title: polyA mRNA RNA-seq from Jurkat clone E61 (ENCLB675DTP)

description:
https://www.encodeproject.org/experiments/ENCSR000BXX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on Jurkat greater than 200bp polyA+
experiment encode accession: ENCSR000BXX
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB675DTP
size range: >200
spikeins used: /references/ENCSR466YMU/

tag: line

value: Jurkat clone E61

value: immortalized cell line

value: T lymphoblastoid derived from an acute T cell leukemia, The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM. - ATCC. (PMID:68013)

value: child

value: 14 year

value: male

value: John Stamatoyannopoulos, UW

tag: health state

value: acute T cell leukemia

tag: link

value: ENCBS407ENC at ENCODE; https://www.encodeproject.org/ENCBS407ENC/

value: Derived from ENCODE donor ENCDO000AAY; https://www.encodeproject.org/ENCDO000AAY/

value: ENCODE dbxrefs Cellosaurus CVCL_0367; http://web.expasy.org/cellosaurus/CVCL_0367

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


title: 60_Wang_input_BWX3690_1mMIPTG_20m

status: Public on Feb 03 2017

type: SRA

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

country: USA

institute: Indiana University at Bloomington

description: Sample 60

library_source: genomic

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Hi-C, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts. For ChIP-seq, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Bacillus subtilis (PY79) genome was divided into restriction fragments (2398 HindIII fragments). Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genome of Bacillus subtilis (PY79) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Genome_build: NC_022898.1
Supplementary_files_format_and_content: *.matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices (i.e. normalized Hi-C interaction scores) with 10kb bins of B. subtilis genome.
Supplementary_files_format_and_content: *.csv: comma-separated values files of ChIP-seq results; number of reads at each genome position

molecule: genomic DNA

organism: Bacillus subtilis PY79

growth_protocol: Bacillus subtilis strains were derived from the prototrophic strain PY79 (Youngman et al 1983, PMID: 6300908). Cells were grown in defined rich medium (CH) (Harwood and Cutting 1990, Molecular Biological Methods for Bacillus) at specified temperature.

extract_protocol:
Hi-C experiments were performed using HindIII according to previous publications (Le et al, 2013, PMID: 24158908; Wang et al 2015, PMID: 26253537). ChIP-seq experiments were performed using anti-SMC, anti-ScpA, anti-ScpB, anti-ParB or anti-GFP antibodies according to previous publication (Graham et al 2014, PMID: 24829297).
the antibody information:
*anti-**SMC: Lindow et al., 2002: Mol Microbiol 46, 997-1009.
*anti-**ParB: Lin et al., 1997: Proc Natl Acad Sci U S A 94, 4721-4726.
*anti-GFP: Rudner et al., 1999: Proc Natl Acad Sci U S A 96, 14765-14770.
*anti-ScpA and anti-ScpB: generated in this study. Procedure described in Experimental Procedures.
Standard library construction protocol was used for Illumina Hiseq2500 sequencing platform (Hi-C) or Illumina Miseq (ChIP-seq). Illumina Truseq indexes were used.

treatment_protocol: Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 20 min, fixed by 3% formaldehyde for 30min at room temperature

tag: sample group

value: CH, 37˚C, 1mM IPTG for 20 min

tag: strain info.

value: parS∆9 no a.b., -94˚ parS no a.b., amyE::Pspank (natRBS) gfp-smc (spec)

tag: chip antibody

value: none (input)


title: LOUCY_DMSO_48h_rep1

city: Gent

first: Sofie

last: Peirs

address: De Pintelaan 185

country: Belgium

institute: Ghent University

description: RNA-sequencing of LOUCY cells treated with DMSO for 48h

library_source: transcriptomic

data_processing:
basecalling with bcl2fastq
Alignment and gene quantification on Gencode_v23 were done with STAR v2.4.2a.
DESeq2 was used for differential expression analisis, using a multifactorial design
Genome_build: hg38
Supplementary_files_format_and_content: STAR raw count data, tdt

molecule: total RNA

organism: Homo sapiens

source_name: LOUCY cells

growth_protocol: Cells were seeded at 0.7 x 10^6 cells/ml. Cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 100 U/ml penicillin, 100 µg/ml streptomycin, 100 µg/ml kanamycin sulfate and 2 mM L-glutamine at 37°C with 5% CO2.

extract_protocol:
RNA was isolated using the miRNeasy mini kit (Qiagen) with on-column DNase digestion. The RNA quality was checked by the Experion RNA StdSens analysis kit (Bio-Rad).
For each sample, 1µg of input material (measured with Ribogreen (Invitrogen)) was used. Libraries were constructed with the Truseq stranded mRNA protocol on the IP-star robot. During the library prep, mRNA was isolated via poly-A capture and cDNA was generated. Next, fragmentation, A-tailing, adaptor ligation and a PCR (13 cycli) were performed on them. The libraries were on average 300bp long. As quality control of the library, analysis on a bioanalyzer chip and a qPCR were done. Libraries were equimolary pooled and 2.4pM of this pool was loaded on the Nextseq500, SR75.

treatment_protocol: Cells were treated with DMSO or 100nM GSK2879552 for 48h

tag: type

value: T-ALL

tag: gender

value: female

tag: treatment

value: DMSO


title: LOUCY_DMSO_48h_rep2


title: 57_Wang_input_BWX3690_0IPTG

description: Sample 57

treatment_protocol: Cells were growing in CH medium at 37˚C, fixed by 3% formaldehyde for 30min at room temperature

value: CH, 37˚C, no IPTG


title: GL261p33

city: Geneva

first: Natacha

last: Civic

address: Rue Michel-Servet 1

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

data_processing:
Illumina Casava1.8.4 software was used for basecalling.
The reads were mapped using TopHat v.2 to the UCSC mm10 genome reference.
The gene features were counted with HTSeq v0.5.3p9 (htseq-count). Normalization and differential expression analysis was performed with the statistical analysis R/Bioconductor package edgeR v. 3.4.2
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab delimited text files with normalized counts and differentially expressed genes with a fold change threshold of 2 and a FDR 5% correction

organism: Mus musculus

source_name: Glioma

growth_protocol: GL261 and U251 GSC cells were grown in Dulbecco's modified Eagle's medium (DMEM) (Gibco) with 10% fetal bovine serum (FBS) (Gibco) and supplements (100 U/ml penicillin G (Sigma-Aldrich), 100 µg/ml streptomycin sulfate (Sigma-Aldrich), 6mM hepes (Applichem), 1.6 mM L-glutamine (Sigma-Aldrich), 50 µM β-mercaptoethanol (Biorad). NSU251 and mNS cells were cultured in neurosphere medium (DMEM/F12) medium supplemented with, 100 U/ml penicillin G, 100 µg/ml streptomycin sulfate, 6mM hepes, 1.6 mM L-glutamine, 50 µM β-mercaptoethanol, B-27 supplement (Invitrogen), 20 ng/mL recombinant basic fibroblast growth factor (basic-FGF) (Invitrogen,) and 20 ng/ml recombinant epidermal growth factor (EGF) (Invitrogen) and 50 U/ml heparin (Sigma). Cells in log phase were harvested at different passage for RNA isolation.

extract_protocol:
Total RNA were isolated from GL261 and mNS using Trizol (Invitrogen) according to the manufacturer's instructions.
The libraries were prepared with the Illumina TruSeq Stranded Total RNA kit according to the Illumina standard protocol.

tag: cell type

value: glioma differentiated cells (GDC)

tag: passages


title: GL261p17


title: TG39_DMSO_rep3

description: RNA-sequencing of P53/R26-Zeb2tg/tg TG39 cells treated with DMSO for 24h

data_processing:
base calling with Casava 1.8
read alignment and gene quantification on ENSG were performed with STAR v2.4.2a
DESeq2 was used for differential expression analisis using a multifactorial design
Genome_build: GRCm38
Supplementary_files_format_and_content: STAR raw count data, tdt

source_name: thymoma primary T-ALL culture

growth_protocol: mouse T-ALL cells were seeded at 0.5 x 10^6 cells/ml. Cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 100 U/ml penicillin, 100 µg/ml streptomycin and 2 mM L-glutamine at 37°C with 5% CO2.

extract_protocol:
RNA was isolated using the RNeasy Plus mini kit (Qiagen).
polyA Illumina Stranded Sample prep

treatment_protocol: Cells were treated with DMSO or 100nM GSK2879552 for 24h


title: 56_Wang_input_BWX3383

description: Sample 56

value: CH, 37˚C

value: parS∆9 no a.b., -153˚ parS (loxP-kan-loxP)


title: TG39_DMSO_rep2


title: polyA mRNA RNA-seq from lung (ENCLB271PTR)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR870AQU/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA-seq of mouse lung tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR870AQU
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB271PTR
size range: 350-450

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

source_name: Mus musculus strain C57BL/6J lung tissue female adult (10 weeks)

extract_protocol:
general protocol: https://www.encodeproject.org/documents/6f6a5d8c-0b06-4457-bfbb-ee4944eab1d6/@@download/attachment/wgEncodeSydhRnaSeq.release2.html.pdf
extraction method: RNeasy Lipid Tissue Mini Kit (QIAGEN cat#74804)

value: lung

value: tissue

tag: biosample encode accession

tag: dev stage

value: adult

tag: age

value: 10 week

tag: Sex

tag: lab

value: Michael Snyder, Stanford

value: ENCBS964PGO at ENCODE; https://www.encodeproject.org/ENCBS964PGO/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: polyA mRNA RNA-seq from spleen (ENCLB726TJR)

description:
https://www.encodeproject.org/experiments/ENCSR966JPL/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA-seq of mouse spleen tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR966JPL
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2015-01-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB726TJR
size range: 350-450

source_name: Mus musculus strain C57BL/6J spleen tissue male adult (10 weeks)

value: spleen

value: male

value: ENCBS614NNG at ENCODE; https://www.encodeproject.org/ENCBS614NNG/


title: polyA mRNA RNA-seq from kidney (ENCLB821KIP)

description:
https://www.encodeproject.org/experiments/ENCSR394YLM/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA-seq of mouse kidney tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR394YLM
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB821KIP
size range: 350-450

source_name: Mus musculus strain C57BL/6J kidney tissue female adult (10 weeks)

value: kidney

value: ENCBS618GAD at ENCODE; https://www.encodeproject.org/ENCBS618GAD/


title: polyA mRNA RNA-seq from brain (ENCLB532QIL)

description:
https://www.encodeproject.org/experiments/ENCSR554PHF/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA-seq of mouse brain tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR554PHF
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2015-01-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB532QIL
size range: 350-450

source_name: Mus musculus strain C57BL/6J brain tissue male adult (10 weeks)

value: brain

value: ENCBS693QXI at ENCODE; https://www.encodeproject.org/ENCBS693QXI/


title: polyA mRNA RNA-seq from sigmoid colon (ENCLB290LAC)

description:
https://www.encodeproject.org/experiments/ENCSR518GDK/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA-seq of mouse sigmoid colon tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR518GDK
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB290LAC
size range: 350-450

source_name: Mus musculus strain C57BL/6J sigmoid colon tissue female adult (10 weeks)

value: sigmoid colon

value: female

value: ENCBS400IVQ at ENCODE; https://www.encodeproject.org/ENCBS400IVQ/


title: polyA mRNA RNA-seq from adrenal gland (ENCLB053GTI)

description:
https://www.encodeproject.org/experiments/ENCSR713OCQ/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA-seq of mouse adrenal gland tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR713OCQ
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB053GTI
size range: 350-450

source_name: Mus musculus strain C57BL/6J adrenal gland tissue female adult (10 weeks)

value: adrenal gland

value: ENCBS816ZVY at ENCODE; https://www.encodeproject.org/ENCBS816ZVY/


title: TG39_DMSO_rep1

value: T-ALL

value: DMSO


title: WT5246_LSD1_rep3

description: RNA-sequencing of P53/R26+/+ WT5246 cells treated with 100nM GSK2879552 for 24h


title: 55_Wang_input_BWX3381

description: Sample 55

value: CH, 37˚C

value: parS∆9 no a.b., -117˚ parS (loxP-kan-loxP)

value: none (input)


title: 53_Wang_input_BWX3377

description: Sample 53

value: parS∆9 no a.b., -59˚ parS (loxP-kan-loxP)


title: WT5246_LSD1_rep2


title: 54_Wang_input_BWX3270

description: Sample 54

value: parS∆9 no a.b., -94˚ parS no a.b.


title: polyA mRNA RNA-seq from testis (ENCLB732YZU)

description:
https://www.encodeproject.org/experiments/ENCSR266ESZ/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA-seq of mouse testis tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR266ESZ
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB732YZU
size range: 350-450

source_name: Mus musculus strain C57BL/6J testis tissue male adult (10 weeks)

value: testis

value: tissue

value: adult

value: 10 week

value: male

value: Michael Snyder, Stanford

value: ENCBS928FOT at ENCODE; https://www.encodeproject.org/ENCBS928FOT/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: polyA mRNA RNA-seq from pancreas (ENCLB093WCA)

description:
https://www.encodeproject.org/experiments/ENCSR248XKS/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA-seq of mouse pancreas tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR248XKS
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2015-01-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB093WCA
size range: 350-450

source_name: Mus musculus strain C57BL/6J pancreas tissue female adult (10 weeks)

value: pancreas

value: female

value: ENCBS508NKR at ENCODE; https://www.encodeproject.org/ENCBS508NKR/


title: polyA mRNA RNA-seq from adipose tissue (ENCLB096OMT)

description:
https://www.encodeproject.org/experiments/ENCSR288TLO/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA-seq of mouse adipose tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR288TLO
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB096OMT
size range: 350-450

source_name: Mus musculus strain C57BL/6J adipose tissue male adult (10 weeks)

value: adipose tissue

value: ENCBS298QDT at ENCODE; https://www.encodeproject.org/ENCBS298QDT/


title: 52_Wang_input_BWX3352_1mMIPTG_25m

description: Sample 52

treatment_protocol: Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 25 min, fixed by 3% formaldehyde for 30min at room temperature

value: CH, 37˚C, 1mM IPTG for 25 min

value: parS∆9 no a.b., ∆spo0J (remains wt parS at -1˚)::spec, yvbJ::Pspank (optRBS) gfp-spo0J(∆parS) (cat)


title: WT5246_LSD1_rep1

value: T-ALL


title: polyA mRNA RNA-seq from small intestine (ENCLB063VIY)

description:
https://www.encodeproject.org/experiments/ENCSR170SVO/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA-seq of mouse small intestine tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR170SVO
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB063VIY
size range: 350-450

source_name: Mus musculus strain C57BL/6J small intestine tissue female adult (10 weeks)

value: small intestine

value: ENCBS443BDC at ENCODE; https://www.encodeproject.org/ENCBS443BDC/


title: WT5246_DMSO_rep3

description: RNA-sequencing of P53/R26+/+ WT5246 cells treated with DMSO for 24h

value: DMSO


title: 51_Wang_input_BWX3352_1mMIPTG_20m

description: Sample 51

value: CH, 37˚C, 1mM IPTG for 20 min

value: none (input)


title: polyA mRNA RNA-seq from heart (ENCLB780BEM)

description:
https://www.encodeproject.org/experiments/ENCSR164BAZ/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA-seq of mouse heart tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR164BAZ
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB780BEM
size range: 350-450

source_name: Mus musculus strain C57BL/6J heart tissue female adult (10 weeks)

value: heart

value: tissue

value: adult

value: 10 week

value: ENCBS183QIH at ENCODE; https://www.encodeproject.org/ENCBS183QIH/


title: WT5246_DMSO_rep2


title: 49_Wang_input_BWX3352_0IPTG

description: Sample 49

value: CH, 37˚C, no IPTG


title: Ring1b-I53A.rep1 [5C]

city: Boston

first: Sharmistha

last: Kundu

state: MA

address: 185 Cambridge St

institute: Massachusetts General Hospital

data_processing:
Library strategy: 5C-seq
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference primer sequence pool using BWA
Top and Bottom Count Primers were removed and primer interactions were normalized using matrix balancing
Supplementary_files_format_and_content: Primer Interaction Frequency text file. 5C primer pairs and normalized interaction frequency

source_name: Illingworth et al., 2015

growth_protocol: ESC were grown in media containing LIF and fetal bovine serum on mitomycin-C inactivated MEF feeder layers. Neural progenitors (NPC) were derived by in vitro differentiation from J1 ESC and maintained using previously described methods (Pollard et al., 2006)

extract_protocol:
5x107 cells were crosslinked for 10 min in 1% formaldehyde. 3C and 5C templates were prepared as described (van Berkum and Dekker, 2009). 5C primers were designed using an alternating primer scheme for available HindIII restriction sites that passed threshold criteria, using my5Csuite primer design tools (Lajoie et al., 2009)
Purified DNA fragments were end repaired, A-tailed, ligated to Illumina adapters and amplified using Illumina barcoded primers.

treatment_protocol: ESC were depleted of feeder cells prior to use in experiments.

tag: genotype/variation


title: Ezh2-KO.rep2 [5C]

source_name: Shen et al., 2008


title: WT5246_DMSO_rep1


title: Ezh2-KO.rep1 [5C]


title: Kdm2b-KO.rep2 [5C]

source_name: Boulard et al., 2015


title: 48_Wang_ChIPGFP_BDR1841

description: Sample 48

value: CH, 37˚C

value: rpoC-gfp (spec)

value: anti-GFP antibodies


title: Phc1-KO.rep2 [5C]

source_name: derived from J1 ESC


title: Kdm2b-KO.rep1 [5C]


title: Ring1b-KO.rep2 [5C]

source_name: Eskeland et al., 2010


title: WT1_DMSO_rep3

description: RNA-sequencing of P53/R26+/+ WT1 cells treated with DMSO for 24h

source_name: thymoma primary T-ALL culture


title: 47_Wang_ChIPGFP_BWX3690_1mMIPTG_25m

description: Sample 47

value: CH, 37˚C, 1mM IPTG for 25 min

value: parS∆9 no a.b., -94˚ parS no a.b., amyE::Pspank (natRBS) gfp-smc (spec)


title: NPC.rep1 [5C]

value: NPC


title: 45_Wang_ChIPGFP_BWX3690_1mMIPTG_15m

description: Sample 45

treatment_protocol: Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 15 min, fixed by 3% formaldehyde for 30min at room temperature

value: CH, 37˚C, 1mM IPTG for 15 min


title: WT1_LSD1i_rep2

description: RNA-sequencing of P53/R26+/+ WT1 cells treated with 100nM GSK2879552 for 24h

value: T-ALL


title: Ring1b-KO.rep1 [5C]


title: 46_Wang_ChIPGFP_BWX3690_1mMIPTG_20m

description: Sample 46


title: Ring1b-I53A.rep2 [5C]


title: WT1_LSD1i_rep1


title: ESC.rep1 [5C]

source_name: J1 ESC

value: ESC


title: NPC.rep2 [5C]


title: 50_Wang_input_BWX3352_1mMIPTG_15m

description: Sample 50

value: parS∆9 no a.b., ∆spo0J (remains wt parS at -1˚)::spec, yvbJ::Pspank (optRBS) gfp-spo0J(∆parS) (cat)


title: ESC.rep2 [5C]


title: polyA mRNA RNA-seq from liver (ENCLB868QQG)

description:
https://www.encodeproject.org/experiments/ENCSR216KLZ/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA-seq of mouse liver tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR216KLZ
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB868QQG
size range: 350-450

source_name: Mus musculus strain C57BL/6J liver tissue female adult (10 weeks)

value: liver

value: female

value: Michael Snyder, Stanford

value: ENCBS391ULH at ENCODE; https://www.encodeproject.org/ENCBS391ULH/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: 44_Wang_ChIPGFP_BWX3690_1mMIPTG_10m

description: Sample 44

treatment_protocol: Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 10 min, fixed by 3% formaldehyde for 30min at room temperature

value: CH, 37˚C, 1mM IPTG for 10 min


title: Phc1-KO.rep1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome mm9 using STAR
Transcript abundance was calculated using Htseq
Genome_build: mm9

extract_protocol:
Total RNA was isolated from two biological replicates of each cell type using TRIzol (Invitrogen), and DNase treated. rRNA was depleted using Ribo-Zero Gold kit (Illumina). Second strand synthesis was done using TruSeq RNA library prep kit (Illumina).
Purified DNA fragments were end repaired, A-tailed, ligated to Illumina adapters and amplified using Illumina barcoded primers.

tag: strain

tag: genotype


title: Phc1-KO.rep1 [5C]


title: NPC.rep1

value: wild type


title: 43_Wang_ChIPGFP_BWX3690_0IPTG

description: Sample 43

value: CH, 37˚C, no IPTG


title: NPC.rep2


title: WT1_DMSO_rep1

value: DMSO


title: Phc1-KO.rep2


title: 42_Wang_ChIPSMC_BWX3690_0IPTG

description: Sample 42

value: anti-SMC antibodies


title: 19_Wang_HiC_BWX3352_1mMIPTG_20m_0m

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Hi-C, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts. For ChIP-seq, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Bacillus subtilis (PY79) genome was divided into restriction fragments (2398 HindIII fragments). Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genome of Bacillus subtilis (PY79) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Genome_build: NC_022898.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv: comma-separated values files of ChIP-seq results.

source_name: Bacillus subtilis PY79

extract_protocol:
Hi-C experiments were performed using HindIII according to previous publications (Le et al, 2013, PMID: 24158908; Wang et al 2015, PMID: 26253537). ChIP-seq experiments were performed using anti-SMC, anti-ScpA, anti-ScpB, anti-ParB or anti-GFP antibodies according to previous publication (Graham et al 2014, PMID: 24829297).
Standard library construction protocol was used for Illumina Hiseq2500 sequencing platform (Hi-C) or Illumina Miseq (ChIP-seq). Illumina Truseq indexes were used.

value: CH, 37˚C, 1mM IPTG for 20 min

tag: restriction enzyme

value: HindIII


title: 41_Wang_ChIPScpB_BWX3383

description: Sample 41

tag: sample group

value: CH, 37˚C

value: parS∆9 no a.b., -153˚ parS (loxP-kan-loxP)

value: anti-ScpB antibodies


title: ESC.rep2

value: ESC


title: WT1_LSD1i_rep3

value: T-ALL


title: NPC2 Input DNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome mm9 using BWA
Wig files were generated by SPP
Genome_build: mm9

extract_protocol:
Cells were crosslinked for 10 mi in 1% formaldehyde at room temperature and quenched with 125mM Glycine. ChIP was performed as previously described (Carey et al., 2009), with minor modifications.
Purified DNA fragments were end repaired, A-tailed, ligated to Illumina adapters and amplified using Illumina barcoded primers.

value: NPC


title: ESC.rep1


title: 39_Wang_ChIPParB_BWX3383

description: Sample 39

tag: strain info.

value: anti-ParB antibodies


title: NPC1 Input DNA

tag: chip antibody


title: 40_Wang_ChIPScpA_BWX3383

description: Sample 40

value: anti-ScpA antibodies


title: NPC H3K27me3 ChIP


title: 25_Wang_HiC_BWX3596_1mMIPTG_25min

description: Sample 25

value: CH, 37˚C, 1mM IPTG for 25 min

value: parS∆9 no a.b., +26˚ parS (loxP-kan-loxP), ∆spo0J (∆parS)::loxP-spec-loxP, yvbJ::Pspank (optRBS) gfp-spo0J (∆parS) (cat)


title: 24_Wang_HiC_BWX3596_1mMIPTG_20min

description: Sample 24


title: 27_Wang_HiC_BWX3596_1mMIPTG_35min

description: Sample 27

treatment_protocol: Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 35 min, fixed by 3% formaldehyde for 30min at room temperature

value: CH, 37˚C, 1mM IPTG for 35 min


title: ESC1 Input DNA


title: 38_Wang_ChIPParB_BWX3381

description: Sample 38

value: parS∆9 no a.b., -117˚ parS (loxP-kan-loxP)


title: WT1_DMSO_rep2

tag: type


title: 26_Wang_HiC_BWX3596_1mMIPTG_30min

description: Sample 26

treatment_protocol: Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 30 min, fixed by 3% formaldehyde for 30min at room temperature

value: CH, 37˚C, 1mM IPTG for 30 min


title: NPC Ezh2 ChIP


title: NPC Cbx2 ChIP


title: 36_Wang_ChIPParB_BWX3377

description: Sample 36

value: parS∆9 no a.b., -59˚ parS (loxP-kan-loxP)


title: 23_Wang_HiC_BWX3596_1mMIPTG_15min

description: Sample 23

value: CH, 37˚C, 1mM IPTG for 15 min


title: 37_Wang_ChIPParB_BWX3270

description: Sample 37

value: parS∆9 no a.b., -94˚ parS no a.b.


title: 22_Wang_HiC_BWX3596_0IPTG

description: Sample 22

value: CH, 37˚C, no IPTG

value: HindIII


title: 35_Wang_ChIPSMC_BWX3383

description: Sample 35

value: CH, 37˚C

value: parS∆9 no a.b., -153˚ parS (loxP-kan-loxP)

value: anti-SMC antibodies


title: ESC H3K27me3 ChIP

value: ESC


title: 21_Wang_HiC_BWX3352_1mMIPTG_20m_15mrif

description: Sample 21

treatment_protocol: Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 20 min, then rifampicin was added to 25ug/ml final concentration for 15 min, fixed by 3% formaldehyde for 30min at room temperature

value: CH, 37˚C, 1mM IPTG for 20 min, then 15 min with 25ug/ul rifampicin

value: parS∆9 no a.b., ∆spo0J (remains wt parS at -1˚)::spec, yvbJ::Pspank (optRBS) gfp-spo0J(∆parS) (cat)


title: ESC2 Input DNA


title: NPC H2AUb ChIP

value: NPC


title: 34_Wang_ChIPSMC_BWX3381

description: Sample 34


title: ESC Cbx2 ChIP


title: ESC Cbx7 ChIP


title: 20_Wang_HiC_BWX3352_1mMIPTG_20m_15m

description: Sample 20

treatment_protocol: Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 20 min, then another 15 min, fixed by 3% formaldehyde for 30min at room temperature

value: CH, 37˚C, 1mM IPTG for 20 min, then 15 min


title: 33_Wang_ChIPSMC_BWX3270

description: Sample 33


title: Untreated-day5

city: Naples

first: Cristina

last: D'Aniello

address: Via Pietro Castellino, 111

country: Italy

institute: IGB-CNR

data_processing:
Illumina casava base calling
FASTQ files were mapped against mm9 with BSMAP v2.88 using the parameters -R -v 0.1 -u -n 1 -s 12 -w 100 -D C-CGG -q 2. We extracted methylation levels per individual C as #C/(#C+#T) with methratio.py from BSMAP v2.88 using the parameters -z -u -g. For further analysis we filtered CGs to have a minimum sequencing depth of 10X.
Genome_build: mm9
Supplementary_files_format_and_content: Bed file containing Cytosine methylation levels and coverage per each CpG

source_name: ESCs

growth_protocol: ESCs were plated at low density in FBS/LIF + VitaminC (500 μM), L-Proline (1 mM) or untreated as control, for 2 and 5 days.

extract_protocol:
DNA was isolated using the WizardR Genomic DNA Purification kit (Promega)
RRBS libraries were prepared for sequencing using standard Illumina protocols

value: Embryonic stem cells


title: ESC Ring1b ChIP


title: Untreated-day2


title: 32_Wang_ChIPSMC_BWX3377

description: Sample 32


title: 18_Wang_HiC_BWX3403_30m_rif

description: Sample 18

treatment_protocol: Cells were growing in CH medium at 37˚C, rifampicin was added to 25ug/ml final concentration for 30 min, fixed by 3% formaldehyde for 30min at room temperature

value: CH, 37˚C, 25ug/ml rifampicin for 30 min

value: parS∆9 no a.b., +26˚ parS (loxP-kan-loxP)


title: NPC Cbx8 ChIP


title: 17_Wang_HiC_BWX3403_10m_rif

description: Sample 17

treatment_protocol: Cells were growing in CH medium at 37˚C, rifampicin was added to 25ug/ml final concentration for 10 min, fixed by 3% formaldehyde for 30min at room temperature

value: CH, 37˚C, 25ug/ml rifampicin for 10 min


title: VitC-day5


title: 16_Wang_HiC_BWX3403

description: Sample 16


title: ESC Ezh2 ChIP


title: VitC-day2


title: NPC Ring1b ChIP


title: 30_Wang_ChIPSMC_BWX3352_1mMIPTG_20m

description: Sample 30

value: CH, 37˚C, 1mM IPTG for 20 min


title: k562_GAL4_t0

city: SAN FRANCISCO

first: John

last: Liu

state: California

address: 35 Medical Center Way

institute: UCSF

description: processed data file: rnaseq_tpm.txt

data_processing:
RNA-seq: Reads were aligned to the human genome (GRCh37) using the spliced read aligner HISAT2 v2.0.3 against an index containing SNP and transcript information (genome_snp_tran). Quantification of Ensembl build 75 genes was carried out with featureCounts using only uniquely mapped reads.
ChIP-seq: Reads were aligned to the human genome (GRCh37) using bowtie v2.2.8. Enrichment at promoter regions, which were defined as +/- 1kb of each TSS and generated from Ensembl GRCh37 build 75, were quantified using featureCounts v1.5.0-p2.
Genome_build: GRCh37

molecule: polyA RNA

growth_protocol: Cells were infected for 48 hr, followed by 2 d puromycin treatment (3 μg/mL) and 2 d recovery

extract_protocol:
DirectZol RNA
TruSeq HT Stranded mRNA

tag: sgrna infected


title: 15_Wang_HiC_BWX3268

description: Sample 15

value: parS∆9 no a.b., -27˚ parS no a.b.


title: ESC H2AUb ChIP


title: 29_Wang_ChIPSMC_BWX3352_1mMIPTG_15m

description: Sample 29

value: CH, 37˚C, 1mM IPTG for 15 min


title: L-Prolin-day5


title: 11_Wang_HiC_BWX3383

description: Sample 11


title: L-Prolin-day2


title: 28_Wang_ChIPSMC_BWX3352_0IPTG

description: Sample 28

value: CH, 37˚C, no IPTG


title: 10_Wang_HiC_BWX3381

description: Sample 10

value: parS∆9 no a.b., -117˚ parS (loxP-kan-loxP)

value: HindIII


title: ESC Phc1 ChIP


title: 09_Wang_HiC_BWX3270

description: Sample 09

value: CH, 37˚C

value: parS∆9 no a.b., -94˚ parS no a.b.


title: L-Prolin-VitC-day2


title: 31_Wang_ChIPSMC_BWX3352_1mMIPTG_25m

description: Sample 31

value: CH, 37˚C, 1mM IPTG for 25 min

value: anti-SMC antibodies


title: F/A_d5

description: Sample 4

data_processing:
Illumina casava base calling
Sequenced reads were mapped to mm9 whole genome using TopHat v 2.0.13 using the annotation file (Mus musculus NCBIM37 release 67) as guide (parameter -G). All the other parameters are set as default.
raw counts have been obtained using HTSeq  (version 0.6.1p1) on intersection-nonempty mode
individual raw count were comnined in a single table of counts and underwent to upper quantile normalization and proportional test filtering
normalization of combined raw counts, filtering and the analysis of differentially expressed genes was performad using RNAseqGUI
Genome_build: mm9
Supplementary_files_format_and_content: bam format was used for the read alignments, tab delimited (txt) for the raw counts

source_name: embryonic stem cells (ESC)

growth_protocol: mir-290_mCherry/mir-302_eGFP dual reporter ESCs (DRESCs) were cultured in serum/LIF + VitaminC (100 μM). L-Pro-treated cells were generated from ESCs plated at low density, in serum/LIF + L-Pro (1 mM) for 5 days. F/A-EpiSCs were generated from ESCs, seeded at low density in N2B27 supplemented with Activin A (20 ng/ml, Invitrogen) and bFGF and cultured for 3 and 5 days.

extract_protocol:
Total RNAs were isolated using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell population

value: mCherry+/eGFP+ (yellow)


title: 08_Wang_HiC_BWX3377

description: Sample 08

value: parS∆9 no a.b., -59˚ parS (loxP-kan-loxP)


title: Pool7_Plasmid

city: Cambridge

first: Sharon

middle: R

last: Grossman

address: 415 Main Street

institute: Broad Institute

description:
fastq of 3' UTR barcode and residual 5' flanking sequencing
processed data file: Pool7_MPRA.txt

data_processing:
Perfect UTR barcode matches were assigned to their respective oligo. Counts for all barcodes assigned to an oligo were summed.
Read counts in RNA and Plasmid libraries summed across all barcodes corresponding to each oligo
Genome_build: mm9

organism: synthetic construct

source_name: plasmid DNA

growth_protocol: 3T3-L1 pre-adipocytes were maintained in DMEM supplemented with 10% calf serum. Two days after confluence, the cells were induced with DMEM supplemented with 10% FBS, 1uM dexamethasone, 1.7uM insulin, and 0.5mM 3-isobutyl-1-methylxanthine (IBMX). 48h later, the medium was replaced with DMEM supplemented with 10% FBS and the cells were fed every two days.

extract_protocol: MPRA libraries were prepared as described by Melnikov et al. (Nat Biotechnol 2012 Feb 26;30(3):271-7. PMID: 22371084)

tag: cell line

value: Plasmid DNA

tag: molecule subtype

value: plasmid DNA


title: LY reactivated SCGs + IFNb, replicate 3

city: New York

first: Mariko

last: Kobayashi

state: NY

address: 1230 York Avenue

department: Molecular Neuro-Oncology

institute: Rockefeller University

data_processing:
Sequencing reads were aligned using the STAR aligner (v2.5.0a) to the Rnor 6.0 genome (Dobin et al., 2013).
Reads were quantified using  featureCounts v1.4.3-p1  (Liao et al., 2014).
Difference analysis of gene expression changes was carried out in R (www.r-project.org; [Ihaka and Gentleman, 1996]) using Bioconductor (Gentleman et al., 2004) and the package edgeR (Robinson and Oshlack, 2010) applying generalized linear model methods to account for biological variation across replicates (McCarthy et al., 2012)
Genome_build: rn6
Supplementary_files_format_and_content: count files of expressed genes used for each pairwise difference analysis, filtered for lowly expressed genes
Supplementary_files_format_and_content: glmEdgeR output files with associated gene name, gene length, and description for pairwise analysis (Reactivated with IFNb; LY+IFNb vs. LY) and (Reactivated with IFNg; LY+IFNg vs. LY)

organism: Rattus norvegicus

source_name: SCG cultures DIV 13-15, harboring reactivating HSV-1

growth_protocol: Superior cervical ganglia (SCG) neurons isolated from E21 Sprague-Dawley rat pups, cultured in neurobasal medium supplemented with NGF (50 ng/ml) and with aphidicolin (5 mM) and 5-fluorouracil (20 mM) to eliminate proliferating cells.  On DIV 5-6, acyclovir (50 mM) was added and 24h later infected with Patton strain HSV-1 EGFP-Us11 at MOI=1.  The virus was removed after 2h and the neurons maintained in culture with ACV until reactivation.

extract_protocol:
total RNA was extracted using Trizol reagent, precipitated with ethanol, DNase-treated, phenol-chloroform extracted, precipitated once more with ethanol and yields determined by absorption spectroscopy using a NanoDrop (NanoDrop Products).
RNA-seq libraries were generated following Illumina TruSeq protocols to remove rRNA using Ribo-Zero, fragmentation, and adaptor ligation.

treatment_protocol: On DIV 12-14, (6-7 days after HSV-1 infection), ACV was removed and cultures were reactivated with LY294002 (20 μM) for 20 h, in presence or absence of IFNβ or IFNγ (100U/ml).

value: Sprague-Dawley

tag: tissue

value: superior cervical ganglia

tag: reactivation condition

value: DIV 13-15 SCG cultures reactivated with LY294002 for 20h

tag: ifn type

value: IFNbeta


title: LY reactivated SCGs, replicate 3

tag: age

value: no IFN


title: LY reactivated SCGs + IFNg, replicate 2

value: IFNgamma


title: F/A_d3

description: Sample 3


title: polyA mRNA RNA-seq from Ishikawa (ENCLB990TKY)

description:
https://www.encodeproject.org/experiments/ENCSR000BYB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on ECC-1 greater than 200bp polyA+ treated with estradiol at 10nM for 4 hours. Note- This experiment previously referred to its biosample as ECC-1, however it has been found that all currently available ECC-1 are actually Ishikawa cells.
experiment encode accession: ENCSR000BYB
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB990TKY
size range: >200
spikeins used: /references/ENCSR466YMU/

source_name: Homo sapiens Ishikawa immortalized cell line treated with 10 nM estradiol for 4 hours

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0f926b2b-f4ce-402a-b936-884770ed81d1/@@download/attachment/wgEncodeHaibRnaSeq.html.pdf

tag: line

value: Ishikawa

value: immortalized cell line

tag: description

value: Endometrial adenocarcinoma Note:This cell line was previously mis-identified as ECC-1 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3432677/).

tag: biosample encode accession

tag: dev stage

value: adult

value: 39 year

tag: Sex

value: female

tag: lab

value: Richard Myers, HAIB

tag: health state

value: endometrial adenocarcinoma

tag: treatments

value: treatment_term_id:CHEBI:23965; treatment_term_name:estradiol; treatment_type:chemical; duration:4; duration_units:hour; UCSC-ENCODE-cv:Estradiol_10nM_4hr;

tag: link

value: ENCBS222DWG at ENCODE; https://www.encodeproject.org/ENCBS222DWG/

value: Derived from ENCODE donor ENCDO000ACV; https://www.encodeproject.org/ENCDO000ACV/

value: ENCODE dbxrefs Cellosaurus CVCL_7260; http://web.expasy.org/cellosaurus/CVCL_7260

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


title: Pool6_Plasmid

description:
fastq of 3' UTR barcode and residual 5' flanking sequencing
processed data file: Pool6_MPRA.txt

value: Plasmid DNA

value: plasmid DNA


title: Pool5_Plasmid

description:
fastq of 3' UTR barcode and residual 5' flanking sequencing
processed data file: Pool5_MPRA.txt


title: LY reactivated SCGs + IFNb, replicate 2

tag: strain

value: Sprague-Dawley

value: superior cervical ganglia

value: DIV 13-15 SCG cultures reactivated with LY294002 for 20h

value: IFNbeta


title: 06_Wang_HiC_BWX3352_1mMIPTG_35m

description: Sample 06

tag: sample group

value: CH, 37˚C, 1mM IPTG for 35 min

tag: strain info.

value: parS∆9 no a.b., ∆spo0J (remains wt parS at -1˚)::spec, yvbJ::Pspank (optRBS) gfp-spo0J(∆parS) (cat)

tag: restriction enzyme

value: HindIII


title: LY reactivated SCGs, replicate 2

tag: tissue

value: no IFN


title: 07_Wang_HiC_BWX3352_1mMIPTG_45m

description: Sample 07

treatment_protocol: Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 45 min, fixed by 3% formaldehyde for 30min at room temperature

value: CH, 37˚C, 1mM IPTG for 45 min


title: L-Pro_d5

description: Sample 2

tag: cell population

value: mCherry+/eGFP+ (yellow)


title: Untreated t0

description: Sample 1


title: L-Prolin-VitC-day5

tag: cell type

value: Embryonic stem cells


title: Pool4_Plasmid

description: fastq of 3' UTR barcode and residual 5' flanking sequencing

data_processing:
Perfect UTR barcode matches were assigned to their respective oligo. Counts for all barcodes assigned to an oligo were summed.
Read counts corresponding to each barcode for each oligo
Genome_build: mm9

tag: cell line

tag: molecule subtype


title: 05_Wang_HiC_BWX3352_1mMIPTG_30m

description: Sample 05

value: CH, 37˚C, 1mM IPTG for 30 min


title: LY reactivated SCGs + IFNg, replicate 1

tag: age

tag: reactivation condition

tag: ifn type

value: IFNgamma


title: LY reactivated SCGs + IFNg, replicate 3


title: 04_Wang_HiC_BWX3352_1mMIPTG_25m

description: Sample 04

value: CH, 37˚C, 1mM IPTG for 25 min


title: Pool2_Plasmid


title: 02_Wang_HiC_BWX3352_1mMIPTG_15m

description: Sample 02

value: CH, 37˚C, 1mM IPTG for 15 min


title: 03_Wang_HiC_BWX3352_1mMIPTG_20m

description: Sample 03

value: CH, 37˚C, 1mM IPTG for 20 min


title: Pool7_barcodes

description: fastq of the barcode linked to oligo

data_processing:
Paired-end reads were aligned to the oligonucleotide pool using Bowtie2 2.1.0 (Langmead and Salzberg, 2012), trimming the tag sequence and adapters. Read pairs that were not aligned in proper pairs, had mapping scores less than 25, or edit distance greater than 5 were discarded. Remaining oligo/barcode pairs were merged. Barcodes that were observed in only 1 read or that matched multiple test sequences were removed from further analysis.
Tab file linking barcodes and oligos
Genome_build: mm9

extract_protocol: Barcode/oligo libraries were prepared as described by Tewkey et al. (Cell 2016 Jun 2;165(6):1519-29. PMID: 27259153)

value: Plasmid DNA

value: plasmid DNA


title: LY reactivated SCGs, replicate 1

value: Sprague-Dawley

value: superior cervical ganglia


title: Pool5_barcodes

description: fastq of the barcode linked to oligo


title: polyA mRNA RNA-seq from small intestine (ENCLB486ZUR)

description:
https://www.encodeproject.org/experiments/ENCSR612HYR/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA-seq of human small intestine tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR612HYR
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB486ZUR
size range: 350-450

source_name: Homo sapiens small intestine tissue female adult (30 years)

extract_protocol:
general protocol: https://www.encodeproject.org/documents/ffef687e-f74d-429e-8799-d16f991bbb11/@@download/attachment/wgEncodeSydhRnaSeq.patch.html.pdf
extraction method: RNeasy Lipid Tissue Mini Kit (QIAGEN cat#74804)

value: small intestine

value: tissue

tag: biosample encode accession

tag: dev stage

value: adult

value: 30 year

tag: Sex

value: female

value: Michael Snyder, Stanford

value: ENCBS487EXT at ENCODE; https://www.encodeproject.org/ENCBS487EXT/

value: Derived from ENCODE donor ENCDO449QPH; https://www.encodeproject.org/ENCDO449QPH/


title: polyA mRNA RNA-seq from spleen (ENCLB680CYA)

description:
https://www.encodeproject.org/experiments/ENCSR448VSW/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA-seq of human spleen tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR448VSW
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-01-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB680CYA
size range: 350-450

source_name: Homo sapiens spleen tissue female adult (30 years)

value: spleen

tag: lab

value: ENCBS167WVB at ENCODE; https://www.encodeproject.org/ENCBS167WVB/

value: Derived from ENCODE donor ENCDO871RXV; https://www.encodeproject.org/ENCDO871RXV/


title: polyA mRNA RNA-seq from heart (ENCLB171YLN)

description:
https://www.encodeproject.org/experiments/ENCSR635GTY/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA-seq of human heart tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR635GTY
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB171YLN
size range: 350-450

source_name: Homo sapiens heart tissue female adult (30 years)

value: heart

tag: link

value: ENCBS227BAN at ENCODE; https://www.encodeproject.org/ENCBS227BAN/


title: polyA mRNA RNA-seq from brain (ENCLB306ITM)

description:
https://www.encodeproject.org/experiments/ENCSR274JRR/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA-seq of human brain tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR274JRR
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-01-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB306ITM
size range: 350-450

source_name: Homo sapiens brain tissue female adult (66 years)

value: brain

value: 66 year

value: ENCBS534KWT at ENCODE; https://www.encodeproject.org/ENCBS534KWT/

value: Derived from ENCODE donor ENCDO691SXZ; https://www.encodeproject.org/ENCDO691SXZ/


title: Pool3_Plasmid

value: Plasmid DNA

value: plasmid DNA


title: polyA mRNA RNA-seq from adipose tissue (ENCLB564EVI)

description:
https://www.encodeproject.org/experiments/ENCSR236OON/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA-seq of human adipose tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR236OON
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB564EVI
size range: 350-450

source_name: Homo sapiens adipose tissue female adult (63 years)

value: adipose tissue

value: tissue

value: adult

value: 63 year

value: ENCBS116JOH at ENCODE; https://www.encodeproject.org/ENCBS116JOH/

value: Derived from ENCODE donor ENCDO828UYN; https://www.encodeproject.org/ENCDO828UYN/


title: polyA mRNA RNA-seq from lung (ENCLB955EVV)

description:
https://www.encodeproject.org/experiments/ENCSR129KCJ/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA-seq of human lung tissue tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR129KCJ
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB955EVV
size range: 350-450

source_name: Homo sapiens lung tissue female adult (30 years)

value: lung

value: 30 year

value: female

value: Michael Snyder, Stanford

value: ENCBS973FZI at ENCODE; https://www.encodeproject.org/ENCBS973FZI/

value: Derived from ENCODE donor ENCDO449QPH; https://www.encodeproject.org/ENCDO449QPH/


title: LY reactivated SCGs + IFNb, replicate 1

tag: strain

value: Sprague-Dawley

value: superior cervical ganglia

value: DIV 13-15 SCG cultures reactivated with LY294002 for 20h

value: IFNbeta


title: polyA mRNA RNA-seq from kidney (ENCLB347INC)

description:
https://www.encodeproject.org/experiments/ENCSR071ZMO/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA-seq of human kidney tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR071ZMO
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB347INC
size range: 350-450

source_name: Homo sapiens kidney tissue male adult (41 year)

value: kidney

value: 41 year

value: male

value: ENCBS314EFM at ENCODE; https://www.encodeproject.org/ENCBS314EFM/

value: Derived from ENCODE donor ENCDO304TKO; https://www.encodeproject.org/ENCDO304TKO/


title: 01_Wang_HiC_BWX3352_0IPTG

description: Sample 01

extract_protocol:
Hi-C experiments were performed using HindIII according to previous publications (Le et al, 2013, PMID: 24158908; Wang et al 2015, PMID: 26253537). ChIP-seq experiments were performed using anti-SMC, anti-ScpA, anti-ScpB, anti-ParB or anti-GFP antibodies according to previous publication (Graham et al 2014, PMID: 24829297).
the antibody information:
*anti-**SMC: Lindow et al., 2002: Mol Microbiol 46, 997-1009.
*anti-**ParB: Lin et al., 1997: Proc Natl Acad Sci U S A 94, 4721-4726.
*anti-GFP: Rudner et al., 1999: Proc Natl Acad Sci U S A 96, 14765-14770.
*anti-ScpA and anti-ScpB: generated in this study. Procedure described in Experimental Procedures.
Standard library construction protocol was used for Illumina Hiseq2500 sequencing platform (Hi-C) or Illumina Miseq (ChIP-seq). Illumina Truseq indexes were used.

tag: sample group

value: CH, 37˚C, no IPTG

value: parS∆9 no a.b., ∆spo0J (remains wt parS at -1˚)::spec, yvbJ::Pspank (optRBS) gfp-spo0J(∆parS) (cat)

value: HindIII


title: Pool1_Plasmid

value: Plasmid DNA

value: plasmid DNA


title: polyA mRNA RNA-seq from pancreas (ENCLB020LQS)

description:
https://www.encodeproject.org/experiments/ENCSR001UXR/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA-seq of human pancreas tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR001UXR
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-01-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB020LQS
size range: 350-450

source_name: Homo sapiens pancreas tissue female adult (30 years)

value: pancreas

value: tissue

value: adult

value: 30 year

value: female

value: Michael Snyder, Stanford

value: ENCBS526GJF at ENCODE; https://www.encodeproject.org/ENCBS526GJF/

value: Derived from ENCODE donor ENCDO871RXV; https://www.encodeproject.org/ENCDO871RXV/


title: polyA mRNA RNA-seq from liver (ENCLB490UAX)

description:
https://www.encodeproject.org/experiments/ENCSR085HNI/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA-seq of human liver tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR085HNI
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB490UAX
size range: 350-450

source_name: Homo sapiens liver tissue male adult (18 years)

value: liver

value: 18 year

value: ENCBS082KWE at ENCODE; https://www.encodeproject.org/ENCBS082KWE/

value: Derived from ENCODE donor ENCDO481HRF; https://www.encodeproject.org/ENCDO481HRF/


title: Pool6_barcodes

description: fastq of the barcode linked to oligo


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cpsf7 knockdown (T0892), replicate 2

status: Public on Feb 02 2017

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: GCGGTATT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab

data_processing:
CASAVA 1.8 was used for base calling.
Fastq files contain demultiplexed reads which were assigned to the appropriate treatment by matching to expected forward and reverse barcodes (sequenced in dedicated reads; not supplied).
Forward and reverse event reads were mapped to custom junction libraries representing all expected splice variants (supplied as processed files), using bowtie with settings --best -v 3 -k 1 --trim3 26 --trim5 20. Trimming was done to remove lower-quality, uninformative ends and because forward reads had a missing base call at position 11 due to a power outage. Junction libraries were first constructed from NCBIm37/mm9 gene annotations, and then refined based on the results of de novo mapping of the reads from one full Illumina lane from each cell line using tophat (default settings with -i 40 and providing Ensembl transcript annotations for NCBIm37), after quality trimming (minimum MAPQ of 33) from the 3'-end with the fastx toolkit. Mapped reads were counted per junction.
Alternative splicing analysis: Percent-spliced-in (PSI) values were calculated for each alternative exon, or part thereof in the case of alternative 5'-/3'-splice sites ('event'), from read tallies as follows: PSI was calculated independently from forward and reverse reads as the percentage of reads supporting inclusion divided by the total number of reads for the event. For alternative 5'/3'-ss events that were part of an alternative exon (Foxm1.A2, Mta1.A1, Uspl1.A3), the PSI was instead calculated with reference to the total reads supporting inclusion of that exon in order to assess independent regulation of alternative splice site usage. Only the read direction in which all reads unambiguously supported either inclusion or exclusion of an event was used, and the average if that applied for both. Exploratory analysis revealed that PSI values showed low-level batch effects per 96-well plate which we moderated by subtracting a weighted plate median in which negative controls (siNT and mock treatment) were given 20x more weight than other samples. To derive variances, and because PSI values are not nearly normally distributed but roughly follow a beta distribution, we elected to fit a beta distribution to each pair of replicate treatments, as well as to all negative controls from both replicates, using maximum-likelihood fitting as implemented in the fitdistr() function from the R package MASS {Venables & Ripley, Modern Applied Statistics with S (2002)}. Iterative optimization of shape parameters was initiated with settings x=PSI, shape1=1, shape2=1, method=”L-BFGS-B”, lower=0.01, and upper=mean number of reads supporting each PSI value. A modified Strictly Standardized Mean Difference (SSMD {Zhang, Genomics (2007)}) was then calculated based on the formula: SSMD = (μt – μc)/SQRT(vart + varc) where μt and μc are the means (corresponding to the PSI), and vart and varc the variances of the beta distributions fitted to the treatment replicates and negative controls, respectively. Events for which not all reads from at least one direction were informative (Mff.A2, Tead1.A2) were excluded from further analysis, as were events in individual treatments with less than 20 reads in one or both replicates (~9% of all event x treatment combinations). Additionally, the following events were removed from further splicing analysis: expression only events or constitutive exons, Fgf4, Gapdh, Srpk2, Srrm4; events with consistently low read counts: Atg13.A1, H2afy.A2, Tcf7l1 (N2A only), Dnmt3b (N2A only); or because measured inclusion was biased by differential length of isoforms:, Fgfr1, Sall4.
Expression analysis: Read counts from all splice variants of each gene were used to estimate relative mRNA expression levels, reads per million reads (RPMs). Differential expression analysis based on raw read counts was performed using the generalized linear models workflow from the R package edgeR. Plate, position (edge/interior) and treatment were used as design factors (where all treatments of each type of control were treated as replicates.) Models fitted using estimateDisp() to estimate the common, trended, and tag-wise dispersion for the CGR8 and N2A data separately. Subsequently, differences attributable to treatment, plate, or position contrasts were extracted with glmLRT() and represented as log2-fold changes with associated FDR. Fold-changes for treatments are relative to the siNT and mock-treatment controls.
Genome_build: NCBIm37/mm9
Supplementary_files_format_and_content: Processed files are either tab-delimited  tables (.tab) or FASTA files (.fa). KnockdownAnnotation.tab contains treatment annotations and well/plate positions. ScreenJuncUp.20-77.tab and ScreenJuncDn.20-77.tab contain the custom junction upstream and downstram junction libraries, respectively, and ScreenEvent_junctions.tab contains the information which junctions were used to calculate PSI for each event. PSI.SSMD.CGR8.tab and PSI.SSMD.N2A.tab contain raw PSI of each replicate and final SSMD. Reads_perEvent_CGR8.tab and Reads_perEvent_N2A.tab contain raw read counts on which expression analyis was based, and Expression.CGR8.treatments.tab and Expression.N2A.treatments.tab contain modeled relative abundance and fold-change with associated FDR for each treatment type.

source_name: Neuroblastoma cells

growth_protocol: CGR8 mouse embryonic stem cells (ESCs) were cultured as described previously on gelatin-coated plates (Gabut et al., Cell (2011), Han  et al., Nature (2013)). Mouse neuroblastoma (N2A) cells were grown in DMEM supplemented with 10% FBS, sodium pyruvate, MEM non-essential amino acids, and penicillin/streptomycin. All cell lines were maintained at 37°C with 5% CO2.

extract_protocol:
Forty-eight hours post-transfection, total RNA were purified from cultured cells using RNeasy Plus 96 Kit (Qiagen), as per the manufacturer’s instructions.
For each sample, a multiplex RT-PCR assay was first applied to simultaneously amplify 50 AS and/or expression events in a single reaction. The multiplex RT-PCR reaction was carried out in 96-well plates using the OneStep RT-PCR kit (Qiagen) as recommended by the manufacturer, with the following changes: reactions were performed in a volume of 20 uL with 2 uL of the purified total RNA as input, and a mixture of 50 pairs of primers was added to each reaction with a final concentration of 0.25 uM for each individual forward and reverse primer. Four identical Veriti 96-well Thermal Cyclers (Applied Biosystems) were used with the following conditions: 50°C for 30 minutes, 95°C for 15 minute, 30 cycles of 94°C for 40 seconds, 58°C for 1 minute (slow ramp rate), 72°C for 3 minutes, and a final extension step at 72°C for 10 minutes. Two sets of barcodes were incorporated into forward and reverse primers, respectively, after the universal adaptors and added to the amplicons in the second PCR reaction to allow demultiplexing all reads that were derived from a particular treatment. Primers sequences were: forward primer, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT (N denotes i5 barcode); reverse primer, CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT (N denotes i7 primer). The second PCR was performed using Phusion High-Fidelity DNA Polymerase (Thermo Scientific), as per the manufacturer’s instructions. For each 20 uL of reaction, 1 uL of the multiplex RT-PCR reaction products was used as templates. The thermal cycling conditions were as follows: 98°C for 30 seconds, 15 cycles of 98°C for 10 seconds, 65°C for 30 seconds, 72°C for 30 seconds, and a final extension step at 72°C for 5 minutes. The resulting libraries were pooled and sequenced.

treatment_protocol: Twenty-four hours prior to transfection, CGR8 and N2A cells were seeded in 96-well plates, 3000 and 5000 cells per well, respectively. Cells were transfected with the SMARTpool siRNAs at 50 nM final concentration using DharmaFECT1 reagent (Dharmacon), as recommended by the manufacturer.


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Adarb2 knockdown (T0887), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: AGCTGAAG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Arrdc4 knockdown (T0884), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: TGCTCTAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Ddx39b knockdown (T0893), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: CCATGGTA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: polyA mRNA RNA-seq from adrenal gland (ENCLB981BIW)

description:
https://www.encodeproject.org/experiments/ENCSR680AAZ/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA-seq of human adrenal gland. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR680AAZ
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB981BIW
size range: 350-450

source_name: Homo sapiens adrenal gland tissue male adult (21 year)

value: adrenal gland

value: 21 year

value: male

value: ENCBS629YZU at ENCODE; https://www.encodeproject.org/ENCBS629YZU/

value: Derived from ENCODE donor ENCDO637AUB; https://www.encodeproject.org/ENCDO637AUB/


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cobra1 knockdown (T0888), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: ATTAGCGC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Adarb1 knockdown (T0885), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: GGTTAACC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Snd1 knockdown (T0886), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: TCCATGCT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Anks1 knockdown (T0883), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: TCGTCATC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zfp868 knockdown (T0882), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: TCTGGTCT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Banf1 knockdown (T0889), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: GATCCTAG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Sun2 knockdown (T0880), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: AGCAAGCA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Gpank1 knockdown (T0879), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: TCCTACGT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Mau2 knockdown (T0881), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: GACTAGAG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, mock (T0891), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: AAGGTACG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Pif1 knockdown (T0877), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: TTGCTTCG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Csdc2 knockdown (T0878), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: ATCCGCTT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: polyA mRNA RNA-seq from sigmoid colon (ENCLB679EPU)

description:
https://www.encodeproject.org/experiments/ENCSR270OKS/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA-seq of human sigmoid colon tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR270OKS
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB679EPU
size range: 350-450

source_name: Homo sapiens sigmoid colon tissue male adult (21 year)

value: sigmoid colon

value: ENCBS511JYL at ENCODE; https://www.encodeproject.org/ENCBS511JYL/


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cwc22 knockdown (T0876), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: AGTCAGAG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Clp1 knockdown (T0875), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: CACTGTGA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: TG39_LSD1i_rep1

description: RNA-sequencing of P53/R26-Zeb2tg/tg  TG39 cells treated with 100nM GSK2879552 for 24h

source_name: thymoma primary T-ALL culture

tag: type

value: T-ALL

tag: treatment


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zc3hav1l knockdown (T0874), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: AGTCGTCA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zc3h11a knockdown (T0873), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: CGGCATTA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Pstk knockdown (T0871), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: GATCTGCA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Bbx knockdown (T0872), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: ATCGATCG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Dus3l knockdown (T0870), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: TGACGAGA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Ino80e knockdown (T0868), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: TCAGTCAG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Snrnp35 knockdown (T0869), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: CAGAAGTG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Adam5 knockdown (T0867), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: ATGCATGC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Actr5 knockdown (T0890), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: GAGAGTCA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, siNT (T0865), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: TGGAGTTC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Celf5 knockdown (T0863), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: ACACGTGT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zcrb1 knockdown (T0861), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: CCAATTGG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Apitd1 knockdown (T0862), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: ACAGTGAG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, mock (T0864), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: ACCTGTAG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zc3h15 knockdown (T0857), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: GAACCTTG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Phf23 knockdown (T0858), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: TTGCTACC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Ska1 knockdown (T0856), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: AGCTACGT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Tspyl4 knockdown (T0853), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: CATGGTAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zcchc12 knockdown (T0850), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: TTGGAAGG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Phf14 knockdown (T0852), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: TGTCTCTG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Spty2d1 knockdown (T0849), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: TTATGCGG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zcchc17 knockdown (T0848), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: ACGTACCA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zfp809 knockdown (T0866), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: AGAGCTCT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Smchd1 knockdown (T0851), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: ACTCACAG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Isy1 knockdown (T0846), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: GCATGGTT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Rnf181 knockdown (T0843), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: GAACTCGT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, 2810432D09Rik knockdown (T0859), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: TGGTCAAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zmat5 knockdown (T0844), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: CTACACCT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zkscan17 knockdown (T0842), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: TAGGCGAA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zcchc7 knockdown (T0840), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: CAGTAGTC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Gpatch4 knockdown (T0841), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: GTGTACAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zfp593 knockdown (T0854), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: CGTAGCTA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, 2410141K09Rik knockdown (T0835), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: GACATGTC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cenpm knockdown (T0836), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: GCAATACC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: polyA mRNA RNA-seq from testis (ENCLB687HNK)

description:
https://www.encodeproject.org/experiments/ENCSR693GGB/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA-seq of human testis tissue. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication (PMID:25413365).
experiment encode accession: ENCSR693GGB
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB687HNK
size range: 350-450

source_name: Homo sapiens testis tissue male adult (44 years)

value: testis

value: tissue

value: adult

value: 44 year

value: ENCBS021ARD at ENCODE; https://www.encodeproject.org/ENCBS021ARD/

value: Derived from ENCODE donor ENCDO730LED; https://www.encodeproject.org/ENCDO730LED/


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zfp954 knockdown (T0833), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: TCCACTTG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, 2610305D13Rik knockdown (T0834), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: TATAGCGC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zfp672 knockdown (T0838), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: CGATCCAA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Dscc1 knockdown (T0831), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: GACAGACA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zfp566 knockdown (T0845), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: TGAGTGTC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Nsun6 knockdown (T0847), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: GCGGAATA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Hnrnpf knockdown (T0832), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: GTGAAGTG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Prpf6 knockdown (T0830), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: ATGCGCTA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Ppwd1 knockdown (T0829), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: GACTCTGA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Rnpc3 knockdown (T0828), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: CATCCATC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cdkn2aip knockdown (T0827), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: TAATGGCC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Rbm42 knockdown (T0826), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: CGTATAGC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Nkap knockdown (T0860), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: TGGTAGGA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Spc24 knockdown (T0824), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: GGCCAATT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, siMbnl (T0825), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: AGCTCATG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, N6amt2 knockdown (T0822), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: ATAAGGCG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zfp799 knockdown (T0821), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: GGTTCCTT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Skiv2l2 knockdown (T0839), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: TCTCGACT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Hnrnpa3 knockdown (T0820), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: TGTGCACA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, N6amt1 knockdown (T0819), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: AGTCTGAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Ube2f knockdown (T0816), replicate 2

description:
Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: GCATAAGG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Tox4 knockdown (T0815), replicate 2

description:
Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: CTCATCAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Specc1l knockdown (T0817), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: GCATATCG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Snrnp25 knockdown (T0814), replicate 2

description:
Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: TACGGCAT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, siNT (T0813), replicate 2

description:
Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: GACTCAGT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Pabpc6 knockdown (T0811), replicate 2

description:
Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: CGATAACC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, siMbnl (T0807), replicate 2

description:
Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: TGCAGTAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Rbm12b knockdown (T0808), replicate 2

description:
Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: ATCCGCAA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Rbm4b knockdown (T0812), replicate 2

description:
Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: GACAGTGA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Rbmx2 knockdown (T0810), replicate 2

description:
Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: CCTATACC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Sohlh2 knockdown (T0809), replicate 2

description:
Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: ACGATCCA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Hormad1 knockdown (T0823), replicate 2

description:
Forward (i5) barcode: CTCTCTAT, reverse (i7) barcode: CTTGCTTG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cdca5 knockdown (T0804), replicate 2

description:
Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: GTTCTGCT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Swi5 knockdown (T0803), replicate 2

description:
Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: CCAACCTT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Wdr77 knockdown (T0806), replicate 2

description:
Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: CTGTACTC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Hnrpll knockdown (T0805), replicate 2

description:
Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: CAAGCTAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Sltm knockdown (T0801), replicate 2

description:
Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: TCGAACGT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Larp6 knockdown (T0802), replicate 2

description:
Forward (i5) barcode: TAGATCGC, reverse (i7) barcode: GAAGTCGA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab