized cell line

value: Michael Snyder, Stanford

value: ENCBS560TQP at ENCODE; https://www.encodeproject.org/ENCBS560TQP/


title: siLuc Chromatin RNA-Seq rep2

data_processing:
library strategy: Chr-Seq
Adapter trimming with Cutadapt v. 1.8.3 in paired end mode with the following parameters: -A GATCGTCGGACTGTAGAACTCTGAAC -a TGGAATTCTCGGGTGCCAAGG --minimum-length 10
Alignment with Tophat v. 2.0.13 and the parameters -g 1 -r 3000 --no-coverage-search to hg19
Extraction of properly paired, properly mapped reads (samflags 0x63, 0x93, 0x53, 0xA3) with SAMtools v. 1.2
For mNET-Seq profiles only the most 3’ nucleotide of the second read was used with the strandedness of the first read
BigWig files were generated from the above bedgraph files through the bedGraphToBigWig tool (Kent et al., 2002).
Data was visualized with Bedtools v. 2.23.0 (genomeCoverageBed).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

source_name: HeLa_siLUC control for EXOC3 KD, Chromatin

value: HeLa

value: siLUC control for EXOC3 KD, Chromatin

value: Chromatin RNA


title: eCLIP from HepG2 (ENCLB169GFJ)

description:
https://www.encodeproject.org/experiments/ENCSR121NVA/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against PRPF8
experiment encode accession: ENCSR121NVA
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR565KBR
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB169GFJ
size range: 175-300

value: Gene Yeo, UCSD

value: ENCBS548DJV at ENCODE; https://www.encodeproject.org/ENCBS548DJV/


title: siLuc Nucleoplasm RNA-Seq rep2

data_processing:
library strategy: NP-Seq
Adapter trimming with Cutadapt v. 1.8.3 in paired end mode with the following parameters: -A GATCGTCGGACTGTAGAACTCTGAAC -a TGGAATTCTCGGGTGCCAAGG --minimum-length 10
Alignment with Tophat v. 2.0.13 and the parameters -g 1 -r 3000 --no-coverage-search to hg19
Extraction of properly paired, properly mapped reads (samflags 0x63, 0x93, 0x53, 0xA3) with SAMtools v. 1.2
For mNET-Seq profiles only the most 3’ nucleotide of the second read was used with the strandedness of the first read
BigWig files were generated from the above bedgraph files through the bedGraphToBigWig tool (Kent et al., 2002).
Data was visualized with Bedtools v. 2.23.0 (genomeCoverageBed).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

source_name: HeLa_siLUC control for EXOC3 KD, Nucleoplasm

value: siLUC control for EXOC3 KD, Nucleoplasm

value: Nucleoplasmic RNA


title: T4P mNET-Seq  siLuc rep2

source_name: T4P mNET-Seq  siLuc

value: siLuc control for CPSF73 KD, Thr4 phospho

value: Polymerase bound RNA


title: siEX3 Nucleoplasm RNA-Seq rep2

source_name: HeLa_EXOC3 KD, Nucleoplasm

value: EXOC3 KD, Nucleoplasm


title: eCLIP from HepG2 (ENCLB655RZE)

description:
https://www.encodeproject.org/experiments/ENCSR121NVA/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against PRPF8
experiment encode accession: ENCSR121NVA
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR565KBR
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB655RZE
size range: 175-300

value: child

value: 15 year

value: male

value: hepatocellular carcinoma

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


title: Total mNET-Seq siEX3 rep1

source_name: Total polymerase, EXOC3 KD

value: EXOC3 KD


title: CCTO43-ORSI-07Oct2011

value: Oregon Siskiyou low elevation


title: ChIP-seq from K562 (ENCLB849NCQ)

description:
https://www.encodeproject.org/experiments/ENCSR117WTM/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF24 ChIP-seq on human K562
experiment encode accession: ENCSR117WTM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR329YMD
encode release date: 2016-03-02
lab: Michael Snyder, Stanford
library encode accession: ENCLB849NCQ
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-ZNF24 fusion protein

value: immortalized cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF24

value: adult

value: 53 year

value: female

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: ENCBS985SCL at ENCODE; https://www.encodeproject.org/ENCBS985SCL/

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

value: ENCODE dbxrefs Cellosaurus CVCL_AW47; http://web.expasy.org/cellosaurus/CVCL_AW47


title: diurnal3B-4400

description: Douglas-fir diurnal transcriptome analysis

data_processing:
Base-calling and demultiplexing was performed using Casava v1.8 (Illumina Inc.).
Transcript read mapping: To quantify transcript abundance in diurnal and RNA-Seq samples, we mapped reads to the pan-transcriptome reference with bowtie2.2.3 (Langmead and Salzberg, 2012) using the following call:  bowtie2 --end-to-end -D 15 -R 2 -L 22 -i S,1,1.15. This allows 15 consecutive seed extension attempts before the aligner moved on (-D 15), a maximum of 2 attempts to re-seed reads with repetitive seeds (-R 2), and a 22 bp seed (-L 22) with zero allowed mismatches in this seed. The function to determine the interval between seed substrings during multi-seed alignment was set to f(x) = 1 + 1.15 * sqrt(x), where x is the read length (-i S,1,1.15) (based on the 101 bp read lengths this resulted in an interval of 13 bp).  Output from this step is provided as processed data file "filename2.gz"
Transcript filtering and normalization: Since many transcripts showed near-zero counts, we excluded transcripts showing median counts below 5 from analyses because they were essentially indistinguishable from background transcription. For transcripts meeting the median cut-off, counts were normalized using DESeq normalization (Anders and Huber, 2010; Bullard et al., 2010; Dillies et al., 2012).
Genome_build: Douglas-fir pan-transcriptome reference v2.03, TSA submission in progress
Supplementary_files_format_and_content: tab-separated text files were generated using  bowtie 2.2.3; Counts represent the number of reads mapping to each transcript model
Supplementary_files_format_and_content: tab-separated text files were generated using DESeq; Counts represent the number of reads mapping to each transcript model, after the application of a normalization factor to correct for library size

growth_protocol: Trees used for the diurnal transcriptome analysis are a sample from a reciprocal translocation study (Harrington et al., 2010) that includes families from multiple geographic sources in the Pacific Northwestern region of North America. Trees used for diurnal analysis derive from a single source from the reciprocal translocation study (Oregon Siskiyou low elevation; 43.3° N, -123.1° W, 429 m elevation), and were grown in Corvallis, Oregon, USA (42.3° N, -122.9° W, 74 m elevation)(Figure S1). For this study, needles were collected from 6 individual trees (3 half sib families, two sibs per family) that were three years old at the time of the study. Needles from the 2012 cohort were first collected at 2 AM on September 7, 2012, and at 4 hour intervals for a total of 48 hours (12 sample points)


title: siEX3 Chromatin RNA-Seq rep2

source_name: HeLa_EXOC3 KD, Chromatin

value: HeLa

value: EXOC3 KD, Chromatin

value: Chromatin RNA


title: ChIP-seq from K562 (ENCLB753TOI)

description:
https://www.encodeproject.org/experiments/ENCSR117WTM/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF24 ChIP-seq on human K562
experiment encode accession: ENCSR117WTM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR329YMD
encode release date: 2016-03-02
lab: Michael Snyder, Stanford
library encode accession: ENCLB753TOI
size range: 450-650

value: ENCBS016MLC at ENCODE; https://www.encodeproject.org/ENCBS016MLC/


title: diurnal3B-4000


title: siEX3 Chromatin RNA-Seq rep1

data_processing:
library strategy: ChrRNA
Adapter trimming with Cutadapt v. 1.8.3 in paired end mode with the following parameters: -A GATCGTCGGACTGTAGAACTCTGAAC -a TGGAATTCTCGGGTGCCAAGG --minimum-length 10
Alignment with Tophat v. 2.0.13 and the parameters -g 1 -r 3000 --no-coverage-search to hg19
Extraction of properly paired, properly mapped reads (samflags 0x63, 0x93, 0x53, 0xA3) with SAMtools v. 1.2
For mNET-Seq profiles only the most 3’ nucleotide of the second read was used with the strandedness of the first read
BigWig files were generated from the above bedgraph files through the bedGraphToBigWig tool (Kent et al., 2002).
Data was visualized with Bedtools v. 2.23.0 (genomeCoverageBed).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

source_name: HeLa_siEX3 Chromatin RNA-Seq

value: HeLa cells


title: ChIP-seq from GM12878 (ENCLB779CDZ)

description:
https://www.encodeproject.org/experiments/ENCSR117KWH/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF207 ChIP-seq on human GM12878
experiment encode accession: ENCSR117KWH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR398JTO
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB779CDZ
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: unknown

value: Michael Snyder, Stanford

value: ENCBS260WJQ at ENCODE; https://www.encodeproject.org/ENCBS260WJQ/

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

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

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


title: siLuc Nucleoplasm RNA-Seq rep1

data_processing:
library strategy: NpRNA-seq
Adapter trimming with Cutadapt v. 1.8.3 in paired end mode with the following parameters: -A GATCGTCGGACTGTAGAACTCTGAAC -a TGGAATTCTCGGGTGCCAAGG --minimum-length 10
Alignment with Tophat v. 2.0.13 and the parameters -g 1 -r 3000 --no-coverage-search to hg19
Extraction of properly paired, properly mapped reads (samflags 0x63, 0x93, 0x53, 0xA3) with SAMtools v. 1.2
For mNET-Seq profiles only the most 3’ nucleotide of the second read was used with the strandedness of the first read
BigWig files were generated from the above bedgraph files through the bedGraphToBigWig tool (Kent et al., 2002).
Data was visualized with Bedtools v. 2.23.0 (genomeCoverageBed).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

source_name: HeLa_siLuc Nucleoplam RNA-Seq

value: siLUC control for EXOC3 KD, Nucleoplasm

value: Nucleoplasmic RNA


title: diurnal3B-3600

value: Oregon Siskiyou low elevation


title: siEX3 Nucleoplasm RNA-Seq rep1

source_name: HeLa_siEX3 Nucleoplam RNA-Seq

value: EXOC3 KD, Nucleoplasm


title: diurnal3B-3200


title: ChIP-seq from K562 (ENCLB968GQF)

description:
https://www.encodeproject.org/experiments/ENCSR115SMW/
***************
biological replicate number: 1
technical replicate number: 1
description: PKNOX1 ChIP-seq on human K562
experiment encode accession: ENCSR115SMW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB968GQF
size range: 450-650

value: immortalized cell line

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

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS048GNZ at ENCODE; https://www.encodeproject.org/ENCBS048GNZ/

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: diurnal3B-2000


title: ChIP-seq from GM12878 (ENCLB260JAG)

description:
https://www.encodeproject.org/experiments/ENCSR117KWH/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF207 ChIP-seq on human GM12878
experiment encode accession: ENCSR117KWH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR398JTO
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB260JAG
size range: 450-650

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

value: unknown

value: Michael Snyder, Stanford

value: ENCBS802GDX at ENCODE; https://www.encodeproject.org/ENCBS802GDX/

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


title: pA+ Nucleoplasm RNA-Seq siLuc

source_name: HeLa_pA+ Nucleoplam RNA-Seq siLuc

value: HeLa cells

value: siLuc treated polyA+ fraction, Nucleoplasm

value: Nucleoplasmic RNA


title: pA- Nucleoplasm RNA-Seq siLuc

source_name: HeLa_pA- Nucleoplam RNA-Seq siLuc

value: siLuc treated polyA- fraction, Nucleoplasm


title: diurnal3B-2400

value: Oregon Siskiyou low elevation


title: diurnal3B-2800


title: ChIP-seq from K562 (ENCLB820SCT)

description:
https://www.encodeproject.org/experiments/ENCSR113LAS/
***************
biological replicate number: 2
technical replicate number: 1
description: MTA2 ChIP-seq on human K562
experiment encode accession: ENCSR113LAS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB820SCT
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line

value: immortalized cell line

value: adult

value: female

value: ENCBS850QNJ at ENCODE; https://www.encodeproject.org/ENCBS850QNJ/


title: eCLIP from HepG2 (ENCLB848HDX)

description:
https://www.encodeproject.org/experiments/ENCSR115GAA/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against PCBP2
experiment encode accession: ENCSR115GAA
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB848HDX
size range: 175-300

value: Control

value: child

value: 15 year

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS548DJV at ENCODE; https://www.encodeproject.org/ENCBS548DJV/

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

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

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


title: S5P mNET-Seq siLuc 2 (Ctrl for siDICER1) rep1

data_processing:
library strategy: mammalian native elongating transcript sequencing (mNET-seq)
Adapter trimming with Cutadapt v. 1.8.3 in paired end mode with the following parameters: -A GATCGTCGGACTGTAGAACTCTGAAC -a TGGAATTCTCGGGTGCCAAGG --minimum-length 10
Alignment with Tophat v. 2.0.13 and the parameters -g 1 -r 3000 --no-coverage-search to hg19
Extraction of properly paired, properly mapped reads (samflags 0x63, 0x93, 0x53, 0xA3) with SAMtools v. 1.2
For mNET-Seq profiles only the most 3’ nucleotide of the second read was used with the strandedness of the first read
BigWig files were generated from the above bedgraph files through the bedGraphToBigWig tool (Kent et al., 2002).
Data was visualized with Bedtools v. 2.23.0 (genomeCoverageBed).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

source_name: HeLa_S5P mNET-Seq siLuc 2 (Ctrl for siDICER1)

value: HeLa cells

value: siLuc control for DICER1 KD, Ser5 phospho

value: Polymerase bound RNA


title: ChIP-seq from K562 (ENCLB342XMG)

description:
https://www.encodeproject.org/experiments/ENCSR115SMW/
***************
biological replicate number: 2
technical replicate number: 1
description: PKNOX1 ChIP-seq on human K562
experiment encode accession: ENCSR115SMW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB342XMG
size range: 450-650

value: immortalized cell line

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

value: 53 year

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)

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

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

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

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


title: CCTO43-ORSI-27Oct2010

description: Douglas-fir annual transcriptome analysis

value: Oregon Siskiyou low elevation


title: Total mNET-Seq siLuc rep1

source_name: Total polymerase, siLuc control for EXOC3 KD

value: HeLa

value: siLuc control for EXOC3 KD


title: diurnal3B-1600


title: S5P mNET-Seq siDICER1 rep1

source_name: HeLa_S5P mNET-Seq siDICER1

value: DICER1 KD, Ser5 phospho


title: diurnal3B-1200


title: ChIP-seq from K562 (ENCLB281FLC)

description:
https://www.encodeproject.org/experiments/ENCSR113LAS/
***************
biological replicate number: 1
technical replicate number: 1
description: MTA2 ChIP-seq on human K562
experiment encode accession: ENCSR113LAS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB281FLC
size range: 450-650

value: adult

value: female

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


title: eCLIP from HepG2 (ENCLB019DSE)

description:
https://www.encodeproject.org/experiments/ENCSR110XNS/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against HNRNPA1
experiment encode accession: ENCSR110XNS
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB019DSE
size range: 175-300

source_name: Homo sapiens HepG2 immortalized cell line

value: Control

value: child

value: 15 year

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS990SBY at ENCODE; https://www.encodeproject.org/ENCBS990SBY/

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

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

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


title: S5P mNET-Seq siLuc 1 (Ctrl for siDGCR8) rep1

source_name: HeLa_S5P mNET-Seq siLuc 1 (Ctrl for siDGCR8)

value: HeLa cells

value: siLuc control for DGCR8 KD, Ser5 phospho

value: Polymerase bound RNA


title: siLuc Chromatin RNA-Seq rep1

source_name: HeLa_siLuc Chromatin RNA-Seq

value: siLUC control for EXOC3 KD, Chromatin

value: Chromatin RNA


title: diurnal3B-0800

value: Oregon Siskiyou low elevation


title: diurnal3B-0400


title: T4P mNET-Seq Empigen treated rep1

source_name: HeLa_T4P mNET-Seq Empigen treated

value: Empigen treated Thr4 phospho


title: diurnal3B-0000


title: ChIP-seq from K562 (ENCLB365EOZ)

description:
https://www.encodeproject.org/experiments/ENCSR108OFV/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-ZNF512 tagged K562 cell ine.
experiment encode accession: ENCSR108OFV
assay title: ChIP-seq
encode release date: 2016-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB365EOZ

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-ZNF512 fusion protein

value: Control

value: immortalized cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF512

value: adult

value: 53 year

value: female

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: ENCBS874FAG at ENCODE; https://www.encodeproject.org/ENCBS874FAG/

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

value: ENCODE dbxrefs Cellosaurus CVCL_HA03; http://web.expasy.org/cellosaurus/CVCL_HA03


title: T4P mNET-Seq (untreated)  rep1

source_name: HeLa_T4P mNET-Seq untreated

value: HeLa cells

value: Control:Empigen untreated Thr4 phospho


title: diurnal3A-4400


title: ChIP-seq from K562 (ENCLB488XXX)

description:
https://www.encodeproject.org/experiments/ENCSR109YGM/
***************
biological replicate number: 1
technical replicate number: 1
description: CREB3L1 ChIP-seq on human K562
experiment encode accession: ENCSR109YGM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB488XXX
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: Michael Snyder, Stanford

value: ENCBS048GNZ at ENCODE; https://www.encodeproject.org/ENCBS048GNZ/

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: diurnal3A-3600

value: Oregon Siskiyou low elevation


title: Y1P mNET-Seq Empigen treated  rep1

source_name: HeLa_Y1P mNET-Seq Empigen treated

value: Empigen treated Tyr1 phospho

value: Polymerase bound RNA


title: diurnal3A-4000


title: ChIP-seq from HEK293 (ENCLB240IEM)

description:
https://www.encodeproject.org/experiments/ENCSR110ZVM/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq on eGFP-ZNF264 tagged human HEK293 cells.
experiment encode accession: ENCSR110ZVM
assay title: ChIP-seq
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB240IEM
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF264 fusion protein

value: Control

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF264 under the control of a CMV promoter.

value: embryonic

value: unknown

value: ENCBS584HTL at ENCODE; https://www.encodeproject.org/ENCBS584HTL/

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


title: Y1P mNET-Seq (untreated)  rep1

source_name: HeLa_Y1P mNET-Seq untreated

value: HeLa cells

value: Control:Empigen untreated Tyr1 phospho


title: ChIP-seq from K562 (ENCLB344DXR)

description:
https://www.encodeproject.org/experiments/ENCSR107RHZ/
***************
biological replicate number: 2
technical replicate number: 1
description: YBX1 ChIP-seq on human K562
experiment encode accession: ENCSR107RHZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB344DXR
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: adult

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS953HJY at ENCODE; https://www.encodeproject.org/ENCBS953HJY/

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


title: S5P mNET-Seq siDGCR8 rep1

source_name: HeLa_S5P mNET-Seq siDGCR8

value: DGCR8 KD, Ser5 phospho

value: Polymerase bound RNA


title: S5P mNET-Seq Empigen treated rep1

source_name: HeLa_S5P mNET-Seq Empigen treated

value: Empigen treated Ser5 phospho


title: diurnal3A-2800

value: Oregon Siskiyou low elevation


title: diurnal3A-3200


title: S2P mNET-Seq Empigen treated rep1

source_name: HeLa_S2P mNET-Seq Empigen treated

value: Empigen treated Ser2 phospho


title: S2P mNET-Seq untreated rep1

source_name: HeLa_S2P mNET-Seq untreated

value: Control:Empigen untreated Ser2 phospho


title: ChIP-seq from K562 (ENCLB321MJU)

description:
https://www.encodeproject.org/experiments/ENCSR107GRP/
***************
biological replicate number: 1
technical replicate number: 1
description: MLLT1 ChIP-seq on human K562
experiment encode accession: ENCSR107GRP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB321MJU
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line

value: immortalized cell line

value: Michael Snyder, Stanford

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

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


title: diurnal3A-2000


title: diurnal3A-2400


title: ChIP-seq from K562 (ENCLB983GRU)

description:
https://www.encodeproject.org/experiments/ENCSR106FRG/
***************
biological replicate number: 1
technical replicate number: 1
description: TAL1 ChIP-seq on human K562
experiment encode accession: ENCSR106FRG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB983GRU
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: ENCBS994WPS at ENCODE; https://www.encodeproject.org/ENCBS994WPS/

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


title: ChIP-seq from K562 (ENCLB709SXN)

description:
https://www.encodeproject.org/experiments/ENCSR106FRG/
***************
biological replicate number: 2
technical replicate number: 1
description: TAL1 ChIP-seq on human K562
experiment encode accession: ENCSR106FRG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB709SXN
size range: 450-650

value: adult

value: 53 year

value: female

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


title: T4P mNET-Seq  siCPSF73 rep1

source_name: HeLa_T4P mNET-Seq  siCPSF73

value: HeLa cells

value: CPSF73 KD, Thr4 phospho


title: S5P mNET-Seq untreated rep1

source_name: HeLa_S5P mNET-Seq untreated

value: Control:Empigen untreated Ser5 phospho

value: Polymerase bound RNA


title: T4P mNET-Seq  siLuc rep1

source_name: HeLa_T4P mNET-Seq  siLuc

value: siLuc control for CPSF73 KD, Thr4 phospho


title: ChIP-seq from K562 (ENCLB300HOB)

description:
https://www.encodeproject.org/experiments/ENCSR109YGM/
***************
biological replicate number: 2
technical replicate number: 1
description: CREB3L1 ChIP-seq on human K562
experiment encode accession: ENCSR109YGM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB300HOB
size range: 450-650

value: chronic myelogenous leukemia (CML)

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


title: diurnal3A-1600

description: Douglas-fir diurnal transcriptome analysis

value: Oregon Siskiyou low elevation


title: FaDu_Snail Cells

city: Taipei

first: Wei-Lun

last: Hwang

address: No.155, Sec.2, Linong Street

department: Department of Biotechnology and Laboratory Science in Medicine

country: Taiwan

institute: National Yang Ming Chiao Tung University

description: stable clones

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat 2.0.8.
Next, We execute transcript assemble using Cufflinks (version 2.1.1) and merge all the assemblies with cuffmerge.
Finally, Cuffdiff quantifies the expression level of each gene in two samples.
The coding RNAs annotated in ensembl database were extracted for gene symbol conversion by DAVID.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: HNSCC cancer cell line

growth_protocol: All cells were cultured in 10% FBS containing RPMI-1640 medium at 37'C under humidified chamber.

extract_protocol:
Total RNA were extratec by TriZol reagent.
The standard Illumia library preparation procedure.

treatment_protocol: vector control and Snail-expressing construct were transduced by lentivirus to generate stable clones.

value: FaDu

tag: protocol

value: Transduced with Snail-expressing vector.


title: S5P mNET-Seq pla-B rep1

source_name: HeLa_S5P mNET-Seq pla-B

value: pla-B treatment, Ser5 phospho


title: ChIP-seq from K562 (ENCLB651CYS)

description:
https://www.encodeproject.org/experiments/ENCSR107RHZ/
***************
biological replicate number: 1
technical replicate number: 1
description: YBX1 ChIP-seq on human K562
experiment encode accession: ENCSR107RHZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB651CYS
size range: 450-650

value: immortalized cell line

value: Michael Snyder, Stanford

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

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


title: w18.40_2h_3 (RNA-Seq)

city: Cologne

first: Barbara

last: Kracher

address: Carl-von-Linné-Weg 10

department: Plant-Microbe Interactions

country: Germany

institute: Max Planck Institute for Plant Breeding Research

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequencing read quality control was performed using FastQC version 0.11.2
Sequenced reads were mapped to the genome of Arabidopsis thaliana (TAIR10) using tophat v2.0.10 with parameters -a 10  -g 10 --library-type fr-firststrand
Read counts per gene per sample were obtained using the htseq-count script in the HTSeq Python package with options -s reverse -t exon
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file including read counts per gene for each sample

source_name: 12 day old seedlings

growth_protocol: Seedlings were grown in1x MS medium supplemented with 0.5 % sucrose and 0.1 % claforan for 12 days in a light chamber at long day conditions (16 h light / 8 h dark).

extract_protocol:
Total RNA was extracted from 100 mg of untreated or flg22-treated seedlings using the TRI Reagent Solution from Applied Biosystems (AM9738) following the manufacturer´s instructions. The RNA was treated with DNAse I (Roche) and purified using the RNeasy MiniElute Cleanup Kit (Qiagen, Germany).
RNA-seq libraries were prepared by the Max Planck Genome Center Cologne (http://mpgc.mpipz.mpg.de) according to the TruSeq Stranded RNA sample preparation v2 guide (Illumina).

treatment_protocol: The seedlings were treated with flg22 by replacing the growth medium with medium containing 1 µM flg22 for 1 h and 2 h.

tag: genotype

value: Col-0 wrky18 wrky40 double mutant

tag: treatment

tag: time-point


title: w18.40_1h_3 (RNA-Seq)


title: S5P mNET-Seq DMSO rep1

source_name: HeLa_S5P mNET-Seq DMSO

tag: cell line

tag: genotype/variation

value: DMSO control for pla-B, Ser5 phospho

tag: molecule subtype


title: S7P mNET-Seq rep1

source_name: HeLa_S7P mNET-Seq

value: HeLa cells

value: Ser7 phospho


title: diurnal3A-1200


title: w18.40_0h_3 (RNA-Seq)

value: untreated


title: diurnal3A-0400


title: diurnal3A-0800


title: w40_1h_3 (RNA-Seq)

value: Col-0 wrky40 mutant


title: T4P mNET-Seq (rep3)

source_name: HeLa_T4P mNET-Seq

value: Thr4 phospho

value: Polymerase bound RNA


title: diurnal3A-0000


title: ChIP-seq from K562 (ENCLB240GID)

description:
https://www.encodeproject.org/experiments/ENCSR107GRP/
***************
biological replicate number: 2
technical replicate number: 1
description: MLLT1 ChIP-seq on human K562
experiment encode accession: ENCSR107GRP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB240GID
size range: 450-650

tag: antibody

tag: line

tag: biosample encode accession

value: adult

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS850QNJ at ENCODE; https://www.encodeproject.org/ENCBS850QNJ/

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


title: Y1P mNET-Seq (rep3)

source_name: HeLa_Y1P mNET-Seq

value: Tyr1 phospho


title: diurnal2B-4000

value: Oregon Siskiyou low elevation


title: diurnal2B-4400


title: w40_2h_3 (RNA-Seq)


title: w40_0h_3 (RNA-Seq)


title: w18_2h_3 (RNA-Seq)

value: Col-0 wrky18 mutant


title: w18_1h_3 (RNA-Seq)


title: diurnal2B-3200


title: w18_0h_3 (RNA-Seq)


title: diurnal2B-2800


title: wt_2h_3 (RNA-Seq)

value: Col-0 WT


title: wt_1h_3 (RNA-Seq)


title: diurnal2B-2000


title: diurnal2B-1600


title: wt_0h_3 (RNA-Seq)


title: w18.40_1h_2 (RNA-Seq)

value: Col-0 wrky18 wrky40 double mutant


title: diurnal2B-0400


title: w40_2h_2 (RNA-Seq)


title: w18.40_2h_2 (RNA-Seq)


title: w40_1h_2 (RNA-Seq)


title: diurnal2B-0800


title: diurnal2B-0000


title: w18.40_0h_2 (RNA-Seq)


title: diurnal2B-3600


title: diurnal2A-4000


title: w18_1h_2 (RNA-Seq)


title: diurnal2A-3600


title: diurnal2A-4400


title: w40_0h_2 (RNA-Seq)


title: diurnal2A-3200


title: FaDu_Control Cells

description: stable clones

value: FaDu

value: Transduced with vector control.


title: diurnal2A-2800


title: diurnal2A-2400


title: diurnal2B-2400


title: w18_0h_2 (RNA-Seq)

value: untreated


title: wt_1h_2 (RNA-Seq)


title: diurnal2A-2000


title: wt_0h_2 (RNA-Seq)


title: diurnal2A-1200


title: w18.40_2h_1 (RNA-Seq)


title: diurnal2A-0800


title: w40_2h_1 (RNA-Seq)

value: Col-0 wrky40 mutant


title: w18.40_1h_1 (RNA-Seq)


title: w18.40_0h_1 (RNA-Seq)


title: w40_1h_1 (RNA-Seq)


title: diurnal1B-4400


title: w40_0h_1 (RNA-Seq)


title: diurnal2A-0000


title: diurnal2A-0400


title: w18_2h_2 (RNA-Seq)


title: diurnal1B-2800


title: diurnal2B-1200


title: diurnal1B-4000


title: w18_0h_1 (RNA-Seq)


title: diurnal1B-3200


title: diurnal1B-2400


title: diurnal2A-1600


title: w18_1h_1 (RNA-Seq)


title: wt_2h_1 (RNA-Seq)


title: wt_2h_2 (RNA-Seq)


title: wt_1h_1 (RNA-Seq)


title: diurnal1B-1600


title: diurnal1B-1200


title: W40HA_2h_2 (ChIP-Seq)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequencing read quality control was performed using FastQC version 0.11.2
Trimming and filtering of LinDA adapters and low quality sequences was performed using 1) cutadapt  v1.2.1 with options –e 0.2, -n 2 and –m 36 and 2) PRINSEQ lite v0.20.2 with options –trim_qual_right/left 20, trim_tail_right/left 3 –min_len 36, -min_qual_mean 25
Sequenced reads were mapped to the Arabidopsis genome (TAIR10) using Bowtie v0.12.7 with options –best –m 1
Peak calling was performed for each replicate using the program QuEST v2.4 in transcription factor mode (option “2”) with permissive parameter settings (option “3”) and suppling the corresponding input or mock-treated sample as negative controls in peak calling
Annotation of peak locations with respect to annotated gene features in TAIR10 was performed using the annotatePeaks.pl function from the Homer suite
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files with peak coordinates, enrichment scores, and annnotation information

extract_protocol:
For the ChIP experiments, 2 g of seedlings were processed as described earlier (Birkenbihl et al., 2012) following the modified protocol of Grendel et al. (2005). For IP was a rabbit polyclonal anti-HA antibody (Sigma-Aldrich, St. Louis, MA) was used. The precipitated DNA was purified with the Qia quick PCR purification kit (Qiagen, Germany) before library construction.
To prepare the ChIP-seq libraries, the DNA was first amplified by two rounds of linear DNA amplification (LinDA) (Shankaranarayanan et al., 2011) and then libraries were constructed with the NEBNext ChIP-seq Library construction kit (New England Biolabs, Ipswich, MA).
The ChIP-seq libraries were sequenced with an Illumina HiSeq2500, resulting in 7-20 million 100 bp single-end reads per sample.

treatment_protocol: The seedlings were treated with flg22 by replacing the growth medium with medium containing 1 µM flg22 for 2 h.

value: Col-0 WRKY40-HA


title: diurnal1B-0800


title: W40HA_0h_2 (ChIP-Seq)


title: diurnal1B-0400


title: diurnal1B-3600


title: diurnal1B-0000


title: W18HA_2h_2 (ChIP-Seq)

value: Col-0 WRKY18-HA


title: W18HA_0h_2 (ChIP-Seq)


title: W33HA_2h_2 (ChIP-Seq)

value: Col-0 WRKY33-HA


title: diurnal1A-3600


title: W33HA_0h_2 (ChIP-Seq)


title: diurnal1B-2000


title: diurnal1A-4000


title: diurnal1A-3200