title: total RNA-seq from T-helper 2 cell (ENCLB977MZE)

description:
https://www.encodeproject.org/experiments/ENCSR588TIV/
***************
biological replicate number: 1
technical replicate number: 1
description: CD4 N (RA+ MACS sort)Th2 (aIFNg 5ug/ml+IL-4 100ng/ml)(day 14)
experiment encode accession: ENCSR588TIV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Barbara Wold, Caltech
library encode accession: ENCLB977MZE
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 (35 years) T-helper 2 primary cell treated with 100 ng/mL Interleukin-4 for 36 hours, 5 ug/mL Interferon-gamma antibody for 36 hours

value: T-helper 2 cell

value: primary cell

value: Homo sapiens

value: male

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:36; duration_units:hour; treatment_term_name:Interferon-gamma antibody; treatment_type:antibody; duration:36; duration_units:hour;

value: ENCBS983OVZ at ENCODE; https://www.encodeproject.org/ENCBS983OVZ/

value: Derived from ENCODE donor ENCDO374BBL; https://www.encodeproject.org/ENCDO374BBL/


title: total RNA-seq from middle frontal area 46 (ENCLB377HSU)

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/ENCSR591NFI/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E2987977_BS146_ENC4_cDNA696
experiment encode accession: ENCSR591NFI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB377HSU
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December

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

value: female

tag: dev stage

value: adult

tag: age

value: 90 or above year

tag: lab

value: Barbara Wold, Caltech

tag: source

value: Rush University

tag: link

value: ENCBS308QTA at ENCODE; https://www.encodeproject.org/ENCBS308QTA/

value: Derived from ENCODE donor ENCDO651VQQ; https://www.encodeproject.org/ENCDO651VQQ/


title: total RNA-seq from layer of hippocampus (ENCLB016QEU)

description:
https://www.encodeproject.org/experiments/ENCSR886NLC/
***************
biological replicate number: 1
technical replicate number: 1
description: 5xFAD X Cast hippocampus_8-10 months female
experiment encode accession: ENCSR886NLC
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-02-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB016QEU
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

organism: Mus musculus

source_name: Mus musculus strain 5xFAD/CAST female adult (8-10 months) layer of hippocampus tissue

value: layer of hippocampus

value: Mus musculus

value: 8-10 month

value: The Jackson Laboratory

value: ENCBS900NRB at ENCODE; https://www.encodeproject.org/ENCBS900NRB/

value: Derived from ENCODE donor ENCDO996MUL; https://www.encodeproject.org/ENCDO996MUL/


title: CRISPR RNA-seq from HepG2 (ENCLB047FQP)

description:
https://www.encodeproject.org/experiments/ENCSR076LFC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ALKBH1. (ALKBH1-BGHcLV24)
experiment encode accession: ENCSR076LFC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR671FDZ
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB047FQP
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting H. sapiens ALKBH1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2ae3596c-e7e4-437e-b159-ac946c68d1a4/@@download/attachment/L-ALKBH1-BGHcLV24-10.pdf

tag: antibody

tag: line

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ALKBH1. (ALKBH1-BGHcLV24-10)

value: Homo sapiens

value: male

tag: health state

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS358QAI at ENCODE; https://www.encodeproject.org/ENCBS358QAI/

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


title: total RNA-seq from left cerebral cortex (ENCLB213ABI)

description:
https://www.encodeproject.org/experiments/ENCSR723XFW/
***************
biological replicate number: 1
technical replicate number: 1
description: 5xFAD X Cast L. cortex (brain)_8-10 months female
experiment encode accession: ENCSR723XFW
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-02-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB213ABI
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: Mus musculus strain 5xFAD/CAST female adult (8-10 months) left cerebral cortex tissue

value: left cerebral cortex

value: tissue

value: female

value: adult

value: Barbara Wold, Caltech

value: ENCBS505BIQ at ENCODE; https://www.encodeproject.org/ENCBS505BIQ/


title: total RNA-seq from middle frontal area 46 (ENCLB939HWC)

description:
https://www.encodeproject.org/experiments/ENCSR102NWB/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E7584572_BS209_ENC4_cDNA764
experiment encode accession: ENCSR102NWB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB939HWC
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 (87 years) with mild cognitive impairment; middle frontal area 46 tissue

value: middle frontal area 46

value: 87 year

value: Rush University

value: ENCBS387BKP at ENCODE; https://www.encodeproject.org/ENCBS387BKP/

value: Derived from ENCODE donor ENCDO354SJE; https://www.encodeproject.org/ENCDO354SJE/


title: total RNA-seq from middle frontal area 46 (ENCLB181HQH)

description:
https://www.encodeproject.org/experiments/ENCSR585EUI/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E2904121_BS150_ENC4_cDNA700
experiment encode accession: ENCSR585EUI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB181HQH
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 (82 years) middle frontal area 46 tissue

value: Homo sapiens

value: 82 year

value: ENCBS952NTO at ENCODE; https://www.encodeproject.org/ENCBS952NTO/

value: Derived from ENCODE donor ENCDO290OPS; https://www.encodeproject.org/ENCDO290OPS/


title: total RNA-seq from middle frontal area 46 (ENCLB515QCU)

description:
https://www.encodeproject.org/experiments/ENCSR096YLM/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E2804864_BS180_ENC4_cDNA734
experiment encode accession: ENCSR096YLM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB515QCU
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) with mild cognitive impairment; middle frontal area 46 tissue

value: male

value: 84 year

value: ENCBS704KLT at ENCODE; https://www.encodeproject.org/ENCBS704KLT/

value: Derived from ENCODE donor ENCDO020PXA; https://www.encodeproject.org/ENCDO020PXA/


title: CRISPR RNA-seq from HepG2 (ENCLB608DYU)

description:
https://www.encodeproject.org/experiments/ENCSR076LFC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ALKBH1. (ALKBH1-BGHcLV24)
experiment encode accession: ENCSR076LFC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR671FDZ
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB608DYU
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/b35fd106-eaca-4bf7-8677-fa4751cc1fc0/@@download/attachment/L-ALKBH1-BGHcLV24-9.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ALKBH1. (ALKBH1-BGHcLV24-9)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS039NUK at ENCODE; https://www.encodeproject.org/ENCBS039NUK/

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


title: total RNA-seq from left cerebral cortex (ENCLB363TPB)

description:
https://www.encodeproject.org/experiments/ENCSR879VZJ/
***************
biological replicate number: 2
technical replicate number: 1
description: B6 X Cast L. cortex (brain)_8-10 months male
experiment encode accession: ENCSR879VZJ
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-11-09
lab: Barbara Wold, Caltech
library encode accession: ENCLB363TPB
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: Mus musculus strain B6CASTF1/J male adult (8-10 months) left cerebral cortex tissue

value: left cerebral cortex

value: tissue

value: B6 X Cast L. cortex (brain)_8-10 months male animal 4_ENC4_cDNA_837

value: Mus musculus

value: adult

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS902QEZ at ENCODE; https://www.encodeproject.org/ENCBS902QEZ/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: total RNA-seq from middle frontal area 46 (ENCLB855LQZ)

description:
https://www.encodeproject.org/experiments/ENCSR090RYJ/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E9716765_BS218_ENC4_cDNA773
experiment encode accession: ENCSR090RYJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB855LQZ
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: Homo sapiens

value: female

value: 90 or above year

value: Rush University

value: ENCBS069FLE at ENCODE; https://www.encodeproject.org/ENCBS069FLE/

value: Derived from ENCODE donor ENCDO170MSG; https://www.encodeproject.org/ENCDO170MSG/


title: CRISPR RNA-seq from HepG2 (ENCLB063ZJC)

description:
https://www.encodeproject.org/experiments/ENCSR085GSF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CNDP2. (CNDP2-BGHcLV29)
experiment encode accession: ENCSR085GSF
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB063ZJC
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens HepG2 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/38a5268e-4787-4dd1-af66-911bb590a7a6/@@download/attachment/L-CNDP2-BGHcLV29-28.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CNDP2. (CNDP2-BGHcLV29-28)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS458NJP at ENCODE; https://www.encodeproject.org/ENCBS458NJP/

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


title: total RNA-seq from heart (ENCLB722KYD)

description:
https://www.encodeproject.org/experiments/ENCSR389GJZ/
***************
biological replicate number: 2
technical replicate number: 1
description: B6 X Cast heart_8-10 months male
experiment encode accession: ENCSR389GJZ
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-11-09
lab: Barbara Wold, Caltech
library encode accession: ENCLB722KYD
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: Mus musculus strain B6CASTF1/J male adult (8-10 months) heart tissue

value: heart

value: tissue

value: B6 X Cast heart_8-10 months male animal 4_ENC4_cDNA_841

value: Mus musculus

value: adult

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS081XNT at ENCODE; https://www.encodeproject.org/ENCBS081XNT/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: CRISPR RNA-seq from HepG2 (ENCLB281QYA)

description:
https://www.encodeproject.org/experiments/ENCSR583SHC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CCDC47. (CCDC47-BGHcLV27)
experiment encode accession: ENCSR583SHC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR650TTU
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB281QYA
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting H. sapiens CCDC47

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8729d730-4c70-4947-9e62-0d9fb3c753ef/@@download/attachment/L-CCDC47-BGHcLV27-45.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CCDC47. (CCDC47-BGHcLV27-45)

value: Homo sapiens

value: male

value: hepatocellular carcinoma

value: ENCBS775FFI at ENCODE; https://www.encodeproject.org/ENCBS775FFI/


title: CRISPR RNA-seq from HepG2 (ENCLB232RAK)

description:
https://www.encodeproject.org/experiments/ENCSR583SHC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CCDC47. (CCDC47-BGHcLV27)
experiment encode accession: ENCSR583SHC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR650TTU
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB232RAK
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/76f3cda2-1760-4ee9-bc19-a90c89b589f4/@@download/attachment/L-CCDC47-BGHcLV27-46.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CCDC47. (CCDC47-BGHcLV27-46)

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS636MAC at ENCODE; https://www.encodeproject.org/ENCBS636MAC/

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


title: total RNA-seq from layer of hippocampus (ENCLB896ZZS)

description:
https://www.encodeproject.org/experiments/ENCSR801JDZ/
***************
biological replicate number: 2
technical replicate number: 1
description: B6 X Cast hippocampus_8-10 months male
experiment encode accession: ENCSR801JDZ
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-11-09
lab: Barbara Wold, Caltech
library encode accession: ENCLB896ZZS
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: Mus musculus strain B6CASTF1/J male adult (8-10 months) layer of hippocampus tissue

value: layer of hippocampus

value: tissue

value: B6 X Cast hippocampus_8-10 months male animal 4_ENC4_cDNA_833

value: Mus musculus

value: adult

value: 8-10 month

value: Barbara Wold, Caltech

value: ENCBS090XCX at ENCODE; https://www.encodeproject.org/ENCBS090XCX/


title: total RNA-seq from natural killer cell (ENCLB919BLQ)

description:
https://www.encodeproject.org/experiments/ENCSR584CVV/
***************
biological replicate number: 1
technical replicate number: 4
description: h.CD56+_DONOR 3: 0 hour no activation
experiment encode accession: ENCSR584CVV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB919BLQ
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

value: natural killer cell

value: primary cell

value: Homo sapiens

value: female

value: 41 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS578OIT at ENCODE; https://www.encodeproject.org/ENCBS578OIT/

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


title: total RNA-seq from heart (ENCLB646FKP)

description:
https://www.encodeproject.org/experiments/ENCSR389GJZ/
***************
biological replicate number: 1
technical replicate number: 1
description: B6 X Cast heart_8-10 months male
experiment encode accession: ENCSR389GJZ
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-11-09
lab: Barbara Wold, Caltech
library encode accession: ENCLB646FKP
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: heart

value: B6 X Cast heart_8-10 months male animal 2_ENC4_cDNA_840

value: male

value: The Jackson Laboratory

value: ENCBS989OMB at ENCODE; https://www.encodeproject.org/ENCBS989OMB/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: total RNA-seq from T-helper 2 cell (ENCLB333MSB)

description:
https://www.encodeproject.org/experiments/ENCSR588TIV/
***************
biological replicate number: 2
technical replicate number: 1
description: CD4 N (RA+ MACS sort)Th2 (aIFNg 5ug/ml+IL-4 100ng/ml)(day 14)
experiment encode accession: ENCSR588TIV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Barbara Wold, Caltech
library encode accession: ENCLB333MSB
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: T-helper 2 cell

value: adult

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

tag: treatments

value: treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:36; duration_units:hour; treatment_term_name:Interferon-gamma antibody; treatment_type:antibody; duration:36; duration_units:hour;

value: ENCBS727FRT at ENCODE; https://www.encodeproject.org/ENCBS727FRT/

value: Derived from ENCODE donor ENCDO374BBL; https://www.encodeproject.org/ENCDO374BBL/


title: total RNA-seq from middle frontal area 46 (ENCLB895NVR)

description:
https://www.encodeproject.org/experiments/ENCSR620YAV/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E1311604_BS172_ENC4_cDNA726
experiment encode accession: ENCSR620YAV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB895NVR
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: female

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS735JRG at ENCODE; https://www.encodeproject.org/ENCBS735JRG/

value: Derived from ENCODE donor ENCDO853KFT; https://www.encodeproject.org/ENCDO853KFT/


title: PRO-cap from HCT116 (ENCLB023WRV)

description:
https://www.encodeproject.org/experiments/ENCSR074XOP/
***************
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 POLR2A_U.
experiment encode accession: ENCSR074XOP
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB023WRV
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

value: cell line

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS729ZZV at ENCODE; https://www.encodeproject.org/ENCBS729ZZV/

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


title: CRISPR RNA-seq from HepG2 (ENCLB391MVV)

description:
https://www.encodeproject.org/experiments/ENCSR077MFQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CARS. (CARS-BGHcLV27)
experiment encode accession: ENCSR077MFQ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR650TTU
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB391MVV
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting H. sapiens CARS

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/85c25740-74c5-47a7-959a-c0f499b82d96/@@download/attachment/L-CARS-BGHcLV27-39.pdf

value: CARS

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CARS. (CARS-BGHcLV27-39)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS916HYF at ENCODE; https://www.encodeproject.org/ENCBS916HYF/

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


title: total RNA-seq from natural killer cell (ENCLB711DOZ)

description:
https://www.encodeproject.org/experiments/ENCSR584CVV/
***************
biological replicate number: 1
technical replicate number: 2
description: h.CD56+_DONOR 3: 0 hour no activation
experiment encode accession: ENCSR584CVV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB711DOZ
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: Homo sapiens

value: female

value: adult

value: 41 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS578OIT at ENCODE; https://www.encodeproject.org/ENCBS578OIT/

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


title: total RNA-seq from layer of hippocampus (ENCLB758ONW)

description:
https://www.encodeproject.org/experiments/ENCSR801JDZ/
***************
biological replicate number: 1
technical replicate number: 1
description: B6 X Cast hippocampus_8-10 months male
experiment encode accession: ENCSR801JDZ
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-11-09
lab: Barbara Wold, Caltech
library encode accession: ENCLB758ONW
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: layer of hippocampus

value: tissue

value: B6 X Cast hippocampus_8-10 months male animal 2_ENC4_cDNA_832

value: Mus musculus

value: male

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS608BJZ at ENCODE; https://www.encodeproject.org/ENCBS608BJZ/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: total RNA-seq from natural killer cell (ENCLB012GRF)

description:
https://www.encodeproject.org/experiments/ENCSR584CVV/
***************
biological replicate number: 1
technical replicate number: 7
description: h.CD56+_DONOR 3: 0 hour no activation
experiment encode accession: ENCSR584CVV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB012GRF
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: Homo sapiens

value: female


title: total RNA-seq from left cerebral cortex (ENCLB707AOQ)

description:
https://www.encodeproject.org/experiments/ENCSR879VZJ/
***************
biological replicate number: 1
technical replicate number: 1
description: B6 X Cast L. cortex (brain)_8-10 months male
experiment encode accession: ENCSR879VZJ
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-11-09
lab: Barbara Wold, Caltech
library encode accession: ENCLB707AOQ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: left cerebral cortex

value: B6 X Cast L. cortex (brain)_8-10 months male animal 2_ENC4_cDNA_836

value: adult

value: ENCBS154EVO at ENCODE; https://www.encodeproject.org/ENCBS154EVO/


title: total RNA-seq from adrenal gland (ENCLB352SNA)

description:
https://www.encodeproject.org/experiments/ENCSR249EFE/
***************
biological replicate number: 1
technical replicate number: 1
description: B6 X Cast adrenal gland_8-10 months male
experiment encode accession: ENCSR249EFE
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-11-09
lab: Barbara Wold, Caltech
library encode accession: ENCLB352SNA
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: Mus musculus strain B6CASTF1/J male adult (8-10 months) adrenal gland tissue

value: adrenal gland

value: tissue

value: B6 X Cast adrenal gland_8-10 months male animal 2_ENC4_cDNA_828

value: ENCBS882DIZ at ENCODE; https://www.encodeproject.org/ENCBS882DIZ/


title: PRO-cap from HCT116 (ENCLB071DKM)

description:
https://www.encodeproject.org/experiments/ENCSR074XOP/
***************
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 POLR2A_U.
experiment encode accession: ENCSR074XOP
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB071DKM
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: ENCBS777WED at ENCODE; https://www.encodeproject.org/ENCBS777WED/

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


title: total RNA-seq from natural killer cell (ENCLB591TNA)

description:
https://www.encodeproject.org/experiments/ENCSR584CVV/
***************
biological replicate number: 1
technical replicate number: 1
description: h.CD56+_DONOR 3: 0 hour no activation
experiment encode accession: ENCSR584CVV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB591TNA
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: Homo sapiens

value: female

value: 41 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS578OIT at ENCODE; https://www.encodeproject.org/ENCBS578OIT/

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


title: CRISPR RNA-seq from K562 (ENCLB075JLP)

description:
https://www.encodeproject.org/experiments/ENCSR071DBC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ALDOA. (ALDOA-BGKcLV26)
experiment encode accession: ENCSR071DBC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB075JLP
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 ALDOA

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/fae6086e-9212-4401-8ad5-5c98ef599a2f/@@download/attachment/L-ALDOA-BGKcLV26-24.pdf

value: ALDOA

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ALDOA. (ALDOA-BGKcLV26-24)

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS326SBM at ENCODE; https://www.encodeproject.org/ENCBS326SBM/

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


title: total RNA-seq from natural killer cell (ENCLB745PXJ)

description:
https://www.encodeproject.org/experiments/ENCSR584CVV/
***************
biological replicate number: 1
technical replicate number: 10
description: h.CD56+_DONOR 3: 0 hour no activation
experiment encode accession: ENCSR584CVV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB745PXJ
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: Homo sapiens


title: total RNA-seq from natural killer cell (ENCLB056OAH)

description:
https://www.encodeproject.org/experiments/ENCSR584CVV/
***************
biological replicate number: 1
technical replicate number: 5
description: h.CD56+_DONOR 3: 0 hour no activation
experiment encode accession: ENCSR584CVV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB056OAH
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 330
nucleic acid starting quantity units: ng

value: female

value: 41 year

value: John Stamatoyannopoulos, UW


title: CRISPR RNA-seq from K562 (ENCLB822KJN)

description:
https://www.encodeproject.org/experiments/ENCSR071DBC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against ALDOA. (ALDOA-BGKcLV26)
experiment encode accession: ENCSR071DBC
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR900GQL
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB822KJN
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/25ee110a-05c0-4c54-9a16-d37b50da626c/@@download/attachment/L-ALDOA-BGKcLV26-23.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against ALDOA. (ALDOA-BGKcLV26-23)

value: ENCBS166ZET at ENCODE; https://www.encodeproject.org/ENCBS166ZET/


title: total RNA-seq from natural killer cell (ENCLB164KVR)

description:
https://www.encodeproject.org/experiments/ENCSR584CVV/
***************
biological replicate number: 1
technical replicate number: 9
description: h.CD56+_DONOR 3: 0 hour no activation
experiment encode accession: ENCSR584CVV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB164KVR
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 330
nucleic acid starting quantity units: ng

value: StemExpress

value: ENCBS578OIT at ENCODE; https://www.encodeproject.org/ENCBS578OIT/

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


title: total RNA-seq from heart (ENCLB472NAX)

description:
https://www.encodeproject.org/experiments/ENCSR674QMU/
***************
biological replicate number: 2
technical replicate number: 1
description: B6 X Cast heart_8-10 months female
experiment encode accession: ENCSR674QMU
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-11-09
lab: Barbara Wold, Caltech
library encode accession: ENCLB472NAX
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: Mus musculus strain B6CASTF1/J female adult (8-10 months) heart tissue

value: heart

value: tissue

value: B6 X Cast heart_8-10 months female animal 3_ENC4_cDNA_839

value: Mus musculus

value: adult

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS825FXB at ENCODE; https://www.encodeproject.org/ENCBS825FXB/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: CRISPR RNA-seq from K562 (ENCLB680UED)

description:
https://www.encodeproject.org/experiments/ENCSR068YPI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SAP30BP. (SAP30BP-BGKcLV33)
experiment encode accession: ENCSR068YPI
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB680UED
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 SEC23IP

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ab08482c-192f-41d3-a285-b02bb56d50ca/@@download/attachment/L-SAP30BP-BGKcLV33-30.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SAP30BP. (SAP30BP-BGKcLV33-30)

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS312BGW at ENCODE; https://www.encodeproject.org/ENCBS312BGW/

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


title: total RNA-seq from natural killer cell (ENCLB630IPB)

description:
https://www.encodeproject.org/experiments/ENCSR584CVV/
***************
biological replicate number: 1
technical replicate number: 3
description: h.CD56+_DONOR 3: 0 hour no activation
experiment encode accession: ENCSR584CVV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB630IPB
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: ENCBS578OIT at ENCODE; https://www.encodeproject.org/ENCBS578OIT/

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


title: total RNA-seq from heart (ENCLB879TDD)

description:
https://www.encodeproject.org/experiments/ENCSR674QMU/
***************
biological replicate number: 1
technical replicate number: 1
description: B6 X Cast heart_8-10 months female
experiment encode accession: ENCSR674QMU
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-11-09
lab: Barbara Wold, Caltech
library encode accession: ENCLB879TDD
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: heart

value: tissue

value: B6 X Cast heart_8-10 months female animal 1_ENC4_cDNA_838

value: Mus musculus

value: adult

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS225NBG at ENCODE; https://www.encodeproject.org/ENCBS225NBG/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: total RNA-seq from natural killer cell (ENCLB252MOE)

description:
https://www.encodeproject.org/experiments/ENCSR584CVV/
***************
biological replicate number: 1
technical replicate number: 8
description: h.CD56+_DONOR 3: 0 hour no activation
experiment encode accession: ENCSR584CVV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB252MOE
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: Homo sapiens

value: female


title: CRISPR RNA-seq from K562 (ENCLB811YBR)

description:
https://www.encodeproject.org/experiments/ENCSR582AOQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CWF19L2. (CWF19L2-BGKcLV28)
experiment encode accession: ENCSR582AOQ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB811YBR
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 CWF19L2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5df423f7-fbe3-49c7-b9da-bbb1d6f4d89f/@@download/attachment/L-CWF19L2-BGKcLV28-55.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CWF19L2. (CWF19L2-BGKcLV28-55)

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS639LVM at ENCODE; https://www.encodeproject.org/ENCBS639LVM/

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


title: total RNA-seq from natural killer cell (ENCLB273QYD)

description:
https://www.encodeproject.org/experiments/ENCSR584CVV/
***************
biological replicate number: 1
technical replicate number: 6
description: h.CD56+_DONOR 3: 0 hour no activation
experiment encode accession: ENCSR584CVV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB273QYD
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 330
nucleic acid starting quantity units: ng

value: primary cell

value: adult

value: 41 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS578OIT at ENCODE; https://www.encodeproject.org/ENCBS578OIT/

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


title: total RNA-seq from adrenal gland (ENCLB303EKT)

description:
https://www.encodeproject.org/experiments/ENCSR249EFE/
***************
biological replicate number: 2
technical replicate number: 1
description: B6 X Cast adrenal gland_8-10 months male
experiment encode accession: ENCSR249EFE
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-11-09
lab: Barbara Wold, Caltech
library encode accession: ENCLB303EKT
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: adrenal gland

value: tissue

value: B6 X Cast adrenal gland_8-10 months male animal 4_ENC4_cDNA_829

value: Mus musculus

value: male

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS962RLX at ENCODE; https://www.encodeproject.org/ENCBS962RLX/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: CRISPR RNA-seq from K562 (ENCLB234HYF)

description:
https://www.encodeproject.org/experiments/ENCSR582AOQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CWF19L2. (CWF19L2-BGKcLV28)
experiment encode accession: ENCSR582AOQ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB234HYF
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/4eedd1a0-c441-447f-87cc-71f6b8a3cc62/@@download/attachment/L-CWF19L2-BGKcLV28-56.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CWF19L2. (CWF19L2-BGKcLV28-56)

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS488OTG at ENCODE; https://www.encodeproject.org/ENCBS488OTG/

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


title: total RNA-seq from adrenal gland (ENCLB830QMM)

description:
https://www.encodeproject.org/experiments/ENCSR173MHB/
***************
biological replicate number: 2
technical replicate number: 1
description: B6 X Cast adrenal gland_8-10 months female
experiment encode accession: ENCSR173MHB
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-11-09
lab: Barbara Wold, Caltech
library encode accession: ENCLB830QMM
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: Mus musculus strain B6CASTF1/J female adult (8-10 months) adrenal gland tissue

value: adrenal gland

value: tissue

value: B6 X Cast adrenal gland_8-10 months female animal 3_ENC4_cDNA_827

value: Mus musculus

value: adult

value: ENCBS858KWH at ENCODE; https://www.encodeproject.org/ENCBS858KWH/


title: total RNA-seq from adrenal gland (ENCLB686XBZ)

description:
https://www.encodeproject.org/experiments/ENCSR173MHB/
***************
biological replicate number: 1
technical replicate number: 1
description: B6 X Cast adrenal gland_8-10 months female
experiment encode accession: ENCSR173MHB
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-11-09
lab: Barbara Wold, Caltech
library encode accession: ENCLB686XBZ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: B6 X Cast adrenal gland_8-10 months female animal 1_ENC4_cDNA_826

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS703JRK at ENCODE; https://www.encodeproject.org/ENCBS703JRK/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: total RNA-seq from layer of hippocampus (ENCLB527VIW)

description:
https://www.encodeproject.org/experiments/ENCSR637GLC/
***************
biological replicate number: 2
technical replicate number: 1
description: B6 X Cast hippocampus_8-10 months female
experiment encode accession: ENCSR637GLC
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-11-09
lab: Barbara Wold, Caltech
library encode accession: ENCLB527VIW
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: Mus musculus strain B6CASTF1/J female adult (8-10 months) layer of hippocampus tissue

value: layer of hippocampus

value: B6 X Cast hippocampus_8-10 months female animal 5_ENC4_cDNA_831

value: female

value: ENCBS812WTH at ENCODE; https://www.encodeproject.org/ENCBS812WTH/


title: CRISPR RNA-seq from HepG2 (ENCLB411FZV)

description:
https://www.encodeproject.org/experiments/ENCSR576ASZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CLTC. (CLTC-BGHcLV29)
experiment encode accession: ENCSR576ASZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB411FZV
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting H. sapiens CLTC

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e7f4b1b9-02d5-4523-86c4-6794697aba9b/@@download/attachment/L-CLTC-BGHcLV29-23.pdf

value: CLTC

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CLTC. (CLTC-BGHcLV29-23)

value: Homo sapiens

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS620CUH at ENCODE; https://www.encodeproject.org/ENCBS620CUH/

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


title: total RNA-seq from middle frontal area 46 (ENCLB256HTL)

description:
https://www.encodeproject.org/experiments/ENCSR082XSF/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E9620322_BS190_ENC4_cDNA744
experiment encode accession: ENCSR082XSF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB256HTL
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: middle frontal area 46

value: tissue

value: adult

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS575OYH at ENCODE; https://www.encodeproject.org/ENCBS575OYH/

value: Derived from ENCODE donor ENCDO680UUE; https://www.encodeproject.org/ENCDO680UUE/


title: total RNA-seq from K562 (ENCLB462QMV)

description:
https://www.encodeproject.org/experiments/ENCSR062FHL/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with DMSO for 4 hours
experiment encode accession: ENCSR062FHL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB462QMV
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 1% DMSO for 4 hours, preserved by flash-freezing

value: cell line

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:DMSO; treatment_type:chemical; duration:4; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS411JWD at ENCODE; https://www.encodeproject.org/ENCBS411JWD/

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


title: total RNA-seq from adrenal gland (ENCLB347GCP)

description:
https://www.encodeproject.org/experiments/ENCSR129DEA/
***************
biological replicate number: 2
technical replicate number: 1
description: 5xFAD X Cast adrenal gland_8-10 months male
experiment encode accession: ENCSR129DEA
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-02-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB347GCP
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: Mus musculus strain 5xFAD/CAST male adult (8-10 months) adrenal gland tissue

value: adrenal gland

value: tissue

value: Mus musculus

value: male

value: 8-10 month

value: The Jackson Laboratory

value: ENCBS515VBP at ENCODE; https://www.encodeproject.org/ENCBS515VBP/

value: Derived from ENCODE donor ENCDO996MUL; https://www.encodeproject.org/ENCDO996MUL/


title: total RNA-seq from K562 (ENCLB084KQI)

description:
https://www.encodeproject.org/experiments/ENCSR062FHL/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with DMSO for 4 hours
experiment encode accession: ENCSR062FHL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB084KQI
size range: 300-600

value: cell line

value: RNA-seq on human cell line K562

value: adult

value: ATCC

value: ENCBS829GTX at ENCODE; https://www.encodeproject.org/ENCBS829GTX/


title: total RNA-seq from middle frontal area 46 (ENCLB555BLE)

description:
https://www.encodeproject.org/experiments/ENCSR080VMJ/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E7244764_BS160_ENC4_cDNA710
experiment encode accession: ENCSR080VMJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB555BLE
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 (89 years) with Alzheimer's disease; middle frontal area 46 tissue

value: middle frontal area 46

value: Homo sapiens

value: female

value: 89 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS960KGD at ENCODE; https://www.encodeproject.org/ENCBS960KGD/

value: Derived from ENCODE donor ENCDO853VGZ; https://www.encodeproject.org/ENCDO853VGZ/


title: CRISPR RNA-seq from HepG2 (ENCLB009WAO)

description:
https://www.encodeproject.org/experiments/ENCSR576ASZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CLTC. (CLTC-BGHcLV29)
experiment encode accession: ENCSR576ASZ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB009WAO
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/4562c2f2-f336-4893-84d1-11047a8da855/@@download/attachment/L-CLTC-BGHcLV29-24.pdf

value: CLTC

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against CLTC. (CLTC-BGHcLV29-24)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS193FMX at ENCODE; https://www.encodeproject.org/ENCBS193FMX/

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


title: total RNA-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB049PQM)

description:
https://www.encodeproject.org/experiments/ENCSR077EAM/
***************
biological replicate number: 1
technical replicate number: 1
description: h.CD4.Treg_DONOR 4: 0 hour no activation
experiment encode accession: ENCSR077EAM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB049PQM
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 (21 years) CD4-positive, CD25-positive, alpha-beta regulatory T primary cell

value: primary cell

value: adult

value: 21 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS007PNL at ENCODE; https://www.encodeproject.org/ENCBS007PNL/

value: Derived from ENCODE donor ENCDO282XZV; https://www.encodeproject.org/ENCDO282XZV/


title: total RNA-seq from layer of hippocampus (ENCLB053CAY)

description:
https://www.encodeproject.org/experiments/ENCSR637GLC/
***************
biological replicate number: 1
technical replicate number: 1
description: B6 X Cast hippocampus_8-10 months female
experiment encode accession: ENCSR637GLC
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-11-09
lab: Barbara Wold, Caltech
library encode accession: ENCLB053CAY
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: layer of hippocampus

value: tissue

value: B6 X Cast hippocampus_8-10 months female animal 1_ENC4_cDNA_830

value: Mus musculus

value: female

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS040JRN at ENCODE; https://www.encodeproject.org/ENCBS040JRN/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: CRISPR RNA-seq from HepG2 (ENCLB895QKE)

description:
https://www.encodeproject.org/experiments/ENCSR060SLE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against BRIX1. (BRIX1-BGHcLV24)
experiment encode accession: ENCSR060SLE
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR671FDZ
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB895QKE
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting H. sapiens BRIX1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/cb1d6152-0ae3-4644-b7ce-f622d58c23e6/@@download/attachment/L-BRIX1-BGHcLV24-20.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against BRIX1. (BRIX1-BGHcLV24-20)

value: Homo sapiens

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS513DCS at ENCODE; https://www.encodeproject.org/ENCBS513DCS/

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


title: total RNA-seq from left cerebral cortex (ENCLB981TXX)

description:
https://www.encodeproject.org/experiments/ENCSR588BJN/
***************
biological replicate number: 1
technical replicate number: 1
description: B6 X Cast L. cortex (brain)_8-10 months female
experiment encode accession: ENCSR588BJN
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-11-09
lab: Barbara Wold, Caltech
library encode accession: ENCLB981TXX
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: Mus musculus strain B6CASTF1/J female adult (8-10 months) left cerebral cortex tissue

value: left cerebral cortex

value: tissue

value: B6 X Cast L. cortex (brain)_8-10 months female animal 1_ENC4_cDNA_834

value: Mus musculus

value: female

value: adult

value: ENCBS779EQI at ENCODE; https://www.encodeproject.org/ENCBS779EQI/


title: total RNA-seq from left cerebral cortex (ENCLB227FLH)

description:
https://www.encodeproject.org/experiments/ENCSR588BJN/
***************
biological replicate number: 2
technical replicate number: 1
description: B6 X Cast L. cortex (brain)_8-10 months female
experiment encode accession: ENCSR588BJN
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-11-09
lab: Barbara Wold, Caltech
library encode accession: ENCLB227FLH
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: B6 X Cast L. cortex (brain)_8-10 months female animal 5_ENC4_cDNA_835

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS379IPL at ENCODE; https://www.encodeproject.org/ENCBS379IPL/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: CRISPR RNA-seq from HepG2 (ENCLB419HQG)

description:
https://www.encodeproject.org/experiments/ENCSR060SLE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against BRIX1. (BRIX1-BGHcLV24)
experiment encode accession: ENCSR060SLE
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR671FDZ
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB419HQG
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/90f887e1-406d-42ff-b5f4-78a0732d9335/@@download/attachment/L-BRIX1-BGHcLV24-19.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against BRIX1. (BRIX1-BGHcLV24-19)

value: Homo sapiens

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS185KSH at ENCODE; https://www.encodeproject.org/ENCBS185KSH/


title: total RNA-seq from gastrocnemius (ENCLB947WJX)

description:
https://www.encodeproject.org/experiments/ENCSR093SMP/
***************
biological replicate number: 2
technical replicate number: 1
description: 5xFAD X Cast gastrocnemius_8-10 months female
experiment encode accession: ENCSR093SMP
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-02-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB947WJX
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: Mus musculus strain 5xFAD/CAST female adult (8-10 months) gastrocnemius tissue

value: gastrocnemius

value: tissue

value: Mus musculus

value: female

value: adult

value: ENCBS370ZSH at ENCODE; https://www.encodeproject.org/ENCBS370ZSH/

value: Derived from ENCODE donor ENCDO996MUL; https://www.encodeproject.org/ENCDO996MUL/


title: CRISPR RNA-seq from K562 (ENCLB473BIQ)

description:
https://www.encodeproject.org/experiments/ENCSR068YPI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SAP30BP. (SAP30BP-BGKcLV33)
experiment encode accession: ENCSR068YPI
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB473BIQ
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/5aebf40c-6cfe-461b-92df-90cd7b7484dd/@@download/attachment/L-SAP30BP-BGKcLV33-29.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SAP30BP. (SAP30BP-BGKcLV33-29)

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ATCC

value: ENCBS042QOZ at ENCODE; https://www.encodeproject.org/ENCBS042QOZ/

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


title: total RNA-seq from motor neuron (ENCLB012HWE)

description:
https://www.encodeproject.org/experiments/ENCSR575MQY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on human motor neuron cell lines
experiment encode accession: ENCSR575MQY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB012HWE
size range: 300-600

source_name: Homo sapiens male adult (49 years) motor neuron in vitro differentiated cells, preserved by flash-freezing

value: motor neuron

value: in vitro differentiated cells

value: RNA-seq on human

value: Homo sapiens

value: male

value: Donor with Amyotrophic Lateral Sclerosis

value: 49 year

value: Michael Snyder, Stanford

value: Cooper-Knock lab, University of Sheffield, UK

value: ENCBS990CZV at ENCODE; https://www.encodeproject.org/ENCBS990CZV/

value: Derived from ENCODE donor ENCDO272LDF; https://www.encodeproject.org/ENCDO272LDF/


title: total RNA-seq from OCI-LY7 (ENCLB591FSV)

description:
https://www.encodeproject.org/experiments/ENCSR073XFZ/
***************
biological replicate number: 2
technical replicate number: 1
description: OCI-LY7 for bru-seq comparison
experiment encode accession: ENCSR073XFZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB591FSV
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 OCI-LY7 cell line

value: cell line

value: B cell lymphoma

value: adult

value: 48 year

value: Mats Ljungman, UMichigan

value: DSMZ

value: ENCBS112SEO at ENCODE; https://www.encodeproject.org/ENCBS112SEO/

value: Derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/


title: total RNA-seq from gastrocnemius (ENCLB461TBH)

description:
https://www.encodeproject.org/experiments/ENCSR093SMP/
***************
biological replicate number: 1
technical replicate number: 1
description: 5xFAD X Cast gastrocnemius_8-10 months female
experiment encode accession: ENCSR093SMP
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-02-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB461TBH
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: gastrocnemius

value: tissue

value: Mus musculus

value: female

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS105OZV at ENCODE; https://www.encodeproject.org/ENCBS105OZV/

value: Derived from ENCODE donor ENCDO996MUL; https://www.encodeproject.org/ENCDO996MUL/


title: total RNA-seq from adrenal gland (ENCLB353HFU)

description:
https://www.encodeproject.org/experiments/ENCSR129DEA/
***************
biological replicate number: 1
technical replicate number: 1
description: 5xFAD X Cast adrenal gland_8-10 months male
experiment encode accession: ENCSR129DEA
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-02-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB353HFU
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: adrenal gland

value: male

value: ENCBS943GNI at ENCODE; https://www.encodeproject.org/ENCBS943GNI/


title: total RNA-seq from middle frontal area 46 (ENCLB947DDT)

description:
https://www.encodeproject.org/experiments/ENCSR078WNY/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E6329379_BS157_ENC4_cDNA707
experiment encode accession: ENCSR078WNY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB947DDT
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 (78 years) middle frontal area 46 tissue

value: middle frontal area 46

value: Homo sapiens

value: adult

value: 78 year

value: Rush University

value: ENCBS804NKI at ENCODE; https://www.encodeproject.org/ENCBS804NKI/

value: Derived from ENCODE donor ENCDO236YSH; https://www.encodeproject.org/ENCDO236YSH/


title: total RNA-seq from middle frontal area 46 (ENCLB942EHE)

description:
https://www.encodeproject.org/experiments/ENCSR579KTN/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E1488495_BS121_ENC4_cDNA683
experiment encode accession: ENCSR579KTN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB942EHE
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December

source_name: Homo sapiens female adult (83 years) middle frontal area 46 tissue

value: tissue

value: 83 year

value: ENCBS168FVU at ENCODE; https://www.encodeproject.org/ENCBS168FVU/

value: Derived from ENCODE donor ENCDO448ZXP; https://www.encodeproject.org/ENCDO448ZXP/


title: total RNA-seq from heart (ENCLB453OZU)

description:
https://www.encodeproject.org/experiments/ENCSR584OSM/
***************
biological replicate number: 2
technical replicate number: 1
description: 5xFAD X Cast heart_8-10 months male
experiment encode accession: ENCSR584OSM
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-02-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB453OZU
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: Mus musculus strain 5xFAD/CAST male adult (8-10 months) heart tissue

value: heart

value: Mus musculus

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS391BLT at ENCODE; https://www.encodeproject.org/ENCBS391BLT/


title: total RNA-seq from middle frontal area 46 (ENCLB560ETQ)

description:
https://www.encodeproject.org/experiments/ENCSR067GOC/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E8522907_BS214_ENC4_cDNA769
experiment encode accession: ENCSR067GOC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB560ETQ
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 Cognitive impairment; middle frontal area 46 tissue

value: middle frontal area 46

value: female

value: 90 or above year

value: ENCBS979TED at ENCODE; https://www.encodeproject.org/ENCBS979TED/

value: Derived from ENCODE donor ENCDO448YMQ; https://www.encodeproject.org/ENCDO448YMQ/


title: total RNA-seq from heart (ENCLB214DCX)

description:
https://www.encodeproject.org/experiments/ENCSR584OSM/
***************
biological replicate number: 1
technical replicate number: 1
description: 5xFAD X Cast heart_8-10 months male
experiment encode accession: ENCSR584OSM
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-02-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB214DCX
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: male

value: adult

value: ENCBS657KFM at ENCODE; https://www.encodeproject.org/ENCBS657KFM/

value: Derived from ENCODE donor ENCDO996MUL; https://www.encodeproject.org/ENCDO996MUL/


title: CRISPR RNA-seq from HepG2 (ENCLB766JBZ)

description:
https://www.encodeproject.org/experiments/ENCSR574ZTO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DARS. (DARS-BGHcLV29)
experiment encode accession: ENCSR574ZTO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB766JBZ
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting H. sapiens DARS

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6cbd6010-e108-48ed-8c2a-75491b8b3144/@@download/attachment/L-DARS-BGHcLV29-57.pdf

value: DARS

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DARS. (DARS-BGHcLV29-57)

value: Homo sapiens

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS993GYU at ENCODE; https://www.encodeproject.org/ENCBS993GYU/

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


title: total RNA-seq from K562 (ENCLB482HQM)

description:
https://www.encodeproject.org/experiments/ENCSR056HPM/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with MB-3 for 12 hours
experiment encode accession: ENCSR056HPM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB482HQM
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 5 uM MB-3 for 12 hours, preserved by flash-freezing

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:12; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS742XYV at ENCODE; https://www.encodeproject.org/ENCBS742XYV/

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


title: total RNA-seq from gastrocnemius (ENCLB718AJF)

description:
https://www.encodeproject.org/experiments/ENCSR086MHH/
***************
biological replicate number: 1
technical replicate number: 1
description: 5xFAD X Cast gastrocnemius_8-10 months male
experiment encode accession: ENCSR086MHH
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-02-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB718AJF
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: Mus musculus strain 5xFAD/CAST male adult (8-10 months) gastrocnemius tissue

value: gastrocnemius

value: tissue

value: Mus musculus

value: male

value: adult

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS480BER at ENCODE; https://www.encodeproject.org/ENCBS480BER/

value: Derived from ENCODE donor ENCDO996MUL; https://www.encodeproject.org/ENCDO996MUL/


title: total RNA-seq from middle frontal area 46 (ENCLB295CPK)

description:
https://www.encodeproject.org/experiments/ENCSR564CRW/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E7334238_BS161_ENC4_cDNA711
experiment encode accession: ENCSR564CRW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB295CPK
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: middle frontal area 46

value: Homo sapiens

value: female

value: 90 or above year

value: Rush University

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

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


title: total RNA-seq from gastrocnemius (ENCLB356QAT)

description:
https://www.encodeproject.org/experiments/ENCSR086MHH/
***************
biological replicate number: 2
technical replicate number: 1
description: 5xFAD X Cast gastrocnemius_8-10 months male
experiment encode accession: ENCSR086MHH
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-02-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB356QAT
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: gastrocnemius

value: ENCBS197MJZ at ENCODE; https://www.encodeproject.org/ENCBS197MJZ/


title: CRISPR RNA-seq from HepG2 (ENCLB880BBL)

description:
https://www.encodeproject.org/experiments/ENCSR574ZTO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DARS. (DARS-BGHcLV29)
experiment encode accession: ENCSR574ZTO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR462MFN
encode release date: 2022-02-14
lab: Brenton Graveley, UConn
library encode accession: ENCLB880BBL
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/ca1410a9-a811-45c4-9f65-ae9bb53f22de/@@download/attachment/L-DARS-BGHcLV29-58.pdf

value: DARS

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against DARS. (DARS-BGHcLV29-58)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS735KRY at ENCODE; https://www.encodeproject.org/ENCBS735KRY/

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


title: total RNA-seq from K562 (ENCLB169BZW)

description:
https://www.encodeproject.org/experiments/ENCSR056HPM/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with MB-3 for 12 hours
experiment encode accession: ENCSR056HPM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB169BZW
size range: 300-600

value: RNA-seq on human cell line K562

value: Homo sapiens

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:12; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS733QES at ENCODE; https://www.encodeproject.org/ENCBS733QES/

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


title: total RNA-seq from middle frontal area 46 (ENCLB314UHC)

description:
https://www.encodeproject.org/experiments/ENCSR563SJY/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E9835349_BS192_ENC4_cDNA746
experiment encode accession: ENCSR563SJY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-06-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB314UHC
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 (87 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: 87 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS135ECM at ENCODE; https://www.encodeproject.org/ENCBS135ECM/

value: Derived from ENCODE donor ENCDO640RUC; https://www.encodeproject.org/ENCDO640RUC/


title: total RNA-seq from activated CD4-positive, alpha-beta T cell (ENCLB646RRY)

description:
https://www.encodeproject.org/experiments/ENCSR052SDT/
***************
biological replicate number: 1
technical replicate number: 1
description: CD4 N (RA+ MACS sort)Th0 (no diff Cytokines)(day 13)+beads (1:3) day 1
experiment encode accession: ENCSR052SDT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Barbara Wold, Caltech
library encode accession: ENCLB646RRY
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 (35 years) activated CD4-positive, alpha-beta T primary cell treated with 10 ng/mL Interleukin-2 for 14 days, anti-CD3 and anti-CD28 coated beads for 24 hours, anti-CD3 and anti-CD28 coated beads for 14 days

value: primary cell

value: male

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:14; duration_units:day; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:14; duration_units:day;

value: ENCBS238ZBD at ENCODE; https://www.encodeproject.org/ENCBS238ZBD/

value: Derived from ENCODE donor ENCDO374BBL; https://www.encodeproject.org/ENCDO374BBL/


title: total RNA-seq from layer of hippocampus (ENCLB136SFU)

description:
https://www.encodeproject.org/experiments/ENCSR549HQM/
***************
biological replicate number: 2
technical replicate number: 1
description: 5xFAD X Cast hippocampus_8-10 months male
experiment encode accession: ENCSR549HQM
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-02-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB136SFU
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: Mus musculus strain 5xFAD/CAST male adult (8-10 months) layer of hippocampus tissue

value: layer of hippocampus

value: Mus musculus

value: adult

value: 8-10 month

value: The Jackson Laboratory

value: ENCBS116ERU at ENCODE; https://www.encodeproject.org/ENCBS116ERU/

value: Derived from ENCODE donor ENCDO996MUL; https://www.encodeproject.org/ENCDO996MUL/


title: total RNA-seq from K562 (ENCLB329UCV)

description:
https://www.encodeproject.org/experiments/ENCSR563ZWI/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 treated with Bortezomib for 4 hours
experiment encode accession: ENCSR563ZWI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB329UCV
size range: 300-600

source_name: Homo sapiens K562 cell line treated with 10 nM Bortezomib for 4 hours, preserved by flash-freezing

value: cell line

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: ATCC

value: treatment_term_name:Bortezomib; treatment_type:chemical; duration:4; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS978JPX at ENCODE; https://www.encodeproject.org/ENCBS978JPX/

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


title: total RNA-seq from K562 (ENCLB411DNX)

description:
https://www.encodeproject.org/experiments/ENCSR563ZWI/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 treated with Bortezomib for 4 hours
experiment encode accession: ENCSR563ZWI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Will Greenleaf, Stanford
library encode accession: ENCLB411DNX
size range: 300-600

value: ENCBS289SBJ at ENCODE; https://www.encodeproject.org/ENCBS289SBJ/


title: total RNA-seq from activated CD4-positive, alpha-beta T cell (ENCLB454DSL)

description:
https://www.encodeproject.org/experiments/ENCSR052SDT/
***************
biological replicate number: 2
technical replicate number: 1
description: CD4 N (RA+ MACS sort)Th0 (no diff Cytokines)(day 13)+beads (1:3) day 1
experiment encode accession: ENCSR052SDT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-07-14
lab: Barbara Wold, Caltech
library encode accession: ENCLB454DSL
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: primary cell

value: male

value: adult

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:14; duration_units:day; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:14; duration_units:day;

value: ENCBS242UJR at ENCODE; https://www.encodeproject.org/ENCBS242UJR/

value: Derived from ENCODE donor ENCDO374BBL; https://www.encodeproject.org/ENCDO374BBL/


title: total RNA-seq from layer of hippocampus (ENCLB686BVP)

description:
https://www.encodeproject.org/experiments/ENCSR549HQM/
***************
biological replicate number: 1
technical replicate number: 1
description: 5xFAD X Cast hippocampus_8-10 months male
experiment encode accession: ENCSR549HQM
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-02-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB686BVP
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: layer of hippocampus

value: tissue

value: Mus musculus

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS830OUL at ENCODE; https://www.encodeproject.org/ENCBS830OUL/

value: Derived from ENCODE donor ENCDO996MUL; https://www.encodeproject.org/ENCDO996MUL/


title: total RNA-seq from OCI-LY7 (ENCLB478LXM)

description:
https://www.encodeproject.org/experiments/ENCSR073XFZ/
***************
biological replicate number: 1
technical replicate number: 1
description: OCI-LY7 for bru-seq comparison
experiment encode accession: ENCSR073XFZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-02-01
lab: Barbara Wold, Caltech
library encode accession: ENCLB478LXM
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: Homo sapiens

value: B cell lymphoma

value: 48 year

value: Mats Ljungman, UMichigan

value: DSMZ

value: ENCBS869GJQ at ENCODE; https://www.encodeproject.org/ENCBS869GJQ/

value: Derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/


title: total RNA-seq from motor neuron (ENCLB634IPO)

description:
https://www.encodeproject.org/experiments/ENCSR575MQY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on human motor neuron cell lines
experiment encode accession: ENCSR575MQY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB634IPO
size range: 300-600

value: motor neuron

value: in vitro differentiated cells

value: RNA-seq on human

value: male

value: Donor with Amyotrophic Lateral Sclerosis

value: adult

value: 49 year

value: Michael Snyder, Stanford

value: Cooper-Knock lab, University of Sheffield, UK

value: ENCBS982BMN at ENCODE; https://www.encodeproject.org/ENCBS982BMN/

value: Derived from ENCODE donor ENCDO272LDF; https://www.encodeproject.org/ENCDO272LDF/


title: CRISPR RNA-seq from K562 (ENCLB156QON)

description:
https://www.encodeproject.org/experiments/ENCSR054DGN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CCT3. (CCT3-BGKcLV28)
experiment encode accession: ENCSR054DGN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB156QON
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 CCT3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/cf39f4d6-e9db-4bfd-a5c8-9df76b196b3c/@@download/attachment/L-CCT3-BGKcLV28-6.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CCT3. (CCT3-BGKcLV28-6)

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS119KBU at ENCODE; https://www.encodeproject.org/ENCBS119KBU/

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


title: PRO-seq from HCT116 (ENCLB319LAD)

description:
https://www.encodeproject.org/experiments/ENCSR545PWV/
***************
biological replicate number: 2
technical replicate number: 1
description: PRO-seq in RAD21_T
experiment encode accession: ENCSR545PWV
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB319LAD
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 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: male

value: colorectal carcinoma

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: ENCBS257FWX at ENCODE; https://www.encodeproject.org/ENCBS257FWX/

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


title: total RNA-seq from adrenal gland (ENCLB028DPC)

description:
https://www.encodeproject.org/experiments/ENCSR511LAZ/
***************
biological replicate number: 2
technical replicate number: 1
description: 5xFAD X Cast adrenal gland_8-10 months female
experiment encode accession: ENCSR511LAZ
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-02-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB028DPC
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: Mus musculus strain 5xFAD/CAST female adult (8-10 months) adrenal gland tissue

value: adrenal gland

value: tissue

value: Mus musculus

value: adult

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS206LPG at ENCODE; https://www.encodeproject.org/ENCBS206LPG/

value: Derived from ENCODE donor ENCDO996MUL; https://www.encodeproject.org/ENCDO996MUL/


title: total RNA-seq from adrenal gland (ENCLB939AXX)

description:
https://www.encodeproject.org/experiments/ENCSR511LAZ/
***************
biological replicate number: 1
technical replicate number: 1
description: 5xFAD X Cast adrenal gland_8-10 months female
experiment encode accession: ENCSR511LAZ
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-02-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB939AXX
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: female

value: ENCBS375TMX at ENCODE; https://www.encodeproject.org/ENCBS375TMX/


title: CRISPR RNA-seq from K562 (ENCLB742CJK)

description:
https://www.encodeproject.org/experiments/ENCSR054DGN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against CCT3. (CCT3-BGKcLV28)
experiment encode accession: ENCSR054DGN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB742CJK
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/7332d389-fcd5-4783-869c-addf6a835465/@@download/attachment/L-CCT3-BGKcLV28-5.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against CCT3. (CCT3-BGKcLV28-5)

value: Homo sapiens

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS711XJR at ENCODE; https://www.encodeproject.org/ENCBS711XJR/

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


title: PRO-seq from HCT116 (ENCLB164YNV)

description:
https://www.encodeproject.org/experiments/ENCSR545GXL/
***************
biological replicate number: 1
technical replicate number: 1
description: PRO-seq in POLR2A_U
experiment encode accession: ENCSR545GXL
assay title: PRO-seq
assembly: GRCh38
encode release date: 2022-07-08
lab: John Lis, Cornell
library encode accession: ENCLB164YNV
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

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS777WED at ENCODE; https://www.encodeproject.org/ENCBS777WED/

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


title: total RNA-seq from gastrocnemius (ENCLB663XSO)

description:
https://www.encodeproject.org/experiments/ENCSR000OCV/
***************
biological replicate number: 2
technical replicate number: 1
description: B6 X Cast gastrocnemius_8-10 months male
experiment encode accession: ENCSR000OCV
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-11-09
lab: Barbara Wold, Caltech
library encode accession: ENCLB663XSO
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: Mus musculus strain B6CASTF1/J male adult (8-10 months) gastrocnemius tissue

value: gastrocnemius

value: tissue

value: B6 X Cast gastrocnemius_8-10 months male animal 4_ENC4_cDNA_845

value: Mus musculus

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS722CXC at ENCODE; https://www.encodeproject.org/ENCBS722CXC/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: total RNA-seq from gastrocnemius (ENCLB844KHN)

description:
https://www.encodeproject.org/experiments/ENCSR000OCV/
***************
biological replicate number: 1
technical replicate number: 1
description: B6 X Cast gastrocnemius_8-10 months male
experiment encode accession: ENCSR000OCV
assay title: total RNA-seq
assembly: mm10
encode release date: 2022-11-09
lab: Barbara Wold, Caltech
library encode accession: ENCLB844KHN
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: 6 X Cast gastrocnemius_8-10 months male animal 2_ENC4_cDNA_844

value: male

value: ENCBS845UIZ at ENCODE; https://www.encodeproject.org/ENCBS845UIZ/


title: CRISPR RNA-seq from K562 (ENCLB696WVQ)

description:
https://www.encodeproject.org/experiments/ENCSR563QCQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPUSD2. (RPUSD2-BGKcLV33)
experiment encode accession: ENCSR563QCQ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB696WVQ
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 RUVBL1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/650357b7-2017-4f58-b115-4702c8bae772/@@download/attachment/L-RPUSD2-BGKcLV33-18.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPUSD2. (RPUSD2-BGKcLV33-18)

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS013NVH at ENCODE; https://www.encodeproject.org/ENCBS013NVH/

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


title: CRISPR RNA-seq from HepG2 (ENCLB570QZE)

description:
https://www.encodeproject.org/experiments/ENCSR051LWN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ADAT1. (ADAT1-BGHcLV25)
experiment encode accession: ENCSR051LWN
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR953VMB
encode release date: 2021-11-04
lab: Brenton Graveley, UConn
library encode accession: ENCLB570QZE
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting H. sapiens ADAT1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6bc35a3d-a6ec-4169-902b-08cd5a38d372/@@download/attachment/L-ADAT1-BGHcLV25-12.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against ADAT1. (ADAT1-BGHcLV25-12)

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS298SZT at ENCODE; https://www.encodeproject.org/ENCBS298SZT/

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


title: CRISPR RNA-seq from K562 (ENCLB101GCF)

description:
https://www.encodeproject.org/experiments/ENCSR563QCQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against RPUSD2. (RPUSD2-BGKcLV33)
experiment encode accession: ENCSR563QCQ
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB101GCF
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/bac02669-9943-4973-ac00-9f34352f0b4c/@@download/attachment/L-RPUSD2-BGKcLV33-17.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against RPUSD2. (RPUSD2-BGKcLV33-17)

value: ENCBS556WPL at ENCODE; https://www.encodeproject.org/ENCBS556WPL/