title: Bru-seq from MCF 10A (ENCLB877GHM)

description:
https://www.encodeproject.org/experiments/ENCSR188PRS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR188PRS
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR444JTC
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB877GHM
size range: 400-500

source_name: Homo sapiens MCF 10A cell line treated with 500 rad irradiation

value: MCF 10A

value: Homo sapiens

value: female

value: fibrocystic disease

value: adult

value: 36 year

value: Mats Ljungman, UMichigan

value: ENCBS418FLR at ENCODE; https://www.encodeproject.org/ENCBS418FLR/

value: Derived from ENCODE donor ENCDO000AAP; https://www.encodeproject.org/ENCDO000AAP/


title: microRNA-seq from middle frontal area 46 (ENCLB937WFA)

status: Public on Dec 04 2022

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR020RPU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR020RPU
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB937WFA
size range: <30

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens female adult (90 or above years) with Alzheimer's disease; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

tag: description

tag: biosample encode accession

tag: organism

tag: Sex

tag: dev stage

tag: age

value: 90 or above year

tag: lab

value: Barbara Wold, Caltech

tag: source

value: Rush University

tag: link

value: ENCBS660AUE at ENCODE; https://www.encodeproject.org/ENCBS660AUE/

value: Derived from ENCODE donor ENCDO223NTQ; https://www.encodeproject.org/ENCDO223NTQ/


title: PRO-seq from HCT116 (ENCLB394VNT)

description:
https://www.encodeproject.org/experiments/ENCSR954XDE/
***************
biological replicate number: 1
technical replicate number: 1
description: PRO-seq in CDK7_T
experiment encode accession: ENCSR954XDE
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB394VNT
spikeins used: The drosophila spike-in reference used for alignment

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CDK7 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

tag: line

value: cell line

value: male

tag: health state

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS143QQX at ENCODE; https://www.encodeproject.org/ENCBS143QQX/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: PRO-seq from HCT116 (ENCLB192CWD)

description:
https://www.encodeproject.org/experiments/ENCSR945WVF/
***************
biological replicate number: 1
technical replicate number: 1
description: PRO-seq in POLR2A_T
experiment encode accession: ENCSR945WVF
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB192CWD
spikeins used: The drosophila spike-in reference used for alignment

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens POLR2A treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: Homo sapiens

value: adult

value: ENCBS486IFU at ENCODE; https://www.encodeproject.org/ENCBS486IFU/


title: microRNA-seq from middle frontal area 46 (ENCLB837JYZ)

description:
https://www.encodeproject.org/experiments/ENCSR493UZT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR493UZT
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB837JYZ
size range: <30

value: middle frontal area 46

value: tissue

value: female

value: 90 or above year

value: ENCBS322PWU at ENCODE; https://www.encodeproject.org/ENCBS322PWU/

value: Derived from ENCODE donor ENCDO427VQK; https://www.encodeproject.org/ENCDO427VQK/


title: Bru-seq from MCF 10A (ENCLB282IHY)

description:
https://www.encodeproject.org/experiments/ENCSR188PRS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR188PRS
assay title: Bru-seq
assembly: GRCh38
possible controls: ENCSR444JTC
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB282IHY
size range: 400-500

value: MCF 10A

value: cell line

value: fibrocystic disease

value: 36 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS591EWF at ENCODE; https://www.encodeproject.org/ENCBS591EWF/

value: Derived from ENCODE donor ENCDO000AAP; https://www.encodeproject.org/ENCDO000AAP/


title: microRNA-seq from middle frontal area 46 (ENCLB757EOX)

description:
https://www.encodeproject.org/experiments/ENCSR010OLA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human Rush brain microRNA-seq from Mortazavi
experiment encode accession: ENCSR010OLA
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB757EOX
size range: <30

source_name: Homo sapiens female adult (88 years) with Alzheimer's disease; middle frontal area 46 tissue

value: Homo sapiens

value: 88 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS485BXU at ENCODE; https://www.encodeproject.org/ENCBS485BXU/

value: Derived from ENCODE donor ENCDO430XKI; https://www.encodeproject.org/ENCDO430XKI/


title: PRO-seq from HCT116 (ENCLB205LAB)

description:
https://www.encodeproject.org/experiments/ENCSR945WVF/
***************
biological replicate number: 2
technical replicate number: 1
description: PRO-seq in POLR2A_T
experiment encode accession: ENCSR945WVF
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB205LAB
spikeins used: The drosophila spike-in reference used for alignment

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS275ZVJ at ENCODE; https://www.encodeproject.org/ENCBS275ZVJ/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: total RNA-seq from middle frontal area 46 (ENCLB185DXZ)

description:
https://www.encodeproject.org/experiments/ENCSR951DTJ/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E1302730_BS147_ENC4_cDNA697
experiment encode accession: ENCSR951DTJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB185DXZ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: middle frontal area 46

value: tissue

value: female

value: 90 or above year

value: ENCBS765SSW at ENCODE; https://www.encodeproject.org/ENCBS765SSW/

value: Derived from ENCODE donor ENCDO847KYQ; https://www.encodeproject.org/ENCDO847KYQ/


title: total RNA-seq from middle frontal area 46 (ENCLB229LDS)

description:
https://www.encodeproject.org/experiments/ENCSR483IHO/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_7948794_BS24_ENC4_cDNA657
experiment encode accession: ENCSR483IHO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Barbara Wold, Caltech
library encode accession: ENCLB229LDS
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: Homo sapiens

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS422TMB at ENCODE; https://www.encodeproject.org/ENCBS422TMB/

value: Derived from ENCODE donor ENCDO470GFA; https://www.encodeproject.org/ENCDO470GFA/


title: total RNA-seq from K562 (ENCLB142RIC)

description:
https://www.encodeproject.org/experiments/ENCSR195JRH/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with JQ1 for 12 hours
experiment encode accession: ENCSR195JRH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB142RIC
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 5 uM JQ1 for 12 hours, preserved by flash-freezing

value: cell line

value: RNA-seq on human cell line K562

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Will Greenleaf, Stanford

value: ATCC

value: treatment_term_name:JQ1; treatment_type:chemical; duration:12; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS287YSQ at ENCODE; https://www.encodeproject.org/ENCBS287YSQ/

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


title: CRISPR RNA-seq from K562 (ENCLB451BYR)

description:
https://www.encodeproject.org/experiments/ENCSR639XFV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SARNP. (SARNP-BGKcLV33)
experiment encode accession: ENCSR639XFV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB451BYR
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 H. sapiens SEC31A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/aef486a4-7807-48ad-8795-8522197d82b3/@@download/attachment/L-SARNP-BGKcLV33-32.pdf

tag: antibody

value: SARNP

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SARNP. (SARNP-BGKcLV33-32)

value: female

value: Brenton Graveley, UConn

value: ENCBS173FOK at ENCODE; https://www.encodeproject.org/ENCBS173FOK/


title: PRO-seq from HCT116 (ENCLB907HED)

description:
https://www.encodeproject.org/experiments/ENCSR929NJH/
***************
biological replicate number: 1
technical replicate number: 1
description: PRO-seq in SMARCA5_U
experiment encode accession: ENCSR929NJH
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB907HED
spikeins used: The drosophila spike-in reference used for alignment

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SMARCA5

value: Homo sapiens

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS141BGY at ENCODE; https://www.encodeproject.org/ENCBS141BGY/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: CRISPR RNA-seq from K562 (ENCLB846SVD)

description:
https://www.encodeproject.org/experiments/ENCSR183WOW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SMG5. (SMG5-BGKcLV33)
experiment encode accession: ENCSR183WOW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB846SVD
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 H. sapiens SMG8

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ee930767-3b2b-4c69-995a-a9663b56457d/@@download/attachment/L-SMG5-BGKcLV33-56.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SMG5. (SMG5-BGKcLV33-56)

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ATCC

value: ENCBS568KMK at ENCODE; https://www.encodeproject.org/ENCBS568KMK/


title: PRO-seq from HCT116 (ENCLB192XSW)

description:
https://www.encodeproject.org/experiments/ENCSR929NJH/
***************
biological replicate number: 2
technical replicate number: 1
description: PRO-seq in SMARCA5_U
experiment encode accession: ENCSR929NJH
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB192XSW
spikeins used: The drosophila spike-in reference used for alignment

value: ENCBS032AKF at ENCODE; https://www.encodeproject.org/ENCBS032AKF/


title: CRISPR RNA-seq from K562 (ENCLB753EDT)

description:
https://www.encodeproject.org/experiments/ENCSR639XFV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SARNP. (SARNP-BGKcLV33)
experiment encode accession: ENCSR639XFV
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB753EDT
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/0238a716-10e0-449d-84bc-bd3b2d19627d/@@download/attachment/L-SARNP-BGKcLV33-31.pdf

value: SARNP

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SARNP. (SARNP-BGKcLV33-31)

value: female

value: Brenton Graveley, UConn

value: ENCBS783LPC at ENCODE; https://www.encodeproject.org/ENCBS783LPC/

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


title: Bru-seq from WTC11 (ENCLB025MTA)

description:
https://www.encodeproject.org/experiments/ENCSR637ZTH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR637ZTH
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB025MTA
size range: 400-500

source_name: Homo sapiens WTC11 cell line

value: Homo sapiens

value: male

value: 30 year

value: Mats Ljungman, UMichigan

value: Coriell

value: ENCBS869SJL at ENCODE; https://www.encodeproject.org/ENCBS869SJL/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: total RNA-seq from middle frontal area 46 (ENCLB765MNE)

description:
https://www.encodeproject.org/experiments/ENCSR959ENR/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E5841627_BS204_ENC4_cDNA759
experiment encode accession: ENCSR959ENR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB765MNE
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 adult (90 or above years) with mild cognitive impairment; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: adult

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS459VZX at ENCODE; https://www.encodeproject.org/ENCBS459VZX/

value: Derived from ENCODE donor ENCDO153NUY; https://www.encodeproject.org/ENCDO153NUY/


title: Bru-seq from WTC11 (ENCLB374BFP)

description:
https://www.encodeproject.org/experiments/ENCSR637ZTH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR637ZTH
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB374BFP
size range: 400-500

value: cell line

value: ENCBS519MHE at ENCODE; https://www.encodeproject.org/ENCBS519MHE/


title: CRISPR RNA-seq from K562 (ENCLB473BZI)

description:
https://www.encodeproject.org/experiments/ENCSR183WOW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SMG5. (SMG5-BGKcLV33)
experiment encode accession: ENCSR183WOW
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB473BZI
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/d16a117e-30f5-4b39-8e00-8ae199cf6aa2/@@download/attachment/L-SMG5-BGKcLV33-55.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SMG5. (SMG5-BGKcLV33-55)

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS085BKT at ENCODE; https://www.encodeproject.org/ENCBS085BKT/

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


title: total RNA-seq from activated T-cell (ENCLB796NXO)

description:
https://www.encodeproject.org/experiments/ENCSR925DZW/
***************
biological replicate number: 1
technical replicate number: 1
description: CD3+_DONOR 1: 72 Hour T cell activation (CD3.CD28 beads) + 50U/ml IL-2
experiment encode accession: ENCSR925DZW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB796NXO
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 330
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (43 years) activated T-cell primary cell treated with 50 U/mL Interleukin-2 for 72 hours, anti-CD3 and anti-CD28 coated beads for 72 hours

value: activated T-cell

value: primary cell

value: male

value: adult

value: 43 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:72; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour;

value: ENCBS969BFR at ENCODE; https://www.encodeproject.org/ENCBS969BFR/

value: Derived from ENCODE donor ENCDO106CDP; https://www.encodeproject.org/ENCDO106CDP/


title: PRO-cap from HCT116 (ENCLB981VPD)

description:
https://www.encodeproject.org/experiments/ENCSR635SXX/
***************
biological replicate number: 2
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in RAD21_U.
experiment encode accession: ENCSR635SXX
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB981VPD
spikeins used: The drosophila spike-in reference used for alignment

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21

value: cell line

value: Homo sapiens

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS645VXU at ENCODE; https://www.encodeproject.org/ENCBS645VXU/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: total RNA-seq from middle frontal area 46 (ENCLB772EEF)

description:
https://www.encodeproject.org/experiments/ENCSR922XPO/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E8277356_BS128_ENC4_cDNA690
experiment encode accession: ENCSR922XPO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB772EEF
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December

source_name: Homo sapiens male adult (90 or above years) with Alzheimer's disease; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS963SPU at ENCODE; https://www.encodeproject.org/ENCBS963SPU/

value: Derived from ENCODE donor ENCDO287LNQ; https://www.encodeproject.org/ENCDO287LNQ/


title: CRISPR RNA-seq from K562 (ENCLB984FET)

description:
https://www.encodeproject.org/experiments/ENCSR166VYI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DCPS. (DCPS-BGKcLV28)
experiment encode accession: ENCSR166VYI
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB984FET
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 H. sapiens DCPS

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/40cbedc0-8c17-461a-bd25-efb6afe2160b/@@download/attachment/L-DCPS-BGKcLV28-64.pdf

value: DCPS

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DCPS. (DCPS-BGKcLV28-64)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS771KWJ at ENCODE; https://www.encodeproject.org/ENCBS771KWJ/

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


title: total RNA-seq from middle frontal area 46 (ENCLB285AQH)

description:
https://www.encodeproject.org/experiments/ENCSR914PRM/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E8973904_BS189_ENC4_cDNA743
experiment encode accession: ENCSR914PRM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB285AQH
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: middle frontal area 46

value: Homo sapiens

value: ENCBS479ZAJ at ENCODE; https://www.encodeproject.org/ENCBS479ZAJ/

value: Derived from ENCODE donor ENCDO658JXQ; https://www.encodeproject.org/ENCDO658JXQ/


title: CRISPR RNA-seq from K562 (ENCLB713SIV)

description:
https://www.encodeproject.org/experiments/ENCSR166VYI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DCPS. (DCPS-BGKcLV28)
experiment encode accession: ENCSR166VYI
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB713SIV
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/3e796a61-79db-4261-8acd-c72bef611094/@@download/attachment/L-DCPS-BGKcLV28-63.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against DCPS. (DCPS-BGKcLV28-63)

value: ENCBS277ZLX at ENCODE; https://www.encodeproject.org/ENCBS277ZLX/


title: total RNA-seq from middle frontal area 46 (ENCLB850NRY)

description:
https://www.encodeproject.org/experiments/ENCSR900GIC/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E2501226_BS144_ENC4_cDNA694
experiment encode accession: ENCSR900GIC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB850NRY
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December

source_name: Homo sapiens female adult (74 years) with Alzheimer's disease; middle frontal area 46 tissue

value: tissue

value: 74 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS177AWD at ENCODE; https://www.encodeproject.org/ENCBS177AWD/

value: Derived from ENCODE donor ENCDO907CMO; https://www.encodeproject.org/ENCDO907CMO/


title: PRO-cap from HCT116 (ENCLB650SGB)

description:
https://www.encodeproject.org/experiments/ENCSR165QKR/
***************
biological replicate number: 2
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in CTCF_U.
experiment encode accession: ENCSR165QKR
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB650SGB
spikeins used: The drosophila spike-in reference used for alignment

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CTCF

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS596YYF at ENCODE; https://www.encodeproject.org/ENCBS596YYF/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: PRO-cap from HCT116 (ENCLB503WZU)

description:
https://www.encodeproject.org/experiments/ENCSR165QKR/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in CTCF_U.
experiment encode accession: ENCSR165QKR
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB503WZU
spikeins used: The drosophila spike-in reference used for alignment

value: cell line

value: Homo sapiens

value: ENCBS440YTE at ENCODE; https://www.encodeproject.org/ENCBS440YTE/


title: CRISPR RNA-seq from K562 (ENCLB015LQY)

description:
https://www.encodeproject.org/experiments/ENCSR633RMN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CAPRIN1. (CAPRIN1-BGKcLV26)
experiment encode accession: ENCSR633RMN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB015LQY
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 H. sapiens CAPRIN1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/279f67d5-ace1-4cdb-8a39-3a0cb7d83c74/@@download/attachment/L-CAPRIN1-BGKcLV26-53.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CAPRIN1. (CAPRIN1-BGKcLV26-53)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS384UVR at ENCODE; https://www.encodeproject.org/ENCBS384UVR/

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


title: CRISPR RNA-seq from K562 (ENCLB216TII)

description:
https://www.encodeproject.org/experiments/ENCSR633RMN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CAPRIN1. (CAPRIN1-BGKcLV26)
experiment encode accession: ENCSR633RMN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB216TII
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/2d4359be-27a2-48ca-a4d7-e60cf02feec6/@@download/attachment/L-CAPRIN1-BGKcLV26-54.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CAPRIN1. (CAPRIN1-BGKcLV26-54)

value: adult

value: ENCBS897FOF at ENCODE; https://www.encodeproject.org/ENCBS897FOF/


title: PRO-seq from HCT116 (ENCLB808BFF)

description:
https://www.encodeproject.org/experiments/ENCSR889SZI/
***************
biological replicate number: 1
technical replicate number: 1
description: PRO-seq in CTCF_U
experiment encode accession: ENCSR889SZI
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB808BFF
spikeins used: The drosophila spike-in reference used for alignment

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki


title: total RNA-seq from natural killer cell (ENCLB359ESJ)

description:
https://www.encodeproject.org/experiments/ENCSR927KSI/
***************
biological replicate number: 1
technical replicate number: 1
description: PBMC (NK MACS sort)NK
experiment encode accession: ENCSR927KSI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Barbara Wold, Caltech
library encode accession: ENCLB359ESJ
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 adult (33 years) natural killer primary cell

value: natural killer cell

value: primary cell

value: Homo sapiens

value: 33 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS190MRQ at ENCODE; https://www.encodeproject.org/ENCBS190MRQ/

value: Derived from ENCODE donor ENCDO195VEA; https://www.encodeproject.org/ENCDO195VEA/


title: total RNA-seq from K562 (ENCLB500FWI)

description:
https://www.encodeproject.org/experiments/ENCSR165GPK/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with AR-42 for 48 hours
experiment encode accession: ENCSR165GPK
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB500FWI
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 10 uM AR-42 for 48 hours, preserved by flash-freezing

value: cell line

value: RNA-seq on human cell line K562

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Will Greenleaf, Stanford

value: ATCC

value: treatment_term_name:AR-42; treatment_type:chemical; duration:48; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS682MKT at ENCODE; https://www.encodeproject.org/ENCBS682MKT/

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


title: total RNA-seq from activated T-cell (ENCLB992WSI)

description:
https://www.encodeproject.org/experiments/ENCSR925DZW/
***************
biological replicate number: 1
technical replicate number: 2
description: CD3+_DONOR 1: 72 Hour T cell activation (CD3.CD28 beads) + 50U/ml IL-2
experiment encode accession: ENCSR925DZW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB992WSI
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 330
nucleic acid starting quantity units: ng

value: activated T-cell

value: primary cell

value: male

value: adult

value: 43 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:72; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour;

value: ENCBS969BFR at ENCODE; https://www.encodeproject.org/ENCBS969BFR/

value: Derived from ENCODE donor ENCDO106CDP; https://www.encodeproject.org/ENCDO106CDP/


title: total RNA-seq from Calu3 (ENCLB783RIR)

description:
https://www.encodeproject.org/experiments/ENCSR897JEH/
***************
biological replicate number: 1
technical replicate number: 1
description: Calu3 for bru-seq comparison
experiment encode accession: ENCSR897JEH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB783RIR
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 Calu3 cell line

value: cell line

value: Homo sapiens

value: Lung adenocarcinoma

value: 25 year

value: Mats Ljungman, UMichigan

value: ENCBS961BBX at ENCODE; https://www.encodeproject.org/ENCBS961BBX/

value: Derived from ENCODE donor ENCDO109DGE; https://www.encodeproject.org/ENCDO109DGE/


title: total RNA-seq from Calu3 (ENCLB726VPH)

description:
https://www.encodeproject.org/experiments/ENCSR897JEH/
***************
biological replicate number: 2
technical replicate number: 1
description: Calu3 for bru-seq comparison
experiment encode accession: ENCSR897JEH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB726VPH
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: ATCC

value: ENCBS806IYJ at ENCODE; https://www.encodeproject.org/ENCBS806IYJ/


title: PRO-seq from HCT116 (ENCLB607PUZ)

description:
https://www.encodeproject.org/experiments/ENCSR889SZI/
***************
biological replicate number: 2
technical replicate number: 1
description: PRO-seq in CTCF_U
experiment encode accession: ENCSR889SZI
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB607PUZ
spikeins used: The drosophila spike-in reference used for alignment

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS596YYF at ENCODE; https://www.encodeproject.org/ENCBS596YYF/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: total RNA-seq from B cell (ENCLB962BPM)

description:
https://www.encodeproject.org/experiments/ENCSR896YYL/
***************
biological replicate number: 1
technical replicate number: 1
description: PBMCCD19+ (B cells) resting
experiment encode accession: ENCSR896YYL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Barbara Wold, Caltech
library encode accession: ENCLB962BPM
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 adult (22 years) B primary cell

value: B cell

value: primary cell

value: adult

value: 22 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS531BSW at ENCODE; https://www.encodeproject.org/ENCBS531BSW/

value: Derived from ENCODE donor ENCDO383AQS; https://www.encodeproject.org/ENCDO383AQS/


title: total RNA-seq from middle frontal area 46 (ENCLB535QFX)

description:
https://www.encodeproject.org/experiments/ENCSR882HXI/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E7404786_BS166_ENC4_cDNA716
experiment encode accession: ENCSR882HXI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB535QFX
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 adult (83 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: 83 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS545PYF at ENCODE; https://www.encodeproject.org/ENCBS545PYF/

value: Derived from ENCODE donor ENCDO592ZWW; https://www.encodeproject.org/ENCDO592ZWW/


title: PRO-cap from HCT116 (ENCLB171EQX)

description:
https://www.encodeproject.org/experiments/ENCSR635SXX/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in RAD21_U.
experiment encode accession: ENCSR635SXX
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB171EQX
spikeins used: The drosophila spike-in reference used for alignment

value: cell line

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS858EAQ at ENCODE; https://www.encodeproject.org/ENCBS858EAQ/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: long read RNA-seq from left cerebral cortex (ENCLB818SSI)

description:
https://www.encodeproject.org/experiments/ENCSR674BKT/
***************
biological replicate number: 1
technical replicate number: 1
description: 5xFAD ctx 8 mo Male
experiment encode accession: ENCSR674BKT
assay title: long read RNA-seq
assembly: mm10
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB818SSI
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

organism: Mus musculus

source_name: Mus musculus strain B6.Cg-Tg(APPSwFlLon,PSEN1*M146L*L286V)6799Vas/Mmjax adult (8 months) left cerebral cortex tissue

value: left cerebral cortex

value: 5xFAD 300ctx 8 mo Male

value: Mus musculus

value: not collected

value: adult

value: 8 month

value: Ali Mortazavi, UCI

value: MODEL-AD

value: ENCBS295DXX at ENCODE; https://www.encodeproject.org/ENCBS295DXX/

value: Derived from ENCODE donor ENCDO835CXP; https://www.encodeproject.org/ENCDO835CXP/


title: total RNA-seq from Caco-2 (ENCLB321GGE)

description:
https://www.encodeproject.org/experiments/ENCSR469WPG/
***************
biological replicate number: 2
technical replicate number: 1
description: Caco-2 for bru-seq comparison
experiment encode accession: ENCSR469WPG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB321GGE
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 Caco-2 cell line

value: cell line

value: Homo sapiens

value: male

value: colorectal adenocarcinoma

value: 72 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS020DQC at ENCODE; https://www.encodeproject.org/ENCBS020DQC/

value: Derived from ENCODE donor ENCDO000ACR; https://www.encodeproject.org/ENCDO000ACR/


title: total RNA-seq from B cell (ENCLB386KNX)

description:
https://www.encodeproject.org/experiments/ENCSR896YYL/
***************
biological replicate number: 2
technical replicate number: 1
description: PBMCCD19+ (B cells) resting
experiment encode accession: ENCSR896YYL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Barbara Wold, Caltech
library encode accession: ENCLB386KNX
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: B cell

value: primary cell

value: 22 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS533MTK at ENCODE; https://www.encodeproject.org/ENCBS533MTK/

value: Derived from ENCODE donor ENCDO383AQS; https://www.encodeproject.org/ENCDO383AQS/


title: total RNA-seq from K562 (ENCLB041GHS)

description:
https://www.encodeproject.org/experiments/ENCSR165EQJ/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with MB-3 for 4 hours
experiment encode accession: ENCSR165EQJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB041GHS
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 5 uM MB-3 for 4 hours, preserved by flash-freezing

value: RNA-seq on human cell line K562

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Will Greenleaf, Stanford

value: treatment_term_name:MB-3; treatment_type:chemical; duration:4; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS754WGW at ENCODE; https://www.encodeproject.org/ENCBS754WGW/

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


title: total RNA-seq from middle frontal area 46 (ENCLB250TFL)

description:
https://www.encodeproject.org/experiments/ENCSR920OZR/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E9972216_BS194_ENC4_cDNA748
experiment encode accession: ENCSR920OZR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB250TFL
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: male

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS786GUA at ENCODE; https://www.encodeproject.org/ENCBS786GUA/

value: Derived from ENCODE donor ENCDO607PIC; https://www.encodeproject.org/ENCDO607PIC/


title: long read RNA-seq from left cerebral cortex (ENCLB005LYV)

description:
https://www.encodeproject.org/experiments/ENCSR674BKT/
***************
biological replicate number: 2
technical replicate number: 1
description: 5xFAD ctx 8 mo Male
experiment encode accession: ENCSR674BKT
assay title: long read RNA-seq
assembly: mm10
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB005LYV
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

value: left cerebral cortex

value: 5xFAD 307ctx 8 mo Male

value: Mus musculus

value: not collected

value: 8 month

value: Ali Mortazavi, UCI

value: MODEL-AD

value: ENCBS255FDH at ENCODE; https://www.encodeproject.org/ENCBS255FDH/

value: Derived from ENCODE donor ENCDO835CXP; https://www.encodeproject.org/ENCDO835CXP/


title: CRISPR RNA-seq from K562 (ENCLB940CDV)

description:
https://www.encodeproject.org/experiments/ENCSR632RWY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RECQL5. (RECQL5-BGKcLV30)
experiment encode accession: ENCSR632RWY
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR347NKX
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB940CDV
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 H. sapiens RECQL5

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e175cb73-a20b-48c9-8386-25c857b85ef5/@@download/attachment/L-RECQL5-BGKcLV30-29.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RECQL5. (RECQL5-BGKcLV30-29)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS210FCU at ENCODE; https://www.encodeproject.org/ENCBS210FCU/

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


title: CRISPR RNA-seq from K562 (ENCLB014SJZ)

description:
https://www.encodeproject.org/experiments/ENCSR632RWY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RECQL5. (RECQL5-BGKcLV30)
experiment encode accession: ENCSR632RWY
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR347NKX
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB014SJZ
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/edfb98da-f1da-44ae-ae7c-246c9a140c46/@@download/attachment/L-RECQL5-BGKcLV30-30.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RECQL5. (RECQL5-BGKcLV30-30)

value: Homo sapiens

value: ENCBS045SWE at ENCODE; https://www.encodeproject.org/ENCBS045SWE/


title: total RNA-seq from K562 (ENCLB046HQG)

description:
https://www.encodeproject.org/experiments/ENCSR165EQJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with MB-3 for 4 hours
experiment encode accession: ENCSR165EQJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB046HQG
size range: 300-600

value: RNA-seq on human cell line K562

value: Will Greenleaf, Stanford

value: treatment_term_name:MB-3; treatment_type:chemical; duration:4; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS977YPE at ENCODE; https://www.encodeproject.org/ENCBS977YPE/


title: total RNA-seq from middle frontal area 46 (ENCLB141ASP)

description:
https://www.encodeproject.org/experiments/ENCSR454MWR/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E4205723_BS199_ENC4_cDNA754
experiment encode accession: ENCSR454MWR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB141ASP
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 adult (90 or above years) with mild cognitive impairment; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS430SUA at ENCODE; https://www.encodeproject.org/ENCBS430SUA/

value: Derived from ENCODE donor ENCDO880FAU; https://www.encodeproject.org/ENCDO880FAU/


title: total RNA-seq from Caco-2 (ENCLB882EHH)

description:
https://www.encodeproject.org/experiments/ENCSR469WPG/
***************
biological replicate number: 1
technical replicate number: 1
description: Caco-2 for bru-seq comparison
experiment encode accession: ENCSR469WPG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB882EHH
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: cell line

value: male

value: colorectal adenocarcinoma

value: adult

value: 72 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS075YII at ENCODE; https://www.encodeproject.org/ENCBS075YII/

value: Derived from ENCODE donor ENCDO000ACR; https://www.encodeproject.org/ENCDO000ACR/


title: total RNA-seq from K562 (ENCLB353WFC)

description:
https://www.encodeproject.org/experiments/ENCSR165GPK/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with AR-42 for 48 hours
experiment encode accession: ENCSR165GPK
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB353WFC
size range: 300-600

value: RNA-seq on human cell line K562

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Will Greenleaf, Stanford

value: treatment_term_name:AR-42; treatment_type:chemical; duration:48; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS433VQN at ENCODE; https://www.encodeproject.org/ENCBS433VQN/

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


title: CRISPR RNA-seq from K562 (ENCLB303SJT)

description:
https://www.encodeproject.org/experiments/ENCSR164POA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CNDP2. (CNDP2-BGKcLV28)
experiment encode accession: ENCSR164POA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB303SJT
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 H. sapiens CNDP2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/78d0ef94-8e36-4c27-a3e2-d20045074514/@@download/attachment/L-CNDP2-BGKcLV28-27.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CNDP2. (CNDP2-BGKcLV28-27)

value: Brenton Graveley, UConn

value: ENCBS051GWD at ENCODE; https://www.encodeproject.org/ENCBS051GWD/


title: total RNA-seq from middle frontal area 46 (ENCLB693CSO)

description:
https://www.encodeproject.org/experiments/ENCSR454GQC/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E3486019_BS181_ENC4_cDNA735
experiment encode accession: ENCSR454GQC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB693CSO
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: middle frontal area 46

value: tissue

value: adult

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS851OMB at ENCODE; https://www.encodeproject.org/ENCBS851OMB/

value: Derived from ENCODE donor ENCDO634UMA; https://www.encodeproject.org/ENCDO634UMA/


title: total RNA-seq from middle frontal area 46 (ENCLB260BZM)

description:
https://www.encodeproject.org/experiments/ENCSR452BSJ/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E4781406_BS151_ENC4_cDNA701
experiment encode accession: ENCSR452BSJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB260BZM
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 adult (90 or above years) with Alzheimer's disease; middle frontal area 46 tissue

value: Homo sapiens

value: female

value: ENCBS141EMN at ENCODE; https://www.encodeproject.org/ENCBS141EMN/

value: Derived from ENCODE donor ENCDO150EBZ; https://www.encodeproject.org/ENCDO150EBZ/


title: CRISPR RNA-seq from K562 (ENCLB840RVK)

description:
https://www.encodeproject.org/experiments/ENCSR631NIZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RNPC3. (RNPC3-BGKcLV30)
experiment encode accession: ENCSR631NIZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR347NKX
encode release date: 2022-02-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB840RVK
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 H. sapiens RNPC3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2e1129ad-de2d-48f9-bef9-739eb3c5bcbd/@@download/attachment/L-RNPC3-BGKcLV30-41.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RNPC3. (RNPC3-BGKcLV30-41)

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ATCC

value: ENCBS692XVD at ENCODE; https://www.encodeproject.org/ENCBS692XVD/

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


title: long read RNA-seq from C2C12 (ENCLB756XOV)

description:
https://www.encodeproject.org/experiments/ENCSR221XGR/
***************
biological replicate number: 1
technical replicate number: 1
description: C2C12 Myoblast
experiment encode accession: ENCSR221XGR
assay title: long read RNA-seq
assembly: mm10
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB756XOV
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

source_name: Mus musculus C2C12 cell line

value: cell line

value: C2C12 myoblast

value: Mus musculus

value: not collected

value: unknown

value: Ali Mortazavi, UCI

value: ENCBS824FPY at ENCODE; https://www.encodeproject.org/ENCBS824FPY/

value: Derived from ENCODE donor ENCDO321TZV; https://www.encodeproject.org/ENCDO321TZV/


title: total RNA-seq from middle frontal area 46 (ENCLB518UYM)

description:
https://www.encodeproject.org/experiments/ENCSR447WLU/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E2129371_BS142_ENC4_cDNA692
experiment encode accession: ENCSR447WLU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB518UYM
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December

source_name: Homo sapiens male adult (78 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: male

value: adult

value: 78 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS611ZGG at ENCODE; https://www.encodeproject.org/ENCBS611ZGG/

value: Derived from ENCODE donor ENCDO623FPG; https://www.encodeproject.org/ENCDO623FPG/


title: total RNA-seq from middle frontal area 46 (ENCLB935SUZ)

description:
https://www.encodeproject.org/experiments/ENCSR446QMB/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E2728434_BS149_ENC4_cDNA749
experiment encode accession: ENCSR446QMB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB935SUZ
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 adult (85 years) middle frontal area 46 tissue

value: female

value: 85 year

value: ENCBS166GKO at ENCODE; https://www.encodeproject.org/ENCBS166GKO/

value: Derived from ENCODE donor ENCDO741DAO; https://www.encodeproject.org/ENCDO741DAO/


title: CRISPR RNA-seq from K562 (ENCLB999ZXT)

description:
https://www.encodeproject.org/experiments/ENCSR163RXI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM8A. (RBM8A-BGKcLV30)
experiment encode accession: ENCSR163RXI
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR347NKX
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB999ZXT
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 H. sapiens RBM8A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/48564c97-a477-4410-bbd6-fa71460883c3/@@download/attachment/L-RBM8A-BGKcLV30-24.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM8A. (RBM8A-BGKcLV30-24)

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS978UDJ at ENCODE; https://www.encodeproject.org/ENCBS978UDJ/

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


title: CRISPR RNA-seq from K562 (ENCLB972SDZ)

description:
https://www.encodeproject.org/experiments/ENCSR631NIZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RNPC3. (RNPC3-BGKcLV30)
experiment encode accession: ENCSR631NIZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR347NKX
encode release date: 2022-02-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB972SDZ
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/c81ba697-f82e-4382-ab1d-bee904633fe3/@@download/attachment/L-RNPC3-BGKcLV30-42.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RNPC3. (RNPC3-BGKcLV30-42)

value: Homo sapiens

value: adult

value: ENCBS813IWN at ENCODE; https://www.encodeproject.org/ENCBS813IWN/


title: CRISPR RNA-seq from K562 (ENCLB741YNX)

description:
https://www.encodeproject.org/experiments/ENCSR163RXI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM8A. (RBM8A-BGKcLV30)
experiment encode accession: ENCSR163RXI
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR347NKX
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB741YNX
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/e86c0ec0-ff8e-4923-9414-e3fb46331924/@@download/attachment/L-RBM8A-BGKcLV30-23.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RBM8A. (RBM8A-BGKcLV30-23)

value: ENCBS374GUN at ENCODE; https://www.encodeproject.org/ENCBS374GUN/


title: CRISPR RNA-seq from K562 (ENCLB160TEX)

description:
https://www.encodeproject.org/experiments/ENCSR164POA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CNDP2. (CNDP2-BGKcLV28)
experiment encode accession: ENCSR164POA
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB160TEX
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/846564bb-561f-4be6-a402-24ecc82d8a96/@@download/attachment/L-CNDP2-BGKcLV28-28.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CNDP2. (CNDP2-BGKcLV28-28)

value: female

value: ENCBS383JOT at ENCODE; https://www.encodeproject.org/ENCBS383JOT/


title: DNase-seq from suppressor macrophage (ENCLB698XOA)

description:
https://www.encodeproject.org/experiments/ENCSR564XXO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR564XXO
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB698XOA
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

library_source: genomic

molecule: genomic DNA

source_name: Homo sapiens male adult (21 years) suppressor macrophage primary cell treated with lipopolysaccharide for 1 hour

value: suppressor macrophage

value: primary cell

value: male

value: 21 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: treatment_term_id:CHEBI:16412; treatment_term_name:lipopolysaccharide; treatment_type:chemical; duration:1; duration_units:hour;

value: ENCBS324LUD at ENCODE; https://www.encodeproject.org/ENCBS324LUD/

value: Derived from ENCODE donor ENCDO733YAB; https://www.encodeproject.org/ENCDO733YAB/


title: long read RNA-seq from C2C12 (ENCLB214KKF)

description:
https://www.encodeproject.org/experiments/ENCSR221XGR/
***************
biological replicate number: 2
technical replicate number: 1
description: C2C12 Myoblast
experiment encode accession: ENCSR221XGR
assay title: long read RNA-seq
assembly: mm10
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB214KKF
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

value: cell line

value: C2C12 myoblast

value: Mus musculus

value: not collected

value: unknown

value: Ali Mortazavi, UCI

value: ATCC

value: ENCBS649CMC at ENCODE; https://www.encodeproject.org/ENCBS649CMC/

value: Derived from ENCODE donor ENCDO321TZV; https://www.encodeproject.org/ENCDO321TZV/


title: total RNA-seq from middle frontal area 46 (ENCLB474YNS)

description:
https://www.encodeproject.org/experiments/ENCSR439PRN/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E1182310_BS120_ENC4_cDNA682
experiment encode accession: ENCSR439PRN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB474YNS
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: adult

value: 83 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS137SYN at ENCODE; https://www.encodeproject.org/ENCBS137SYN/

value: Derived from ENCODE donor ENCDO161NAR; https://www.encodeproject.org/ENCDO161NAR/


title: total RNA-seq from middle frontal area 46 (ENCLB937LOM)

description:
https://www.encodeproject.org/experiments/ENCSR863EIY/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E1554367_BS148_ENC4_cDNA698
experiment encode accession: ENCSR863EIY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB937LOM
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 adult (82 years) middle frontal area 46 tissue

value: male

value: 82 year

value: ENCBS870MVU at ENCODE; https://www.encodeproject.org/ENCBS870MVU/

value: Derived from ENCODE donor ENCDO407UTA; https://www.encodeproject.org/ENCDO407UTA/


title: total RNA-seq from K562 (ENCLB760SYA)

description:
https://www.encodeproject.org/experiments/ENCSR161RSX/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with MB-3 for 24 hours
experiment encode accession: ENCSR161RSX
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB760SYA
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 5 uM MB-3 for 24 hours, preserved by flash-freezing

value: cell line

value: RNA-seq on human cell line K562

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Will Greenleaf, Stanford

value: treatment_term_name:MB-3; treatment_type:chemical; duration:24; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS669SHO at ENCODE; https://www.encodeproject.org/ENCBS669SHO/

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


title: total RNA-seq from K562 (ENCLB366URZ)

description:
https://www.encodeproject.org/experiments/ENCSR161RSX/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with MB-3 for 24 hours
experiment encode accession: ENCSR161RSX
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB366URZ
size range: 300-600

value: Homo sapiens

value: adult

value: ATCC

value: ENCBS781FVE at ENCODE; https://www.encodeproject.org/ENCBS781FVE/


title: total RNA-seq from middle frontal area 46 (ENCLB826ECW)

description:
https://www.encodeproject.org/experiments/ENCSR443ASQ/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E8583444_BS184_ENC4_cDNA738
experiment encode accession: ENCSR443ASQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB826ECW
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 adult (83 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: 83 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS314RQJ at ENCODE; https://www.encodeproject.org/ENCBS314RQJ/

value: Derived from ENCODE donor ENCDO394FZZ; https://www.encodeproject.org/ENCDO394FZZ/


title: total RNA-seq from natural killer cell (ENCLB961ZIH)

description:
https://www.encodeproject.org/experiments/ENCSR842NDO/
***************
biological replicate number: 1
technical replicate number: 1
description: h.CD56+_DONOR 3: 72 hour activation IL-12+IL-15+IL-18, 100ng/ml
experiment encode accession: ENCSR842NDO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB961ZIH
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 330
nucleic acid starting quantity units: ng

source_name: Homo sapiens female adult (41 years) natural killer primary cell treated with 100 ng/mL Interleukin-12 subunit alpha for 72 hours, 100 ng/mL Interleukin-15 for 72 hours, 100 ng/mL Interleukin-12 subunit beta for 72 hours, 100 ng/mL Interleukin-18 for...

value: natural killer cell

value: primary cell

value: female

value: 41 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein; duration:72; duration_units:hour; treatment_term_id:UniProtKB:Q14116; treatment_term_name:Interleukin-18; treatment_type:protein; duration:72; duration_units:hour;

value: ENCBS734EVS at ENCODE; https://www.encodeproject.org/ENCBS734EVS/

value: Derived from ENCODE donor ENCDO911LCI; https://www.encodeproject.org/ENCDO911LCI/


title: total RNA-seq from WTC11 (ENCLB694LYB)

description:
https://www.encodeproject.org/experiments/ENCSR723OPL/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens cardiomyocytes in vitro differentiated originated from WTC11 cells, 4 days after differentiation
experiment encode accession: ENCSR723OPL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-22
lab: Will Greenleaf, Stanford
library encode accession: ENCLB694LYB

source_name: Homo sapiens WTC11 cell line treated with 7.5 uM IWP-2 for 48 hours, 4 days post differentiation, preserved by flash-freezing

value: cell line

value: iPSC differentiation in to cardiomycytes

value: Homo sapiens

value: male

value: adult

value: 30 year

value: Will Greenleaf, Stanford

value: Coriell

value: treatment_term_id:CHEBI:125649; treatment_term_name:IWP-2; treatment_type:chemical; duration:48; duration_units:hour;

value: ENCBS761UUN at ENCODE; https://www.encodeproject.org/ENCBS761UUN/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: CRISPR RNA-seq from K562 (ENCLB328TSU)

description:
https://www.encodeproject.org/experiments/ENCSR159HPD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CAST. (CAST-BGKcLV26)
experiment encode accession: ENCSR159HPD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB328TSU
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 H. sapiens CAST

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7fefecbe-398b-49a6-bfc8-4498e0bd7b7c/@@download/attachment/L-CAST-BGKcLV26-59.pdf

value: CAST

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CAST. (CAST-BGKcLV26-59)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS676SDY at ENCODE; https://www.encodeproject.org/ENCBS676SDY/

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


title: long read RNA-seq from left cerebral cortex (ENCLB440QNX)

description:
https://www.encodeproject.org/experiments/ENCSR644GDT/
***************
biological replicate number: 2
technical replicate number: 1
description: Cortex from 6 mo C57BL/6 male
experiment encode accession: ENCSR644GDT
assay title: long read RNA-seq
assembly: mm10
encode release date: 2020-03-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB440QNX
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Mus musculus strain B6NCrl adult (6 months) left cerebral cortex tissue

value: left cerebral cortex

value: tissue

value: Cortex from 6 mo C57BL/6 male

value: Mus musculus

value: not collected

value: 6 month

value: Ali Mortazavi, UCI

value: MODEL-AD

value: ENCBS913WLS at ENCODE; https://www.encodeproject.org/ENCBS913WLS/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: CRISPR RNA-seq from K562 (ENCLB282FGR)

description:
https://www.encodeproject.org/experiments/ENCSR159HPD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CAST. (CAST-BGKcLV26)
experiment encode accession: ENCSR159HPD
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB282FGR
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/62fe08da-f306-4735-a15d-2927280ba34f/@@download/attachment/L-CAST-BGKcLV26-60.pdf

value: CAST

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CAST. (CAST-BGKcLV26-60)

value: Homo sapiens

value: female

value: adult

value: ENCBS336JAA at ENCODE; https://www.encodeproject.org/ENCBS336JAA/


title: long read RNA-seq from left cerebral cortex (ENCLB287KUK)

description:
https://www.encodeproject.org/experiments/ENCSR644GDT/
***************
biological replicate number: 1
technical replicate number: 1
description: Cortex from 6 mo C57BL/6 male
experiment encode accession: ENCSR644GDT
assay title: long read RNA-seq
assembly: mm10
encode release date: 2020-03-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB287KUK
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: left cerebral cortex

value: ENCBS375QEH at ENCODE; https://www.encodeproject.org/ENCBS375QEH/


title: total RNA-seq from natural killer cell (ENCLB715DGZ)

description:
https://www.encodeproject.org/experiments/ENCSR842NDO/
***************
biological replicate number: 1
technical replicate number: 2
description: h.CD56+_DONOR 3: 72 hour activation IL-12+IL-15+IL-18, 100ng/ml
experiment encode accession: ENCSR842NDO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB715DGZ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 330
nucleic acid starting quantity units: ng

value: natural killer cell

value: primary cell

value: 41 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein; duration:72; duration_units:hour; treatment_term_id:UniProtKB:Q14116; treatment_term_name:Interleukin-18; treatment_type:protein; duration:72; duration_units:hour;

value: ENCBS734EVS at ENCODE; https://www.encodeproject.org/ENCBS734EVS/

value: Derived from ENCODE donor ENCDO911LCI; https://www.encodeproject.org/ENCDO911LCI/


title: total RNA-seq from middle frontal area 46 (ENCLB518FPG)

description:
https://www.encodeproject.org/experiments/ENCSR832YWU/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E3291783_BS154_ENC4_cDNA704
experiment encode accession: ENCSR832YWU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB518FPG
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 adult (87 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: male

value: 87 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS506TDA at ENCODE; https://www.encodeproject.org/ENCBS506TDA/

value: Derived from ENCODE donor ENCDO123QRW; https://www.encodeproject.org/ENCDO123QRW/


title: total RNA-seq from WTC11 (ENCLB087WSY)

description:
https://www.encodeproject.org/experiments/ENCSR914ALB/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens cardiomyocytes in vitro differentiated originated from WTC11 cells, 6 days after differentiation
experiment encode accession: ENCSR914ALB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-22
lab: Will Greenleaf, Stanford
library encode accession: ENCLB087WSY

source_name: Homo sapiens WTC11 cell line, 6 days post differentiation, preserved by flash-freezing

value: cell line

value: iPSC differentiation in to cardiomycytes

value: Homo sapiens

value: adult

value: 30 year

value: Will Greenleaf, Stanford

value: Coriell

value: ENCBS180JSX at ENCODE; https://www.encodeproject.org/ENCBS180JSX/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: Bru-seq from HCT116 (ENCLB626YWF)

description:
https://www.encodeproject.org/experiments/ENCSR626FRT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR626FRT
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB626YWF
size range: 400-500

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS851OSG at ENCODE; https://www.encodeproject.org/ENCBS851OSG/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: total RNA-seq from T-helper 17 cell (ENCLB561AVL)

description:
https://www.encodeproject.org/experiments/ENCSR831GLL/
***************
biological replicate number: 1
technical replicate number: 1
description: h.CD4.Th17_DONOR 6: 0 hour no activation
experiment encode accession: ENCSR831GLL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB561AVL
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 330
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (50 years) T-helper 17 primary cell

value: T-helper 17 cell

value: primary cell

value: male

value: 50 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS075VXO at ENCODE; https://www.encodeproject.org/ENCBS075VXO/

value: Derived from ENCODE donor ENCDO641WTL; https://www.encodeproject.org/ENCDO641WTL/


title: Bru-seq from HCT116 (ENCLB304FDM)

description:
https://www.encodeproject.org/experiments/ENCSR626FRT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR626FRT
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-10-04
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB304FDM
size range: 400-500

value: cell line

value: Homo sapiens

value: adult

value: ENCBS654QXD at ENCODE; https://www.encodeproject.org/ENCBS654QXD/


title: total RNA-seq from middle frontal area 46 (ENCLB182KFG)

description:
https://www.encodeproject.org/experiments/ENCSR418WMG/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E8792932_BS215_ENC4_cDNA770
experiment encode accession: ENCSR418WMG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB182KFG
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 adult (89 years) with mild cognitive impairment; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: 89 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS589OUP at ENCODE; https://www.encodeproject.org/ENCBS589OUP/

value: Derived from ENCODE donor ENCDO697SWU; https://www.encodeproject.org/ENCDO697SWU/


title: total RNA-seq from WTC11 (ENCLB133IHR)

description:
https://www.encodeproject.org/experiments/ENCSR723OPL/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens cardiomyocytes in vitro differentiated originated from WTC11 cells, 4 days after differentiation
experiment encode accession: ENCSR723OPL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-22
lab: Will Greenleaf, Stanford
library encode accession: ENCLB133IHR

value: iPSC differentiation in to cardiomycytes

value: male

value: 30 year

value: Will Greenleaf, Stanford

value: Coriell

value: treatment_term_id:CHEBI:125649; treatment_term_name:IWP-2; treatment_type:chemical; duration:48; duration_units:hour;

value: ENCBS811FZJ at ENCODE; https://www.encodeproject.org/ENCBS811FZJ/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: PRO-cap from K562 (ENCLB290TVD)

description:
https://www.encodeproject.org/experiments/ENCSR882DWM/
***************
biological replicate number: 2
technical replicate number: 1
description: CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, only uncapped nascent RNA was selected and no PCR amplification was done.
experiment encode accession: ENCSR882DWM
assay title: PRO-cap
assembly: GRCh38
encode release date: 2021-12-14
lab: John Lis, Cornell
library encode accession: ENCLB290TVD

source_name: Homo sapiens K562 cell line

value: cell line

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: John Lis, Cornell

value: ATCC

value: ENCBS800REP at ENCODE; https://www.encodeproject.org/ENCBS800REP/

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


title: PRO-cap from K562 (ENCLB465HHU)

description:
https://www.encodeproject.org/experiments/ENCSR882DWM/
***************
biological replicate number: 1
technical replicate number: 1
description: CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, only uncapped nascent RNA was selected and no PCR amplification was done.
experiment encode accession: ENCSR882DWM
assay title: PRO-cap
assembly: GRCh38
encode release date: 2021-12-14
lab: John Lis, Cornell
library encode accession: ENCLB465HHU

value: ENCBS154MMU at ENCODE; https://www.encodeproject.org/ENCBS154MMU/


title: PRO-seq from HCT116 (ENCLB674REX)

description:
https://www.encodeproject.org/experiments/ENCSR404RZX/
***************
biological replicate number: 1
technical replicate number: 1
description: PRO-seq in BRD4_U
experiment encode accession: ENCSR404RZX
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB674REX
spikeins used: The drosophila spike-in reference used for alignment

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens BRD4

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS214JQO at ENCODE; https://www.encodeproject.org/ENCBS214JQO/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: total RNA-seq from middle frontal area 46 (ENCLB590ZXZ)

description:
https://www.encodeproject.org/experiments/ENCSR826FNO/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E7148318_BS165_ENC4_cDNA715
experiment encode accession: ENCSR826FNO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB590ZXZ
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 adult (84 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: Homo sapiens

value: 84 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS934BVK at ENCODE; https://www.encodeproject.org/ENCBS934BVK/

value: Derived from ENCODE donor ENCDO999WDR; https://www.encodeproject.org/ENCDO999WDR/


title: PRO-seq from HCT116 (ENCLB945LTZ)

description:
https://www.encodeproject.org/experiments/ENCSR404RZX/
***************
biological replicate number: 2
technical replicate number: 1
description: PRO-seq in BRD4_U
experiment encode accession: ENCSR404RZX
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB945LTZ
spikeins used: The drosophila spike-in reference used for alignment

value: cell line

value: adult

value: ENCBS930EMD at ENCODE; https://www.encodeproject.org/ENCBS930EMD/


title: CRISPR RNA-seq from K562 (ENCLB521CIG)

description:
https://www.encodeproject.org/experiments/ENCSR157IJG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SMG7. (SMG7-BGKcLV33)
experiment encode accession: ENCSR157IJG
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB521CIG
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 H. sapiens SMG9

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/88b3b0b9-97cf-45e4-8c51-8803fec468a2/@@download/attachment/L-SMG7-BGKcLV33-58.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SMG7. (SMG7-BGKcLV33-58)

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS248EXP at ENCODE; https://www.encodeproject.org/ENCBS248EXP/

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


title: PRO-cap from K562 (ENCLB049AQJ)

description:
https://www.encodeproject.org/experiments/ENCSR882DWM/
***************
biological replicate number: 2
technical replicate number: 2
description: CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, only uncapped nascent RNA was selected and no PCR amplification was done.
experiment encode accession: ENCSR882DWM
assay title: PRO-cap
assembly: GRCh38
encode release date: 2021-12-14
lab: John Lis, Cornell
library encode accession: ENCLB049AQJ

value: Homo sapiens

value: John Lis, Cornell

value: ENCBS800REP at ENCODE; https://www.encodeproject.org/ENCBS800REP/


title: CRISPR RNA-seq from K562 (ENCLB394CWU)

description:
https://www.encodeproject.org/experiments/ENCSR157IJG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SMG7. (SMG7-BGKcLV33)
experiment encode accession: ENCSR157IJG
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB394CWU
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/16463a6e-b162-4f50-8bb2-6ace4a18b177/@@download/attachment/L-SMG7-BGKcLV33-57.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SMG7. (SMG7-BGKcLV33-57)

value: ENCBS385NOB at ENCODE; https://www.encodeproject.org/ENCBS385NOB/


title: BruChase-seq from endothelial cell of umbilical vein (ENCLB623RRZ)

description:
https://www.encodeproject.org/experiments/ENCSR624MRE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR624MRE
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR849FAX
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB623RRZ
size range: 400-500

source_name: Homo sapiens male newborn endothelial of umbilical vein primary cell, subjected to a 2 hour pulse-chase

value: endothelial cell of umbilical vein

value: primary cell

value: male

value: newborn

value: unknown

value: Mats Ljungman, UMichigan

value: Lonza

value: ENCBS356JLC at ENCODE; https://www.encodeproject.org/ENCBS356JLC/

value: Derived from ENCODE donor ENCDO628LXZ; https://www.encodeproject.org/ENCDO628LXZ/


title: BruChase-seq from endothelial cell of umbilical vein (ENCLB496IZJ)

description:
https://www.encodeproject.org/experiments/ENCSR624MRE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR624MRE
assay title: BruChase-seq
assembly: GRCh38
possible controls: ENCSR849FAX
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB496IZJ
size range: 400-500

value: ENCBS838SCE at ENCODE; https://www.encodeproject.org/ENCBS838SCE/


title: microRNA-seq from HL-60 (ENCLB353YIJ)

description:
https://www.encodeproject.org/experiments/ENCSR865XJM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation HL-60 derived M2 macrophages (differentiated 24hr) microRNA-seq from Mortazavi
experiment encode accession: ENCSR865XJM
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB353YIJ
size range: <30

source_name: Homo sapiens HL-60 cell line treated with 10 uM phorbol 13-acetate 12-myristate for 120 hours, 10 ng/mL interleukin-13 for 24 hours, 10 ng/mL interleukin-4 for 24 hours

value: cell line

value: HL-60 derived M2A macrophages (24hr)

value: female

value: acute promyelocytic leukemia

value: adult

value: 36 year

value: Ali Mortazavi, UCI

value: ATCC

value: treatment_term_id:CHEBI:37537; treatment_term_name:phorbol 13-acetate 12-myristate; treatment_type:chemical; duration:120; duration_units:hour; treatment_term_id:UniProtKB:P35225; treatment_term_name:interleukin-13; treatment_type:protein; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P05112; treatment_term_name:interleukin-4; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS172TZS at ENCODE; https://www.encodeproject.org/ENCBS172TZS/

value: Derived from ENCODE donor ENCDO000AAM; https://www.encodeproject.org/ENCDO000AAM/


title: microRNA-seq from HL-60 (ENCLB927ILN)

description:
https://www.encodeproject.org/experiments/ENCSR865XJM/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA Evaluation HL-60 derived M2 macrophages (differentiated 24hr) microRNA-seq from Mortazavi
experiment encode accession: ENCSR865XJM
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB927ILN
size range: <30

value: Homo sapiens

value: ENCBS486WPL at ENCODE; https://www.encodeproject.org/ENCBS486WPL/


title: total RNA-seq from MCF 10A (ENCLB815KYI)

description:
https://www.encodeproject.org/experiments/ENCSR815NTL/
***************
biological replicate number: 2
technical replicate number: 1
description: MFC 10A for bru-seq comparison
experiment encode accession: ENCSR815NTL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB815KYI
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 MCF 10A cell line

value: MCF 10A

value: fibrocystic disease

value: Mats Ljungman, UMichigan

value: ENCBS863SFU at ENCODE; https://www.encodeproject.org/ENCBS863SFU/

value: Derived from ENCODE donor ENCDO000AAP; https://www.encodeproject.org/ENCDO000AAP/


title: total RNA-seq from A549 (ENCLB747WSO)

description:
https://www.encodeproject.org/experiments/ENCSR155ZTO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR155ZTO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB747WSO
size range: 200-300

source_name: Homo sapiens A549 cell line treated with 1 uM AZD2906 (agonist) for 4 hours

extract_protocol:
extraction protocol: https://www.encodeproject.org/documents/e4e1b09a-8fe8-4212-9e76-a2fd6d0c8b49/@@download/attachment/supplemental%20PolyA%20plus%20RNA-seq%20library%20construction%20protocol.pdf
general protocol: https://www.encodeproject.org/documents/c2499c10-935d-4bc9-b374-5a40f69d4af9/@@download/attachment/Reddy_Lab_RNAseq_ENCODE_protocol.pdf
extraction method: Qiagen RNA extraction

value: cell line

value: male

value: 58 year

value: Tim Reddy, Duke

value: treatment_term_name:AZD2906; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS600HFC at ENCODE; https://www.encodeproject.org/ENCBS600HFC/

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


title: total RNA-seq from A549 (ENCLB497IPY)

description:
https://www.encodeproject.org/experiments/ENCSR155ZTO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR155ZTO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Tim Reddy, Duke
library encode accession: ENCLB497IPY
size range: 200-300

value: adult

value: ATCC

value: ENCBS828KDP at ENCODE; https://www.encodeproject.org/ENCBS828KDP/


title: total RNA-seq from activated B cell (ENCLB415NAG)

description:
https://www.encodeproject.org/experiments/ENCSR398REC/
***************
biological replicate number: 2
technical replicate number: 1
description: PBMCCD19+ (B cells) activatedCPG ODN2006 24h
experiment encode accession: ENCSR398REC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Barbara Wold, Caltech
library encode accession: ENCLB415NAG
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 adult (22 years) activated B primary cell treated with 0.5 uM CpG ODN for 24 hours

value: activated B cell

value: primary cell

value: Homo sapiens

value: 22 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_name:CpG ODN; treatment_type:chemical; duration:24; duration_units:hour;

value: ENCBS430TYQ at ENCODE; https://www.encodeproject.org/ENCBS430TYQ/

value: Derived from ENCODE donor ENCDO383AQS; https://www.encodeproject.org/ENCDO383AQS/


title: total RNA-seq from WTC11 (ENCLB888WEL)

description:
https://www.encodeproject.org/experiments/ENCSR914ALB/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens cardiomyocytes in vitro differentiated originated from WTC11 cells, 6 days after differentiation
experiment encode accession: ENCSR914ALB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-22
lab: Will Greenleaf, Stanford
library encode accession: ENCLB888WEL

value: cell line

value: iPSC differentiation in to cardiomycytes

value: male

value: 30 year

value: Will Greenleaf, Stanford

value: Coriell

value: ENCBS817RRI at ENCODE; https://www.encodeproject.org/ENCBS817RRI/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: PRO-cap from K562 (ENCLB264LBO)

description:
https://www.encodeproject.org/experiments/ENCSR882DWM/
***************
biological replicate number: 1
technical replicate number: 2
description: CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, only uncapped nascent RNA was selected and no PCR amplification was done.
experiment encode accession: ENCSR882DWM
assay title: PRO-cap
assembly: GRCh38
encode release date: 2021-12-14
lab: John Lis, Cornell
library encode accession: ENCLB264LBO

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: John Lis, Cornell

value: ATCC

value: ENCBS154MMU at ENCODE; https://www.encodeproject.org/ENCBS154MMU/

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


title: total RNA-seq from MCF 10A (ENCLB290MLO)

description:
https://www.encodeproject.org/experiments/ENCSR815NTL/
***************
biological replicate number: 1
technical replicate number: 1
description: MFC 10A for bru-seq comparison
experiment encode accession: ENCSR815NTL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB290MLO
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: MCF 10A

value: Homo sapiens

value: fibrocystic disease

value: 36 year

value: Mats Ljungman, UMichigan

value: ENCBS534SPQ at ENCODE; https://www.encodeproject.org/ENCBS534SPQ/

value: Derived from ENCODE donor ENCDO000AAP; https://www.encodeproject.org/ENCDO000AAP/