title: ChIPSeq_Input_24h2i

source_name: ChIPSeq Input 24h2i

extract_protocol:
ChIP-Seq: Cells were cross-linked with 1% methanol-free formaldehyde in fresh medium for 10 minutes. Cross-linking reaction was quenched with glycine at a final concentration of 0.2M. Cells were then washed twice with ice-cold PBS and harvested. Cell pellets were then resuspended in LB1 buffer (50 mM Hepes–KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA;10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100, protease inhibitors) for 10 minutes at 4°C, pelleted and resuspended in LB2 buffer (10 mM Tris–HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA, protease inhibitors) for 10 minutes at 4°C. Cells were pelleted, resuspended in LB3 buffer (10 mM Tris–HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na–Deoxycholate; 0.5% N-lauroylsarcosine, protease inhibitors) and sonicated using Misonix Sonicator 3000. After addition of Triton-X to a final concentration of 1%, the lysate was centrifuged at 20,000g for 10 minutes to pellet debris. Sonicate chromatin was then added to the bead-antibody complexes and incubated overnight at 4°C. Bead-antibody were prepared as follows: Protein G-coupled Dynabeads were incubated overnight with primary antibodies (anti-H3K9me2; Abcam ab1220) in PBS added with 5 mg/ml BSA. Beads were washed extensively with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCL), once with 1x TE buffer and eluted in 200ul of buffer containing 1% SDS and 0.1M NaHCO3. Cross-linking was reversed by incubation at 65°C overnight, followed by RNase A treatment at 37°C for 1 hour and Proteinase K treatment at 55°C for 2 hours. DNA was then extracted using Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions. Eluted DNA was then used to perform ChIP-Seq library preparation using the MicroPlex Library Preparation Kit v2 (Diagenode)
Genomic DNA and total RNA were isolated from the samples using the Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions.
RNASeq: RNA was used for library preparation using TruSeq RNA Library Prep Kit v2 (Illumina) following the manufacturer’s instructions. Libraries were indexed either using Illumina Indexes and 50 bp single-end sequencing was performed on Illumina HiSeq 2000 instruments using TruSeq reagents (Illumina, San Diego, CA, USA), according to manufacturer’s instructions.
RRBS-Seq was performed as described previously (Smallwood et al, 2011)
ChIP-Seq: Cells were cross-linked with 1% methanol-free formaldehyde in fresh medium for 10 minutes. Cross-linking reaction was quenched with glycine at a final concentration of 0.2M. Cells were then washed twice with ice-cold PBS and harvested. Cell pellets were then resuspended in LB1 buffer (50 mM Hepes–KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA;10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100, protease inhibitors) for 10 minutes at 4°C, pelleted and resuspended in LB2 buffer (10 mM Tris–HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA, protease inhibitors) for 10 minutes at 4°C. Cells were pelleted, resuspended in LB3 buffer (10 mM Tris–HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na–Deoxycholate; 0.5% N-lauroylsarcosine, protease inhibitors) and sonicated using Misonix Sonicator 3000. After addition of Triton-X to a final concentration of 1%, the lysate was centrifuged at 20,000g for 10 minutes to pellet debris. Sonicate chromatin was then added to the bead-antibody complexes and incubated overnight at 4°C. Bead-antibody were prepared as follows: Protein G-coupled Dynabeads were incubated overnight with primary antibodies (anti-H3K9me2; Abcam ab1220) in PBS added with 5 mg/ml BSA. Beads were washed extensively with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCL), once with 1x TE buffer and eluted in 200ul of buffer containing 1% SDS and 0.1M NaHCO3. Cross-linking was reversed by incubation at 65°C overnight, followed by RNase A treatment at 37°C for 1 hour and Proteinase K treatment at 55°C for 2 hours. DNA was then extracted using Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions. Eluted DNA was then used to perform ChIP-Seq library preparation using the MicroPlex Library Preparation Kit v2 (Diagenode)
ChIP-BS-Seq: Cells were cross-linked with 1% methanol-free formaldehyde in fresh medium for 10 minutes. Cross-linking reaction was quenched with glycine at a final concentration of 0.2M. Cells were then washed twice with ice-cold PBS and harvested. Cell pellets were then resuspended in LB1 buffer (50 mM Hepes–KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA;10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100, protease inhibitors) for 10 minutes at 4°C, pelleted and resuspended in LB2 buffer (10 mM Tris–HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA, protease inhibitors) for 10 minutes at 4°C. Cells were pelleted, resuspended in LB3 buffer (10 mM Tris–HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na–Deoxycholate; 0.5% N-lauroylsarcosine, protease inhibitors) and sonicated using Misonix Sonicator 3000. After addition of Triton-X to a final concentration of 1%, the lysate was centrifuged at 20,000g for 10 minutes to pellet debris. Sonicate chromatin was then added to the bead-antibody complexes and incubated overnight at 4°C. Bead-antibody were prepared as follows: Protein G-coupled Dynabeads were incubated overnight with primary antibodies (anti-H3K9me2; Abcam ab1220) in PBS added with 5 mg/ml BSA. Beads were washed extensively with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCL), once with 1x TE buffer and eluted in 200ul of buffer containing 1% SDS and 0.1M NaHCO3. Cross-linking was reversed by incubation at 65°C overnight, followed by RNase A treatment at 37°C for 1 hour and Proteinase K treatment at 55°C for 2 hours. DNA was then extracted using Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions. Eluted DNA was then treated for WGBS as described before


title: shRNA RNA-seq from HepG2 (ENCLB236VAS)

status: Public on May 26 2016

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR622MCX/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against U2AF2 in HepG2 cells followed by RNA-seq. (U2AF2 BGHLV14)
experiment encode accession: ENCSR622MCX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB236VAS
size range: >200
spikeins used: /references/ENCSR449DXG/

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting U2AF2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/00ced242-6e55-402b-828c-d6e09c3a92e1/@@download/attachment/L-U2AF2_BGHLV14-65.pdf

tag: antibody

tag: line

value: immortalized cell line

tag: description

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against U2AF2. (U2AF2_BGHLV14-65)

tag: biosample encode accession

tag: age

value: 15 year

tag: dev stage

value: child

tag: Sex

value: male

tag: health state

value: hepatocellular carcinoma

tag: lab

value: Brenton Graveley, UConn

tag: link

value: ENCBS970EPG at ENCODE; https://www.encodeproject.org/ENCBS970EPG/

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

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


title: ChIPSeq_Input_LT2i

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

library_source: genomic

data_processing:
RNA-Seq: Raw FastQ data were trimmed with Trim Galore (v0.3.5, default parameters) and mapped to the mouse GRCm38 genome assembly using TopHat v2.0.11, guided by gene models from Ensembl v61. Data were quantitated at mRNA level using the RNA-seq quantitation pipeline in SeqMonk software (www.bioinformatics.babraham.ac.uk/projects/seqmonk/) applying transcript length correction and 75th percentile normalisation.
Genome_build: GRCm38
RRBS and ChIP-BS-Seq: Trimmed sequences were mapped to the mouse NCBIM37 genome using Bismark (Krueger and Andrews, 2011) (v0.12.3); CpG methylation calls were extracted and analysed using SeqMonk (www.bioinformatics.babraham.ac.uk/projects/seqmonk/) and custom R scripts.
ChIP-Seq: Trimmed sequences were mapped to the mouse NCBIM37 genome using Bowtie 2; Read counts over 2kb tiles were normalied for total reads and the largest data store and log2 transformed. Tiles with <3 normlized read counts in all input samples were excluded.
Genome_build: NCBIM37
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>
Supplementary_files_format_and_content: Quantitated RNA-Seq data file is tab delimited and contains the following 17 columns: (1) mRNA name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6-17) log2 RPKM values for each sample
Supplementary_files_format_and_content: Quantitated H3K9me2 data file is tab delimited and contains the following 12 columns: (1) Chromosome; (2) Start; (3) End; (4-12) log2 readcount for each sample

molecule: genomic DNA

organism: Mus musculus

source_name: ChIPSeq Input LT2i

tag: background strain

tag: cell type

value: ESC

tag: genotype

value: Wild-type

tag: chip antibody


title: ChIPSeq_H3K9me2_LT2i_2

source_name: ChIPSeq H3K9me2 LT2i 2

value: anti-H3K9me2; Abcam ab1220


title: ChIPSeq_Input_Ser

source_name: ChIPSeq Input Ser


title: shRNA RNA-seq from HepG2 (ENCLB948TVP)

description:
https://www.encodeproject.org/experiments/ENCSR622MCX/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against U2AF2 in HepG2 cells followed by RNA-seq. (U2AF2 BGHLV14)
experiment encode accession: ENCSR622MCX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB948TVP
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/14f45398-7c49-47ae-aca7-75466e2ab82f/@@download/attachment/L-U2AF2_BGHLV14-66.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against U2AF2. (U2AF2_BGHLV14-66)

value: ENCBS727GLB at ENCODE; https://www.encodeproject.org/ENCBS727GLB/


title: ChIPSeq_H3K9me2_LT2i_1

source_name: ChIPSeq H3K9me2 LT2i 1


title: RNA_ImmB_Eb_rep1

city: New York

first: Jane

last: Skok

state: NY

address: 550 First Ave, Smillow 307

institute: NYU

description:
ribodepleted RNA
count data: htseq_counts_ImmB.txt

data_processing:
Paired-end reads were mapped to the mm10 genome using TopHat2 (parameters: --no-coverage-search --no-discordant --no-mixed --b2-very-sensitive –N 1).
Counts for Refseq genes were obtained using htseq-counts
Genome_build: mm10
Supplementary_files_format_and_content: tdf

source_name: CD19+IgD-B220+IgM+ Eb-/- immature B cells

growth_protocol: Animals were bred and maintained in the animal facility. Animal care was approved by Institutional Animal Care and Use Committee (protocol number 150606-01, NYU School of Medicine).

extract_protocol:
Cells were lysed with RLT buffer, total RNA was extracted with Qiagen kit.
Ribo-depleted RNA was fragmented and reverse-transcribed.  Illumina adapters were attached to cDNA through T-A overhand ligation and the library was amplified.

treatment_protocol: Cells were sorted ex vivo and processed immediatelly.

tag: strain

tag: tissue

value: bone marrow

value: 5-7 weeks old

value: CD19+IgD-B220+IgM+ immature B cells


title: shRNA RNA-seq from K562 (ENCLB921YNH)

description:
https://www.encodeproject.org/experiments/ENCSR611ZAL/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against TAF15 in K562 cells followed by RNA-seq. (TAF15-LV08)
experiment encode accession: ENCSR611ZAL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR344XID
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB921YNH
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting TAF15

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e14956cf-691a-42ab-beb4-ef1249bad736/@@download/attachment/L-TAF15-LV08-57.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against TAF15. (TAF15-LV08-57)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS823LKQ at ENCODE; https://www.encodeproject.org/ENCBS823LKQ/

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

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


title: ChIPSeq_H3K9me2_24h2i_2

source_name: ChIPSeq H3K9me2 24h2i 2

value: ESC


title: shRNA RNA-seq from K562 (ENCLB751QRU)

description:
https://www.encodeproject.org/experiments/ENCSR611ZAL/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against TAF15 in K562 cells followed by RNA-seq. (TAF15-LV08)
experiment encode accession: ENCSR611ZAL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR344XID
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB751QRU
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/83a7dbda-9afb-4a69-81b0-df381ec732bf/@@download/attachment/L-TAF15-LV08-58.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against TAF15. (TAF15-LV08-58)

value: Brenton Graveley, UConn

value: ENCBS693EWC at ENCODE; https://www.encodeproject.org/ENCBS693EWC/


title: ChIPSeq_H3K9me2_24h2i_1

source_name: ChIPSeq H3K9me2 24h2i 1

value: Wild-type

value: anti-H3K9me2; Abcam ab1220


title: ChIPSeq_H3K9me2_Ser_2

source_name: ChIPSeq H3K9me2 Ser 2


title: RRBS_TET_TKO_168h2i_2

source_name: RRBS TET TKO 168h2i 2

extract_protocol:
RRBS-Seq was performed as described previously (Smallwood et al, 2011)
Genomic DNA and total RNA were isolated from the samples using the Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions.
RNASeq: RNA was used for library preparation using TruSeq RNA Library Prep Kit v2 (Illumina) following the manufacturer’s instructions. Libraries were indexed either using Illumina Indexes and 50 bp single-end sequencing was performed on Illumina HiSeq 2000 instruments using TruSeq reagents (Illumina, San Diego, CA, USA), according to manufacturer’s instructions.
RRBS-Seq was performed as described previously (Smallwood et al, 2011)
ChIP-Seq: Cells were cross-linked with 1% methanol-free formaldehyde in fresh medium for 10 minutes. Cross-linking reaction was quenched with glycine at a final concentration of 0.2M. Cells were then washed twice with ice-cold PBS and harvested. Cell pellets were then resuspended in LB1 buffer (50 mM Hepes–KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA;10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100, protease inhibitors) for 10 minutes at 4°C, pelleted and resuspended in LB2 buffer (10 mM Tris–HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA, protease inhibitors) for 10 minutes at 4°C. Cells were pelleted, resuspended in LB3 buffer (10 mM Tris–HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na–Deoxycholate; 0.5% N-lauroylsarcosine, protease inhibitors) and sonicated using Misonix Sonicator 3000. After addition of Triton-X to a final concentration of 1%, the lysate was centrifuged at 20,000g for 10 minutes to pellet debris. Sonicate chromatin was then added to the bead-antibody complexes and incubated overnight at 4°C. Bead-antibody were prepared as follows: Protein G-coupled Dynabeads were incubated overnight with primary antibodies (anti-H3K9me2; Abcam ab1220) in PBS added with 5 mg/ml BSA. Beads were washed extensively with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCL), once with 1x TE buffer and eluted in 200ul of buffer containing 1% SDS and 0.1M NaHCO3. Cross-linking was reversed by incubation at 65°C overnight, followed by RNase A treatment at 37°C for 1 hour and Proteinase K treatment at 55°C for 2 hours. DNA was then extracted using Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions. Eluted DNA was then used to perform ChIP-Seq library preparation using the MicroPlex Library Preparation Kit v2 (Diagenode)
ChIP-BS-Seq: Cells were cross-linked with 1% methanol-free formaldehyde in fresh medium for 10 minutes. Cross-linking reaction was quenched with glycine at a final concentration of 0.2M. Cells were then washed twice with ice-cold PBS and harvested. Cell pellets were then resuspended in LB1 buffer (50 mM Hepes–KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA;10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100, protease inhibitors) for 10 minutes at 4°C, pelleted and resuspended in LB2 buffer (10 mM Tris–HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA, protease inhibitors) for 10 minutes at 4°C. Cells were pelleted, resuspended in LB3 buffer (10 mM Tris–HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na–Deoxycholate; 0.5% N-lauroylsarcosine, protease inhibitors) and sonicated using Misonix Sonicator 3000. After addition of Triton-X to a final concentration of 1%, the lysate was centrifuged at 20,000g for 10 minutes to pellet debris. Sonicate chromatin was then added to the bead-antibody complexes and incubated overnight at 4°C. Bead-antibody were prepared as follows: Protein G-coupled Dynabeads were incubated overnight with primary antibodies (anti-H3K9me2; Abcam ab1220) in PBS added with 5 mg/ml BSA. Beads were washed extensively with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCL), once with 1x TE buffer and eluted in 200ul of buffer containing 1% SDS and 0.1M NaHCO3. Cross-linking was reversed by incubation at 65°C overnight, followed by RNase A treatment at 37°C for 1 hour and Proteinase K treatment at 55°C for 2 hours. DNA was then extracted using Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions. Eluted DNA was then treated for WGBS as described before


title: ChIP-BS_H3K9me2_Ser_1

description: ChIP-BS-Seq

source_name: ChIP-BS H3K9me2 Ser 1

extract_protocol:
ChIP-BS-Seq: Cells were cross-linked with 1% methanol-free formaldehyde in fresh medium for 10 minutes. Cross-linking reaction was quenched with glycine at a final concentration of 0.2M. Cells were then washed twice with ice-cold PBS and harvested. Cell pellets were then resuspended in LB1 buffer (50 mM Hepes–KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA;10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100, protease inhibitors) for 10 minutes at 4°C, pelleted and resuspended in LB2 buffer (10 mM Tris–HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA, protease inhibitors) for 10 minutes at 4°C. Cells were pelleted, resuspended in LB3 buffer (10 mM Tris–HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na–Deoxycholate; 0.5% N-lauroylsarcosine, protease inhibitors) and sonicated using Misonix Sonicator 3000. After addition of Triton-X to a final concentration of 1%, the lysate was centrifuged at 20,000g for 10 minutes to pellet debris. Sonicate chromatin was then added to the bead-antibody complexes and incubated overnight at 4°C. Bead-antibody were prepared as follows: Protein G-coupled Dynabeads were incubated overnight with primary antibodies (anti-H3K9me2; Abcam ab1220) in PBS added with 5 mg/ml BSA. Beads were washed extensively with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCL), once with 1x TE buffer and eluted in 200ul of buffer containing 1% SDS and 0.1M NaHCO3. Cross-linking was reversed by incubation at 65°C overnight, followed by RNase A treatment at 37°C for 1 hour and Proteinase K treatment at 55°C for 2 hours. DNA was then extracted using Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions. Eluted DNA was then treated for WGBS as described before
Genomic DNA and total RNA were isolated from the samples using the Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions.
RNASeq: RNA was used for library preparation using TruSeq RNA Library Prep Kit v2 (Illumina) following the manufacturer’s instructions. Libraries were indexed either using Illumina Indexes and 50 bp single-end sequencing was performed on Illumina HiSeq 2000 instruments using TruSeq reagents (Illumina, San Diego, CA, USA), according to manufacturer’s instructions.
RRBS-Seq was performed as described previously (Smallwood et al, 2011)
ChIP-Seq: Cells were cross-linked with 1% methanol-free formaldehyde in fresh medium for 10 minutes. Cross-linking reaction was quenched with glycine at a final concentration of 0.2M. Cells were then washed twice with ice-cold PBS and harvested. Cell pellets were then resuspended in LB1 buffer (50 mM Hepes–KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA;10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100, protease inhibitors) for 10 minutes at 4°C, pelleted and resuspended in LB2 buffer (10 mM Tris–HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA, protease inhibitors) for 10 minutes at 4°C. Cells were pelleted, resuspended in LB3 buffer (10 mM Tris–HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na–Deoxycholate; 0.5% N-lauroylsarcosine, protease inhibitors) and sonicated using Misonix Sonicator 3000. After addition of Triton-X to a final concentration of 1%, the lysate was centrifuged at 20,000g for 10 minutes to pellet debris. Sonicate chromatin was then added to the bead-antibody complexes and incubated overnight at 4°C. Bead-antibody were prepared as follows: Protein G-coupled Dynabeads were incubated overnight with primary antibodies (anti-H3K9me2; Abcam ab1220) in PBS added with 5 mg/ml BSA. Beads were washed extensively with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCL), once with 1x TE buffer and eluted in 200ul of buffer containing 1% SDS and 0.1M NaHCO3. Cross-linking was reversed by incubation at 65°C overnight, followed by RNase A treatment at 37°C for 1 hour and Proteinase K treatment at 55°C for 2 hours. DNA was then extracted using Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions. Eluted DNA was then used to perform ChIP-Seq library preparation using the MicroPlex Library Preparation Kit v2 (Diagenode)
ChIP-BS-Seq: Cells were cross-linked with 1% methanol-free formaldehyde in fresh medium for 10 minutes. Cross-linking reaction was quenched with glycine at a final concentration of 0.2M. Cells were then washed twice with ice-cold PBS and harvested. Cell pellets were then resuspended in LB1 buffer (50 mM Hepes–KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA;10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100, protease inhibitors) for 10 minutes at 4°C, pelleted and resuspended in LB2 buffer (10 mM Tris–HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA, protease inhibitors) for 10 minutes at 4°C. Cells were pelleted, resuspended in LB3 buffer (10 mM Tris–HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na–Deoxycholate; 0.5% N-lauroylsarcosine, protease inhibitors) and sonicated using Misonix Sonicator 3000. After addition of Triton-X to a final concentration of 1%, the lysate was centrifuged at 20,000g for 10 minutes to pellet debris. Sonicate chromatin was then added to the bead-antibody complexes and incubated overnight at 4°C. Bead-antibody were prepared as follows: Protein G-coupled Dynabeads were incubated overnight with primary antibodies (anti-H3K9me2; Abcam ab1220) in PBS added with 5 mg/ml BSA. Beads were washed extensively with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCL), once with 1x TE buffer and eluted in 200ul of buffer containing 1% SDS and 0.1M NaHCO3. Cross-linking was reversed by incubation at 65°C overnight, followed by RNase A treatment at 37°C for 1 hour and Proteinase K treatment at 55°C for 2 hours. DNA was then extracted using Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions. Eluted DNA was then treated for WGBS as described before


title: ChIPSeq_H3K9me2_Ser_1

source_name: ChIPSeq H3K9me2 Ser 1


title: RRBS_TET_TKO_168h2i_1

source_name: RRBS TET TKO 168h2i 1


title: shRNA RNA-seq from HepG2 (ENCLB875XIP)

description:
https://www.encodeproject.org/experiments/ENCSR610AEI/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RBM25 in HepG2 cells followed by RNA-seq. (RBM25-BGHLV12)
experiment encode accession: ENCSR610AEI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR603TCV
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB875XIP
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting RBM25

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/33a4cc35-79dc-42c2-a8a6-3eac9a093296/@@download/attachment/L-RBM25-BGHLV12-65.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM25. (RBM25-BGHLV12-65)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS242YTF at ENCODE; https://www.encodeproject.org/ENCBS242YTF/

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

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


title: shRNA RNA-seq from HepG2 (ENCLB363LPJ)

description:
https://www.encodeproject.org/experiments/ENCSR610AEI/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against RBM25 in HepG2 cells followed by RNA-seq. (RBM25-BGHLV12)
experiment encode accession: ENCSR610AEI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR603TCV
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB363LPJ
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b73a2f14-689b-49e5-9710-f80c4d07463c/@@download/attachment/L-RBM25-BGHLV12-66.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM25. (RBM25-BGHLV12-66)

value: ENCBS912TCF at ENCODE; https://www.encodeproject.org/ENCBS912TCF/


title: RRBS_TET_TKO_96h2i_1

source_name: RRBS TET TKO 96h2i 1

value: ESC


title: shRNA RNA-seq from HepG2 (ENCLB935HOL)

description:
https://www.encodeproject.org/experiments/ENCSR603TCV/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHLV12-93-94)
experiment encode accession: ENCSR603TCV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB935HOL
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/dcc706b7-cbd2-4664-bb32-c294f442ee18/@@download/attachment/L-NT-BGHLV12-94.pdf

value: Control

value: RNA-seq on HepG2 cells treated with an Control shRNA against no target (NT-BGHLV12-02-94)

value: ENCBS638ASL at ENCODE; https://www.encodeproject.org/ENCBS638ASL/


title: RRBS_TET_TKO_ser_2

source_name: RRBS TET TKO ser 2


title: RRBS_TET_TKO_48h2i_2

source_name: RRBS TET TKO 48h2i 2


title: RRBS_TET_WT_168h2i_1

source_name: RRBS TET WT 168h2i 1

value: Wild-type


title: RRBS_TET_TKO_96h2i_2

source_name: RRBS TET TKO 96h2i 2


title: RRBS_TET_TKO_48h2i_1

source_name: RRBS TET TKO 48h2i 1


title: RRBS_TET_TKO_ser_1

source_name: RRBS TET TKO ser 1


title: RRBS_TET_WT_96h2i_1

source_name: RRBS TET WT 96h2i 1


title: RRBS_TET_WT_96h2i_2

source_name: RRBS TET WT 96h2i 2


title: RRBS_TET_WT_48h2i_2

source_name: RRBS TET WT 48h2i 2


title: RRBS_TET_WT_48h2i_1

source_name: RRBS TET WT 48h2i 1


title: RRBS_TET_WT_ser_2

source_name: RRBS TET WT ser 2


title: shRNA RNA-seq from HepG2 (ENCLB519QTS)

description:
https://www.encodeproject.org/experiments/ENCSR597XHH/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SRSF9 in HepG2 cells followed by RNA-seq. (SRSF9-BGHLV12)
experiment encode accession: ENCSR597XHH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR603TCV
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB519QTS
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SRSF9

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d7aa34a1-ba00-47ff-be03-7c31293a13a9/@@download/attachment/L-SRSF9-BGHLV12-79.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SRSF9. (SRSF9-BGHLV12-79)

value: Brenton Graveley, UConn

value: ENCBS937LVM at ENCODE; https://www.encodeproject.org/ENCBS937LVM/


title: shRNA RNA-seq from HepG2 (ENCLB063LKH)

description:
https://www.encodeproject.org/experiments/ENCSR597IYB/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against EXOSC9 in HepG2 cells followed by RNA-seq. (EXOSC9 BGHLV14)
experiment encode accession: ENCSR597IYB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR003EKR
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB063LKH
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting EXOSC9

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0dd40b68-8b86-433f-8588-5e20fa9ba3c5/@@download/attachment/L-EXOSC9_BGHLV14-18.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against EXOSC9. (EXOSC9_BGHLV14-18)

value: 15 year

value: child

value: ENCBS479RLA at ENCODE; https://www.encodeproject.org/ENCBS479RLA/


title: RRBS_TET_WT_ser_1

source_name: RRBS TET WT ser 1


title: shRNA RNA-seq from HepG2 (ENCLB879LSE)

description:
https://www.encodeproject.org/experiments/ENCSR597IYB/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against EXOSC9 in HepG2 cells followed by RNA-seq. (EXOSC9 BGHLV14)
experiment encode accession: ENCSR597IYB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR003EKR
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB879LSE
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f21ec0c0-a7b4-4d09-902e-822c969b97d5/@@download/attachment/L-EXOSC9_BGHLV14-17.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against EXOSC9. (EXOSC9_BGHLV14-17)

value: male

value: hepatocellular carcinoma

value: ENCBS341ITG at ENCODE; https://www.encodeproject.org/ENCBS341ITG/

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


title: RRBS_UHRF1_KO_168h2i_2

source_name: RRBS UHRF1 KO 168h2i 2

value: ESC


title: shRNA RNA-seq from K562 (ENCLB811MJH)

description:
https://www.encodeproject.org/experiments/ENCSR577XBW/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against FXR2 in K562 cells followed by RNA-seq. (FXR2-LV08)
experiment encode accession: ENCSR577XBW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB811MJH
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting FXR2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/97e9a26b-b875-4ce4-b71a-6d9f0ae14a19/@@download/attachment/L-FXR2-LV08-32.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against FXR2. (FXR2-LV08-32)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS645RVR at ENCODE; https://www.encodeproject.org/ENCBS645RVR/

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

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


title: RRBS_UHRF1_KO_96h2i_1

source_name: RRBS UHRF1 KO 96h2i 1


title: RRBS_UHRF1_KO_96h2i_2

source_name: RRBS UHRF1 KO 96h2i 2


title: RRBS_UHRF1_KO_168h2i_1

source_name: RRBS UHRF1 KO 168h2i 1


title: shRNA RNA-seq from HepG2 (ENCLB268NYD)

description:
https://www.encodeproject.org/experiments/ENCSR603TCV/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHLV12-93-94)
experiment encode accession: ENCSR603TCV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB268NYD
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/44b4b76e-c323-45f9-aff8-07eef1e9caf0/@@download/attachment/L-NT-BGHLV12-93.pdf

value: Control

value: RNA-seq on HepG2 cells treated with an Control shRNA against no target (NT-BGHLV12-01-93)

value: 15 year

value: child

value: Brenton Graveley, UConn

value: ENCBS623BZF at ENCODE; https://www.encodeproject.org/ENCBS623BZF/

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


title: shRNA RNA-seq from K562 (ENCLB809VKL)

description:
https://www.encodeproject.org/experiments/ENCSR577XBW/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against FXR2 in K562 cells followed by RNA-seq. (FXR2-LV08)
experiment encode accession: ENCSR577XBW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB809VKL
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e83fb250-48c6-4555-9078-eaa3249ede1f/@@download/attachment/L-FXR2-LV08-31.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against FXR2. (FXR2-LV08-31)

value: ENCBS181AJG at ENCODE; https://www.encodeproject.org/ENCBS181AJG/


title: shRNA RNA-seq from HepG2 (ENCLB844JCM)

description:
https://www.encodeproject.org/experiments/ENCSR597XHH/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SRSF9 in HepG2 cells followed by RNA-seq. (SRSF9-BGHLV12)
experiment encode accession: ENCSR597XHH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR603TCV
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB844JCM
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7983be0f-9dfa-4d7e-a1bc-77d4bd8eaee8/@@download/attachment/L-SRSF9-BGHLV12-80.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SRSF9. (SRSF9-BGHLV12-80)

value: male

value: hepatocellular carcinoma

value: ENCBS810JOY at ENCODE; https://www.encodeproject.org/ENCBS810JOY/

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


title: RRBS_UHRF1_KO_72h2i_1

source_name: RRBS UHRF1 KO 72h2i 1

value: ESC


title: shRNA RNA-seq from HepG2 (ENCLB418FPY)

description:
https://www.encodeproject.org/experiments/ENCSR576GOW/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against RAVER1 in HepG2 cells followed by RNA-seq. (RAVER1 BGHLV14)
experiment encode accession: ENCSR576GOW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB418FPY
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting RAVER1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b4cdf15c-0b41-4d59-a4f0-9d53241b26ee/@@download/attachment/L-RAVER1_BGHLV14-34.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RAVER1. (RAVER1_BGHLV14-34)

value: ENCBS354ZLY at ENCODE; https://www.encodeproject.org/ENCBS354ZLY/


title: RRBS_UHRF1_KO_72h2i_2

source_name: RRBS UHRF1 KO 72h2i 2


title: RRBS_UHRF1_KO_48h2i_2

source_name: RRBS UHRF1 KO 48h2i 2


title: RRBS_UHRF1_KO_24h2i_2

source_name: RRBS UHRF1 KO 24h2i 2


title: RRBS_UHRF1_KO_48h2i_1

source_name: RRBS UHRF1 KO 48h2i 1


title: RRBS_UHRF1_WT_168h2i_2

source_name: RRBS UHRF1 WT 168h2i 2

value: Wild-type


title: RRBS_UHRF1_WT_168h2i_1

source_name: RRBS UHRF1 WT 168h2i 1


title: RRBS_UHRF1_KO_ser_2

source_name: RRBS UHRF1 KO ser 2


title: RRBS_UHRF1_KO_ser_1

source_name: RRBS UHRF1 KO ser 1


title: RRBS_UHRF1_KO_24h2i_1

source_name: RRBS UHRF1 KO 24h2i 1


title: shRNA RNA-seq from HepG2 (ENCLB518ANZ)

description:
https://www.encodeproject.org/experiments/ENCSR572AMC/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against RECQL in HepG2 cells followed by RNA-seq. (RECQL-BGHLV12)
experiment encode accession: ENCSR572AMC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR603TCV
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB518ANZ
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b24846a4-7b72-4ec3-9ec0-554fd032949a/@@download/attachment/L-RECQL-BGHLV12-72.pdf

value: RECQL

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RECQL. (RECQL-BGHLV12-72)

value: 15 year

value: ENCBS120JBW at ENCODE; https://www.encodeproject.org/ENCBS120JBW/


title: shRNA RNA-seq from K562 (ENCLB335UBZ)

description:
https://www.encodeproject.org/experiments/ENCSR561CBC/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against KHSRP in K562 cells followed by RNA-seq. (KHSRP-LV11)
experiment encode accession: ENCSR561CBC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB335UBZ
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/22130674-cc07-4214-b534-9341f4fbce5d/@@download/attachment/L-KHSRP-LV11-23.pdf

value: KHSRP

value: RNA-seq on K562 cells treated with an shRNA knockdown against KHSRP. (KHSRP-LV11-23)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS855MYK at ENCODE; https://www.encodeproject.org/ENCBS855MYK/

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

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


title: shRNA RNA-seq from HepG2 (ENCLB053CNL)

description:
https://www.encodeproject.org/experiments/ENCSR576GOW/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RAVER1 in HepG2 cells followed by RNA-seq. (RAVER1 BGHLV14)
experiment encode accession: ENCSR576GOW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB053CNL
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/232f94ea-a002-4e71-ac58-0c36b75f67b7/@@download/attachment/L-RAVER1_BGHLV14-33.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RAVER1. (RAVER1_BGHLV14-33)

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS854HTL at ENCODE; https://www.encodeproject.org/ENCBS854HTL/

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

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


title: RRBS_UHRF1_WT_96h2i_2

source_name: RRBS UHRF1 WT 96h2i 2

value: ESC

value: Wild-type


title: shRNA RNA-seq from HepG2 (ENCLB294EZL)

description:
https://www.encodeproject.org/experiments/ENCSR572AMC/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RECQL in HepG2 cells followed by RNA-seq. (RECQL-BGHLV12)
experiment encode accession: ENCSR572AMC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR603TCV
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB294EZL
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1d6447e8-035b-4bbb-a598-9024b370adf8/@@download/attachment/L-RECQL-BGHLV12-71.pdf

value: RECQL

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RECQL. (RECQL-BGHLV12-71)

value: 15 year

value: ENCBS133GYV at ENCODE; https://www.encodeproject.org/ENCBS133GYV/


title: RRBS_UHRF1_WT_72h2i_2

source_name: RRBS UHRF1 WT 72h2i 2

extract_protocol:
RRBS-Seq was performed as described previously (Smallwood et al, 2011)
Genomic DNA and total RNA were isolated from the samples using the Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions.
RNASeq: RNA was used for library preparation using TruSeq RNA Library Prep Kit v2 (Illumina) following the manufacturer’s instructions. Libraries were indexed either using Illumina Indexes and 50 bp single-end sequencing was performed on Illumina HiSeq 2000 instruments using TruSeq reagents (Illumina, San Diego, CA, USA), according to manufacturer’s instructions.
RRBS-Seq was performed as described previously (Smallwood et al, 2011)
ChIP-Seq: Cells were cross-linked with 1% methanol-free formaldehyde in fresh medium for 10 minutes. Cross-linking reaction was quenched with glycine at a final concentration of 0.2M. Cells were then washed twice with ice-cold PBS and harvested. Cell pellets were then resuspended in LB1 buffer (50 mM Hepes–KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA;10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100, protease inhibitors) for 10 minutes at 4°C, pelleted and resuspended in LB2 buffer (10 mM Tris–HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA, protease inhibitors) for 10 minutes at 4°C. Cells were pelleted, resuspended in LB3 buffer (10 mM Tris–HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na–Deoxycholate; 0.5% N-lauroylsarcosine, protease inhibitors) and sonicated using Misonix Sonicator 3000. After addition of Triton-X to a final concentration of 1%, the lysate was centrifuged at 20,000g for 10 minutes to pellet debris. Sonicate chromatin was then added to the bead-antibody complexes and incubated overnight at 4°C. Bead-antibody were prepared as follows: Protein G-coupled Dynabeads were incubated overnight with primary antibodies (anti-H3K9me2; Abcam ab1220) in PBS added with 5 mg/ml BSA. Beads were washed extensively with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCL), once with 1x TE buffer and eluted in 200ul of buffer containing 1% SDS and 0.1M NaHCO3. Cross-linking was reversed by incubation at 65°C overnight, followed by RNase A treatment at 37°C for 1 hour and Proteinase K treatment at 55°C for 2 hours. DNA was then extracted using Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions. Eluted DNA was then used to perform ChIP-Seq library preparation using the MicroPlex Library Preparation Kit v2 (Diagenode)
ChIP-BS-Seq: Cells were cross-linked with 1% methanol-free formaldehyde in fresh medium for 10 minutes. Cross-linking reaction was quenched with glycine at a final concentration of 0.2M. Cells were then washed twice with ice-cold PBS and harvested. Cell pellets were then resuspended in LB1 buffer (50 mM Hepes–KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA;10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100, protease inhibitors) for 10 minutes at 4°C, pelleted and resuspended in LB2 buffer (10 mM Tris–HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA, protease inhibitors) for 10 minutes at 4°C. Cells were pelleted, resuspended in LB3 buffer (10 mM Tris–HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na–Deoxycholate; 0.5% N-lauroylsarcosine, protease inhibitors) and sonicated using Misonix Sonicator 3000. After addition of Triton-X to a final concentration of 1%, the lysate was centrifuged at 20,000g for 10 minutes to pellet debris. Sonicate chromatin was then added to the bead-antibody complexes and incubated overnight at 4°C. Bead-antibody were prepared as follows: Protein G-coupled Dynabeads were incubated overnight with primary antibodies (anti-H3K9me2; Abcam ab1220) in PBS added with 5 mg/ml BSA. Beads were washed extensively with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCL), once with 1x TE buffer and eluted in 200ul of buffer containing 1% SDS and 0.1M NaHCO3. Cross-linking was reversed by incubation at 65°C overnight, followed by RNase A treatment at 37°C for 1 hour and Proteinase K treatment at 55°C for 2 hours. DNA was then extracted using Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions. Eluted DNA was then treated for WGBS as described before


title: RRBS_UHRF1_WT_72h2i_1

source_name: RRBS UHRF1 WT 72h2i 1


title: RRBS_UHRF1_WT_48h2i_2

source_name: RRBS UHRF1 WT 48h2i 2


title: RRBS_UHRF1_WT_48h2i_1

source_name: RRBS UHRF1 WT 48h2i 1


title: RRBS_UHRF1_WT_24h2i_2

source_name: RRBS UHRF1 WT 24h2i 2


title: RRBS_UHRF1_WT_24h2i_1

source_name: RRBS UHRF1 WT 24h2i 1


title: shRNA RNA-seq from K562 (ENCLB682GRV)

description:
https://www.encodeproject.org/experiments/ENCSR560AYQ/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against RBM34 in K562 cells followed by RNA-seq. (RBM34-LV11)
experiment encode accession: ENCSR560AYQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB682GRV
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting RBM34

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/34cf2911-394a-4eb9-a5cb-d360aca9102b/@@download/attachment/L-RBM34-LV11-44.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against RBM34. (RBM34-LV11-44)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS306NPK at ENCODE; https://www.encodeproject.org/ENCBS306NPK/


title: RRBS_UHRF1_WT_ser_2

source_name: RRBS UHRF1 WT ser 2


title: RRBS_UHRF1_WT_ser_1

source_name: RRBS UHRF1 WT ser 1


title: shRNA RNA-seq from K562 (ENCLB811VGS)

description:
https://www.encodeproject.org/experiments/ENCSR546MBH/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against EIF2S1 in K562 cells followed by RNA-seq. (EIF2S1-LV08)
experiment encode accession: ENCSR546MBH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB811VGS
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting EIF2S1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/aa62f151-8042-481a-8f99-7df2f4ddc428/@@download/attachment/L-EIF2S1-LV08-19.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against EIF2S1. (EIF2S1-LV08-19)

value: ENCBS603PMU at ENCODE; https://www.encodeproject.org/ENCBS603PMU/

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

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


title: RRBS_UHRF1_WT_96h2i_1

source_name: RRBS UHRF1 WT 96h2i 1

value: ESC

value: Wild-type


title: RRBS_E14_168h2i_2

source_name: RRBS E14 168h2i 2


title: RRBS_E14_168h2i_1

source_name: RRBS E14 168h2i 1


title: RRBS_E14_96h2i_2

source_name: RRBS E14 96h2i 2


title: shRNA RNA-seq from K562 (ENCLB171LPD)

description:
https://www.encodeproject.org/experiments/ENCSR545AIK/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against PCBP1 in K562 cells followed by RNA-seq. (PCBP1-LV11)
experiment encode accession: ENCSR545AIK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB171LPD
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting PCBP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/dbff74ce-8b5a-403d-bad1-312081730cef/@@download/attachment/L-PCBP1-LV11-29.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PCBP1. (PCBP1-LV11-29)

value: ENCBS413UCH at ENCODE; https://www.encodeproject.org/ENCBS413UCH/


title: shRNA RNA-seq from K562 (ENCLB579ENS)

description:
https://www.encodeproject.org/experiments/ENCSR546MBH/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against EIF2S1 in K562 cells followed by RNA-seq. (EIF2S1-LV08)
experiment encode accession: ENCSR546MBH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB579ENS
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6a76d217-a303-462b-a9b2-8f6d03d52d05/@@download/attachment/L-EIF2S1-LV08-20.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against EIF2S1. (EIF2S1-LV08-20)

value: ENCBS026IRF at ENCODE; https://www.encodeproject.org/ENCBS026IRF/


title: RRBS_E14_96h2i_1

source_name: RRBS E14 96h2i 1


title: RRBS_E14_72h2i_1

source_name: RRBS E14 72h2i 1


title: shRNA RNA-seq from K562 (ENCLB759JWZ)

description:
https://www.encodeproject.org/experiments/ENCSR545AIK/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against PCBP1 in K562 cells followed by RNA-seq. (PCBP1-LV11)
experiment encode accession: ENCSR545AIK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB759JWZ
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/42aff424-35e0-4044-a313-0f087704172e/@@download/attachment/L-PCBP1-LV11-30.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PCBP1. (PCBP1-LV11-30)

value: 53 year

value: ENCBS561DIS at ENCODE; https://www.encodeproject.org/ENCBS561DIS/


title: shRNA RNA-seq from K562 (ENCLB365YTZ)

description:
https://www.encodeproject.org/experiments/ENCSR561CBC/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against KHSRP in K562 cells followed by RNA-seq. (KHSRP-LV11)
experiment encode accession: ENCSR561CBC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB365YTZ
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/dbf01133-857e-454b-91dc-4ac1e5021280/@@download/attachment/L-KHSRP-LV11-24.pdf

value: KHSRP

value: RNA-seq on K562 cells treated with an shRNA knockdown against KHSRP. (KHSRP-LV11-24)

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS053JIZ at ENCODE; https://www.encodeproject.org/ENCBS053JIZ/


title: RRBS_E14_48h2i_2

source_name: RRBS E14 48h2i 2


title: RRBS_E14_72h2i_2

source_name: RRBS E14 72h2i 2


title: RRBS_E14_48h2i_1

source_name: RRBS E14 48h2i 1


title: shRNA RNA-seq from K562 (ENCLB354FDS)

description:
https://www.encodeproject.org/experiments/ENCSR560AYQ/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RBM34 in K562 cells followed by RNA-seq. (RBM34-LV11)
experiment encode accession: ENCSR560AYQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB354FDS
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6d67e3d9-a872-4bb8-b702-835b7892fbe6/@@download/attachment/L-RBM34-LV11-43.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against RBM34. (RBM34-LV11-43)

value: Brenton Graveley, UConn

value: ENCBS049QOP at ENCODE; https://www.encodeproject.org/ENCBS049QOP/

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


title: RRBS_E14_24h2i_1

source_name: RRBS E14 24h2i 1

value: ESC

value: Wild-type


title: shRNA RNA-seq from HepG2 (ENCLB503IXQ)

description:
https://www.encodeproject.org/experiments/ENCSR533HXS/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against EIF2C1 in HepG2 cells followed by RNA-seq. (EIF2C1 BGHLV14)
experiment encode accession: ENCSR533HXS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR003EKR
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB503IXQ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting AGO1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/28138897-95cf-48a9-9e90-db5023b348ee/@@download/attachment/L-EIF2C1_BGHLV14-14.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF2C1. (EIF2C1_BGHLV14-14)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS030ZIT at ENCODE; https://www.encodeproject.org/ENCBS030ZIT/

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

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


title: RRBS_E14_24h2i_2

source_name: RRBS E14 24h2i 2


title: shRNA RNA-seq from HepG2 (ENCLB416HXZ)

description:
https://www.encodeproject.org/experiments/ENCSR533HXS/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against EIF2C1 in HepG2 cells followed by RNA-seq. (EIF2C1 BGHLV14)
experiment encode accession: ENCSR533HXS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR003EKR
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB416HXZ
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4daedebd-d56c-48b5-9241-253a683dedee/@@download/attachment/L-EIF2C1_BGHLV14-13.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF2C1. (EIF2C1_BGHLV14-13)

value: ENCBS817NZJ at ENCODE; https://www.encodeproject.org/ENCBS817NZJ/


title: shRNA RNA-seq from HepG2 (ENCLB466HKN)

description:
https://www.encodeproject.org/experiments/ENCSR529QEZ/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against PRPF6 in HepG2 cells followed by RNA-seq. (PRPF6 BGHLV14)
experiment encode accession: ENCSR529QEZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB466HKN
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting PRPF6

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/29f1f822-9bb4-4850-a7b3-cbd6531e48ca/@@download/attachment/L-PRPF6_BGHLV14-31.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PRPF6. (PRPF6_BGHLV14-31)

value: ENCBS857THE at ENCODE; https://www.encodeproject.org/ENCBS857THE/


title: shRNA RNA-seq from HepG2 (ENCLB257QDM)

description:
https://www.encodeproject.org/experiments/ENCSR529QEZ/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against PRPF6 in HepG2 cells followed by RNA-seq. (PRPF6 BGHLV14)
experiment encode accession: ENCSR529QEZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB257QDM
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/04204be8-9c8f-4da5-b4fb-6ad3d0a7c609/@@download/attachment/L-PRPF6_BGHLV14-32.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PRPF6. (PRPF6_BGHLV14-32)

value: Brenton Graveley, UConn

value: ENCBS525TLA at ENCODE; https://www.encodeproject.org/ENCBS525TLA/


title: RRBS_E14_ser_2

source_name: RRBS E14 ser 2

value: ESC

value: Wild-type


title: RRBS_E14_ser_1

source_name: RRBS E14 ser 1


title: RNA_Seq_E14_2i_72h_2

description: ExpValuesRNASeq.txt

source_name: RNA Seq E14 2i 72h 2

extract_protocol:
RNASeq: RNA was used for library preparation using TruSeq RNA Library Prep Kit v2 (Illumina) following the manufacturer’s instructions. Libraries were indexed either using Illumina Indexes and 50 bp single-end sequencing was performed on Illumina HiSeq 2000 instruments using TruSeq reagents (Illumina, San Diego, CA, USA), according to manufacturer’s instructions.
Genomic DNA and total RNA were isolated from the samples using the Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions.
RNASeq: RNA was used for library preparation using TruSeq RNA Library Prep Kit v2 (Illumina) following the manufacturer’s instructions. Libraries were indexed either using Illumina Indexes and 50 bp single-end sequencing was performed on Illumina HiSeq 2000 instruments using TruSeq reagents (Illumina, San Diego, CA, USA), according to manufacturer’s instructions.
RRBS-Seq was performed as described previously (Smallwood et al, 2011)
ChIP-Seq: Cells were cross-linked with 1% methanol-free formaldehyde in fresh medium for 10 minutes. Cross-linking reaction was quenched with glycine at a final concentration of 0.2M. Cells were then washed twice with ice-cold PBS and harvested. Cell pellets were then resuspended in LB1 buffer (50 mM Hepes–KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA;10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100, protease inhibitors) for 10 minutes at 4°C, pelleted and resuspended in LB2 buffer (10 mM Tris–HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA, protease inhibitors) for 10 minutes at 4°C. Cells were pelleted, resuspended in LB3 buffer (10 mM Tris–HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na–Deoxycholate; 0.5% N-lauroylsarcosine, protease inhibitors) and sonicated using Misonix Sonicator 3000. After addition of Triton-X to a final concentration of 1%, the lysate was centrifuged at 20,000g for 10 minutes to pellet debris. Sonicate chromatin was then added to the bead-antibody complexes and incubated overnight at 4°C. Bead-antibody were prepared as follows: Protein G-coupled Dynabeads were incubated overnight with primary antibodies (anti-H3K9me2; Abcam ab1220) in PBS added with 5 mg/ml BSA. Beads were washed extensively with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCL), once with 1x TE buffer and eluted in 200ul of buffer containing 1% SDS and 0.1M NaHCO3. Cross-linking was reversed by incubation at 65°C overnight, followed by RNase A treatment at 37°C for 1 hour and Proteinase K treatment at 55°C for 2 hours. DNA was then extracted using Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions. Eluted DNA was then used to perform ChIP-Seq library preparation using the MicroPlex Library Preparation Kit v2 (Diagenode)
ChIP-BS-Seq: Cells were cross-linked with 1% methanol-free formaldehyde in fresh medium for 10 minutes. Cross-linking reaction was quenched with glycine at a final concentration of 0.2M. Cells were then washed twice with ice-cold PBS and harvested. Cell pellets were then resuspended in LB1 buffer (50 mM Hepes–KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA;10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100, protease inhibitors) for 10 minutes at 4°C, pelleted and resuspended in LB2 buffer (10 mM Tris–HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA, protease inhibitors) for 10 minutes at 4°C. Cells were pelleted, resuspended in LB3 buffer (10 mM Tris–HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na–Deoxycholate; 0.5% N-lauroylsarcosine, protease inhibitors) and sonicated using Misonix Sonicator 3000. After addition of Triton-X to a final concentration of 1%, the lysate was centrifuged at 20,000g for 10 minutes to pellet debris. Sonicate chromatin was then added to the bead-antibody complexes and incubated overnight at 4°C. Bead-antibody were prepared as follows: Protein G-coupled Dynabeads were incubated overnight with primary antibodies (anti-H3K9me2; Abcam ab1220) in PBS added with 5 mg/ml BSA. Beads were washed extensively with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCL), once with 1x TE buffer and eluted in 200ul of buffer containing 1% SDS and 0.1M NaHCO3. Cross-linking was reversed by incubation at 65°C overnight, followed by RNase A treatment at 37°C for 1 hour and Proteinase K treatment at 55°C for 2 hours. DNA was then extracted using Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions. Eluted DNA was then treated for WGBS as described before


title: shRNA RNA-seq from K562 (ENCLB352CGS)

description:
https://www.encodeproject.org/experiments/ENCSR529JNJ/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against HNRNPK in K562 cells followed by RNA-seq. (HNRNPK-LV11)
experiment encode accession: ENCSR529JNJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB352CGS
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/766c74aa-8697-4799-962d-27b4b1839981/@@download/attachment/L-HNRNPK-LV11-15.pdf

value: HNRNPK

value: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPK. (HNRNPK-LV11-15)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS153VBF at ENCODE; https://www.encodeproject.org/ENCBS153VBF/

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

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


title: RNA_Seq_E14_2i_72h_1

description: ExpValuesRNASeq.txt

source_name: RNA Seq E14 2i 72h 1


title: RNA_Seq_E14_2i_24h_3

description: ExpValuesRNASeq.txt

source_name: RNA Seq E14 2i 24h 3


title: RNA_Seq_E14_2i_6h_3

description: ExpValuesRNASeq.txt

source_name: RNA Seq E14 2i 6h 3


title: shRNA RNA-seq from K562 (ENCLB449OXL)

description:
https://www.encodeproject.org/experiments/ENCSR529JNJ/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against HNRNPK in K562 cells followed by RNA-seq. (HNRNPK-LV11)
experiment encode accession: ENCSR529JNJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB449OXL
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1ff3ea8e-992f-4642-b534-dab00d5f15ad/@@download/attachment/L-HNRNPK-LV11-16.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPK. (HNRNPK-LV11-16)

value: ENCBS871KRX at ENCODE; https://www.encodeproject.org/ENCBS871KRX/


title: RNA_Seq_E14_2i_24h_1

description: ExpValuesRNASeq.txt

source_name: RNA Seq E14 2i 24h 1


title: RNA_Seq_E14_2i_24h_2

description: ExpValuesRNASeq.txt

source_name: RNA Seq E14 2i 24h 2


title: RNA_Seq_E14_2i_6h_2

description: ExpValuesRNASeq.txt

source_name: RNA Seq E14 2i 6h 2


title: shRNA RNA-seq from K562 (ENCLB734AEK)

description:
https://www.encodeproject.org/experiments/ENCSR527IVX/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against PTBP1 in K562 cells followed by RNA-seq. (PTBP1-LV11)
experiment encode accession: ENCSR527IVX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB734AEK
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting PTBP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/22c7d085-5526-49d2-88c0-b7bdb939027d/@@download/attachment/L-PTBP1-LV11-36.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PTBP1. (PTBP1-LV11-36)

value: ENCBS600EDY at ENCODE; https://www.encodeproject.org/ENCBS600EDY/


title: RNA_Seq_E14_2i_6h_1

description: ExpValuesRNASeq.txt

source_name: RNA Seq E14 2i 6h 1


title: RNA_Seq_E14_ser_1

description: ExpValuesRNASeq.txt

source_name: RNA Seq E14 ser 1


title: RNA_Seq_E14_ser_2

description: ExpValuesRNASeq.txt

source_name: RNA Seq E14 ser 2


title: shRNA RNA-seq from HepG2 (ENCLB873ZLB)

description:
https://www.encodeproject.org/experiments/ENCSR500WHE/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against XRCC6 in HepG2 cells followed by RNA-seq. (XRCC BGHLV14)
experiment encode accession: ENCSR500WHE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB873ZLB
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting XRCC6

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4666a200-a700-41ca-a39e-f9811b974101/@@download/attachment/L-XRCC6_BGHLV14-70.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against XRCC6. (XRCC6_BGHLV14-70)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS019LAC at ENCODE; https://www.encodeproject.org/ENCBS019LAC/

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

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


title: shRNA RNA-seq from K562 (ENCLB663UDQ)

description:
https://www.encodeproject.org/experiments/ENCSR527IVX/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against PTBP1 in K562 cells followed by RNA-seq. (PTBP1-LV11)
experiment encode accession: ENCSR527IVX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB663UDQ
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/66641fc6-f2b1-4268-85de-a5217959bee1/@@download/attachment/L-PTBP1-LV11-35.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PTBP1. (PTBP1-LV11-35)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS870PSR at ENCODE; https://www.encodeproject.org/ENCBS870PSR/


title: RNA_Seq_E14_2i_72h_3

description: ExpValuesRNASeq.txt

source_name: RNA Seq E14 2i 72h 3

value: ESC

value: Wild-type


title: shRNA RNA-seq from HepG2 (ENCLB420LUW)

description:
https://www.encodeproject.org/experiments/ENCSR492UFS/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against MATR3 in HepG2 cells followed by RNA-seq. (MATR3 17-BGHLV12)
experiment encode accession: ENCSR492UFS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB420LUW
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting MATR3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/422d7fef-15db-4d8e-9cc0-28263b2dbb4c/@@download/attachment/L-MATR3_17-BGHLV12-49.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against MATR3. (MATR3_17-BGHLV12-49)

value: ENCBS301LDQ at ENCODE; https://www.encodeproject.org/ENCBS301LDQ/


city: San Francisco

first: UCSF-UBC

last: CENTER

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: miRNA-Seq analysis of H1 embryonic stem cell line (m00741) using Illumina Genome Analyzer IIx
library name: m00741
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RIN N/A
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: N/A ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

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

tag: submitted sample id

value: cell line

value: male

tag: body site

value: Embryo ICM

tag: histological type

value: Embryonic stem cell

tag: is tumor

value: No


title: shRNA RNA-seq from HepG2 (ENCLB634VMX)

description:
https://www.encodeproject.org/experiments/ENCSR491FOC/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT BGHLV14)
experiment encode accession: ENCSR491FOC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB634VMX
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5d5c566e-d572-4a61-bb40-33341afbed1e/@@download/attachment/L-NT_BGHLV14-2.pdf

tag: antibody

value: Control

tag: line

tag: description

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

tag: biosample encode accession

value: 15 year

value: child

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

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

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

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


title: shRNA RNA-seq from HepG2 (ENCLB010AEB)

description:
https://www.encodeproject.org/experiments/ENCSR478FJK/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against IGF2BP2 in HepG2 cells followed by RNA-seq. (IGF2BP2-BGHLV12)
experiment encode accession: ENCSR478FJK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB010AEB
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting IGF2BP2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/df14af59-74e1-4984-9f92-5bf8f74e8fbf/@@download/attachment/L-IGF2BP2-BGHLV12-42.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against IGF2BP2. (IGF2BP2-BGHLV12-42)

tag: age

tag: dev stage

tag: Sex

tag: health state

value: ENCBS511ZQV at ENCODE; https://www.encodeproject.org/ENCBS511ZQV/


title: shRNA RNA-seq from HepG2 (ENCLB701RLL)

description:
https://www.encodeproject.org/experiments/ENCSR485ZTC/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against DDX21 in HepG2 cells followed by RNA-seq. (DDX21 BGHLV14)
experiment encode accession: ENCSR485ZTC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR003EKR
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB701RLL
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting DDX21

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/614634c7-04a9-49a3-97a1-1da406898511/@@download/attachment/L-DDX21_BGHLV14-9.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX21. (DDX21_BGHLV14-9)

tag: lab

tag: link

value: ENCBS793GXQ at ENCODE; https://www.encodeproject.org/ENCBS793GXQ/


title: shRNA RNA-seq from HepG2 (ENCLB848OMP)

description:
https://www.encodeproject.org/experiments/ENCSR491FOC/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT BGHLV14)
experiment encode accession: ENCSR491FOC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB848OMP
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7462b134-6fc6-4c07-9501-e72abdb0c24d/@@download/attachment/L-NT_BGHLV14-1.pdf

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

value: male

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


title: shRNA RNA-seq from HepG2 (ENCLB495XFU)

description:
https://www.encodeproject.org/experiments/ENCSR478FJK/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against IGF2BP2 in HepG2 cells followed by RNA-seq. (IGF2BP2-BGHLV12)
experiment encode accession: ENCSR478FJK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB495XFU
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/27ab20e9-7187-4ec0-a162-162e61511fca/@@download/attachment/L-IGF2BP2-BGHLV12-41.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against IGF2BP2. (IGF2BP2-BGHLV12-41)

value: ENCBS016WDR at ENCODE; https://www.encodeproject.org/ENCBS016WDR/


title: RNA_Seq_E14_ser_3

description: ExpValuesRNASeq.txt

source_name: RNA Seq E14 ser 3

tag: background strain

tag: cell type

value: ESC

tag: genotype

value: Wild-type


title: shRNA RNA-seq from K562 (ENCLB915VNI)

description:
https://www.encodeproject.org/experiments/ENCSR464ADT/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SRSF7 in K562 cells followed by RNA-seq. (SRSF7-LV11)
experiment encode accession: ENCSR464ADT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB915VNI
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting SRSF7

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c8dc6068-14ae-4341-8f71-0e25b14bddb7/@@download/attachment/L-SRSF7-LV11-54.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SRSF7. (SRSF7-LV11-54)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS626OHB at ENCODE; https://www.encodeproject.org/ENCBS626OHB/

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

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


title: shRNA RNA-seq from K562 (ENCLB661NRH)

description:
https://www.encodeproject.org/experiments/ENCSR464ADT/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SRSF7 in K562 cells followed by RNA-seq. (SRSF7-LV11)
experiment encode accession: ENCSR464ADT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB661NRH
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/82d634f3-eb23-4496-a4f1-7c2fd74b1ecb/@@download/attachment/L-SRSF7-LV11-53.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against SRSF7. (SRSF7-LV11-53)

value: Brenton Graveley, UConn

value: ENCBS182RTT at ENCODE; https://www.encodeproject.org/ENCBS182RTT/


title: microRNA-seq from H1-hESC (ENCLB501BZS)

description:
https://www.encodeproject.org/experiments/ENCSR430YFL/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human H1-hESC
experiment encode accession: ENCSR430YFL
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-02-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB501BZS
size range: <30

source_name: Homo sapiens H1-hESC stem cell male embryo

value: stem cell

value: embryonic stem cells

value: unknown

value: embryonic

value: male

value: healthy

value: Barbara Wold, Caltech

value: ENCBS051SJH at ENCODE; https://www.encodeproject.org/ENCBS051SJH/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/

value: ENCODE dbxrefs Cellosaurus CVCL_9771; http://web.expasy.org/cellosaurus/CVCL_9771

value: ENCODE dbxrefs H1-hESC; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=H1-hESC


title: shRNA RNA-seq from HepG2 (ENCLB069ZEJ)

description:
https://www.encodeproject.org/experiments/ENCSR500WHE/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against XRCC6 in HepG2 cells followed by RNA-seq. (XRCC BGHLV14)
experiment encode accession: ENCSR500WHE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB069ZEJ
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d1e53bc1-35e0-42d5-b36c-76d9edf45081/@@download/attachment/L-XRCC6_BGHLV14-69.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against XRCC6. (XRCC6_BGHLV14-69)

value: 15 year

value: child

value: hepatocellular carcinoma

value: ENCBS104QEK at ENCODE; https://www.encodeproject.org/ENCBS104QEK/

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

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


title: microRNA-seq from H1-hESC (ENCLB323PIN)

description:
https://www.encodeproject.org/experiments/ENCSR430YFL/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human H1-hESC
experiment encode accession: ENCSR430YFL
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-02-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB323PIN
size range: <30

value: stem cell

value: embryonic stem cells

value: ENCBS716AAA at ENCODE; https://www.encodeproject.org/ENCBS716AAA/


title: shRNA RNA-seq from HepG2 (ENCLB102PAG)

description:
https://www.encodeproject.org/experiments/ENCSR455VZH/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against PABPC4 in HepG2 cells followed by RNA-seq. (PABPC4-BGHLV12)
experiment encode accession: ENCSR455VZH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB102PAG
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting PABPC4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/fa748129-439b-4e7b-9cf7-d745e582425f/@@download/attachment/L-PABPC4-BGHLV12-54.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PABPC4. (PABPC4-BGHLV12-54)

value: male

value: Brenton Graveley, UConn

value: ENCBS354PIF at ENCODE; https://www.encodeproject.org/ENCBS354PIF/


title: shRNA RNA-seq from K562 (ENCLB087WMO)

description:
https://www.encodeproject.org/experiments/ENCSR694LKY/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against TIA1 in K562 cells followed by RNA-seq. (TIA1-LV11)
experiment encode accession: ENCSR694LKY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB087WMO
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting TIA1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/89b09ce6-9d11-47fb-96fa-132576e94b2b/@@download/attachment/L-TIA1-LV11-60.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against TIA1. (TIA1-LV11-60)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS757HMX at ENCODE; https://www.encodeproject.org/ENCBS757HMX/

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

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


title: shRNA RNA-seq from HepG2 (ENCLB280IGO)

description:
https://www.encodeproject.org/experiments/ENCSR424YSV/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against AATF in HepG2 cells followed by RNA-seq. (AATF BGHLV14)
experiment encode accession: ENCSR424YSV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR003EKR
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB280IGO
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0cd48076-fd96-438e-a679-aecb6e313ad6/@@download/attachment/L-AATF_BGHLV14-3.pdf

value: AATF

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against AATF. (AATF_BGHLV14-3)

value: 15 year

value: child

value: hepatocellular carcinoma

value: ENCBS023JBH at ENCODE; https://www.encodeproject.org/ENCBS023JBH/

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

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


title: shRNA RNA-seq from HepG2 (ENCLB245IZU)

description:
https://www.encodeproject.org/experiments/ENCSR455VZH/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against PABPC4 in HepG2 cells followed by RNA-seq. (PABPC4-BGHLV12)
experiment encode accession: ENCSR455VZH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB245IZU
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8925311a-0b0c-4b29-8975-911d5c15332f/@@download/attachment/L-PABPC4-BGHLV12-53.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PABPC4. (PABPC4-BGHLV12-53)

value: male

value: Brenton Graveley, UConn

value: ENCBS896YYX at ENCODE; https://www.encodeproject.org/ENCBS896YYX/


title: shRNA RNA-seq from HepG2 (ENCLB695KHS)

description:
https://www.encodeproject.org/experiments/ENCSR492UFS/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against MATR3 in HepG2 cells followed by RNA-seq. (MATR3 17-BGHLV12)
experiment encode accession: ENCSR492UFS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB695KHS
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4bae9a0d-9519-4979-911e-ddfa00b3ade6/@@download/attachment/L-MATR3_17-BGHLV12-50.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against MATR3. (MATR3_17-BGHLV12-50)

value: ENCBS204FOO at ENCODE; https://www.encodeproject.org/ENCBS204FOO/


title: shRNA RNA-seq from HepG2 (ENCLB057GGB)

description:
https://www.encodeproject.org/experiments/ENCSR424YSV/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against AATF in HepG2 cells followed by RNA-seq. (AATF BGHLV14)
experiment encode accession: ENCSR424YSV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR003EKR
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB057GGB
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/fd40c901-ef62-4171-a428-e187b2c8e67e/@@download/attachment/L-AATF_BGHLV14-4.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against AATF. (AATF_BGHLV14-4)

value: ENCBS557NDG at ENCODE; https://www.encodeproject.org/ENCBS557NDG/


title: shRNA RNA-seq from HepG2 (ENCLB445HTU)

description:
https://www.encodeproject.org/experiments/ENCSR410UHJ/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against RPS10 in HepG2 cells followed by RNA-seq. (RPS10 BGHLV14)
experiment encode accession: ENCSR410UHJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB445HTU
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting RPS10

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1ff7b9c9-226d-42f0-8b9a-5cb57bcd4ba4/@@download/attachment/L-RPS10_BGHLV14-42.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RPS10. (RPS10_BGHLV14-42)

value: ENCBS476TPW at ENCODE; https://www.encodeproject.org/ENCBS476TPW/


title: shRNA RNA-seq from HepG2 (ENCLB562IJY)

description:
https://www.encodeproject.org/experiments/ENCSR398LZW/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SND1 in HepG2 cells followed by RNA-seq. (SND1 BGHLV14)
experiment encode accession: ENCSR398LZW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB562IJY
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SND1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/55d481de-f641-41af-ae4d-e49726260a3a/@@download/attachment/L-SND1_BGHLV14-51.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SND1. (SND1_BGHLV14-51)

value: 15 year

value: ENCBS338VUB at ENCODE; https://www.encodeproject.org/ENCBS338VUB/