title: shRNA RNA-seq from HepG2 (ENCLB977BNI)

description:
https://www.encodeproject.org/experiments/ENCSR057GCF/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against TIA1 in HepG2 cells followed by RNA-seq. (TIA1-BGHLV12)
experiment encode accession: ENCSR057GCF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR603TCV
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB977BNI
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f04e6442-998b-4484-88dc-6e3d0618d133/@@download/attachment/L-TIA1-BGHLV12-87.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against TIA1. (TIA1-BGHLV12-87)

value: 15 year

value: child

value: ENCBS422FYC at ENCODE; https://www.encodeproject.org/ENCBS422FYC/


title: shRNA RNA-seq from K562 (ENCLB738SZX)

status: Public on May 26 2016

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/ENCSR056QEW/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against CIRBP in K562 cells followed by RNA-seq. (CIRBP-LV11)
experiment encode accession: ENCSR056QEW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB738SZX
size range: >200
spikeins used: /references/ENCSR449DXG/

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 transiently expressing shRNA targeting CIRBP

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/abceccc0-8ab4-45c7-884e-0489d3bd638a/@@download/attachment/L-CIRBP-LV11-3.pdf

tag: antibody

value: CIRBP

tag: line

value: immortalized cell line

tag: description

value: RNA-seq on K562 cells treated with an shRNA knockdown against CIRBP. (CIRBP-LV11-3)

tag: biosample encode accession

tag: age

value: 53 year

tag: dev stage

value: adult

tag: Sex

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: lab

value: Brenton Graveley, UConn

tag: link

value: ENCBS193QNA at ENCODE; https://www.encodeproject.org/ENCBS193QNA/

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: MCF-7 cells treated with 10nM TCDD, replicate 1

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

data_processing:
Alignment to hg19 using TopHat 2.0.7 with BowTie 0.12.9 and SamTools 0.1.18
Counts by gene calculated using R/Bioconductor packages GenomicFeatures and GenomicRanges, with Ensembl gene annotations
Normalized counts calculated using DESeq
Differential Gene expression calculated using DESeq (version 1) with treatment as the single variable
Genome_build: hg19
Supplementary_files_format_and_content: counts_10nM_TCDD.txt is a tab-delimited text file containing raw read counts per gene
Supplementary_files_format_and_content: normalized_counts_10nM_TCDD.txt is a tab-delimited text file containing counts per gene after normalization by the estimateSizeFactors function in the Bioconductor package DESeq

source_name: MCF-7 breast cancer cells

growth_protocol: 250,000 MCF-7 cells were seeded in 35 mm plates in DMEM supplemented with 10 % FBS for 24 hr, followed by overnight serum-starvation in phenol red-free DMEM

extract_protocol:
Total RNA purification kits from Qiagen (Valencia, CA) were used according to manufacturers instructions
Libraries were prepared from 1 µg of total RNA using a TruSeq RNA Prep Kit (Illumina Inc., San Diego, CA)

treatment_protocol: 6hrs treatment with either vehicle (DMSO) or TCDD

tag: treatment

value: TCDD

tag: concentration


title: MCF-7 cells treated with 10nM TCDD, replicate 3


title: shRNA RNA-seq from K562 (ENCLB051HTR)

description:
https://www.encodeproject.org/experiments/ENCSR047EEG/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against PABPC4 in K562 cells followed by RNA-seq. (PABPC4-LV08)
experiment encode accession: ENCSR047EEG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR344XID
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB051HTR
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting PABPC4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3d98ab75-a886-4dd3-a356-af0b92b13bb1/@@download/attachment/L-PABPC4-LV08-38.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PABPC4. (PABPC4-LV08-38)

value: ENCBS946FNG at ENCODE; https://www.encodeproject.org/ENCBS946FNG/


title: shRNA RNA-seq from HepG2 (ENCLB877VPD)

description:
https://www.encodeproject.org/experiments/ENCSR064DXG/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against PTBP1 in HepG2 cells followed by RNA-seq. (PTBP1-BGHLV12)
experiment encode accession: ENCSR064DXG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR603TCV
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB877VPD
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting PTBP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/95df3f36-5921-4409-b740-0298bd78dcf5/@@download/attachment/L-PTBP1-BGHLV12-59.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PTBP1. (PTBP1-BGHLV12-59)

value: 15 year

value: male

value: hepatocellular carcinoma

value: ENCBS042JDA at ENCODE; https://www.encodeproject.org/ENCBS042JDA/

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

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


title: MCF-7 cells treated with DMSO, replicate 4

value: DMSO


title: MCF-7 cells treated with DMSO, replicate 3


title: shRNA RNA-seq from HepG2 (ENCLB177FPZ)

description:
https://www.encodeproject.org/experiments/ENCSR017PRS/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SRSF7 in HepG2 cells followed by RNA-seq. (SRSF7-BGHLV12)
experiment encode accession: ENCSR017PRS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR603TCV
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB177FPZ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SRSF7

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f2dc14e5-d25e-4b57-a2fa-da13256f83fb/@@download/attachment/L-SRSF7-BGHLV12-78.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SRSF7. (SRSF7-BGHLV12-78)

value: child

value: ENCBS815MFP at ENCODE; https://www.encodeproject.org/ENCBS815MFP/


title: Evx1Δfs Clone 14 Rep2

city: Brisbane

first: Charles

middle: Cameron

last: Bell

state: Queensland

address: 37 Kent Street

country: Australia

institute: Mater Research

description: Differentiation performed in serum

data_processing:
RNAseq data was mapped to the Mus musculus reference genome (mm9) using TopHat2 and then TMAP (Kim et al. 2013). Tophat2 is required to map spliced junctions, while TMAP is designed for IonTorrent sequencing data and therefore performs better with IonTorrent data. Transcript counts were obtained by using HTSeq on the mapped data using the standard settings (Anders et al. 2013). Differential gene expression analysis was performed on the HTSeq output using DESeq2 using the standard settings (Love et al. 2014).
Genome_build: mm9
Supplementary_files_format_and_content: CSV file containing normalized counts for each replicate as calculated by DESeq2.

organism: Mus musculus

source_name: D4 Embryoid Bodies

growth_protocol: Evx1Δfs and Del#3 mESCs were maintained in 1000U/ml LIF on gelatanized plates in standard embryonic stem cell media at 37 degrees C and 5% CO2.

extract_protocol:
RNA was extracted from the embryoid bodies using Trizol according to manufactors instructions.
Total RNA was analysed on the Bioanalyser (Agilent) to confirm high RNA quality (Rinn value > 8). mRNA selection of total RNA was performed using Ambion Dynabeads© mRNA DIRECT Micro Purification Kit (#61021, Life Technologies). Barcoded RNAseq libraries were generated from the mRNA using the Ion Total RNAseq Kit v3 (#4475936) and Ion Xpress RNAseq Barcode 1-16 Kit (#4475485, Life Technologies). RNAseq libraries were sequenced on the Ion Proton sequencing instrument using the Ion P1 Hi-Q Sequencing 200 Kit with the Ion P1 v2 chip. Each sample was sequenced to a depth of least 15 million reads.

treatment_protocol: Cells were seeded at 2x104 cells/ml in embryonic stem cell media without LIF, as described previously (Bruce et al. 2007). Cells were then grown in this serum containing media for 4 days. Samples being compared were set up on the same day at the same time.

tag: tissue

value: Day 4 embryoid bodies

tag: cell type

value: W9.5 mESCs (derived from)


title: MCF-7 cells treated with DMSO, replicate 2


title: MCF-7 cells treated with DMSO, replicate 1


title: MCF-7 cells treated with 10nM TCDD, replicate 4

value: TCDD


title: MCF-7 cells treated with 10nM TCDD, replicate 2


title: shRNA RNA-seq from HepG2 (ENCLB196GBO)

description:
https://www.encodeproject.org/experiments/ENCSR030ARO/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against NCBP2 in HepG2 cells followed by RNA-seq. (NCBP2-BGHLV12)
experiment encode accession: ENCSR030ARO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB196GBO
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting NCBP2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ebe6fd51-77e6-41b7-a303-c16ccb1375a6/@@download/attachment/L-NCBP2-BGHLV12-51.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against NCBP2. (NCBP2-BGHLV12-51)

value: Brenton Graveley, UConn

value: ENCBS437UIO at ENCODE; https://www.encodeproject.org/ENCBS437UIO/


title: u500high_v4-bulk

city: Seattle

first: Jay

last: Shendure

state: Wa

address: 6528 19th Avenue NE

department: Genome Sciences

institute: University of Washington

description:
GESTALT_Barcode
DNA readout of V3 lineage tracing barcode - high DsRed levels
sample106

library_source: genomic

data_processing:
Sequences were trimmed, filtered and called according to the v1.0 of the FateMap pipeline publicly available here: https://github.com/shendurelab/Cas9FateMapping
Genome_build: HG19
Supplementary_files_format_and_content: called UMI file (.stats.txt): A file containing rows for the sequencing read recovered (when done without UMIs) or the UMI sequence.  Each row contains the name, whether the read was 2) kept after filtering, 3) if the read couldn't be merged, did the calls per-target site conflict?, 3) were the calls from paired reads or a merged read, 4+) the indel events over each of the targets in the read
Supplementary_files_format_and_content: annotations file: the annotations of node names in the PHYLIP MIX input file to their event identity
Supplementary_files_format_and_content: MIX data matrix: the data matrix input to the PHYLIP mix tool
Supplementary_files_format_and_content: JSON tree file: a richly annotated lineage tree stored in the JSON format, compatible with D3 tree visualization
Supplementary_files_format_and_content: MIX genotype output: the raw output file containing genotypes produced by PHYLIP MIX
Supplementary_files_format_and_content: MIX newick tree output: the newick trees produced as output from PHYLIP MIX

molecule: genomic DNA

extract_protocol:
Kapa High Fidelity Polymerase was used for all barcode amplification steps. Gradient PCRs were performed to optimize annealing temperatures for amplification from gDNA. For experiments performed without UMIs, up to 250 ng of gDNA was loaded into a single 50 µl PCR reaction and amplified using primers immediately flanking the barcode (see table S4 for oligo sequences). If there was less than 250 ng from a sample, all of it was used in a single reaction. For experiments performed with UMIs, a primer with a sequencing adapter and 10 nt of fully degenerate sequence 5' to the barcode-flanking sequence was used for a single prolonged extension step, in which the temperature was ramped between annealing and extending for five cycles (without a denaturing step to prevent re-sampling of gDNA barcodes). All cell culture experiments and v6 zebrafish embryos received a single extension to incorporate UMIs, whereas v7 embryo time-course experiments and all ADR1 tissues (also v7) received 2 UMI incorporation cycles due to having low gDNA consequent to fewer cells being present in early embryo and sorted heart samples. To minimize repetitive amplification of the same barcode, no reverse primer was included in UMI-tagging reactions. DNA was then purified using AMPure beads (Agencourt), and loaded into a PCR primed from the sequencing adapter flanking each UMI and a site immediately 3' of the barcode.
For all experiments, two ensuing qPCRs were performed prior to sequencing to incorporate sequencing adapters, sample indexes, and flow cell adapters. AMPure beads were used to purify PCR products after each reaction.

tag: cell line


title: Del3 (Evx1/Evx1asΔ2.6kb) Rep1

description: Differentiation performed in serum


title: r50high_v2-bulk

description:
GESTALT_Barcode
DNA readout of V3 lineage tracing barcode - high DsRed levels
sample9


title: shRNA RNA-seq from HepG2 (ENCLB002YTJ)

description:
https://www.encodeproject.org/experiments/ENCSR030GZQ/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against TRA2A in HepG2 cells followed by RNA-seq. (TRA2A BGHLV14)
experiment encode accession: ENCSR030GZQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB002YTJ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting TRA2A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6aef5911-719e-42b5-a135-50af926e6958/@@download/attachment/L-TRA2A_BGHLV14-62.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against TRA2A. (TRA2A_BGHLV14-62)

value: 15 year

value: ENCBS147BEL at ENCODE; https://www.encodeproject.org/ENCBS147BEL/


title: shRNA RNA-seq from HepG2 (ENCLB895NHT)

description:
https://www.encodeproject.org/experiments/ENCSR010ZMZ/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against HLTF in HepG2 cells followed by RNA-seq. (HLTF BGHLV14)
experiment encode accession: ENCSR010ZMZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB895NHT
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting HLTF

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/fa27da25-d512-4148-8348-2c90e2c8fcea/@@download/attachment/L-HLTF_BGHLV14-26.pdf

value: HLTF

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against HLTF. (HLTF_BGHLV14-26)

value: male

value: hepatocellular carcinoma

value: ENCBS138OWD at ENCODE; https://www.encodeproject.org/ENCBS138OWD/


title: shRNA RNA-seq from HepG2 (ENCLB517MGJ)

description:
https://www.encodeproject.org/experiments/ENCSR028ITN/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against PCBP2 in HepG2 cells followed by RNA-seq. (PCBP2 BGHLV14)
experiment encode accession: ENCSR028ITN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB517MGJ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting PCBP2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d2d0494a-21f8-45dc-9233-2af3ded65e85/@@download/attachment/L-PCBP2_BGHLV14-29.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PCBP2. (PCBP2_BGHLV14-29)

value: ENCBS753KCK at ENCODE; https://www.encodeproject.org/ENCBS753KCK/

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

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


title: shRNA RNA-seq from HepG2 (ENCLB324DZV)

description:
https://www.encodeproject.org/experiments/ENCSR010ZMZ/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against HLTF in HepG2 cells followed by RNA-seq. (HLTF BGHLV14)
experiment encode accession: ENCSR010ZMZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB324DZV
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/94b850b9-e0f9-4f6c-abae-01cfaa009f81/@@download/attachment/L-HLTF_BGHLV14-25.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against HLTF. (HLTF_BGHLV14-25)

value: child

value: ENCBS885FSX at ENCODE; https://www.encodeproject.org/ENCBS885FSX/


title: t1high_v1-bulk

description:
GESTALT_Barcode
DNA readout of V3 lineage tracing barcode - high DsRed levels
sample103


title: M3-2

description:
GESTALT_Barcode
DNA readout of V5 lineage tracing barcode -sorted on medium DsRed levels
sample93


title: shRNA RNA-seq from HepG2 (ENCLB648OBM)

description:
https://www.encodeproject.org/experiments/ENCSR016IDR/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against AKAP1 in HepG2 cells followed by RNA-seq. (AKAP1-BGHLV12)
experiment encode accession: ENCSR016IDR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB648OBM
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting AKAP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/303a7fe2-6a83-4893-a367-9f54291aa851/@@download/attachment/L-AKAP1-BGHLV12-4.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against AKAP1. (AKAP1-BGHLV12-4)

value: Brenton Graveley, UConn

value: ENCBS113GKP at ENCODE; https://www.encodeproject.org/ENCBS113GKP/


title: shRNA RNA-seq from HepG2 (ENCLB757ABL)

description:
https://www.encodeproject.org/experiments/ENCSR016IDR/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against AKAP1 in HepG2 cells followed by RNA-seq. (AKAP1-BGHLV12)
experiment encode accession: ENCSR016IDR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB757ABL
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/df99501f-b562-4d96-a332-0786fadf15f6/@@download/attachment/L-AKAP1-BGHLV12-3.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against AKAP1. (AKAP1-BGHLV12-3)

value: 15 year

value: ENCBS045GOD at ENCODE; https://www.encodeproject.org/ENCBS045GOD/


title: shRNA RNA-seq from HepG2 (ENCLB108KLY)

description:
https://www.encodeproject.org/experiments/ENCSR030ARO/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against NCBP2 in HepG2 cells followed by RNA-seq. (NCBP2-BGHLV12)
experiment encode accession: ENCSR030ARO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB108KLY
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/cdc8fcd5-7bf1-4aac-8560-9517ce0ec4e6/@@download/attachment/L-NCBP2-BGHLV12-52.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against NCBP2. (NCBP2-BGHLV12-52)

value: male

value: ENCBS704AVG at ENCODE; https://www.encodeproject.org/ENCBS704AVG/


title: shRNA RNA-seq from HepG2 (ENCLB081GDF)

description:
https://www.encodeproject.org/experiments/ENCSR003EKR/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT BGHLV14 1)
experiment encode accession: ENCSR003EKR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB081GDF
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting Non-specific target control

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/842a227d-6f54-441b-a0d8-860b71f34e2d/@@download/attachment/L-NT_BGHLV14-2_1.pdf

value: Control

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an Control shRNA against no target. (NT_BGHLV14-2)

value: hepatocellular carcinoma

value: ENCBS628IQK at ENCODE; https://www.encodeproject.org/ENCBS628IQK/


title: shRNA RNA-seq from HepG2 (ENCLB091JLI)

description:
https://www.encodeproject.org/experiments/ENCSR017PRS/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SRSF7 in HepG2 cells followed by RNA-seq. (SRSF7-BGHLV12)
experiment encode accession: ENCSR017PRS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR603TCV
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB091JLI
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4c8713d6-3064-4577-8d46-1685a0df6861/@@download/attachment/L-SRSF7-BGHLV12-77.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SRSF7. (SRSF7-BGHLV12-77)

value: ENCBS974ELC at ENCODE; https://www.encodeproject.org/ENCBS974ELC/

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

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


title: r10high_v3-bulk

description:
GESTALT_Barcode
DNA readout of V3 lineage tracing barcode - high DsRed levels
sample116


title: shRNA RNA-seq from HepG2 (ENCLB238SWB)

description:
https://www.encodeproject.org/experiments/ENCSR009PPI/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against FXR1 in HepG2 cells followed by RNA-seq. (FXR1-BGHLV12)
experiment encode accession: ENCSR009PPI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB238SWB
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting FXR1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c5b8d6df-787f-4af7-9b96-54c4a61b822a/@@download/attachment/L-FXR1-BGHLV12-29.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against FXR1. (FXR1-BGHLV12-29)

value: child

value: Brenton Graveley, UConn

value: ENCBS959DVN at ENCODE; https://www.encodeproject.org/ENCBS959DVN/


title: M4-1

description:
GESTALT_Barcode
DNA readout of V5 lineage tracing barcode -sorted on medium DsRed levels
sample109


title: HT29_ShFra1-2_rep2

city: Amsterdam

first: Oscar

last: Krijgsman

state: Outside the US or Canada

address: Plesmanlaan 121

department: Molecular Oncology and Immunology

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Read mapping was performed using TopHat version 2.0.9 with the NCBI Build 37 reference genome
Read counts per gene were quantified using HTSeq version 0.5.4
Read count data was normalized to 10Million reads per sample.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix with read count data normalised to 10 million reads per sample.

extract_protocol: Total RNA was isolated using trisol followed by Illumina TruSeq RNA Sample Prep Kit according to manufacturers specifications.

value: colorectal adenocarcinoma cell line

tag: fra-1 status

value: knock-down


title: shRNA RNA-seq from HepG2 (ENCLB900ZWL)

description:
https://www.encodeproject.org/experiments/ENCSR009PPI/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against FXR1 in HepG2 cells followed by RNA-seq. (FXR1-BGHLV12)
experiment encode accession: ENCSR009PPI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB900ZWL
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4ad34e8b-7d36-41c5-bf33-d3dfcd058535/@@download/attachment/L-FXR1-BGHLV12-30.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against FXR1. (FXR1-BGHLV12-30)

value: 15 year

value: male

value: ENCBS049QKG at ENCODE; https://www.encodeproject.org/ENCBS049QKG/


title: Lenti_Crispr_HEK4_V2_D14

description:
GESTALT_Barcode
Lineage barcode V2 with lenticrisprV2 genome integration
sample87


title: HT29_ShFra1-2_rep1


title: shRNA RNA-seq from K562 (ENCLB710ZUJ)

description:
https://www.encodeproject.org/experiments/ENCSR000KYM/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against DDX3X in K562 cells followed by RNA-seq. (DDX3X-LV08)
experiment encode accession: ENCSR000KYM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB710ZUJ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting DDX3X

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/038da087-71a6-41c2-a677-94a57dfc8cc0/@@download/attachment/L-DDX3X-LV08-15.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against DDX3X. (DDX3X-LV08-15)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS406BAI at ENCODE; https://www.encodeproject.org/ENCBS406BAI/

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: L7-2

description:
GESTALT_Barcode
DNA readout of V5 lineage tracing barcode-- sorted on low DsRed
sample110


title: shRNA RNA-seq from HepG2 (ENCLB280UZM)

description:
https://www.encodeproject.org/experiments/ENCSR003EKR/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT BGHLV14 1)
experiment encode accession: ENCSR003EKR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB280UZM
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6ed6fd56-f76a-4e91-a038-e3cd67a78f90/@@download/attachment/L-NT_BGHLV14-1_1.pdf

value: Control

value: RNA-seq on HepG2 cells treated with an Control shRNA against no target. (NT_BGHLV14-1)

value: child

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS984EPA at ENCODE; https://www.encodeproject.org/ENCBS984EPA/

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

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


title: shRNA RNA-seq from HepG2 (ENCLB796JAA)

description:
https://www.encodeproject.org/experiments/ENCSR028ITN/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against PCBP2 in HepG2 cells followed by RNA-seq. (PCBP2 BGHLV14)
experiment encode accession: ENCSR028ITN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB796JAA
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/465187b8-bfd3-40f9-b5b7-5c9a1bc3cc46/@@download/attachment/L-PCBP2_BGHLV14-30.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PCBP2. (PCBP2_BGHLV14-30)

value: 15 year

value: male

value: ENCBS740QWK at ENCODE; https://www.encodeproject.org/ENCBS740QWK/


title: HT29_ShFra1-1_rep2

value: colorectal adenocarcinoma cell line

value: knock-down


title: HT29_ShFra1-1_rep1


title: cell_culture_9

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample100


title: HT29_KH_rep3

value: WT


title: shRNA RNA-seq from K562 (ENCLB213KRS)

description:
https://www.encodeproject.org/experiments/ENCSR000KYM/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against DDX3X in K562 cells followed by RNA-seq. (DDX3X-LV08)
experiment encode accession: ENCSR000KYM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB213KRS
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/26986325-1074-41af-beb4-a0936d98549a/@@download/attachment/L-DDX3X-LV08-16.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against DDX3X. (DDX3X-LV08-16)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS441PSF at ENCODE; https://www.encodeproject.org/ENCBS441PSF/

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: cell_culture_8

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample98

extract_protocol:
Kapa High Fidelity Polymerase was used for all barcode amplification steps. Gradient PCRs were performed to optimize annealing temperatures for amplification from gDNA. For experiments performed without UMIs, up to 250 ng of gDNA was loaded into a single 50 µl PCR reaction and amplified using primers immediately flanking the barcode (see table S4 for oligo sequences). If there was less than 250 ng from a sample, all of it was used in a single reaction. For experiments performed with UMIs, a primer with a sequencing adapter and 10 nt of fully degenerate sequence 5' to the barcode-flanking sequence was used for a single prolonged extension step, in which the temperature was ramped between annealing and extending for five cycles (without a denaturing step to prevent re-sampling of gDNA barcodes). All cell culture experiments and v6 zebrafish embryos received a single extension to incorporate UMIs, whereas v7 embryo time-course experiments and all ADR1 tissues (also v7) received 2 UMI incorporation cycles due to having low gDNA consequent to fewer cells being present in early embryo and sorted heart samples. To minimize repetitive amplification of the same barcode, no reverse primer was included in UMI-tagging reactions. DNA was then purified using AMPure beads (Agencourt), and loaded into a PCR primed from the sequencing adapter flanking each UMI and a site immediately 3' of the barcode.
For all experiments, two ensuing qPCRs were performed prior to sequencing to incorporate sequencing adapters, sample indexes, and flow cell adapters. AMPure beads were used to purify PCR products after each reaction.


title: cell_culture_6

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample80


title: HT29_ShFra1-2_rep3


title: cell_culture_7

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample72


title: M2-1

description:
GESTALT_Barcode
DNA readout of V5 lineage tracing barcode -sorted on medium DsRed levels
sample95


title: HT29_ShFra1-1_rep3


title: cell_culture_5

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample126


title: HT29_KH_rep1


title: cell_culture_36_12b

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample32


title: Post-treatment from PDX of sample M029

data_processing:
Read mapping was performed using TopHat version 2.0.9 with the NCBI Build 37 reference genome
Read counts per gene were quantified using HTSeq version 0.5.4
Read count data was normalized to 10Million reads per sample.
Genome_build: hg19
Supplementary_files_format_and_content: fastq filesand text file with normalized read count data

source_name: Melanoma tumor

extract_protocol:
total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

value: post-treatment Vemurafenib

tag: tumor

value: PDX

tag: material

value: Fresh Frozen


title: Post-treatment patient sample M029R

value: Patient material

value: FFPE


title: Pre-treatment from PDX of sample M029

value: pre-treatment


title: Pre-treatment from PDX of sample M026


title: cell_culture_4

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample36


title: Post-treatment patient sample M026


title: cell_culture_34_11b

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample13


title: cell_culture_35_12a

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample29


title: cell_culture_3

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample34


title: cell_culture_29_9a

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample118


title: Post-treatment patient sample M019


title: cell_culture_32_10b

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample47


title: Post-treatment from PDX of sample M019


title: Pre-treatment from PDX of sample M019


title: HT29_KH_rep2

value: colorectal adenocarcinoma cell line


title: cell_culture_28_8b

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample128


title: cell_culture_27_8a

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample123


title: Pre-treatment from PDX of sample M005


title: Evx1Δfs Clone 14 Rep1

description: Differentiation performed in serum

extract_protocol:
RNA was extracted from the embryoid bodies using Trizol according to manufactors instructions.
Total RNA was analysed on the Bioanalyser (Agilent) to confirm high RNA quality (Rinn value > 8). mRNA selection of total RNA was performed using Ambion Dynabeads© mRNA DIRECT Micro Purification Kit (#61021, Life Technologies). Barcoded RNAseq libraries were generated from the mRNA using the Ion Total RNAseq Kit v3 (#4475936) and Ion Xpress RNAseq Barcode 1-16 Kit (#4475485, Life Technologies). RNAseq libraries were sequenced on the Ion Proton sequencing instrument using the Ion P1 Hi-Q Sequencing 200 Kit with the Ion P1 v2 chip. Each sample was sequenced to a depth of least 15 million reads.

value: Day 4 embryoid bodies

value: W9.5 mESCs (derived from)


title: cell_culture_25_7a

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample4


title: Pre-treatment patient sample M019


title: cell_culture_31_10a

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample31


title: cell_culture_26_7b

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample112


title: Post-treatment patient sample M005


title: cell_culture_24_6b

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample133


title: Pre-treatment patient sample M005


title: cell_culture_23_6a

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample136


title: cell_culture_30_9b

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample117


title: Pre-treatment patient sample M026


city: San Francisco

first: UCSF-UBC

last: CENTER

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: miRNA-Seq analysis of foreskin melanocyte from skin03 (m05799) using Illumina HiSeq 2000
library name: m05799
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RIN 9
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 2.124 ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing: Various levels of processed data files will be made available as this project proceeds.

extract_protocol: library construction protocol: Refer to document 'miRNA3 - Plate Format miRNA Library Construction' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

value: male

tag: body site

value: Penis

tag: histological type

value: Melanocyte

tag: is tumor

value: No

value: primary cell culture

value: foreskin melanocyte


description:
design description: miRNA-Seq analysis of pancreas islet from ZD4 273 (m08319) using Illumina HiSeq 2000
library name: m08319
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RIN 7.7
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 1.008 ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Pancreas

value: Islet

value: primary cell

value: pancreas islet


description:
design description: miRNA-Seq analysis of peripheral mononuclear cell from TC016 (m09073) using Illumina HiSeq 2000
library name: m09073
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RQS 5.6
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 1.2169 ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: female

value: Blood

value: Peripheral blood mononuclear cell


title: cell_culture_20_4b

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample22


title: cell_culture_17_3a

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample102


title: cell_culture_22_5b

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample129


description:
design description: MeDIP-Seq analysis of fetal brain tissue from H22911 (A02297) using Illumina HiSeq 2000
library name: A02297
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 25 min
MeDIP_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MeDIP_PROTOCOL_DNA_AMOUNT: 2 ug
MeDIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
MeDIP_PROTOCOL_BEAD_AMOUNT: 100 ul
MeDIP_PROTOCOL_ANTIBODY_AMOUNT: 1 ug
MeDIP_ANTIBODY: Methylcytidine
MeDIP_ANTIBODY_PROVIDER: Eurogentec
MeDIP_ANTIBODY_CATALOG: BI-MECY-0100
MeDIP_ANTIBODY_LOT: 80808
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

extract_protocol: library construction protocol: Refer to document 'MeDIP-seq library construction protocol v2' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

value: Brain

value: Brain tissue

value: primary tissue

value: fetal brain tissue


description:
design description: RNA-Seq analysis of brain (germinal matrix) tissue from HuFGM02 (A21768) using Illumina HiSeq 2000
library name: A21768
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 13
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 5.2
RNA_PREPARATION_INITIAL_RNA_QNTY: 4.07 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 240-420 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

extract_protocol: library construction protocol: Refer to document 'Strand Specific 96-well Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

value: male

value: Germinal matrix tissue

value: brain (germinal matrix) tissue


title: cell_culture_21_5a

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample131


title: cell_culture_19_4a

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample53


title: cell_culture_16_2b

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample37


title: cell_culture_14_1b

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample99


title: Post-treatment from PDX of sample M005

value: post-treatment Vemurafenib

value: PDX

value: Fresh Frozen


title: cell_culture_18_3b

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample56


title: cell_culture_13_1a

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample91


description:
design description: RNA-Seq analysis of peripheral mononuclear cell from TC016 (A21769) using Illumina HiSeq 2000
library name: A21769
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 13
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 6.9
RNA_PREPARATION_INITIAL_RNA_QNTY: 3.67 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 240-420 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: No


title: cell_culture_1

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample107


title: cell_culture_11

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample19


title: cell_culture_10

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample11


title: 8-DsRed-High-v5

description:
GESTALT_Barcode
DNA readout of V5 lineage tracing barcode - sorted on high DsRed levels
sample57


title: embryos_3_13_v6_unedited

description:
GESTALT_Barcode
barcode readout of 30 hours post fertilization embryo with lineage barcode V6
sample25

organism: Danio rerio

tag: developmental stage


title: cell_culture_12

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample27


title: embryos_3_14_v6_unedited

description:
GESTALT_Barcode
barcode readout of 30 hours post fertilization embryo with lineage barcode V6
sample70


title: embryos_1_8_v6

description:
GESTALT_Barcode
barcode readout of 30 hours post fertilization embryo with lineage barcode V6
sample62


title: cell_culture_33_11a

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample39


title: 3-DsRed-Med-v1

description:
GESTALT_Barcode
DNA readout of V1 lineage tracing barcode - medium DsRed levels
sample86


title: embryos_1_6_v6

description:
GESTALT_Barcode
barcode readout of 30 hours post fertilization embryo with lineage barcode V6
sample119


title: embryos_1_7_v6

description:
GESTALT_Barcode
barcode readout of 30 hours post fertilization embryo with lineage barcode V6
sample38


title: embryos_1_5_v6

description:
GESTALT_Barcode
barcode readout of 30 hours post fertilization embryo with lineage barcode V6
sample81


title: cell_culture_15_2a

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample16


title: embryos_1_4_v6

description:
GESTALT_Barcode
barcode readout of 30 hours post fertilization embryo with lineage barcode V6
sample84


title: embryos_1_2_v6

description:
GESTALT_Barcode
barcode readout of 30 hours post fertilization embryo with lineage barcode V6
sample12


title: embryos_1_3_v6

description:
GESTALT_Barcode
barcode readout of 30 hours post fertilization embryo with lineage barcode V6
sample3


title: R9_v1-mono-3-dsRed-high

description:
GESTALT_Barcode
RNA readout of V1 lineage tracing barcode - sorted on high DsRed levels
sample1


title: R8-v1-mono-2-dsRed-high-RNA

description:
GESTALT_Barcode
RNA readout of V1 lineage tracing barcode - sorted on high DsRed levels
sample18


title: embryos_1_1_v6

description:
GESTALT_Barcode
barcode readout of 30 hours post fertilization embryo with lineage barcode V6
sample67


title: R7-v1-mono-1-dsRed-high-RNA

description:
GESTALT_Barcode
RNA readout of V1 lineage tracing barcode - sorted on high DsRed levels
sample122


title: 2-DsRed-Low-v1

description:
GESTALT_Barcode
DNA readout of V1 lineage tracing barcode - low DsRed levels
sample111


title: AtWTInf_3

status: Public on May 25 2016

city: University Park

first: Michael

middle: J

last: Axtell

state: Pennsylvania

address: 208 Mueller Lab

department: Biology

institute: Penn State University

description:
small RNA
WT3
AtWTInflorescense3_R1
Processed data file: mir_expression_raw_RPM.txt

data_processing:
Adapter discovery was performed using an in-house script (find_3p_adap.pl) (http://sites.psu.edu/axtell/software/misc-tools/), and trimmed using cutadapt under default settings.
Trimmed libraries were then aligned to TAIR10 reference genome, using multiple alignment principles (ShortStack, Bowtie, Novoalign, BWA).
Alignments of mature miRNA transcripts were extracted, quantified and normalized by the amount of total aligned reads in millions (RPM).
Genome_build: TAIR10
Supplementary_files_format_and_content: mir_expression_raw_RPM.txt: Tab-delimited text file includes expression in RPM for 11 miRNA loci using various alignment principles in 3 libraries.
Alignment principles:
u (ShortStack -mmap u), f (ShortStack -mmap f), r (ShortStack -mmap r), n (ShortStack -mmap n), bow (bowtie -v 1 --best -k 1), bowm (bowtie -v 1 --best --strata -m 1), bwa (bwa aln -k 1) and novo (novoalign in default).

organism: Arabidopsis thaliana

source_name: inflorescense, WT

extract_protocol:
RNA extraction was performed using tri-reagent based protocol.
Libraries were constructed using the TruSeq Small RNA Library prep kit (Illumina, RS-200-0012) per the manufacturer instructions.

tag: ecotype

value: Columbia

tag: genotype/variation

value: wild type

value: inflorescence


title: bZIP_tnt.bZIP53_col_v3b

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-bZIP_tnt-bZIP53_col-chr1-5_GEM_events.narrowPeak

data_processing:
library strategy: DAP-seq
Base calling was done with Illumina Offline Base Caller (OLB 1.9.4).
Reads were aligned by bowtie2 version 2.0.0-beta7 against the Arabidopsis TAIR10 genome assembly or Zea mays genome assembly B73 with default parameters, and additionally filter for highest scoring MAPQ alignments only (score=254).
Peaks were called using GEM peak caller version 2.3 with the default version 2.3 read distribution, TAIR10 genome sequences and parameters " --k_min 6 --k_max 20 --k_seqs 250 --outNP --k_neg_dinu_shuffle".
Genome_build: Arabidopsis TAIR10 or maize B73
Supplementary_files_format_and_content: Peak regions in narrowPeak format were created by GEM.

source_name: young leaf

extract_protocol:
Genomic DNA is extracted from Arabidopsis young leaves by phenol:chloroform:isoamyl alchohol (25:24:1) followed by a chloroform  extraction, ethanol precipitation and resuspension in Tris/EDTA buffer.  The DAP-Seq DNA library is prepared from fragmented naked genomic DNA ligated with a short DNA sequence (20bp) encoding a truncated Illumina TruSeq adapter.  Separately, a construct containing an affinity-tagged transcription factor (GST or HALO) is translated by either heterologous (E. coli) or in vitro (wheat germ) expression system. The affinity-tagged protein is immobilized on the appropriate affinity resin.  The DNA affinity purification step begins by combining the DNA library with the immobilized transcription factor. After the wash steps remove the unbound DNA, the bound DNA fraction is eluted.
The eluted DNA fragments are PCR amplified with a full-length indexed TruSeq primer and directly sequenced on the Illumina HiSeq 2500.

tag: protein

tag: gene id

tag: protein family

value: bZIP

tag: protein source

value: Arabidopsis thaliana

tag: protein affinity tag

value: Halo

tag: expression system

value: tnt

tag: dna source

value: col

tag: replicate

tag: subset

value: motif+TFBS


title: bZIP_tnt.bZIP44_col_v3a

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-bZIP_tnt-bZIP44_col-chr1-5_GEM_events.narrowPeak


title: bZIP_tnt.bZIP53_col_v3a


title: 4-DsRed-High-v1

description:
GESTALT_Barcode
DNA readout of V1 lineage tracing barcode - sorted on high DsRed levels
sample78

tag: cell line


title: 1-unedited_v1

description:
GESTALT_Barcode
DNA readout of V1 lineage tracing barcode - control
sample89


title: bZIP_tnt.TGA3_col_v3b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-bZIP_tnt-TGA3_col-chr1-5_GEM_events.narrowPeak


title: bZIP_tnt.TGA3_col_v3a


title: bZIP_tnt.bZIP44_col_v3b


title: bZIP_tnt.TGA1_col_v3a

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-bZIP_tnt-TGA1_col-chr1-5_GEM_events.narrowPeak


title: bZIP_tnt.GBF6_col_v3b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-bZIP_tnt-GBF6_col-chr1-5_GEM_events.narrowPeak


title: bZIP_tnt.GBF6_col_v3a


title: bZIP_tnt.GBF3_colamp_v3e

description:
A. thaliana Col-0 input DNA library was PCR amplifed (ampDAP-Seq library) before affinity purification.
processed data file: DAPSeq-bZIP_tnt-GBF3_colamp-chr1-5_GEM_events.narrowPeak

value: colamp


title: bZIP_tnt.GBF3_colamp_v3d


title: bZIP_tnt.TGA2_col_v3a

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-bZIP_tnt-TGA2_col-chr1-5_GEM_events.narrowPeak


title: AtWTInf_1

description:
small RNA
WT1
AtWTInflorescense1_R1
Processed data file: mir_expression_raw_RPM.txt

tag: tissue


title: bZIP_tnt.GBF3_col_v3b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-bZIP_tnt-GBF3_col-chr1-5_GEM_events.narrowPeak


title: AtWTInf_2

description:
small RNA
WT2
AtWTInflorescense2_R1
Processed data file: mir_expression_raw_RPM.txt


title: bZIP_tnt.GBF3_col_v3a


title: bHLH_tnt.bHLH31_col_b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-bHLH_tnt-bHLH31_col-chr1-5_GEM_events.narrowPeak

value: bHLH

value: b


title: bHLH_tnt.bHLH34_col_b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-bHLH_tnt-bHLH34_col-chr1-5_GEM_events.narrowPeak

value: motif


title: bHLH_tnt.bHLH31_col200_a

value: a


title: bHLH_tnt.bHLH34_col_a


title: bHLH_tnt.BIM2_colamp_v3b

description:
A. thaliana Col-0 input DNA library was PCR amplifed (ampDAP-Seq library) before affinity purification.
processed data file: DAPSeq-bHLH_tnt-BIM2_colamp-chr1-5_GEM_events.narrowPeak


title: bHLH_tnt.BIM2_colamp_v3a


title: cell_culture_2

description:
GESTALT_Barcode
barcode readout of cellculture artifical lineage line with V1 lineage barcode
sample65


title: WRKY_tnt.WRKY8_col_b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-WRKY_tnt-WRKY8_col-chr1-5_GEM_events.narrowPeak

value: WRKY


title: WRKY_tnt.WRKY7_col_b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-WRKY_tnt-WRKY7_col-chr1-5_GEM_events.narrowPeak


title: WRKY_tnt.WRKY70_col_b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-WRKY_tnt-WRKY70_col-chr1-5_GEM_events.narrowPeak


title: WRKY_tnt.WRKY7_col100_a


title: WRKY_tnt.WRKY8_col100_a


title: WRKY_tnt.WRKY40_col_a

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-WRKY_tnt-WRKY40_col-chr1-5_GEM_events.narrowPeak


title: WRKY_tnt.WRKY22_col_b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-WRKY_tnt-WRKY22_col-chr1-5_GEM_events.narrowPeak


title: WRKY_tnt.WRKY22_col100_a


title: WRKY_tnt.WRKY40_col_v31


title: bZIP_tnt.TGA1_col_v3b


title: WRKY_tnt.WRKY21_col_a

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-WRKY_tnt-WRKY21_col-chr1-5_GEM_events.narrowPeak


title: TCP_tnt.TCP3_col_a

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-TCP_tnt-TCP3_col-chr1-5_GEM_events.narrowPeak

value: TCP


title: Trihelix_tnt.At3g14180_col100_a

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-Trihelix_tnt-At3g14180_col-chr1-5_GEM_events.narrowPeak

value: Trihelix


title: TCP_tnt.TCP3_col_b


title: TCP_tnt.TCP24_col_b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-TCP_tnt-TCP24_col-chr1-5_GEM_events.narrowPeak


title: WRKY_tnt.WRKY21_col_b


title: TCP_tnt.TCP24_col200_a


title: RAV_tnt.RAV1_col100_a

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-RAV_tnt-RAV1_col-chr1-5_GEM_events.narrowPeak

value: RAV


title: TCP_tnt.At1g72010_col_b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-TCP_tnt-At1g72010_col-chr1-5_GEM_events.narrowPeak


title: TCP_tnt.At1g72010_col200_a


title: NAC_tnt.VND4_col_v3a

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-NAC_tnt-VND4_col-chr1-5_GEM_events.narrowPeak

value: NAC


title: NAC_tnt.VND4_col_v3b


title: NAC_tnt.VND3_col_v3b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-NAC_tnt-VND3_col-chr1-5_GEM_events.narrowPeak


title: NAC_tnt.VND3_col_v3a


title: RAV_tnt.RAV1_col_b


title: Trihelix_tnt.At3g14180_col_b


title: WRKY_tnt.WRKY70_col200_a


title: NAC_tnt.NTL8_col_v3b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-NAC_tnt-NTL8_col-chr1-5_GEM_events.narrowPeak


title: NAC_tnt.CUC2_col_v3a

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-NAC_tnt-CUC2_col-chr1-5_GEM_events.narrowPeak


title: NAC_tnt.ANAC096_col_v3b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-NAC_tnt-ANAC096_col-chr1-5_GEM_events.narrowPeak


title: NAC_tnt.ANAC070_col_v3a

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-NAC_tnt-ANAC070_col-chr1-5_GEM_events.narrowPeak


title: NAC_tnt.ANAC079_col_v3a

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-NAC_tnt-ANAC079_col-chr1-5_GEM_events.narrowPeak


title: NAC_tnt.ANAC062_col_v3b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-NAC_tnt-ANAC062_col-chr1-5_GEM_events.narrowPeak


title: NAC_tnt.ANAC096_col_v3a


title: NAC_tnt.ANAC062_col_v3a


title: NAC_tnt.CUC2_col_v3b


title: NAC_tnt.ANAC055_col_v3b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-NAC_tnt-ANAC055_col-chr1-5_GEM_events.narrowPeak


title: NAC_tnt.ANAC047_col_v3b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-NAC_tnt-ANAC047_col-chr1-5_GEM_events.narrowPeak


title: NAC_tnt.ANAC053_col_v3a

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-NAC_tnt-ANAC053_col-chr1-5_GEM_events.narrowPeak


title: NAC_tnt.ANAC047_col_v3a


title: NAC_tnt.ANAC046_col_v3b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-NAC_tnt-ANAC046_col-chr1-5_GEM_events.narrowPeak


title: NAC_tnt.ANAC046_col_v3a


title: NAC_tnt.ANAC017_col_v3a

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-NAC_tnt-ANAC017_col-chr1-5_GEM_events.narrowPeak


title: MYBrelated_tnt.TRP1_col_a

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-MYBrelated_tnt-TRP1_col-chr1-5_GEM_events.narrowPeak

value: MYBrelated


title: NAC_tnt.NTL8_col_v3a


title: NAC_tnt.ANAC079_col_v3b


title: MYBrelated_tnt.LCL1_col_b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-MYBrelated_tnt-LCL1_col-chr1-5_GEM_events.narrowPeak


title: NAC_tnt.ANAC055_col_v3a


title: MYBrelated_tnt.EPR1_col_b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-MYBrelated_tnt-EPR1_col-chr1-5_GEM_events.narrowPeak


title: MYB_tnt.MYB74_col_b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-MYB_tnt-MYB74_col-chr1-5_GEM_events.narrowPeak

value: MYB


title: NAC_tnt.ANAC034_col_v3b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-NAC_tnt-ANAC034_col-chr1-5_GEM_events.narrowPeak

value: Arabidopsis thaliana


title: NAC_tnt.ANAC034_col_v3a

value: Halo


title: MYBrelated_tnt.TRP1_col_b

value: tnt


title: MYBrelated_tnt.EPR1_col200_a

value: col


title: MYBrelated_tnt.LCL1_col_a

value: motif+TFBS


title: NAC_tnt.ANAC053_col_v3b


title: MYB_tnt.MYB55_col_b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-MYB_tnt-MYB55_col-chr1-5_GEM_events.narrowPeak


title: NAC_tnt.ANAC070_col_v3b


title: MYB_tnt.MYB60_col200_a

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-MYB_tnt-MYB60_col-chr1-5_GEM_events.narrowPeak


title: MYB_tnt.MYB44_col_b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-MYB_tnt-MYB44_col-chr1-5_GEM_events.narrowPeak


title: MYB_tnt.MYB55_col_a


title: NAC_tnt.ANAC017_col_v3b


title: MYB_tnt.MYB44_col100_a


title: Homeobox_tnt.PDF2_col_a

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-Homeobox_tnt-PDF2_col-chr1-5_GEM_events.narrowPeak

value: Homeobox


title: Homeobox_tnt.EDT1_col200_a

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-Homeobox_tnt-EDT1_col-chr1-5_GEM_events.narrowPeak


title: MYB_tnt.MYB74_col_a


title: MYB_tnt.MYB60_col_b


title: G2like_tnt.At1g25550_col_b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-G2like_tnt-At1g25550_col-chr1-5_GEM_events.narrowPeak


title: G2like_tnt.At2g01060_col_b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-G2like_tnt-At2g01060_col-chr1-5_GEM_events.narrowPeak


title: G2like_tnt.At1g68670_col_b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-G2like_tnt-At1g68670_col-chr1-5_GEM_events.narrowPeak


title: Homeobox_tnt.EDT1_100ng20cy_b


title: CPP_tnt.SOL1_col_b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-CPP_tnt-SOL1_col-chr1-5_GEM_events.narrowPeak

value: CPP


title: G2like_tnt.At1g25550_col100_a


title: CPP_tnt.SOL1_col_a


title: C2H2_tnt.At5g66730_col_a

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-C2H2_tnt-At5g66730_col-chr1-5_GEM_events.narrowPeak


title: C2H2_tnt.IDD5_col_a

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-C2H2_tnt-IDD5_col-chr1-5_GEM_events.narrowPeak


title: C2H2_tnt.IDD5_col_b

value: b


title: G2like_tnt.At1g68670_col100_a


title: G2like_tnt.At2g01060_col_a


title: HSF_tnt.HSFA6B_col100_a

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-HSF_tnt-HSFA6B_col-chr1-5_GEM_events.narrowPeak

value: HSF


title: AP2EREBP_tnt.ERF15_col_b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-AP2EREBP_tnt-ERF15_col-chr1-5_GEM_events.narrowPeak


title: AP2EREBP_tnt.ERF6_col_b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-AP2EREBP_tnt-ERF6_col-chr1-5_GEM_events.narrowPeak

value: motif


title: AP2EREBP_tnt.ERF105_col_b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-AP2EREBP_tnt-ERF105_col-chr1-5_GEM_events.narrowPeak


title: C2H2_tnt.At5g66730_col_b


title: AP2EREBP_tnt.ERF15_col100_a

value: a


title: HSF_tnt.HSFA6B_col_b


title: Homeobox_tnt.PDF2_col_b


title: AP2EREBP_tnt.At4g32800_col200_a

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-AP2EREBP_tnt-At4g32800_col-chr1-5_GEM_events.narrowPeak


title: AP2EREBP_tnt.At4g32800_col_b


title: AP2EREBP_tnt.ERF6_col_a


title: C2H2_tnt.STZ_col100_a

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-C2H2_tnt-STZ_col-chr1-5_GEM_events.narrowPeak

value: STZ


title: C2H2_tnt.STZ_col_b


title: AP2EREBP_tnt.At2g33710_col_b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-AP2EREBP_tnt-At2g33710_col-chr1-5_GEM_events.narrowPeak


title: AP2EREBP_tnt.At2g33710_col_a


title: AP2EREBP_tnt.ERF105_col_a


title: mTERF_tnt.AT5G23930_col_a

description: A. thaliana Col-0 input DNA library

value: mTERF


title: bZIP_tnt.bZIP69_colamp_a

description: A. thaliana Col-0 input DNA library was PCR amplifed (ampDAP-Seq library) before affinity purification.

value: bZIP

value: colamp


title: AP2EREBP_tnt.At1g22810_col_a

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-AP2EREBP_tnt-At1g22810_col-chr1-5_GEM_events.narrowPeak


title: bZIP_tnt.bZIP68_col_a

description: A. thaliana Col-0 input DNA library


title: zfGRF_tnt.AT3G42860_col_a

description: A. thaliana Col-0 input DNA library

value: zfGRF


title: bZIP_tnt.bZIP69_col_a

description: A. thaliana Col-0 input DNA library


title: bZIP_tnt.bZIP48_col_a

description: A. thaliana Col-0 input DNA library


title: bZIP_tnt.bZIP50_colamp_v31


title: bZIP_tnt.bZIP42_colamp_a


title: bZIP_tnt.bZIP52_col_v31

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.At1g22810_col_b


title: bZIP_tnt.bZIP3_col_a

description: A. thaliana Col-0 input DNA library


description:
design description: RNA-Seq analysis of fetal brain tissue from HuFNSC02 (A03492) using Illumina HiSeq 2000
library name: A03492
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 6.8
RNA_PREPARATION_INITIAL_RNA_QNTY: 6 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 300-400 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

tag: submitted sample id

tag: Sex

value: female

tag: body site

value: Brain

value: Brain tissue

value: No

value: primary tissue

value: fetal brain tissue


title: bZIP_tnt.bZIP16_col_v3a

description: A. thaliana Col-0 input DNA library

value: Arabidopsis thaliana

value: Halo

value: tnt

value: col

value: motif+TFBS


title: bZIP_tnt.bZIP28_col_a

description: A. thaliana Col-0 input DNA library

value: a


title: bZIP_tnt.bZIP48_colamp_a


title: bZIP_tnt.bZIP53_colamp_a


title: bZIP_tnt.bZIP43_col_a

description: A. thaliana Col-0 input DNA library

value: motif


title: bZIP_tnt.bZIP52_colamp_a


title: bZIP_tnt.bZIP50_col_v31

description: A. thaliana Col-0 input DNA library


title: bZIP_tnt.bZIP18_col_v31

description: A. thaliana Col-0 input DNA library


title: bZIP_tnt.bZIP44_colamp_a


title: bZIP_tnt.bZIP42_col_a

description: A. thaliana Col-0 input DNA library


title: bZIP_tnt.bZIP16_colamp_a


title: bZIP_tnt.VIP1_col_v3a

description: A. thaliana Col-0 input DNA library


title: bZIP_tnt.TGA9_col_a

description: A. thaliana Col-0 input DNA library


title: bZIP_tnt.VIP1_colamp_a


title: bZIP_tnt.TGA9_colamp_a


title: bZIP_tnt.TGA2_col_v3b

description:
A. thaliana Col-0 input DNA library
processed data file: DAPSeq-bZIP_tnt-TGA2_col-chr1-5_GEM_events.narrowPeak


title: bZIP_tnt.TGA4_colamp_a


title: bZIP_tnt.TGA5_col_v3a

description: A. thaliana Col-0 input DNA library


title: bZIP_tnt.TGA2_colamp_v31


title: bZIP_tnt.TGA3_colamp_a


title: bZIP_tnt.TGA4_col_a

description: A. thaliana Col-0 input DNA library


title: bZIP_tnt.ABI5_col_v3h

description: A. thaliana Col-0 input DNA library


title: bZIP_tnt.GBF5_colamp_a


title: bZIP_tnt.AREB3_colamp_a


title: bZIP_tnt.HY5_colamp_v3a


title: bZIP_tnt.GBF5_col_v3a

description: A. thaliana Col-0 input DNA library


title: bZIP_tnt.GBF6_colamp_a


title: bZIP_tnt.TGA10_col_a

description: A. thaliana Col-0 input DNA library


title: bHLH_tnt.bHLH80_col_a

description: A. thaliana Col-0 input DNA library

value: bHLH


title: bHLH_tnt.bHLH74_col_a

description: A. thaliana Col-0 input DNA library


title: bHLH_tnt.bHLH80_colamp_a


title: bZIP_tnt.bZIP18_colamp_a

value: bZIP


title: bZIP_tnt.ABI5_colamp_v3b

value: colamp


title: bZIP_tnt.AREB3_col_v31

description: A. thaliana Col-0 input DNA library


title: bHLH_tnt.bHLH77_col_a

description: A. thaliana Col-0 input DNA library


title: bZIP_tnt.TGA1_colamp_a


title: bHLH_tnt.bHLH69_col_a

description: A. thaliana Col-0 input DNA library


title: bHLH_tnt.bHLH74_colamp_a


title: bZIP_tnt.TGA6_colamp_a


title: bZIP_tnt.TGA6_col_a

description: A. thaliana Col-0 input DNA library


title: bHLH_tnt.bHLH64_col_a

description: A. thaliana Col-0 input DNA library


title: bHLH_tnt.bHLH34_colamp_a


title: bZIP_tnt.TGA10_colamp_a


title: bHLH_tnt.bHLH28_col_a

description: A. thaliana Col-0 input DNA library


title: bHLH_tnt.bHLH18_col_a

description: A. thaliana Col-0 input DNA library


title: bZIP_tnt.ABF2_col_v3a

description: A. thaliana Col-0 input DNA library


title: bHLH_tnt.bHLH157_col_a

description: A. thaliana Col-0 input DNA library


title: bHLH_tnt.bHLH130_col_a

description: A. thaliana Col-0 input DNA library


title: bHLH_tnt.bHLH10_col_a

description: A. thaliana Col-0 input DNA library


title: bHLH_tnt.bHLH122_col100_a

description: A. thaliana Col-0 input DNA library


title: bHLH_tnt.BIM1_col_a

description: A. thaliana Col-0 input DNA library


title: bHLH_tnt.BIM1_colamp_a


title: bHLH_tnt.BIM2_col_v3b

description: A. thaliana Col-0 input DNA library


title: ZFHD_tnt.ATHB33_col_a

description: A. thaliana Col-0 input DNA library

value: ZFHD


title: bHLH_tnt.bHLH10_colamp_a


title: bHLH_tnt.bHLH122_colamp_a


title: ZFHD_tnt.ATHB34_colamp_a


title: ZFHD_tnt.ATHB33_colamp_a


title: bHLH_tnt.BIM3_col_a

description: A. thaliana Col-0 input DNA library


title: ZFHD_tnt.ATHB34_col_a

description: A. thaliana Col-0 input DNA library


title: ZFHD_tnt.ATHB25_colamp_a


title: ZFHD_tnt.ATHB24_colamp_a


title: ZFHD_tnt.ATHB23_col_b

description: A. thaliana Col-0 input DNA library

value: b


title: ZFHD_tnt.ATHB25_col_a

description: A. thaliana Col-0 input DNA library


title: ZFHD_tnt.ATHB23_colamp_a


title: bHLH_tnt.PIF7_col_a

description: A. thaliana Col-0 input DNA library


title: ZFHD_tnt.AtHB32_col200_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY8_colamp_a

value: WRKY


title: ZFHD_tnt.ATHB24_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY75_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY75_colamp_a


title: WRKY_tnt.WRKY7_colamp_a


title: WRKY_tnt.WRKY65_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY71_col_a

description: A. thaliana Col-0 input DNA library


title: bHLH_tnt.bHLH104_col_b

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY6_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY65_colamp_a


title: WRKY_tnt.WRKY59_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY50_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY50_colamp_a


title: WRKY_tnt.WRKY47_colamp_a


title: WRKY_tnt.WRKY43_colamp_a


title: WRKY_tnt.WRKY55_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY45_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY46_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY42_colamp_a


title: WRKY_tnt.WRKY46_colamp_a


title: WRKY_tnt.WRKY42_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY43_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY33_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY40_colamp_a


title: WRKY_tnt.WRKY28_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY28_colamp_a


title: WRKY_tnt.WRKY45_colamp_a


title: WRKY_tnt.WRKY31_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY30_colamp_a


title: WRKY_tnt.WRKY29_colamp_a


title: WRKY_tnt.WRKY6_colamp_a


title: WRKY_tnt.WRKY27_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY29_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY26_colamp_a


title: WRKY_tnt.WRKY27_colamp_a


title: WRKY_tnt.WRKY47_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY25_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY31_colamp_a


title: WRKY_tnt.WRKY30_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY25_colamp_a


title: WRKY_tnt.WRKY18_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY21_colamp_a


title: WRKY_tnt.WRKY20_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY22_colamp_a


title: WRKY_tnt.WRKY24_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY24_colamp_a


title: WRKY_tnt.WRKY18_colamp_a


title: WRKY_tnt.WRKY15_col_b

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY14_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY15_colamp_a


title: Trihelix_tnt.GT2_col_a

description: A. thaliana Col-0 input DNA library

value: Trihelix


title: Trihelix_tnt.GTL1_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY14_colamp_a


title: Trihelix_tnt.GT3a_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY11_col_a

description: A. thaliana Col-0 input DNA library


title: Trihelix_tnt.GTL1_colamp_a


title: Trihelix_tnt.GT1_col_a

description: A. thaliana Col-0 input DNA library


title: Trihelix_tnt.AT5G05550_colamp_a


title: Trihelix_tnt.AT5G47660_colamp_a


title: Trihelix_tnt.AT5G47660_col_a

description: A. thaliana Col-0 input DNA library


title: Trihelix_tnt.GT2_colamp_a


title: Trihelix_tnt.AT5G05550_col_a

description: A. thaliana Col-0 input DNA library


title: Trihelix_tnt.AT3G25990_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY17_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY17_colamp_a


title: Trihelix_tnt.AT3G10030_col_a

description: A. thaliana Col-0 input DNA library


title: Trihelix_tnt.AT3G25990_colamp_a


title: Trihelix_tnt.AT2G33550_colamp_a


title: Trihelix_tnt.AT1G76880_col_a

description: A. thaliana Col-0 input DNA library


title: Trihelix_tnt.AT3G10030_colamp_a


title: Trihelix_tnt.AT1G76870_col_b

description: A. thaliana Col-0 input DNA library


title: Trihelix_tnt.AT3G58630_colamp_a


title: TCP_tnt.TCP7_col_a

description: A. thaliana Col-0 input DNA library

value: TCP


title: TCP_tnt.TCP24_colamp_a


title: TCP_tnt.TCP20_colamp_a


title: TCP_tnt.TCP16_col_a

description: A. thaliana Col-0 input DNA library


title: TCP_tnt.TCP16_colamp_a


title: TCP_tnt.TCP17_colamp_a


title: TCP_tnt.TCP14_col_b

description: A. thaliana Col-0 input DNA library


title: TCP_tnt.TCP17_col_a

description: A. thaliana Col-0 input DNA library


title: Trihelix_tnt.AT3G58630_col_a

description: A. thaliana Col-0 input DNA library


title: TCP_tnt.TCP1_col_a

description: A. thaliana Col-0 input DNA library


title: TCP_tnt.At5g08330_col_a

description: A. thaliana Col-0 input DNA library


title: WRKY_tnt.WRKY26_col_a

description: A. thaliana Col-0 input DNA library


title: TCP_tnt.PTF1_col_a

description: A. thaliana Col-0 input DNA library


title: TCP_tnt.At2g45680_col_b

description: A. thaliana Col-0 input DNA library


title: TCP_tnt.PTF1_colamp_a


title: TCP_tnt.At5g08330_colamp_a


title: TCP_tnt.At1g69690_col_a

description: A. thaliana Col-0 input DNA library


title: TCP_tnt.At2g45680_colamp_a


title: Trihelix_tnt.AT2G33550_col_a

description: A. thaliana Col-0 input DNA library


title: TCP_tnt.At1g72010_colamp_a


title: TCP_tnt.At1g69690_colamp_a


title: SRS_tnt.SRS7_col_a

description: A. thaliana Col-0 input DNA library

value: SRS


title: TCP_tnt.TCP20_col_a

description: A. thaliana Col-0 input DNA library


title: SBP_tnt.SPL9_col_a

description: A. thaliana Col-0 input DNA library

value: SBP


title: SBP_tnt.SPL5_colamp_a

value: Arabidopsis thaliana


title: SBP_tnt.SPL5_col_a

description: A. thaliana Col-0 input DNA library

value: Halo


title: SRS_tnt.SRS7_colamp_a

value: tnt


title: TCP_tnt.TCP3_colamp_a


title: SBP_tnt.SPL3_col_a

description: A. thaliana Col-0 input DNA library

value: col


title: SBP_tnt.SPL3_colamp_a


title: SBP_tnt.SPL15_colamp_a

value: motif+TFBS


title: SBP_tnt.SPL15_col_a

description: A. thaliana Col-0 input DNA library

value: a


title: SBP_tnt.SPL14_col_a

description: A. thaliana Col-0 input DNA library


title: SBP_tnt.SPL13_col_a

description: A. thaliana Col-0 input DNA library


title: SBP_tnt.SPL11_col100_a

description: A. thaliana Col-0 input DNA library

value: motif


title: SBP_tnt.SPL1_col_a

description: A. thaliana Col-0 input DNA library


title: RWPRK_tnt.RKD2_col_a

description: A. thaliana Col-0 input DNA library

value: RWPRK


title: RWPRK_tnt.RKD2_colamp_a


title: RWPRK_tnt.NLP7_col_a

description: A. thaliana Col-0 input DNA library


title: REMB3_tnt.AT2G31460_col_a

description: A. thaliana Col-0 input DNA library


title: REM_tnt.REM19_colamp_a

value: REM


title: SBP_tnt.SPL1_colamp_a

value: colamp


title: REM_tnt.REM19_col_a

description: A. thaliana Col-0 input DNA library


title: S1Falike_tnt.AT3G09735_col_a

description: A. thaliana Col-0 input DNA library


title: Orphan_tnt.BBX31_col_a

description: A. thaliana Col-0 input DNA library

value: Orphan


title: RAV_tnt.RAV1_colamp_a

value: RAV


title: PLATZ_tnt.AT2G01818_col_a

description: A. thaliana Col-0 input DNA library

value: PLATZ


title: Orphan_tnt.AT1G24250_col_a

description: A. thaliana Col-0 input DNA library


title: SBP_tnt.SPL9_colamp_a


title: ND_tnt.AT1G63040_col_a

description: A. thaliana Col-0 input DNA library

value: ND


title: ND_tnt.ASHR1_col_a

description: A. thaliana Col-0 input DNA library


title: ND_tnt.FRS9_col_a

description: A. thaliana Col-0 input DNA library


title: ND_tnt.AT2G28920_col_a

description: A. thaliana Col-0 input DNA library


title: ND_tnt.FRS9_colamp_a


title: NAC_tnt.VND6_col_v31

description: A. thaliana Col-0 input DNA library

value: NAC


title: NAC_tnt.VND6_colamp_a


title: ND_tnt.AGL95_col_a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.VND3_colamp_a


title: NAC_tnt.VND4_colamp_a


title: NAC_tnt.VND2_colamp_a


title: NAC_tnt.VND2_col_a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.SND2_col_a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.SND2_colamp_a


title: NAC_tnt.NTM1_col_a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.SMB_colamp_a

value: SMB


title: NAC_tnt.SMB_col_a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.SND3_colamp_a


title: NAC_tnt.NST1_col_v31

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.NTM2_col_b

description: A. thaliana Col-0 input DNA library

value: b


title: NAC_tnt.VND1_col_a

description: A. thaliana Col-0 input DNA library

value: Arabidopsis thaliana


title: Orphan_tnt.AT1G23810_col_a

description: A. thaliana Col-0 input DNA library

value: Halo


title: NLP_tnt.AtNLP4_col_b

description: A. thaliana Col-0 input DNA library

value: NLP

value: tnt


title: NAC_tnt.NST1_colamp_a

value: motif+TFBS


title: NAC_tnt.SND3_col_b

description: A. thaliana Col-0 input DNA library

value: col


title: NAC_tnt.NAM_col_v3a

description: A. thaliana Col-0 input DNA library

value: NAM


title: NAC_tnt.NAP_colamp_a

value: NAP

value: a


title: NAC_tnt.NAC2_colamp_a

value: colamp


title: NAC_tnt.CUC3_col_a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.NTM1_colamp_a


title: NAC_tnt.NAP_col_v3a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.NAC2_col_v3a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.CUC3_colamp_a

value: motif


title: NAC_tnt.NAM_colamp_a


title: NAC_tnt.CUC2_colamp_a


title: NAC_tnt.CUC1_col_v31

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.CUC1_colamp_a


title: NAC_tnt.ATAF1_colamp_a


title: NAC_tnt.ATAF1_col_a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.ANAC096_colamp_a


title: NAC_tnt.AT1G19040_col_a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.ANAC103_col_a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.AT3G12910_col_a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.ANAC092_col_v3a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.ANAC103_colamp_a


title: NAC_tnt.ANAC094_col_a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.ANAC092_colamp_a


title: NAC_tnt.ANAC083_col_v3a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.ANAC087_col_v3a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.ANAC087_colamp_a


title: NAC_tnt.ANAC079_colamp_a


title: NAC_tnt.ANAC071_col_a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.ANAC070_colamp_a


title: NAC_tnt.ANAC075_col_a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.ANAC083_colamp_a


title: NAC_tnt.ANAC058_col_a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.ANAC071_colamp_a


title: NAC_tnt.ANAC057_col_a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.ANAC058_colamp_a


title: NAC_tnt.ANAC050_col_v3a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.ANAC062_colamp_a


title: NAC_tnt.ANAC050_colamp_a


title: NAC_tnt.ANAC047_colamp_a


title: NAC_tnt.ANAC046_colamp_a


title: WRKY_tnt.WRKY3_col_a

description: A. thaliana Col-0 input DNA library

value: WRKY


title: NAC_tnt.ANAC045_col_a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.ANAC028_col_a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.ANAC042_col_a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.ANAC016_col_a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.ANAC020_col_v31

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.ANAC038_colamp_a


title: NAC_tnt.ANAC017_colamp_v31


title: NAC_tnt.ANAC005_col_a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.ANAC013_col_a

description: A. thaliana Col-0 input DNA library


title: MYBrelated_tnt.TRP2_col_a

description: A. thaliana Col-0 input DNA library

value: MYBrelated


title: NAC_tnt.ANAC013_colamp_a


title: NAC_tnt.ANAC004_colamp_a


title: NAC_tnt.ANAC057_colamp_a


title: NAC_tnt.ANAC011_col_a

description: A. thaliana Col-0 input DNA library


title: MYBrelated_tnt.TBP3_col_a

description: A. thaliana Col-0 input DNA library


title: MYBrelated_tnt.RVE1_colamp_a


title: MYBrelated_tnt.TBP3_colamp_a


title: MYBrelated_tnt.TRP2_colamp_a


title: NAC_tnt.ANAC053_colamp_a


title: MYBrelated_tnt.RVE1_col_a

description: A. thaliana Col-0 input DNA library


title: MYBrelated_tnt.LHY1_colamp_a


title: NAC_tnt.ANAC045_colamp_a


title: MYBrelated_tnt.At5g58900_col_a

description: A. thaliana Col-0 input DNA library


title: MYBrelated_tnt.At5g58900_colamp_a


title: MYBrelated_tnt.LHY1_col_a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.ANAC016_colamp_a


title: NAC_tnt.ANAC004_col_a

description: A. thaliana Col-0 input DNA library


title: NAC_tnt.ANAC038_col_a

description: A. thaliana Col-0 input DNA library


title: MYBrelated_tnt.At5g52660_col_a

description: A. thaliana Col-0 input DNA library


title: MYBrelated_tnt.At5g47390_col_b

description: A. thaliana Col-0 input DNA library


title: MYBrelated_tnt.At5g47390_colamp_a


title: MYBrelated_tnt.At5g08520_col_b

description: A. thaliana Col-0 input DNA library


title: MYBrelated_tnt.At5g05790_col_a

description: A. thaliana Col-0 input DNA library


title: MYBrelated_tnt.At4g01280_col_a

description: A. thaliana Col-0 input DNA library


title: MYBrelated_tnt.At4g01280_colamp_a


title: MYBrelated_tnt.At3g11280_col_a

description: A. thaliana Col-0 input DNA library


title: MYBrelated_tnt.At3g11280_colamp_a


title: MYBrelated_tnt.LCL1_colamp_a


title: MYBrelated_tnt.At3g09600_col_a

description: A. thaliana Col-0 input DNA library


title: MYBrelated_tnt.At2g38090_col_a

description: A. thaliana Col-0 input DNA library


title: MYBrelated_tnt.At1g74840_col100_a

description: A. thaliana Col-0 input DNA library


title: MYBrelated_tnt.EPR1_colamp_a


title: MYBrelated_tnt.At1g74840_colamp_a


title: MYBrelated_tnt.At1g19000_col_a

description: A. thaliana Col-0 input DNA library


title: MYBrelated_tnt.At1g49010_col_a

description: A. thaliana Col-0 input DNA library


title: MYBrelated_tnt.At1g19000_colamp_a


title: MYBrelated_tnt.At3g09600_colamp_a


title: MYBrelated_tnt.AT5G56840_colamp_a


title: MYBrelated_tnt.AT5G61620_colamp_a


title: MYBrelated_tnt.AT5G61620_col_a

description: A. thaliana Col-0 input DNA library


title: MYBrelated_tnt.At5g08520_colamp_a


title: MYBrelated_tnt.AT4G12670_col_a

description: A. thaliana Col-0 input DNA library


title: MYBrelated_tnt.At1g49010_colamp_a


title: MYBrelated_tnt.AT5G56840_col_a

description: A. thaliana Col-0 input DNA library


title: MYBrelated_tnt.AT3G10580_colamp_a


title: MYBrelated_tnt.AT1G72740_col_a

description: A. thaliana Col-0 input DNA library


title: MYBrelated_tnt.AT4G12670_colamp_a


title: MYBrelated_tnt.AT1G18960_col_a

description: A. thaliana Col-0 input DNA library


title: MYBrelated_tnt.AT3G10113_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB99_col_a

description: A. thaliana Col-0 input DNA library

value: MYB


title: MYBrelated_tnt.AT1G72740_colamp_a


title: MYBrelated_tnt.At5g52660_colamp_a


title: MYB_tnt.MYB96_col_b

description: A. thaliana Col-0 input DNA library


title: MYBrelated_tnt.AT3G10580_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB96_colamp_a


title: MYB_tnt.MYB98_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB94_col_b

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB92_colamp_a


title: MYB_tnt.MYB88_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB93_colamp_a


title: MYB_tnt.MYB92_100ng20cy_b

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB88_colamp_a


title: MYB_tnt.MYB93_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB83_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB83_colamp_a


title: MYB_tnt.MYB81_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB81_colamp_a