title: Uhrf_TKOL_rep2

status: Public on Jun 18 2021

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

institute: Max Planck Institute for Molecular Genetics

description: ChIPmentation

data_processing:
The ChIPseq data as well as the control input sequencing were aligned to the mouse mm9 reference genome using BWA mem using the default parameter. Duplicate reads were removed using GATK MarkDuplicates (v4.1.0.0).
Peaks were called using the MACS2 peakcall (2.1.2_dev) function with default parameters.
Genome build: mm9
processed data files format and content: bigWig coverage files

source_name: J1 mESC

growth_protocol: mES cells were cultured in Knock Out DMEM media (Gibco) containing 15% FBS, 1% PEN/STREP, 1% glutamine, 1% NEAA, and 105 U LIF. For ES cell maintenance, dishes were coated with 0.2% gelatin and irradiated CD1 mouse embryonic fibroblasts (MEFs) were plated as a confluent layer of feeder cells. mES cells were seeded at a density of 50,000 cells per well of a six-well plate and were split every 3–4 days.

extract_protocol:
Cells were washed once with PBS and fixed with 1% formaldehyde (methanol-free) for 10 minutes at room temperature with rotation. The formaldehyde was quenched with 125 mM glycine for five minutes at room temperature. Cells were spun at 500g for 10 minutes at 4°C and washed twice with ice-cold PBS supplemented with Protease Inhibitor cOmpleteTM. Subsequent work was performed on ice and with buffers cooled to 4°C. The pellet was lysed in L3B buffer (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Sodium Deoxycholate (DOC), 0.5% N-lauroylsarcosine, 1x protease inhibitors) and sonicated in a 130 µL milliTUBE in a Covaris E220 for 7 min until most of the fragments were 200- 700 base pairs long (settings: duty cycle 5%, peak incident power 140 Watts, cycles per burst 200). Lysates were supplemented with 1% Triton-X-100 and centrifuged at full speed for five minutes at 4°C, the supernatant containing the sonicated chromatin was transferred to a new tube.
In parallel, Protein G magnetic beads (Invitrogen) were blocked and conjugated to an antibody by washing them twice in PBS with 0.5% BSA and resuspended in 200 μl of PBS with 0.5% BSA per IP. Anti-Flag (1 μg, Millipore/Sigma F1804) was added and bound to the beads by rotating >1 hour at room temperature. Blocked antibody conjugated magnetic beads were added to the tube containing the chromatin and incubated over night at 4°C. The beads were then washed twice with each of the following: TFWBI (20 mM Tris-HCl/pH 7.4, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA), TF-WBIII (250 mM LiCl, 1% Triton X-100, 0.7% DOC, 10 mM Tris-HCl/pH 8, 1 mM EDTA), and 10 mM Tris-HCl pH8. Beads were resuspended in 24 μl of tagmentation buffer and 1 μl of Tn5 transposase (Illumina 15027866, 15027865) and then incubated at 37ºC for five minutes in a thermocycler. Tagmentation reactions were removed and beads were washed twice with WBI and TET (0.2% Tween-20, 10 mM Tris-HCl/pH 8.0, 1 mM EDTA) (twice). Beads were then incubated with 70 μl elution buffer (0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris HCl pH 8.0) containing 2 μl of Proteinase K (NEB) for 1 hour at 55°C and 8 hours at 65°C to reverse crosslink, and supernatant was transferred to a new tube. Another 30 μl of elution buffer was added to the beads and incubated with another 1 μl of Proteinase K for 1 hour at 55°C, eluates were combined. Finally, DNA was purified with AMPure XP beads (sample-to-beads ratio 1:2). Relative quantitation was performed using SYBR-green as in (Schmidl et al, 2015; PMID:26280331) using 2 μl of DNA. Libraries were amplified according to the Cq values obtained in the previous step (12 cycles were used), purified using AMPure XP beads and eluted in 15 μl of water.

value: mESC

value: Dnmt3a + Dnmt3b KO + Dnmt1 shRNA + Uhrf1 FLAG TAG


title: Trim28_DKO0_rep1

type: SRA

country: Germany

description: ChIP-seq

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
5 (histone) or 25 (Trim28) million cells were crosslinked with 1% FA for 5 or 8 minutes respectively at RT. Glycine was added to a final concentration of 125mM and mixed for 5 minutes at RT. Crosslinked cells were washed with DPBS 2x then spun down 3min 15000g.  Cells were then incubated with 500µL cell lysis buffer (20 mM Tris-HCl ph8.0, 85 mM KCl, 0.5% NP 40) for 10 minutes on ice then spun down for 3min at 2500g. Supernatant was removed and the cell pellet was resuspended in 500µL of nuclear lysis buffer (10 mM Tris–HCl, pH 7.5, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS) then incubated for 10 minutes on ice. Volume was increased to 1mL using Nuclei Lysis Buffer then sonicated on a Covaris E220 Evolution sonicator (PIP = 140.0, Duty Factor = 5.0, Cycles/Burst = 200, 10minutes).
After sonication, chromatin was spun down at 15000g for 10 minutes to pellet insoluble material. Volume was increased to 1.5mL with Chip Dilution Buffer (0.01% SDS, 1.1% Triton X-100,1.2mM EDTA, 16.7mM Tris-HCl pH 8.1, 167mM NaCl) and 2ug of H3K4me3 antibody (Abcam: ab8580), H3K36me3 (Active Motif 61101), H3K9me3 (Abcam, ab8898), or Trim28(Abcam, ab22553) were added. Immunoprecipitation mixture was allowed to rotate overnight at 4°C. The next day, 40µLs of Protein A Dynabeads (Thermo, 10001D) were added to the IP mixture and allowed to rotate for 4 hours at 4°C. This was followed by two washes of each: low salt wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl  pH 8.1, 150mM NaCl); high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20mM Tris, pH 8.1, 500 mM NaCl); LiCl wash buffer (0.25M LCl, 1% NP40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl pH 8.1); and TE buffer pH 8.0 (10mM Tris-HCl, pH 8.0, 1mM EDTA pH 8.0). DNA was eluted twice using 50µLs of elution buffer (0.5 to 1% SDS and 0.1 M NaHCO3) at 65°C for 15 minutes. 16µL of reverse crosslinking salt mixture (250 mM Tris-HCl, pH 6.5, 62.5 mM EDTA pH 8.0, 1.25 M NaCl, 5mg/ml Proteinase K) was added and samples were allowed to incubate at 65°C overnight. For library preparation, DNA was purified using AMPure XP beads (Beckman-Coulter) and treated with DNase-free RNase (Roche) for 30 minutes at 37 °C. DNA libraries were then end repaired and A-tailed using Ultra II End Repair/dA-Tailing Module (NEB) and adapters (Broad Institute, single index P7) were ligated using Blunt/TA Ligase Master Mix (NEB). Next, libraries were PCR amplified using Pfu Ultra II Fusion High-fidelity DNA Polymerase (Agilent) then size selected on a gel for fragments between 200-1000bp

tag: cell type

tag: strain

tag: genotype

value: Dnmt3a + Dnmt3b KO


title: Tbx18 Sham (Heart)

status: Public on Jun 19 2021

city: Los Angeles

first: Reza

last: Ardehali

state: CA

address: 675 Charles E Young Dr S

department: Internal Medicine, Division of Cardiology

country: USA

institute: David Geffen School of Medicine at UCLA

library_source: transcriptomic

data_processing:
CellRanger mkfastq was used to demultiplex the base call files
CellRanger (v3.0.2) count with mm10 genome reference was used to perform read alignment and UMI counting and generate filtered feature barcode matrices
Filtering cells (Seurat v3): minimum features >500
Filtering features (Seurat v3): minimum cells >3
Normalization (Seurat v3): logNormalization
Number of variable features: (Brain) 7500; (Heart) 2000
Scaling (Seurat v3, default): ScaleData
Batch correction (Seurat v3): FindIntegrationAnchors & IntegrateData; Heart(dim=20, anchor.features=2000); Brain(dim=75, anchor.features=7500)
Dimensional reduction (Seurat v3): RunPCA; Heart (pca, dim = 30); Brain (pca, dim = 50)
Clustering (Seurat v3): FindNeighbors (Heart: dim = 20; Brain: dim = 50); FindClusters (resolution = 0.5)
Differential expression (Seurat v3):FindMarkers (min.pct=0.25)
Genome_build: mm10
Supplementary_files_format_and_content: Data is from filtered feature-barcode matrices generated by cellranger count. mtx (matrix table of count values for genes and samples) and tsv files (features/cellular barcodes)

molecule: total RNA

source_name: Ventricles of the heart

growth_protocol: Intraperitoneal tamoxifen administration for 4 days followed by week washout period.

extract_protocol:
In the heart, atria were removed, and enzymatic digestion was performed using a Collagenase (Worthington) and Dispase (Sigma) mix. Cells were then sorted for tdT expression using fluorescence activated cell sorting. In the brain, cortical tissue was dissected and digested using the Miltenyi® Adult Brain Dissociation Kit. Cells were sorted for tdT expression using fluorescence activated cell sorting.
RNA libraries were prepared for sequencing using 3' 10X Genomics v.3

treatment_protocol: LAD ligation in the heart tissue. Photothrombosis in the brain tissue.

tag: tissue

value: heart

tag: treatment

value: Sham Surgery


title: Trim28_WT_rep2

description: ChIP-seq

source_name: V65 mESC

value: WT


title: Tbx18 MI Peri-Infarct

source_name: Peri-infarct area of Heart (minus atria)

value: LAD Ligation


title: Trim28_TKOL_rep2

description: ChIP-seq

value: Dnmt3a + Dnmt3b KO + Dnmt1 shRNA


title: Trim28_TKOL_rep1

description: ChIP-seq


title: Uhrf_TKOL_rep1

description: ChIPmentation


title: Trim28_DKO0_rep2

description: ChIP-seq


title: Trim28_WT_rep1

description: ChIP-seq


title: Uhrf_WT_rep2

description: ChIPmentation

value: WT + Uhrf1 FLAG TAG


title: Uhrf_DKO0_rep1

description: ChIPmentation

value: Dnmt3a + Dnmt3b KO + Uhrf1 FLAG TAG


title: Uhrf_WT_rep1

description: ChIPmentation


title: H3K9me3_WT_rep1

description: ChIP-seq


title: H3K9me3_TKOL_rep1

description: ChIP-seq


title: Uhrf_DKO0_rep2

description: ChIPmentation


title: H3K9me3_TKOL_rep2

description: ChIP-seq


title: Tbx18 Sham (Brain)

source_name: Brain

value: brain


title: Tbx18 Stroke Peri-Infarct

source_name: Peri-infarct area of Brain

value: PT Stroke


title: total RNA-seq from placenta (ENCLB784DQM)

status: Public on Jun 15 2021

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR899OKE/
***************
biological replicate number: 1
technical replicate number: 1
description: Stam Placenta 11008
experiment encode accession: ENCSR899OKE
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB784DQM
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

organism: Homo sapiens

source_name: Homo sapiens female embryo placenta tissue

value: placenta

value: tissue

tag: biosample encode accession

tag: Sex

value: female

tag: dev stage

value: embryonic

tag: age

value: not collected

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: John Stamatoyannopoulos

tag: link

value: ENCBS599XLB at ENCODE; https://www.encodeproject.org/ENCBS599XLB/

value: Derived from ENCODE donor ENCDO818SNP; https://www.encodeproject.org/ENCDO818SNP/


title: H3K9me3_DKO0_rep1

description: ChIP-seq

value: mESC

value: Dnmt3a + Dnmt3b KO


title: H3K9me3_DKO0_rep2

description: ChIP-seq


title: H3K9me3_WT_rep2

description: ChIP-seq

value: WT


title: shRNA RNA-seq from K562 (ENCLB881NBZ)

description:
https://www.encodeproject.org/experiments/ENCSR898ABR/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT-BGKLV36-D)
experiment encode accession: ENCSR898ABR
assay title: shRNA RNA-seq
assembly: GRCh38
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB881NBZ
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 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/8869138a-9c01-4dd5-9dfe-2d0c3dd19ceb/@@download/attachment/L-NT-BGKLV36-1D.pdf

tag: line

value: cell line

tag: description

value: RNA-seq on K562 cells treated with an shRNA knockdown against non-target. (NT_BGKLV36-1)

value: 53 year

value: adult

tag: health state

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS405CUM at ENCODE; https://www.encodeproject.org/ENCBS405CUM/

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


title: shRNA RNA-seq from K562 (ENCLB298XGW)

description:
https://www.encodeproject.org/experiments/ENCSR898ABR/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT-BGKLV36-D)
experiment encode accession: ENCSR898ABR
assay title: shRNA RNA-seq
assembly: GRCh38
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB298XGW
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0269b0cf-d861-4315-bd21-a56dd7fc3d5c/@@download/attachment/L-NT-BGKLV36-2D.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against non-target. (NT_BGKLV36-2)

value: female

value: ENCBS131LFM at ENCODE; https://www.encodeproject.org/ENCBS131LFM/


title: shRNA RNA-seq from K562 (ENCLB669KKH)

description:
https://www.encodeproject.org/experiments/ENCSR953IQF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against NUP35. (NUP35-BGKLV38-C)
experiment encode accession: ENCSR953IQF
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR260BQC
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB669KKH
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens K562 cell line expressing RNAi targeting NUP35

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b1570f64-2807-411f-b539-fb2117422fcb/@@download/attachment/L-NUP35-BGKLV38-41C.pdf

tag: antibody

value: RNA-seq on K562 cells treated with an shRNA knockdown against NUP35. (NUP35-BGKLV38-41C)

value: ATCC

value: ENCBS893MGB at ENCODE; https://www.encodeproject.org/ENCBS893MGB/


title: polyA plus RNA-seq from A549 (ENCLB234SUZ)

description:
https://www.encodeproject.org/experiments/ENCSR964GKZ/
***************
biological replicate number: 2
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 15 mins.
experiment encode accession: ENCSR964GKZ
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB234SUZ
fragmentation methods: chemical (RNase III)
size range: >200
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 15 minutes

extract_protocol:
treatment protocol: https://www.encodeproject.org/documents/c5b10eee-de7f-4845-a387-e73980ef5a19/@@download/attachment/RNA_DEX_treatment.pdf
general protocol: https://www.encodeproject.org/documents/5533fb32-41f1-4c7a-b62d-0095a33cab20/@@download/attachment/01_RNA_HARVEST_and_ISOLATION_Reddy_GGR.pdf
extraction protocol: https://www.encodeproject.org/documents/53726435-7acc-4248-a5df-3eef6ea3b422/@@download/attachment/02_Rev%20D%20Quick%20Reference%20Card%2C%20PrepX%20PolyA%2048%20Protocol.pdf
extraction protocol: https://www.encodeproject.org/documents/5f9d4f74-4e39-4818-9ee9-d8e9b8004ceb/@@download/attachment/03_RevC%20Quick%20Reference%20Card%2C%20PrepX%20mRNA%2048%20Protocol.pdf
extraction protocol: https://www.encodeproject.org/documents/c72e898e-82c7-478d-b043-8945133a7724/@@download/attachment/04_Rev%20C%20Quick%20Reference%20Card%2C%20PrepX%20PCR%20Cleanup%2048%20Protocol.pdf
general protocol: https://www.encodeproject.org/documents/7a683e77-85ac-45f9-b1fa-b6ceb50ca1bc/@@download/attachment/05_POST_RNA_LIB_PREP_Reddy_GGR.pdf
extraction method: RNeasy Plus Mini Kit Qiagen cat#74134 plus additional on column Dnase treatment

value: male

value: 58 year

value: Tim Reddy, Duke

tag: treatments

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:15; duration_units:minute;

value: ENCBS013HGJ at ENCODE; https://www.encodeproject.org/ENCBS013HGJ/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: polyA plus RNA-seq from A549 (ENCLB363UBQ)

description:
https://www.encodeproject.org/experiments/ENCSR964GKZ/
***************
biological replicate number: 1
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 15 mins.
experiment encode accession: ENCSR964GKZ
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB363UBQ
fragmentation methods: chemical (RNase III)
size range: >200
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: cell line

value: adult

value: ENCBS645JZI at ENCODE; https://www.encodeproject.org/ENCBS645JZI/


title: polyA plus RNA-seq from A549 (ENCLB940JYF)

description:
https://www.encodeproject.org/experiments/ENCSR964GKZ/
***************
biological replicate number: 3
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 15 mins.
experiment encode accession: ENCSR964GKZ
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB940JYF
fragmentation methods: chemical (RNase III)
size range: >200
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS326TJA at ENCODE; https://www.encodeproject.org/ENCBS326TJA/


title: shRNA RNA-seq from K562 (ENCLB459XYW)

description:
https://www.encodeproject.org/experiments/ENCSR953IQF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against NUP35. (NUP35-BGKLV38-C)
experiment encode accession: ENCSR953IQF
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR260BQC
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB459XYW
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0d1d9676-665e-433b-ab21-3afbb00d883a/@@download/attachment/L-NUP35-BGKLV38-42C.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against NUP35. (NUP35-BGKLV38-42C)

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS863OOF at ENCODE; https://www.encodeproject.org/ENCBS863OOF/

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


title: CRISPR RNA-seq from K562 (ENCLB474UTT)

description:
https://www.encodeproject.org/experiments/ENCSR972AZD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SRSF9. (SRSF9-BGKcLV06)
experiment encode accession: ENCSR972AZD
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR341TTW
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB474UTT
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting SRSF9

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/71bc0735-5e2f-42ba-9951-014521e984c7/@@download/attachment/L-SRSF9-BGKcLV06-36.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SRSF9. (SRSF9-BGKcLV06-36)

value: female

value: ATCC

value: ENCBS327DJT at ENCODE; https://www.encodeproject.org/ENCBS327DJT/


title: shRNA RNA-seq from K562 (ENCLB602OWI)

description:
https://www.encodeproject.org/experiments/ENCSR967QNT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against GPKOW. (GPKOW_BGKLV36)
experiment encode accession: ENCSR967QNT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR424QCW
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB602OWI
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

source_name: Homo sapiens K562 cell line expressing RNAi targeting GPKOW

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/bb4cd770-5c94-469a-a424-4224dd40c7d2/@@download/attachment/L-GPKOW_BGKLV36-28.pdf

value: GPKOW

value: RNA-seq on K562 cells treated with an shRNA knockdown against GPKOW. (GPKOW_BGKLV36-28)

value: ENCBS368KDK at ENCODE; https://www.encodeproject.org/ENCBS368KDK/


title: shRNA RNA-seq from HepG2 (ENCLB352YLJ)

description:
https://www.encodeproject.org/experiments/ENCSR997HCQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV37)
experiment encode accession: ENCSR997HCQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB352YLJ
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

source_name: Homo sapiens HepG2 cell line expressing RNAi

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/394c78e1-9c55-4355-8fa7-e58c6763b85e/@@download/attachment/L-NT_BGHLV37-2.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against non-target. (NT_BGHLV37-2)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS135CDE at ENCODE; https://www.encodeproject.org/ENCBS135CDE/

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


title: CRISPR RNA-seq from K562 (ENCLB944DOX)

description:
https://www.encodeproject.org/experiments/ENCSR889MBF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against TRNAU1AP. (TRNAU1AP-BGKcLV06)
experiment encode accession: ENCSR889MBF
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR341TTW
encode release date: 2017-12-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB944DOX
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting TRNAU1AP

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3173488c-e749-4278-ba76-94acabf74332/@@download/attachment/L-TRNAU1AP-BGKcLV06-39.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against TRNAU1AP. (TRNAU1AP-BGKcLV06-39)

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS993YVS at ENCODE; https://www.encodeproject.org/ENCBS993YVS/


title: CRISPR RNA-seq from HepG2 (ENCLB543MPG)

description:
https://www.encodeproject.org/experiments/ENCSR991XFO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DROSHA. (DROSHA_BGHcLV05)
experiment encode accession: ENCSR991XFO
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR481WJH
encode release date: 2017-01-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB543MPG
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting DROSHA

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/69575b1c-aa0b-48a9-94a9-a8fb68fa6135/@@download/attachment/L-DROSHA_BGHcLV05-13.pdf

value: DROSHA

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DROSHA. (DROSHA_BGHcLV05-13)

value: ATCC

value: ENCBS047KDJ at ENCODE; https://www.encodeproject.org/ENCBS047KDJ/


title: CRISPR RNA-seq from K562 (ENCLB858UZD)

description:
https://www.encodeproject.org/experiments/ENCSR972AZD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SRSF9. (SRSF9-BGKcLV06)
experiment encode accession: ENCSR972AZD
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR341TTW
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB858UZD
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5b52a69e-d852-415f-addd-8704015898ee/@@download/attachment/L-SRSF9-BGKcLV06-35.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SRSF9. (SRSF9-BGKcLV06-35)

value: female

value: ENCBS375GMU at ENCODE; https://www.encodeproject.org/ENCBS375GMU/

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


title: CRISPR RNA-seq from HepG2 (ENCLB972DDL)

description:
https://www.encodeproject.org/experiments/ENCSR959HPB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NOLC1. (NOLC1-BGHcLV07)
experiment encode accession: ENCSR959HPB
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR521WAI
encode release date: 2017-12-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB972DDL
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting NOLC1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3c507d23-3d2b-4340-af9b-c299c83082cf/@@download/attachment/L-NOLC1-BGHcLV07-19.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NOLC1. (NOLC1-BGHcLV07-19)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS989VXW at ENCODE; https://www.encodeproject.org/ENCBS989VXW/


title: CRISPR RNA-seq from K562 (ENCLB355TBA)

description:
https://www.encodeproject.org/experiments/ENCSR889MBF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against TRNAU1AP. (TRNAU1AP-BGKcLV06)
experiment encode accession: ENCSR889MBF
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR341TTW
encode release date: 2017-12-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB355TBA
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8a49e38f-1ca9-4fd2-aec5-82973498e334/@@download/attachment/L-TRNAU1AP-BGKcLV06-40.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against TRNAU1AP. (TRNAU1AP-BGKcLV06-40)

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS229BUY at ENCODE; https://www.encodeproject.org/ENCBS229BUY/


title: CRISPR RNA-seq from K562 (ENCLB196NNX)

description:
https://www.encodeproject.org/experiments/ENCSR974RYS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ZNF800. (ZNF800-BGKcLV06)
experiment encode accession: ENCSR974RYS
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR341TTW
encode release date: 2017-12-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB196NNX
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting ZNF800

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2d4808e9-7d31-4c61-a0e7-c2f7b5dac13f/@@download/attachment/L-ZNF800-BGKcLV06-47.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ZNF800. (ZNF800-BGKcLV06-47)

value: ATCC

value: ENCBS182NRR at ENCODE; https://www.encodeproject.org/ENCBS182NRR/


title: CRISPR RNA-seq from HepG2 (ENCLB337KXE)

description:
https://www.encodeproject.org/experiments/ENCSR991XFO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DROSHA. (DROSHA_BGHcLV05)
experiment encode accession: ENCSR991XFO
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR481WJH
encode release date: 2017-01-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB337KXE
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/da7cc632-9f5e-4005-9f74-a3f458c610a8/@@download/attachment/L-DROSHA_BGHcLV05-14.pdf

value: DROSHA

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DROSHA. (DROSHA_BGHcLV05-14)

value: ENCBS076OJD at ENCODE; https://www.encodeproject.org/ENCBS076OJD/

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


title: CRISPR RNA-seq from HepG2 (ENCLB868OKH)

description:
https://www.encodeproject.org/experiments/ENCSR959HPB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NOLC1. (NOLC1-BGHcLV07)
experiment encode accession: ENCSR959HPB
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR521WAI
encode release date: 2017-12-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB868OKH
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ee96ac26-06fc-43ab-9718-b788b0948fb7/@@download/attachment/L-NOLC1-BGHcLV07-20.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against NOLC1. (NOLC1-BGHcLV07-20)

value: male

value: hepatocellular carcinoma

value: child

value: ENCBS347KEX at ENCODE; https://www.encodeproject.org/ENCBS347KEX/


title: CRISPR RNA-seq from HepG2 (ENCLB097UFL)

description:
https://www.encodeproject.org/experiments/ENCSR964YLV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF3H. (EIF3H-BGHcLV05-B)
experiment encode accession: ENCSR964YLV
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR853AOV
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB097UFL
fragmentation methods: chemical (Illumina TruSeq)
size range: >200

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting EIF3H

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/dbf13ec8-0b8f-477e-bd81-ebf7f330b369/@@download/attachment/L-EIF3H-BGHcLV05-16B.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF3H. (EIF3H-BGHcLV05-16B)

value: 15 year

value: ENCBS731URN at ENCODE; https://www.encodeproject.org/ENCBS731URN/


title: CRISPR RNA-seq from HepG2 (ENCLB203VPC)

description:
https://www.encodeproject.org/experiments/ENCSR964YLV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF3H. (EIF3H-BGHcLV05-B)
experiment encode accession: ENCSR964YLV
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR853AOV
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB203VPC
fragmentation methods: chemical (Illumina TruSeq)
size range: >200

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3bc80e3b-b812-4c0c-a36c-c87103ee7464/@@download/attachment/L-EIF3H-BGHcLV05-15B.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF3H. (EIF3H-BGHcLV05-15B)

value: Brenton Graveley, UConn

value: ENCBS443YFV at ENCODE; https://www.encodeproject.org/ENCBS443YFV/


title: shRNA RNA-seq from K562 (ENCLB943GXQ)

description:
https://www.encodeproject.org/experiments/ENCSR967QNT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against GPKOW. (GPKOW_BGKLV36)
experiment encode accession: ENCSR967QNT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR424QCW
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB943GXQ
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/fb93dea1-94f8-4aa7-ae84-db1f6731d674/@@download/attachment/L-GPKOW_BGKLV36-27.pdf

value: GPKOW

value: cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against GPKOW. (GPKOW_BGKLV36-27)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ATCC

value: ENCBS229FEA at ENCODE; https://www.encodeproject.org/ENCBS229FEA/

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


title: shRNA RNA-seq from K562 (ENCLB256CZL)

description:
https://www.encodeproject.org/experiments/ENCSR949RMX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against XRN1. (XRN1-BGKLV38-C)
experiment encode accession: ENCSR949RMX
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR260BQC
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB256CZL
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens K562 cell line expressing RNAi targeting XRN1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f5f47e06-88ce-427b-8c4c-311758e2f37e/@@download/attachment/L-XRN1-BGKLV38-130C.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against XRN1. (XRN1-BGKLV38-130C)

value: ENCBS625KVU at ENCODE; https://www.encodeproject.org/ENCBS625KVU/


title: CRISPR RNA-seq from K562 (ENCLB935DXR)

description:
https://www.encodeproject.org/experiments/ENCSR974RYS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ZNF800. (ZNF800-BGKcLV06)
experiment encode accession: ENCSR974RYS
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR341TTW
encode release date: 2017-12-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB935DXR
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8b0e8868-10f1-4ef9-94e4-c17518efebf5/@@download/attachment/L-ZNF800-BGKcLV06-48.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ZNF800. (ZNF800-BGKcLV06-48)

value: ENCBS892HDF at ENCODE; https://www.encodeproject.org/ENCBS892HDF/


title: shRNA RNA-seq from K562 (ENCLB290XZA)

description:
https://www.encodeproject.org/experiments/ENCSR940GIC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against CKAP4. (CKAP4-BGKLV36-D)
experiment encode accession: ENCSR940GIC
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR898ABR
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB290XZA
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line expressing RNAi targeting CKAP4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c8aa39ee-48f3-4f61-930b-51f7f0cada07/@@download/attachment/L-CKAP4-BGKLV36-9D.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against CKAP4. (CKAP4-BGKLV36-9B)

value: ENCBS704TWA at ENCODE; https://www.encodeproject.org/ENCBS704TWA/


title: shRNA RNA-seq from HepG2 (ENCLB471LNG)

description:
https://www.encodeproject.org/experiments/ENCSR997HCQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV37)
experiment encode accession: ENCSR997HCQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB471LNG
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/20b7c721-1bfc-4b04-a96d-8e639b35eaaa/@@download/attachment/L-NT_BGHLV37-1.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against non-target. (NT_BGHLV37-1)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS496TVI at ENCODE; https://www.encodeproject.org/ENCBS496TVI/

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


title: CRISPR RNA-seq from HepG2 (ENCLB734HEX)

description:
https://www.encodeproject.org/experiments/ENCSR845MNM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SRSF7. (SRSF7_BGHcLV03)
experiment encode accession: ENCSR845MNM
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR105NML
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB734HEX
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting SRSF7

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1d669ecc-1953-4511-91e1-cc055bfd8340/@@download/attachment/L-SRSF7_BGHcLV03-6.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SRSF7. (SRSF7_BGHcLV03-6)

value: ATCC

value: ENCBS670FFG at ENCODE; https://www.encodeproject.org/ENCBS670FFG/


title: CRISPR RNA-seq from HepG2 (ENCLB607VLU)

description:
https://www.encodeproject.org/experiments/ENCSR853AOV/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV05-B)
experiment encode accession: ENCSR853AOV
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB607VLU
fragmentation methods: chemical (Illumina TruSeq)
size range: >200

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b3242413-5fa8-40ea-aa53-f8f7849e8edb/@@download/attachment/L-NT-BGHcLV05-2B.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against non target. (NT_BGHcLV05-2)

value: ENCBS901AHP at ENCODE; https://www.encodeproject.org/ENCBS901AHP/


title: CRISPR RNA-seq from HepG2 (ENCLB204AKA)

description:
https://www.encodeproject.org/experiments/ENCSR834IFU/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV05-C)
experiment encode accession: ENCSR834IFU
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB204AKA
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/831f41ac-ec12-4332-8a45-ec0d08ba16cb/@@download/attachment/L-NT-BGHcLV05-2C.pdf


title: total RNA-seq from placenta (ENCLB081RMC)

description:
https://www.encodeproject.org/experiments/ENCSR942YMN/
***************
biological replicate number: 1
technical replicate number: 1
description: Stam Placenta 11010
experiment encode accession: ENCSR942YMN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB081RMC
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male embryo placenta tissue

value: placenta

value: tissue

value: embryonic

value: not collected

value: John Stamatoyannopoulos, UW

value: John Stamatoyannopoulos

value: ENCBS111SJN at ENCODE; https://www.encodeproject.org/ENCBS111SJN/

value: Derived from ENCODE donor ENCDO824PZQ; https://www.encodeproject.org/ENCDO824PZQ/


title: shRNA RNA-seq from K562 (ENCLB849YAI)

description:
https://www.encodeproject.org/experiments/ENCSR952OOP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against CKAP4. (CKAP4-BGKLV36-B)
experiment encode accession: ENCSR952OOP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR324WIS
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB849YAI
fragmentation methods: chemical (Illumina TruSeq)
size range: >200

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/71e2d7ad-7606-4166-b69b-7ed32f53da03/@@download/attachment/L-CKAP4-BGKLV36-9B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against CKAP4. (CKAP4-BGKLV36-9B)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS704TWA at ENCODE; https://www.encodeproject.org/ENCBS704TWA/

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


title: CRISPR RNA-seq from K562 (ENCLB044YOW)

description:
https://www.encodeproject.org/experiments/ENCSR939BTN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SRSF4. (SRSF4-BGKcLV04-C)
experiment encode accession: ENCSR939BTN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR005JBU
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB044YOW
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting SRSF4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c74e8ce4-9dd1-471f-849f-b9f56637b0a8/@@download/attachment/L-SRSF4-BGKcLV04-29C.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SRSF4. (SRSF4-BGKcLV04-29B)

value: ATCC

value: ENCBS217XMV at ENCODE; https://www.encodeproject.org/ENCBS217XMV/


title: shRNA RNA-seq from K562 (ENCLB302IVR)

description:
https://www.encodeproject.org/experiments/ENCSR949RMX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against XRN1. (XRN1-BGKLV38-C)
experiment encode accession: ENCSR949RMX
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR260BQC
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB302IVR
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8c5912e3-257f-47a9-a0d2-47783e625b3f/@@download/attachment/L-XRN1-BGKLV38-129C.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against XRN1. (XRN1-BGKLV38-129C)

value: ENCBS735PDF at ENCODE; https://www.encodeproject.org/ENCBS735PDF/


title: shRNA RNA-seq from K562 (ENCLB224ZMX)

description:
https://www.encodeproject.org/experiments/ENCSR940GIC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against CKAP4. (CKAP4-BGKLV36-D)
experiment encode accession: ENCSR940GIC
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR898ABR
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB224ZMX
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4678d699-2b1f-4ef4-91e1-7bb9f558da76/@@download/attachment/L-CKAP4-BGKLV36-10D.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against CKAP4. (CKAP4-BGKLV36-10B)

value: ENCBS672MAJ at ENCODE; https://www.encodeproject.org/ENCBS672MAJ/


title: shRNA RNA-seq from K562 (ENCLB495NWR)

description:
https://www.encodeproject.org/experiments/ENCSR952QDQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against METAP2. (METAP2_BGKLV36)
experiment encode accession: ENCSR952QDQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR424QCW
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB495NWR
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

source_name: Homo sapiens K562 cell line expressing RNAi targeting METAP2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/25fde143-31fa-4df7-87e1-d9146d302da2/@@download/attachment/L-METAP2_BGKLV36-36.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against METAP2. (METAP2_BGKLV36-36)

value: ENCBS632CZP at ENCODE; https://www.encodeproject.org/ENCBS632CZP/


title: CRISPR RNA-seq from HepG2 (ENCLB708RGH)

description:
https://www.encodeproject.org/experiments/ENCSR845MNM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SRSF7. (SRSF7_BGHcLV03)
experiment encode accession: ENCSR845MNM
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR105NML
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB708RGH
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/76d6aef6-7ea7-48e0-a15e-2f329fd927c2/@@download/attachment/L-SRSF7_BGHcLV03-5.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against SRSF7. (SRSF7_BGHcLV03-5)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS111IHC at ENCODE; https://www.encodeproject.org/ENCBS111IHC/

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


title: CRISPR RNA-seq from K562 (ENCLB818QPB)

description:
https://www.encodeproject.org/experiments/ENCSR939BTN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SRSF4. (SRSF4-BGKcLV04-C)
experiment encode accession: ENCSR939BTN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR005JBU
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB818QPB
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/93e6e763-83d9-4003-a440-3c5ce0f1ee9d/@@download/attachment/L-SRSF4-BGKcLV04-30C.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SRSF4. (SRSF4-BGKcLV04-30B)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS578FNZ at ENCODE; https://www.encodeproject.org/ENCBS578FNZ/

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


title: polyA plus RNA-seq from A549 (ENCLB546CDK)

description:
https://www.encodeproject.org/experiments/ENCSR937WIG/
***************
biological replicate number: 2
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 0 mins.
experiment encode accession: ENCSR937WIG
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB546CDK
fragmentation methods: chemical (RNase III)
size range: >200
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Homo sapiens A549 cell line

extract_protocol:
treatment protocol: https://www.encodeproject.org/documents/c5b10eee-de7f-4845-a387-e73980ef5a19/@@download/attachment/RNA_DEX_treatment.pdf
general protocol: https://www.encodeproject.org/documents/5533fb32-41f1-4c7a-b62d-0095a33cab20/@@download/attachment/01_RNA_HARVEST_and_ISOLATION_Reddy_GGR.pdf
extraction protocol: https://www.encodeproject.org/documents/53726435-7acc-4248-a5df-3eef6ea3b422/@@download/attachment/02_Rev%20D%20Quick%20Reference%20Card%2C%20PrepX%20PolyA%2048%20Protocol.pdf
extraction protocol: https://www.encodeproject.org/documents/5f9d4f74-4e39-4818-9ee9-d8e9b8004ceb/@@download/attachment/03_RevC%20Quick%20Reference%20Card%2C%20PrepX%20mRNA%2048%20Protocol.pdf
extraction protocol: https://www.encodeproject.org/documents/c72e898e-82c7-478d-b043-8945133a7724/@@download/attachment/04_Rev%20C%20Quick%20Reference%20Card%2C%20PrepX%20PCR%20Cleanup%2048%20Protocol.pdf
general protocol: https://www.encodeproject.org/documents/7a683e77-85ac-45f9-b1fa-b6ceb50ca1bc/@@download/attachment/05_POST_RNA_LIB_PREP_Reddy_GGR.pdf
extraction method: RNeasy Plus Mini Kit Qiagen cat#74134 plus additional on column Dnase treatment

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: ENCBS961BTU at ENCODE; https://www.encodeproject.org/ENCBS961BTU/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: CRISPR RNA-seq from HepG2 (ENCLB592MWK)

description:
https://www.encodeproject.org/experiments/ENCSR834IFU/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV05-C)
experiment encode accession: ENCSR834IFU
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB592MWK
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6c6a9433-7839-4f3b-b9bc-5c8a70971dc7/@@download/attachment/L-NT-BGHcLV05-1C.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against non target. (NT_BGHcLV05-1)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS332SEB at ENCODE; https://www.encodeproject.org/ENCBS332SEB/


title: shRNA RNA-seq from HepG2 (ENCLB114ADK)

description:
https://www.encodeproject.org/experiments/ENCSR840QOH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against ETF1. (ETF1_BGHLV37)
experiment encode accession: ENCSR840QOH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR997HCQ
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB114ADK
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

source_name: Homo sapiens HepG2 cell line expressing RNAi targeting ETF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/dea60349-cb09-4f4f-974e-1bd7d9eee873/@@download/attachment/L-ETF1_BGHLV37-20.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ETF1. (ETF1_BGHLV37-20)

value: ENCBS714ECQ at ENCODE; https://www.encodeproject.org/ENCBS714ECQ/

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


title: shRNA RNA-seq from K562 (ENCLB992BJN)

description:
https://www.encodeproject.org/experiments/ENCSR952OOP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against CKAP4. (CKAP4-BGKLV36-B)
experiment encode accession: ENCSR952OOP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR324WIS
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB992BJN
fragmentation methods: chemical (Illumina TruSeq)
size range: >200

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/92c9711b-ca7a-48a7-b1a7-6318e86ce076/@@download/attachment/L-CKAP4-BGKLV36-10B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against CKAP4. (CKAP4-BGKLV36-10B)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS672MAJ at ENCODE; https://www.encodeproject.org/ENCBS672MAJ/


title: shRNA RNA-seq from K562 (ENCLB408YEW)

description:
https://www.encodeproject.org/experiments/ENCSR952QDQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against METAP2. (METAP2_BGKLV36)
experiment encode accession: ENCSR952QDQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR424QCW
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB408YEW
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ce9b9191-23b3-43b9-8c57-0a64d2b810ea/@@download/attachment/L-METAP2_BGKLV36-35.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against METAP2. (METAP2_BGKLV36-35)

value: ATCC

value: ENCBS888WCD at ENCODE; https://www.encodeproject.org/ENCBS888WCD/

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


title: polyA plus RNA-seq from A549 (ENCLB738AQA)

description:
https://www.encodeproject.org/experiments/ENCSR937WIG/
***************
biological replicate number: 3
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 0 mins.
experiment encode accession: ENCSR937WIG
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB738AQA
fragmentation methods: chemical (RNase III)
size range: >200
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: male

value: 58 year

value: Tim Reddy, Duke

value: ENCBS060XOR at ENCODE; https://www.encodeproject.org/ENCBS060XOR/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: shRNA RNA-seq from HepG2 (ENCLB244VSF)

description:
https://www.encodeproject.org/experiments/ENCSR840QOH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against ETF1. (ETF1_BGHLV37)
experiment encode accession: ENCSR840QOH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR997HCQ
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB244VSF
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8bf21605-98a4-4588-96dc-a8f8b241c630/@@download/attachment/L-ETF1_BGHLV37-19.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ETF1. (ETF1_BGHLV37-19)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS232YHB at ENCODE; https://www.encodeproject.org/ENCBS232YHB/

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


title: polyA plus RNA-seq from A549 (ENCLB941MPO)

description:
https://www.encodeproject.org/experiments/ENCSR831FZM/
***************
biological replicate number: 1
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 20 mins.
experiment encode accession: ENCSR831FZM
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB941MPO
fragmentation methods: chemical (RNase III)
size range: >200
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 20 minutes

value: adult

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:20; duration_units:minute;

value: ENCBS725ZWM at ENCODE; https://www.encodeproject.org/ENCBS725ZWM/


title: polyA plus RNA-seq from A549 (ENCLB473OZV)

description:
https://www.encodeproject.org/experiments/ENCSR831FZM/
***************
biological replicate number: 2
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 20 mins.
experiment encode accession: ENCSR831FZM
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB473OZV
fragmentation methods: chemical (RNase III)
size range: >200
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ATCC

value: ENCBS879LDL at ENCODE; https://www.encodeproject.org/ENCBS879LDL/


title: polyA plus RNA-seq from A549 (ENCLB467ESB)

description:
https://www.encodeproject.org/experiments/ENCSR937WIG/
***************
biological replicate number: 1
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 0 mins.
experiment encode accession: ENCSR937WIG
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB467ESB
fragmentation methods: chemical (RNase III)
size range: >200
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: male

value: ENCBS443EUC at ENCODE; https://www.encodeproject.org/ENCBS443EUC/


title: polyA plus RNA-seq from A549 (ENCLB279LZS)

description:
https://www.encodeproject.org/experiments/ENCSR831FZM/
***************
biological replicate number: 3
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 20 mins.
experiment encode accession: ENCSR831FZM
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB279LZS
fragmentation methods: chemical (RNase III)
size range: >200
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: 58 year

value: Tim Reddy, Duke

value: ENCBS565NTN at ENCODE; https://www.encodeproject.org/ENCBS565NTN/


title: CRISPR RNA-seq from HepG2 (ENCLB682CGV)

description:
https://www.encodeproject.org/experiments/ENCSR853AOV/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV05-B)
experiment encode accession: ENCSR853AOV
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB682CGV
fragmentation methods: chemical (Illumina TruSeq)
size range: >200

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/29e6e702-ccf4-4840-8a66-4e3814cc37dc/@@download/attachment/L-NT-BGHcLV05-1B.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against non target. (NT_BGHcLV05-1)

value: Brenton Graveley, UConn

value: ENCBS332SEB at ENCODE; https://www.encodeproject.org/ENCBS332SEB/


title: shRNA RNA-seq from HepG2 (ENCLB321UHL)

description:
https://www.encodeproject.org/experiments/ENCSR902VPO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against WDR3. (WDR3-BGHLV37-C)
experiment encode accession: ENCSR902VPO
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR225PRV
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB321UHL
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens HepG2 cell line expressing RNAi targeting WDR3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8e1222d2-effb-414a-bb40-fe4e11bb0788/@@download/attachment/L-WDR3-BGHLV37-76C.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against WDR3. (WDR3-BGHLV37-76C)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS286UBI at ENCODE; https://www.encodeproject.org/ENCBS286UBI/


title: CRISPR RNA-seq from HepG2 (ENCLB817XVM)

description:
https://www.encodeproject.org/experiments/ENCSR805TIZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV05-D)
experiment encode accession: ENCSR805TIZ
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB817XVM
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/355dcf8c-7cdf-4d95-8875-d8115db6989d/@@download/attachment/L-NT-BGHcLV05-1D.pdf

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


title: total RNA-seq from placenta (ENCLB979UQX)

description:
https://www.encodeproject.org/experiments/ENCSR903XMI/
***************
biological replicate number: 1
technical replicate number: 1
description: Stam Placenta 11009
experiment encode accession: ENCSR903XMI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB979UQX
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens female embryo placenta tissue

value: placenta

value: tissue

value: female

value: embryonic

value: not collected

value: John Stamatoyannopoulos, UW

value: John Stamatoyannopoulos

value: ENCBS148EVO at ENCODE; https://www.encodeproject.org/ENCBS148EVO/

value: Derived from ENCODE donor ENCDO496RNL; https://www.encodeproject.org/ENCDO496RNL/


title: shRNA RNA-seq from K562 (ENCLB975QGI)

description:
https://www.encodeproject.org/experiments/ENCSR793QPX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HDGF. (HDGF-BGKLV36-C)
experiment encode accession: ENCSR793QPX
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR619PCR
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB975QGI
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens K562 cell line expressing RNAi targeting HDGF

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/199f8199-fe11-470a-a35d-24c79099b9d3/@@download/attachment/L-HDGF-BGKLV36-30.pdf

value: HDGF

value: cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against HDGF. (HDGF-BGKLV36-30)

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS882LEE at ENCODE; https://www.encodeproject.org/ENCBS882LEE/

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


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB581DTX)

description:
https://www.encodeproject.org/experiments/ENCSR669ZGZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human CD4-positive, CD25-positive, alpha-beta regulatory T cell
experiment encode accession: ENCSR669ZGZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR079AKM
encode release date: 2020-12-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB581DTX
fragmentation methods: none

source_name: Homo sapiens CD4-positive, CD25-positive, alpha-beta regulatory T primary cell

value: primary cell

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS342CPO at ENCODE; https://www.encodeproject.org/ENCBS342CPO/

value: Derived from ENCODE donor ENCDO258PRN; https://www.encodeproject.org/ENCDO258PRN/


title: shRNA RNA-seq from HepG2 (ENCLB512JKW)

description:
https://www.encodeproject.org/experiments/ENCSR902VPO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against WDR3. (WDR3-BGHLV37-C)
experiment encode accession: ENCSR902VPO
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR225PRV
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB512JKW
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3d4fae86-59ba-4528-81e5-1f27ea2135d1/@@download/attachment/L-WDR3-BGHLV37-75C.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against WDR3. (WDR3-BGHLV37-75C)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS952ZRG at ENCODE; https://www.encodeproject.org/ENCBS952ZRG/

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


title: shRNA RNA-seq from K562 (ENCLB112BHZ)

description:
https://www.encodeproject.org/experiments/ENCSR793QPX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HDGF. (HDGF-BGKLV36-C)
experiment encode accession: ENCSR793QPX
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR619PCR
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB112BHZ
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7efd2f01-0f90-4a59-a6bd-23b45bab14b8/@@download/attachment/L-HDGF-BGKLV36-29.pdf

value: HDGF

value: RNA-seq on K562 cells treated with an shRNA knockdown against HDGF. (HDGF-BGKLV36-29)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS663QKK at ENCODE; https://www.encodeproject.org/ENCBS663QKK/

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


title: total RNA-seq from chondrocyte (ENCLB706JRN)

description:
https://www.encodeproject.org/experiments/ENCSR774MGO/
***************
biological replicate number: 2
technical replicate number: 1
description: WA09 derived chondrocytes
experiment encode accession: ENCSR774MGO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB706JRN
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens female embryo (5 days) chondrocyte in vitro differentiated cells

value: chondrocyte

value: in vitro differentiated cells

value: WA09 derived chondrocytes

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS524YKH at ENCODE; https://www.encodeproject.org/ENCBS524YKH/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: CRISPR RNA-seq from K562 (ENCLB565YRN)

description:
https://www.encodeproject.org/experiments/ENCSR905NIK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SRSF4. (SRSF4-BGKcLV04-B)
experiment encode accession: ENCSR905NIK
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR772DUM
encode release date: 2017-12-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB565YRN
fragmentation methods: chemical (Illumina TruSeq)
size range: >200

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0ff5c0f8-613f-461a-9e98-3a3646d6a129/@@download/attachment/L-SRSF4-BGKcLV04-29B.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SRSF4. (SRSF4-BGKcLV04-29B)

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS217XMV at ENCODE; https://www.encodeproject.org/ENCBS217XMV/


title: total RNA-seq from chondrocyte (ENCLB641ESO)

description:
https://www.encodeproject.org/experiments/ENCSR774MGO/
***************
biological replicate number: 3
technical replicate number: 1
description: WA09 derived chondrocytes
experiment encode accession: ENCSR774MGO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB641ESO
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: ENCBS668AFC at ENCODE; https://www.encodeproject.org/ENCBS668AFC/


title: shRNA RNA-seq from K562 (ENCLB861VHS)

description:
https://www.encodeproject.org/experiments/ENCSR774AEQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT-BGKLV34-B)
experiment encode accession: ENCSR774AEQ
assay title: shRNA RNA-seq
assembly: GRCh38
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB861VHS
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens K562 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/de61554d-7ab4-4bd5-aa41-08d185ab27c6/@@download/attachment/L-NT-BGKLV34-1B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against non-target. (NT_BGKLV34-1)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS922JMC at ENCODE; https://www.encodeproject.org/ENCBS922JMC/

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


title: shRNA RNA-seq from K562 (ENCLB169DYG)

description:
https://www.encodeproject.org/experiments/ENCSR655JYC/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT-BGKLV38-D)
experiment encode accession: ENCSR655JYC
assay title: shRNA RNA-seq
assembly: GRCh38
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB169DYG
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens K562 cell line expressing RNAi

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/32f5fe73-cf53-4e01-9427-24e8cb2ae3c7/@@download/attachment/L-NT-BGKLV38-2D.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against non-target. (NT_BGKLV38-2)

value: ATCC

value: ENCBS865TCO at ENCODE; https://www.encodeproject.org/ENCBS865TCO/


title: shRNA RNA-seq from HepG2 (ENCLB328NIU)

description:
https://www.encodeproject.org/experiments/ENCSR676SDU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against XRN1. (XRN1-BGHLV37-C)
experiment encode accession: ENCSR676SDU
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR225PRV
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB328NIU
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens HepG2 cell line expressing RNAi targeting XRN1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7fed9a91-c4c0-4b8d-b8e4-54cd97802423/@@download/attachment/L-XRN1-BGHLV37-100C.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against XRN1. (XRN1-BGHLV37-100C)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS482SUX at ENCODE; https://www.encodeproject.org/ENCBS482SUX/

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


title: total RNA-seq from chondrocyte (ENCLB492DNB)

description:
https://www.encodeproject.org/experiments/ENCSR774MGO/
***************
biological replicate number: 1
technical replicate number: 1
description: WA09 derived chondrocytes
experiment encode accession: ENCSR774MGO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB492DNB
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: chondrocyte

value: in vitro differentiated cells

value: WA09 derived chondrocytes

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS434FZQ at ENCODE; https://www.encodeproject.org/ENCBS434FZQ/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: CRISPR RNA-seq from K562 (ENCLB889RIG)

description:
https://www.encodeproject.org/experiments/ENCSR905NIK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SRSF4. (SRSF4-BGKcLV04-B)
experiment encode accession: ENCSR905NIK
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR772DUM
encode release date: 2017-12-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB889RIG
fragmentation methods: chemical (Illumina TruSeq)
size range: >200

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2d6612b2-994c-4742-88d3-566f16531195/@@download/attachment/L-SRSF4-BGKcLV04-30B.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SRSF4. (SRSF4-BGKcLV04-30B)

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS578FNZ at ENCODE; https://www.encodeproject.org/ENCBS578FNZ/

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


title: shRNA RNA-seq from HepG2 (ENCLB415PXJ)

description:
https://www.encodeproject.org/experiments/ENCSR676SDU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against XRN1. (XRN1-BGHLV37-C)
experiment encode accession: ENCSR676SDU
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR225PRV
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB415PXJ
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f85d2f90-ca68-4ab7-8bce-f7c7d387476c/@@download/attachment/L-XRN1-BGHLV37-99C.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against XRN1. (XRN1-BGHLV37-99C)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS469EOJ at ENCODE; https://www.encodeproject.org/ENCBS469EOJ/

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


title: shRNA RNA-seq from K562 (ENCLB050JFV)

description:
https://www.encodeproject.org/experiments/ENCSR688GVV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against FTO. (FTO_BGKLV36)
experiment encode accession: ENCSR688GVV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR424QCW
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB050JFV
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

source_name: Homo sapiens K562 cell line expressing RNAi targeting FTO

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/69394468-fcc2-4827-a8ef-3ea0e9a4079c/@@download/attachment/L-FTO_BGKLV36-25.pdf

value: FTO

value: RNA-seq on K562 cells treated with an shRNA knockdown against FTO. (FTO_BGKLV36-25)

value: female

value: ENCBS166GHD at ENCODE; https://www.encodeproject.org/ENCBS166GHD/


title: shRNA RNA-seq from K562 (ENCLB349BMJ)

description:
https://www.encodeproject.org/experiments/ENCSR774AEQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT-BGKLV34-B)
experiment encode accession: ENCSR774AEQ
assay title: shRNA RNA-seq
assembly: GRCh38
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB349BMJ
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/9444d697-02d9-4e0e-b0c6-bd34e98e798d/@@download/attachment/L-NT-BGKLV34-2B.pdf

value: cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against non-target. (NT_BGKLV34-2)

value: adult

value: chronic myelogenous leukemia (CML)

value: ENCBS645VVV at ENCODE; https://www.encodeproject.org/ENCBS645VVV/


title: total RNA-seq from placenta (ENCLB445WKP)

description:
https://www.encodeproject.org/experiments/ENCSR648YUM/
***************
biological replicate number: 1
technical replicate number: 1
description: Stam Placenta 11012
experiment encode accession: ENCSR648YUM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB445WKP
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: placenta

value: tissue

value: embryonic

value: not collected

value: John Stamatoyannopoulos, UW

value: John Stamatoyannopoulos

value: ENCBS604CSM at ENCODE; https://www.encodeproject.org/ENCBS604CSM/

value: Derived from ENCODE donor ENCDO353NXC; https://www.encodeproject.org/ENCDO353NXC/


title: CRISPR RNA-seq from K562 (ENCLB695OAJ)

description:
https://www.encodeproject.org/experiments/ENCSR828YEB/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT_BGKcLV04)
experiment encode accession: ENCSR828YEB
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
encode release date: 2017-01-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB695OAJ
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d7ffa98a-ff4e-4efa-8bec-e389a02a50a9/@@download/attachment/L-NT_BGKcLV04-2.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against non target. (NT_BGKcLV04-2)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS906RHA at ENCODE; https://www.encodeproject.org/ENCBS906RHA/

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


title: shRNA RNA-seq from K562 (ENCLB795HBL)

description:
https://www.encodeproject.org/experiments/ENCSR688GVV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against FTO. (FTO_BGKLV36)
experiment encode accession: ENCSR688GVV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR424QCW
encode release date: 2017-01-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB795HBL
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ea7f35fa-3ad2-440d-b595-ae15fc420276/@@download/attachment/L-FTO_BGKLV36-26.pdf

value: FTO

value: cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against FTO. (FTO_BGKLV36-26)

value: female

value: adult

value: ENCBS258AXV at ENCODE; https://www.encodeproject.org/ENCBS258AXV/


title: shRNA RNA-seq from K562 (ENCLB037RHF)

description:
https://www.encodeproject.org/experiments/ENCSR655JYC/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT-BGKLV38-D)
experiment encode accession: ENCSR655JYC
assay title: shRNA RNA-seq
assembly: GRCh38
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB037RHF
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/eb95e218-79d3-4a0a-a887-b4e2a07e0f93/@@download/attachment/L-NT-BGKLV38-1D.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against non-target. (NT_BGKLV38-1)

value: chronic myelogenous leukemia (CML)

value: ENCBS479HRC at ENCODE; https://www.encodeproject.org/ENCBS479HRC/


title: shRNA RNA-seq from HepG2 (ENCLB790TRW)

description:
https://www.encodeproject.org/experiments/ENCSR756VLW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against ABT1. (ABT1-BGHLV37-C)
experiment encode accession: ENCSR756VLW
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR225PRV
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB790TRW
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens HepG2 cell line expressing RNAi targeting ABT1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c9212e82-0d5b-435c-9f98-dfbe52461107/@@download/attachment/L-ABT1-BGHLV37-3C.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ABT1. (ABT1-BGHLV37-3C)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS561WGB at ENCODE; https://www.encodeproject.org/ENCBS561WGB/

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


title: shRNA RNA-seq from HepG2 (ENCLB858UHU)

description:
https://www.encodeproject.org/experiments/ENCSR756VLW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against ABT1. (ABT1-BGHLV37-C)
experiment encode accession: ENCSR756VLW
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR225PRV
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB858UHU
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2100078e-f7a7-429a-877a-1f49721e2964/@@download/attachment/L-ABT1-BGHLV37-4C.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ABT1. (ABT1-BGHLV37-4C)

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS157VRK at ENCODE; https://www.encodeproject.org/ENCBS157VRK/


title: shRNA RNA-seq from HepG2 (ENCLB273CEJ)

description:
https://www.encodeproject.org/experiments/ENCSR696JWA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against ZC3H8. (ZC3H8-BGHLV37-B)
experiment encode accession: ENCSR696JWA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR584UYK
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB273CEJ
fragmentation methods: chemical (Illumina TruSeq)
size range: >200

source_name: Homo sapiens HepG2 cell line expressing RNAi targeting ZC3H8

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3766afd2-5e3e-49d1-99f2-11954918bb56/@@download/attachment/L-ZC3H8-BGHLV37-115B.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ZC3H8. (ZC3H8-BGHLV37-115B)

value: ENCBS699OQY at ENCODE; https://www.encodeproject.org/ENCBS699OQY/


title: CRISPR RNA-seq from K562 (ENCLB818QII)

description:
https://www.encodeproject.org/experiments/ENCSR772DUM/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV04-B)
experiment encode accession: ENCSR772DUM
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
encode release date: 2017-12-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB818QII
fragmentation methods: chemical (Illumina TruSeq)
size range: >200

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/56672c83-5885-4639-8dc1-7c01e7a0573f/@@download/attachment/L-NT-BGKcLV04-1B.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against non target. (NT_BGKcLV04-1)

value: female

value: adult

value: 53 year

value: ENCBS981XHM at ENCODE; https://www.encodeproject.org/ENCBS981XHM/

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


title: CRISPR RNA-seq from K562 (ENCLB606CNC)

description:
https://www.encodeproject.org/experiments/ENCSR772DUM/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV04-B)
experiment encode accession: ENCSR772DUM
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
encode release date: 2017-12-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB606CNC
fragmentation methods: chemical (Illumina TruSeq)
size range: >200

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b8e4b970-0e04-4dfd-9f41-05a3c38dc11e/@@download/attachment/L-NT-BGKcLV04-2B.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against non target. (NT_BGKcLV04-2)

value: chronic myelogenous leukemia (CML)

value: ENCBS906RHA at ENCODE; https://www.encodeproject.org/ENCBS906RHA/


title: shRNA RNA-seq from K562 (ENCLB043HQL)

description:
https://www.encodeproject.org/experiments/ENCSR818TZM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against UTP3. (UTP3-BGKLV38-B)
experiment encode accession: ENCSR818TZM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR024FOF
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB043HQL
fragmentation methods: chemical (Illumina TruSeq)
size range: >200

source_name: Homo sapiens K562 cell line expressing RNAi targeting UTP3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/9a417710-a651-4dd5-b11f-f3e521201e06/@@download/attachment/L-UTP3-BGKLV38-103B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against UTP3. (UTP3-BGKLV38-103B)

value: ENCBS742THM at ENCODE; https://www.encodeproject.org/ENCBS742THM/


title: CRISPR RNA-seq from K562 (ENCLB101IFA)

description:
https://www.encodeproject.org/experiments/ENCSR680OJB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SYNCRIP. (SYNCRIP-BGKcLV06)
experiment encode accession: ENCSR680OJB
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR341TTW
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB101IFA
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting SYNCRIP

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e71dd4f7-e8c2-49dd-aca9-ea014971eda5/@@download/attachment/L-SYNCRIP-BGKcLV06-38.pdf

value: SYNCRIP

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SYNCRIP. (SYNCRIP-BGKcLV06-38)

value: Brenton Graveley, UConn

value: ENCBS137STC at ENCODE; https://www.encodeproject.org/ENCBS137STC/


title: CRISPR RNA-seq from K562 (ENCLB072HVI)

description:
https://www.encodeproject.org/experiments/ENCSR642GBC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS3. (RPS3-BGKcLV04-B)
experiment encode accession: ENCSR642GBC
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR772DUM
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB072HVI
fragmentation methods: chemical (Illumina TruSeq)
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting RPS3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ad17d7a3-d3c8-4e13-bc1d-34930b32384c/@@download/attachment/L-RPS3-BGKcLV04-25B.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPS3. (RPS3-BGKcLV04-25B)

value: ATCC

value: ENCBS640DOL at ENCODE; https://www.encodeproject.org/ENCBS640DOL/


title: shRNA RNA-seq from K562 (ENCLB552BCG)

description:
https://www.encodeproject.org/experiments/ENCSR818TZM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against UTP3. (UTP3-BGKLV38-B)
experiment encode accession: ENCSR818TZM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR024FOF
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB552BCG
fragmentation methods: chemical (Illumina TruSeq)
size range: >200

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f1b1cfd3-9792-4ff6-98e7-d8904e50f9ca/@@download/attachment/L-UTP3-BGKLV38-104B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against UTP3. (UTP3-BGKLV38-104B)

value: female

value: adult

value: ENCBS532TPY at ENCODE; https://www.encodeproject.org/ENCBS532TPY/


title: CRISPR RNA-seq from K562 (ENCLB573FZT)

description:
https://www.encodeproject.org/experiments/ENCSR828YEB/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT_BGKcLV04)
experiment encode accession: ENCSR828YEB
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
encode release date: 2017-01-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB573FZT
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2c4fea8d-7fda-4e69-bd30-2cb276f0f892/@@download/attachment/L-NT_BGKcLV04-1.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against non target. (NT_BGKcLV04-1)

value: 53 year

value: ENCBS981XHM at ENCODE; https://www.encodeproject.org/ENCBS981XHM/

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