title: CRISPR RNA-seq from K562 (ENCLB574CXI)

description:
https://www.encodeproject.org/experiments/ENCSR226KWO/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT_BGKcLV04_B)
experiment encode accession: ENCSR226KWO
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
encode release date: 2017-01-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB574CXI
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4e99bfe0-c22a-428f-9ccb-619a01f2b799/@@download/attachment/L-NT_BGKcLV04-2B.pdf

value: cell line

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

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

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

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


title: shRNA RNA-seq from K562 (ENCLB801KTL)

status: Public on Jun 15 2021

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/ENCSR016OIX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against MARK2. (MARK2-BGKLV36-C)
experiment encode accession: ENCSR016OIX
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR619PCR
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB801KTL
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens K562 cell line expressing RNAi targeting MARK2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/50cd40f2-c32f-48f2-b24f-b4be3e7e7f39/@@download/attachment/L-MARK2-BGKLV36-33.pdf

tag: antibody

tag: line

tag: description

value: RNA-seq on K562 cells treated with an shRNA knockdown against MARK2. (MARK2-BGKLV36-33)

tag: biosample encode accession

tag: Sex

value: female

tag: health state

tag: dev stage

tag: age

tag: lab

tag: source

tag: link

value: ENCBS705OBP at ENCODE; https://www.encodeproject.org/ENCBS705OBP/


title: microRNA-seq from endodermal cell (ENCLB764YNB)

description:
https://www.encodeproject.org/experiments/ENCSR820BMF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation H1-derived endodermal cells microRNA-seq from Mortazavi
experiment encode accession: ENCSR820BMF
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB764YNB
size range: <30

source_name: Homo sapiens male embryo endodermal in vitro differentiated cells originated from H1, preserved by flash-freezing

value: endodermal cell

value: in vitro differentiated cells

value: male

value: embryonic

value: unknown

value: Job Dekker, UMass

value: René Maehr

value: healthy

value: ENCBS017VBO at ENCODE; https://www.encodeproject.org/ENCBS017VBO/

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


title: shRNA RNA-seq from K562 (ENCLB678JSW)

description:
https://www.encodeproject.org/experiments/ENCSR231PWH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against NKRF. (NKRF-BGKLV36-C)
experiment encode accession: ENCSR231PWH
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR619PCR
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB678JSW
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens K562 cell line expressing RNAi targeting NKRF

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/66ccf205-4792-4c40-bd9a-f226f1f4c699/@@download/attachment/L-NKRF-BGKLV36-40.pdf

value: NKRF

value: cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against NKRF. (NKRF-BGKLV36-40)

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS314LSG at ENCODE; https://www.encodeproject.org/ENCBS314LSG/


title: CRISPR RNA-seq from K562 (ENCLB718YID)

description:
https://www.encodeproject.org/experiments/ENCSR226KWO/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT_BGKcLV04_B)
experiment encode accession: ENCSR226KWO
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
encode release date: 2017-01-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB718YID
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/27948b8e-a9fe-49be-ad0c-75b7be66327c/@@download/attachment/L-NT_BGKcLV04-1B.pdf

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

value: female

value: ATCC

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

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


title: shRNA RNA-seq from HepG2 (ENCLB358ATO)

description:
https://www.encodeproject.org/experiments/ENCSR204QKA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against YWHAG. (YWHAG-BGHLV37-C)
experiment encode accession: ENCSR204QKA
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR225PRV
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB358ATO
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens HepG2 cell line expressing RNAi targeting YWHAG

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/69328506-286c-4529-a42a-f38387fd8085/@@download/attachment/L-YWHAG-BGHLV37-112C.pdf

value: YWHAG

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against YWHAG. (YWHAG-BGHLV37-112C)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS869OTH at ENCODE; https://www.encodeproject.org/ENCBS869OTH/

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


title: shRNA RNA-seq from HepG2 (ENCLB243SYA)

description:
https://www.encodeproject.org/experiments/ENCSR215FRI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against PRPF4. (PRPF4-BGHLV37-B)
experiment encode accession: ENCSR215FRI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR584UYK
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB243SYA
fragmentation methods: chemical (Illumina TruSeq)
size range: >200

source_name: Homo sapiens HepG2 cell line expressing RNAi targeting PRPF4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6dd3662e-724b-4aea-a039-84262a3528ab/@@download/attachment/L-PRPF4-BGHLV37-42B.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PRPF4. (PRPF4-BGHLV37-42B)

value: ENCBS334WBP at ENCODE; https://www.encodeproject.org/ENCBS334WBP/


title: shRNA RNA-seq from HepG2 (ENCLB264DJX)

description:
https://www.encodeproject.org/experiments/ENCSR215FRI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against PRPF4. (PRPF4-BGHLV37-B)
experiment encode accession: ENCSR215FRI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR584UYK
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB264DJX
fragmentation methods: chemical (Illumina TruSeq)
size range: >200

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4f0ea94c-8580-4619-905a-e855b845c87d/@@download/attachment/L-PRPF4-BGHLV37-41B.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PRPF4. (PRPF4-BGHLV37-41B)

value: Brenton Graveley, UConn

value: ENCBS528KLM at ENCODE; https://www.encodeproject.org/ENCBS528KLM/


title: microRNA-seq from aorta (ENCLB526KVI)

description:
https://www.encodeproject.org/experiments/ENCSR812JKX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W61 aorta microRNA-seq from Mortazavi
experiment encode accession: ENCSR812JKX
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-10-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB526KVI
size range: <30

source_name: Homo sapiens female adult (41 years) aorta tissue, preserved by flash-freezing

value: aorta

value: tissue

value: female

value: adult

value: 41 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: DM:no; HTN:no; CAD:no

value: ENCBS481ZAB at ENCODE; https://www.encodeproject.org/ENCBS481ZAB/

value: Derived from ENCODE donor ENCDO575WHY; https://www.encodeproject.org/ENCDO575WHY/


title: shRNA RNA-seq from K562 (ENCLB435UUX)

description:
https://www.encodeproject.org/experiments/ENCSR024FOF/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT-BGKLV38-B)
experiment encode accession: ENCSR024FOF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB435UUX
fragmentation methods: chemical (Illumina TruSeq)
size range: >200

source_name: Homo sapiens K562 cell line expressing RNAi

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/42529f79-0699-49f9-a80f-7ee5dd95d5ed/@@download/attachment/L-NT-BGKLV38-2B.pdf

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

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ATCC

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

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


title: shRNA RNA-seq from K562 (ENCLB106VWJ)

description:
https://www.encodeproject.org/experiments/ENCSR024FOF/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT-BGKLV38-B)
experiment encode accession: ENCSR024FOF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB106VWJ
fragmentation methods: chemical (Illumina TruSeq)
size range: >200

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/fcc8db56-8147-43cc-9aa1-5a8acfff9262/@@download/attachment/L-NT-BGKLV38-1B.pdf

value: cell line

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

value: Brenton Graveley, UConn

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


title: shRNA RNA-seq from K562 (ENCLB630WQU)

description:
https://www.encodeproject.org/experiments/ENCSR016OIX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against MARK2. (MARK2-BGKLV36-C)
experiment encode accession: ENCSR016OIX
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR619PCR
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB630WQU
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/57d9c403-6821-4561-8301-f806f231f8e7/@@download/attachment/L-MARK2-BGKLV36-34.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against MARK2. (MARK2-BGKLV36-34)

value: female

value: adult

value: ENCBS477ORG at ENCODE; https://www.encodeproject.org/ENCBS477ORG/


title: CRISPR RNA-seq from HepG2 (ENCLB559KQO)

description:
https://www.encodeproject.org/experiments/ENCSR805TIZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHcLV05-D)
experiment encode accession: ENCSR805TIZ
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB559KQO
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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/01b141fb-c8ac-4fa9-8a12-a4f1c3cfb147/@@download/attachment/L-NT-BGHcLV05-2D.pdf

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

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

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

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


title: CRISPR RNA-seq from K562 (ENCLB977VXZ)

description:
https://www.encodeproject.org/experiments/ENCSR005JBU/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in K562 cells followed by RNA-seq. (NT-BGKcLV04-C)
experiment encode accession: ENCSR005JBU
assay title: CRISPR RNA-seq
assembly: GRCh38
encode release date: 2021-04-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB977VXZ
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins
instrument models: Illumina HiSeq 2500,Illumina MiSeq

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f8a1d262-e393-4028-a973-4c336548df6e/@@download/attachment/L-NT-BGKcLV04-2C.pdf

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

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ATCC

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


title: microRNA-seq from endodermal cell (ENCLB148HQN)

description:
https://www.encodeproject.org/experiments/ENCSR820BMF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation H1-derived endodermal cells microRNA-seq from Mortazavi
experiment encode accession: ENCSR820BMF
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB148HQN
size range: <30

value: endodermal cell

value: in vitro differentiated cells

value: embryonic

value: unknown

value: Job Dekker, UMass

value: René Maehr

value: healthy

value: ENCBS360LED at ENCODE; https://www.encodeproject.org/ENCBS360LED/

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


title: shRNA RNA-seq from HepG2 (ENCLB251LBI)

description:
https://www.encodeproject.org/experiments/ENCSR204QKA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against YWHAG. (YWHAG-BGHLV37-C)
experiment encode accession: ENCSR204QKA
assay title: shRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR225PRV
encode release date: 2021-01-28
lab: Brenton Graveley, UConn
library encode accession: ENCLB251LBI
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/890a2d34-bb09-42ed-9ef9-d05a5bdabd04/@@download/attachment/L-YWHAG-BGHLV37-111C.pdf

value: YWHAG

value: cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against YWHAG. (YWHAG-BGHLV37-111C)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS112LZE at ENCODE; https://www.encodeproject.org/ENCBS112LZE/


title: microRNA-seq from endodermal cell (ENCLB535GAU)

description:
https://www.encodeproject.org/experiments/ENCSR820BMF/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA Evaluation H1-derived endodermal cells microRNA-seq from Mortazavi
experiment encode accession: ENCSR820BMF
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB535GAU
size range: <30

value: endodermal cell

value: in vitro differentiated cells

value: ENCBS251IOF at ENCODE; https://www.encodeproject.org/ENCBS251IOF/


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB266OOV)

description:
https://www.encodeproject.org/experiments/ENCSR785RXZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR785RXZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR934ZBY
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB266OOV
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

library_source: genomic

molecule: genomic DNA

source_name: Homo sapiens CD4-positive, alpha-beta memory T primary cell, preserved by cryopreservation

value: CD4-positive, alpha-beta memory T cell

value: primary cell

value: CD4+ memory CD3+ CD4+ CD8- CD45RA- CD45RO+ nonTreg

value: not collected

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS668VBU at ENCODE; https://www.encodeproject.org/ENCBS668VBU/

value: Derived from ENCODE donor ENCDO922TOC; https://www.encodeproject.org/ENCDO922TOC/


title: CRISPR RNA-seq from HepG2 (ENCLB770SIK)

description:
https://www.encodeproject.org/experiments/ENCSR105NML/
***************
biological replicate number: 2
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHcLV03)
experiment encode accession: ENCSR105NML
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB770SIK
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/33823c61-fe7f-4d65-a043-8f56cca82071/@@download/attachment/L-NT_BGHcLV03-2.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against non target. (NT_BGHcLV03-2)

value: male

value: hepatocellular carcinoma

value: ATCC

value: ENCBS987KVB at ENCODE; https://www.encodeproject.org/ENCBS987KVB/

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


title: CRISPR RNA-seq from HepG2 (ENCLB951JHO)

description:
https://www.encodeproject.org/experiments/ENCSR105NML/
***************
biological replicate number: 1
technical replicate number: 1
description: Control CRISPR gRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHcLV03)
experiment encode accession: ENCSR105NML
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB951JHO
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6f6d219a-1548-4cb6-a2df-b30f351b6041/@@download/attachment/L-NT_BGHcLV03-1.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against non target. (NT_BGHcLV03-1)

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS949DPY at ENCODE; https://www.encodeproject.org/ENCBS949DPY/


title: total RNA-seq from macrophage (ENCLB335PGQ)

description:
https://www.encodeproject.org/experiments/ENCSR992IIX/
***************
biological replicate number: 3
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 40 minute.
experiment encode accession: ENCSR992IIX
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB335PGQ
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

organism: Mus musculus

source_name: Mus musculus strain C57BL/6J macrophage primary cell chromatin fraction

value: macrophage

value: primary cell

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

tag: subcellular fraction term name

value: chromatin

value: ENCBS244WKV at ENCODE; https://www.encodeproject.org/ENCBS244WKV/

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


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB489WZH)

description:
https://www.encodeproject.org/experiments/ENCSR796MKZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR796MKZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR934ZBY
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB489WZH
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

value: CD4-positive, alpha-beta memory T cell

value: CD4+ memory CD3+ CD4+ CD8- CD45RA- CD45RO+ nonTreg

value: healthy

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS668VBU at ENCODE; https://www.encodeproject.org/ENCBS668VBU/

value: Derived from ENCODE donor ENCDO922TOC; https://www.encodeproject.org/ENCDO922TOC/


title: CRISPR RNA-seq from HepG2 (ENCLB710LCN)

description:
https://www.encodeproject.org/experiments/ENCSR666QJU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against AGGF1. (AGGF1-BGHcLV05-D)
experiment encode accession: ENCSR666QJU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR805TIZ
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB710LCN
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 AGGF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/43f5e77d-41b9-4fb9-8f38-2af37bb1133d/@@download/attachment/L-AGGF1-BGHcLV05-5D.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against AGGF1. (AGGF1-BGHcLV05-5B)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS048KGW at ENCODE; https://www.encodeproject.org/ENCBS048KGW/

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


title: microRNA-seq from spleen (ENCLB119SKB)

description:
https://www.encodeproject.org/experiments/ENCSR678BDA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W61 spleen microRNA-seq from Mortazavi
experiment encode accession: ENCSR678BDA
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-06-11
lab: Ali Mortazavi, UCI
library encode accession: ENCLB119SKB
size range: <30

source_name: Homo sapiens female adult (41 years) spleen tissue, preserved by flash-freezing

value: spleen

value: tissue

value: female

value: adult

value: 41 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: DM:no; HTN:no; CAD:no

value: ENCBS411TAI at ENCODE; https://www.encodeproject.org/ENCBS411TAI/

value: Derived from ENCODE donor ENCDO575WHY; https://www.encodeproject.org/ENCDO575WHY/


title: CRISPR RNA-seq from K562 (ENCLB154DOT)

description:
https://www.encodeproject.org/experiments/ENCSR103NNB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SDAD1. (SDAD1-BGKcLV06)
experiment encode accession: ENCSR103NNB
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR341TTW
encode release date: 2017-12-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB154DOT
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting SDAD1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/13877f84-6b07-4bbf-9845-93e7af34ce5d/@@download/attachment/L-SDAD1-BGKcLV06-31.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SDAD1. (SDAD1-BGKcLV06-31)

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS880QCJ at ENCODE; https://www.encodeproject.org/ENCBS880QCJ/

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


title: CRISPR RNA-seq from HepG2 (ENCLB644OBV)

description:
https://www.encodeproject.org/experiments/ENCSR666QJU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against AGGF1. (AGGF1-BGHcLV05-D)
experiment encode accession: ENCSR666QJU
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR805TIZ
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB644OBV
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/3450e2e2-ca23-4e20-9294-069f29c3b303/@@download/attachment/L-AGGF1-BGHcLV05-6D.pdf

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against AGGF1. (AGGF1-BGHcLV05-6B)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS010LBN at ENCODE; https://www.encodeproject.org/ENCBS010LBN/

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


title: total RNA-seq from macrophage (ENCLB515HIQ)

description:
https://www.encodeproject.org/experiments/ENCSR896LKP/
***************
biological replicate number: 3
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 15 minute.
experiment encode accession: ENCSR896LKP
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB515HIQ
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Mus musculus strain C57BL/6J macrophage primary cell cytosolic fraction

value: macrophage

value: primary cell

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: cytosol

value: ENCBS787HRW at ENCODE; https://www.encodeproject.org/ENCBS787HRW/

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


title: polyA plus RNA-seq from macrophage (ENCLB950NJI)

description:
https://www.encodeproject.org/experiments/ENCSR879BNI/
***************
biological replicate number: 1
technical replicate number: 1
description: mRNA-seq on whole cell extract RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for30 minutes.
experiment encode accession: ENCSR879BNI
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB950NJI
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Mus musculus strain C57BL/6J macrophage primary cell originated from bone marrow treated with 100 ng/mL lipoprotein A for 30 minutes

tag: treatments

value: treatment_term_name:lipoprotein A; treatment_type:protein; duration:30; duration_units:minute;

value: ENCBS275UTU at ENCODE; https://www.encodeproject.org/ENCBS275UTU/


title: total RNA-seq from macrophage (ENCLB732FGB)

description:
https://www.encodeproject.org/experiments/ENCSR998WNE/
***************
biological replicate number: 3
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 10 minute.
experiment encode accession: ENCSR998WNE
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB732FGB
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS510HPZ at ENCODE; https://www.encodeproject.org/ENCBS510HPZ/


title: microRNA-seq from mesenteric fat pad (ENCLB951HLN)

description:
https://www.encodeproject.org/experiments/ENCSR796JPP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W73 mesenteric fat pad microRNA-seq from Mortazavi
experiment encode accession: ENCSR796JPP
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-10-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB951HLN
size range: <30

source_name: Homo sapiens female adult (59 years) mesenteric fat pad tissue, preserved by flash-freezing

value: mesenteric fat pad

value: tissue

value: female

value: adult

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: DM:yes; HTN:yes; CAD:no

value: ENCBS232CCX at ENCODE; https://www.encodeproject.org/ENCBS232CCX/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: total RNA-seq from macrophage (ENCLB425SDZ)

description:
https://www.encodeproject.org/experiments/ENCSR998WNE/
***************
biological replicate number: 2
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 10 minute.
experiment encode accession: ENCSR998WNE
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB425SDZ
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: macrophage

value: primary cell

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: ENCBS941ZTJ at ENCODE; https://www.encodeproject.org/ENCBS941ZTJ/


title: total RNA-seq from macrophage (ENCLB826UTC)

description:
https://www.encodeproject.org/experiments/ENCSR982MXJ/
***************
biological replicate number: 3
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 25 minute.
experiment encode accession: ENCSR982MXJ
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB826UTC
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: cytosol

value: ENCBS517MSJ at ENCODE; https://www.encodeproject.org/ENCBS517MSJ/

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


title: total RNA-seq from macrophage (ENCLB734ODT)

description:
https://www.encodeproject.org/experiments/ENCSR982MXJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 25 minute.
experiment encode accession: ENCSR982MXJ
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB734ODT
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS395MVN at ENCODE; https://www.encodeproject.org/ENCBS395MVN/


title: CRISPR RNA-seq from K562 (ENCLB125DBW)

description:
https://www.encodeproject.org/experiments/ENCSR103NNB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SDAD1. (SDAD1-BGKcLV06)
experiment encode accession: ENCSR103NNB
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR341TTW
encode release date: 2017-12-09
lab: Brenton Graveley, UConn
library encode accession: ENCLB125DBW
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6ac8d5b9-ca3f-481c-8d40-43b42567d4d8/@@download/attachment/L-SDAD1-BGKcLV06-32.pdf

value: cell line

value: RNA-seq on K562 cells treated with a CRISPR gRNA against SDAD1. (SDAD1-BGKcLV06-32)

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS367HEP at ENCODE; https://www.encodeproject.org/ENCBS367HEP/

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


title: CRISPR RNA-seq from K562 (ENCLB351UTS)

description:
https://www.encodeproject.org/experiments/ENCSR105LOV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against PCBP3. (PCBP3-BGKcLV06)
experiment encode accession: ENCSR105LOV
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR341TTW
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB351UTS
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting PCBP3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b0414012-9678-414d-ad4c-4b850adf1e2a/@@download/attachment/L-PCBP3-BGKcLV06-24.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against PCBP3. (PCBP3-BGKcLV06-24)

value: ENCBS694ZGH at ENCODE; https://www.encodeproject.org/ENCBS694ZGH/


title: CRISPR RNA-seq from K562 (ENCLB650KWL)

description:
https://www.encodeproject.org/experiments/ENCSR105LOV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against PCBP3. (PCBP3-BGKcLV06)
experiment encode accession: ENCSR105LOV
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR341TTW
encode release date: 2017-12-06
lab: Brenton Graveley, UConn
library encode accession: ENCLB650KWL
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 15 spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/45dba180-b9a8-4af1-8e30-8498d3bb78ed/@@download/attachment/L-PCBP3-BGKcLV06-23.pdf

value: RNA-seq on K562 cells treated with a CRISPR gRNA against PCBP3. (PCBP3-BGKcLV06-23)

value: ENCBS799AGZ at ENCODE; https://www.encodeproject.org/ENCBS799AGZ/


title: total RNA-seq from macrophage (ENCLB037SGI)

description:
https://www.encodeproject.org/experiments/ENCSR896LKP/
***************
biological replicate number: 2
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 15 minute.
experiment encode accession: ENCSR896LKP
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB037SGI
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: macrophage

value: primary cell

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: cytosol

value: ENCBS217CCH at ENCODE; https://www.encodeproject.org/ENCBS217CCH/


title: total RNA-seq from macrophage (ENCLB740LTP)

description:
https://www.encodeproject.org/experiments/ENCSR982MXJ/
***************
biological replicate number: 2
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 25 minute.
experiment encode accession: ENCSR982MXJ
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB740LTP
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS645BOX at ENCODE; https://www.encodeproject.org/ENCBS645BOX/

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


title: total RNA-seq from macrophage (ENCLB724YDP)

description:
https://www.encodeproject.org/experiments/ENCSR868ZAZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 75 minute.
experiment encode accession: ENCSR868ZAZ
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB724YDP
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS366XDU at ENCODE; https://www.encodeproject.org/ENCBS366XDU/


title: CRISPR RNA-seq from HepG2 (ENCLB353DAN)

description:
https://www.encodeproject.org/experiments/ENCSR000SKS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPLP0. (RPLP0_BGHcLV03)
experiment encode accession: ENCSR000SKS
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR105NML
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB353DAN
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

source_name: Homo sapiens HepG2 cell line genetically modified (deletion) using CRISPR targeting RPLP0

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f671b0f9-51d2-4bd7-9b1b-5c90b255dc75/@@download/attachment/L-RPLP0_BGHcLV03-18.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPLP0. (RPLP0_BGHcLV03-18)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS199RMB at ENCODE; https://www.encodeproject.org/ENCBS199RMB/

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


title: total RNA-seq from macrophage (ENCLB089VZC)

description:
https://www.encodeproject.org/experiments/ENCSR864RGP/
***************
biological replicate number: 2
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 90 minute.
experiment encode accession: ENCSR864RGP
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB089VZC
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 250
nucleic acid starting quantity units: ng

value: macrophage

value: primary cell

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: chromatin

value: ENCBS480OCU at ENCODE; https://www.encodeproject.org/ENCBS480OCU/


title: total RNA-seq from macrophage (ENCLB112ANB)

description:
https://www.encodeproject.org/experiments/ENCSR857KZU/
***************
biological replicate number: 2
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 120 minute.
experiment encode accession: ENCSR857KZU
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB112ANB
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: Alexander Hoffmann

value: cytosol

value: ENCBS613NIW at ENCODE; https://www.encodeproject.org/ENCBS613NIW/

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


title: total RNA-seq from macrophage (ENCLB051NOM)

description:
https://www.encodeproject.org/experiments/ENCSR896LKP/
***************
biological replicate number: 4
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 15 minute.
experiment encode accession: ENCSR896LKP
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB051NOM
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS459QAB at ENCODE; https://www.encodeproject.org/ENCBS459QAB/


title: polyA plus RNA-seq from macrophage (ENCLB009AQC)

description:
https://www.encodeproject.org/experiments/ENCSR879BNI/
***************
biological replicate number: 2
technical replicate number: 1
description: mRNA-seq on whole cell extract RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for30 minutes.
experiment encode accession: ENCSR879BNI
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB009AQC
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: treatment_term_name:lipoprotein A; treatment_type:protein; duration:30; duration_units:minute;

value: ENCBS475IIX at ENCODE; https://www.encodeproject.org/ENCBS475IIX/


title: total RNA-seq from macrophage (ENCLB967CIA)

description:
https://www.encodeproject.org/experiments/ENCSR868ZAZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 75 minute.
experiment encode accession: ENCSR868ZAZ
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB967CIA
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS515LXN at ENCODE; https://www.encodeproject.org/ENCBS515LXN/


title: CRISPR RNA-seq from HepG2 (ENCLB766IYQ)

description:
https://www.encodeproject.org/experiments/ENCSR000SKS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPLP0. (RPLP0_BGHcLV03)
experiment encode accession: ENCSR000SKS
assay title: CRISPR RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR105NML
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB766IYQ
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: NIST profile 78B spike-ins

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e8c2cdd5-9230-4add-b445-f04b71bd524d/@@download/attachment/L-RPLP0_BGHcLV03-17.pdf

value: cell line

value: RNA-seq on HepG2 cells treated with a CRISPR gRNA against RPLP0. (RPLP0_BGHcLV03-17)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

value: ENCBS956FFN at ENCODE; https://www.encodeproject.org/ENCBS956FFN/


title: total RNA-seq from macrophage (ENCLB200ZQY)

description:
https://www.encodeproject.org/experiments/ENCSR992IIX/
***************
biological replicate number: 2
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 40 minute.
experiment encode accession: ENCSR992IIX
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB200ZQY
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 250
nucleic acid starting quantity units: ng

value: macrophage

value: primary cell

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: chromatin

value: ENCBS702ZPR at ENCODE; https://www.encodeproject.org/ENCBS702ZPR/


title: total RNA-seq from macrophage (ENCLB335VLD)

description:
https://www.encodeproject.org/experiments/ENCSR837DAP/
***************
biological replicate number: 3
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 0 minute.
experiment encode accession: ENCSR837DAP
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB335VLD
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: ENCBS487ZJC at ENCODE; https://www.encodeproject.org/ENCBS487ZJC/

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


title: total RNA-seq from macrophage (ENCLB805MFU)

description:
https://www.encodeproject.org/experiments/ENCSR965WQM/
***************
biological replicate number: 2
technical replicate number: 1
description: Ribo depletion RNA-seq on nucleoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 25 minute.
experiment encode accession: ENCSR965WQM
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB805MFU
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Mus musculus strain C57BL/6J macrophage primary cell nuclear fraction

value: nucleus

value: ENCBS796FBB at ENCODE; https://www.encodeproject.org/ENCBS796FBB/


title: total RNA-seq from macrophage (ENCLB835LAI)

description:
https://www.encodeproject.org/experiments/ENCSR864RGP/
***************
biological replicate number: 3
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 90 minute.
experiment encode accession: ENCSR864RGP
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB835LAI
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: ENCBS435MUT at ENCODE; https://www.encodeproject.org/ENCBS435MUT/


title: total RNA-seq from macrophage (ENCLB157TTZ)

description:
https://www.encodeproject.org/experiments/ENCSR940IMN/
***************
biological replicate number: 2
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 10 minute.
experiment encode accession: ENCSR940IMN
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB157TTZ
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 250
nucleic acid starting quantity units: ng

value: ENCBS109JNO at ENCODE; https://www.encodeproject.org/ENCBS109JNO/


title: total RNA-seq from macrophage (ENCLB548HPD)

description:
https://www.encodeproject.org/experiments/ENCSR842HHZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 35 minute.
experiment encode accession: ENCSR842HHZ
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB548HPD
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: cytosol

value: ENCBS420ZKH at ENCODE; https://www.encodeproject.org/ENCBS420ZKH/


title: total RNA-seq from macrophage (ENCLB283DHL)

description:
https://www.encodeproject.org/experiments/ENCSR965WQM/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on nucleoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 25 minute.
experiment encode accession: ENCSR965WQM
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB283DHL
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: ENCBS070DUB at ENCODE; https://www.encodeproject.org/ENCBS070DUB/


title: total RNA-seq from macrophage (ENCLB965XYE)

description:
https://www.encodeproject.org/experiments/ENCSR837DAP/
***************
biological replicate number: 2
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 0 minute.
experiment encode accession: ENCSR837DAP
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB965XYE
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 250
nucleic acid starting quantity units: ng

value: macrophage

value: ENCBS317KGE at ENCODE; https://www.encodeproject.org/ENCBS317KGE/


title: polyA plus RNA-seq from macrophage (ENCLB795ZGO)

description:
https://www.encodeproject.org/experiments/ENCSR938LWT/
***************
biological replicate number: 2
technical replicate number: 1
description: mRNA-seq on whole cell extract RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for120 minutes.
experiment encode accession: ENCSR938LWT
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB795ZGO
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Mus musculus strain C57BL/6J macrophage primary cell originated from bone marrow treated with 100 ng/mL lipoprotein A for 120 minutes

value: primary cell

value: not collected

value: treatment_term_name:lipoprotein A; treatment_type:protein; duration:120; duration_units:minute;

value: ENCBS526PRG at ENCODE; https://www.encodeproject.org/ENCBS526PRG/


title: total RNA-seq from macrophage (ENCLB065LZK)

description:
https://www.encodeproject.org/experiments/ENCSR924IHS/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 0 minute.
experiment encode accession: ENCSR924IHS
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB065LZK
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 250
nucleic acid starting quantity units: ng

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: chromatin

value: ENCBS173TER at ENCODE; https://www.encodeproject.org/ENCBS173TER/


title: total RNA-seq from macrophage (ENCLB129LBU)

description:
https://www.encodeproject.org/experiments/ENCSR940IMN/
***************
biological replicate number: 3
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 10 minute.
experiment encode accession: ENCSR940IMN
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB129LBU
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: ENCBS710HYS at ENCODE; https://www.encodeproject.org/ENCBS710HYS/

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


title: polyA plus RNA-seq from macrophage (ENCLB328DAI)

description:
https://www.encodeproject.org/experiments/ENCSR822FMG/
***************
biological replicate number: 3
technical replicate number: 1
description: mRNA-seq on whole cell extract RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for180 minutes.
experiment encode accession: ENCSR822FMG
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB328DAI
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Mus musculus strain C57BL/6J macrophage primary cell originated from bone marrow treated with 100 ng/mL lipoprotein A for 180 minutes

value: treatment_term_name:lipoprotein A; treatment_type:protein; duration:180; duration_units:minute;

value: ENCBS118JNF at ENCODE; https://www.encodeproject.org/ENCBS118JNF/


title: total RNA-seq from macrophage (ENCLB771UCJ)

description:
https://www.encodeproject.org/experiments/ENCSR959OQW/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on nucleoplasmic fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 75 minute.
experiment encode accession: ENCSR959OQW
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB771UCJ
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: nucleus

value: ENCBS980LYL at ENCODE; https://www.encodeproject.org/ENCBS980LYL/


title: polyA plus RNA-seq from macrophage (ENCLB752RLK)

description:
https://www.encodeproject.org/experiments/ENCSR822FMG/
***************
biological replicate number: 2
technical replicate number: 1
description: mRNA-seq on whole cell extract RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for180 minutes.
experiment encode accession: ENCSR822FMG
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB752RLK
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: macrophage

value: ENCBS162FMY at ENCODE; https://www.encodeproject.org/ENCBS162FMY/


title: total RNA-seq from macrophage (ENCLB973KOU)

description:
https://www.encodeproject.org/experiments/ENCSR924IHS/
***************
biological replicate number: 2
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 0 minute.
experiment encode accession: ENCSR924IHS
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB973KOU
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: primary cell

value: ENCBS121ODP at ENCODE; https://www.encodeproject.org/ENCBS121ODP/


title: total RNA-seq from macrophage (ENCLB363DFF)

description:
https://www.encodeproject.org/experiments/ENCSR839HSB/
***************
biological replicate number: 2
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 60 minute.
experiment encode accession: ENCSR839HSB
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB363DFF
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: not collected

value: cytosol

value: ENCBS567YAS at ENCODE; https://www.encodeproject.org/ENCBS567YAS/


title: total RNA-seq from macrophage (ENCLB672PIG)

description:
https://www.encodeproject.org/experiments/ENCSR857KZU/
***************
biological replicate number: 3
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 120 minute.
experiment encode accession: ENCSR857KZU
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB672PIG
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: unknown

value: Alexander Hoffmann, UCLA

value: ENCBS759IWP at ENCODE; https://www.encodeproject.org/ENCBS759IWP/


title: total RNA-seq from macrophage (ENCLB063CSZ)

description:
https://www.encodeproject.org/experiments/ENCSR839HSB/
***************
biological replicate number: 3
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 60 minute.
experiment encode accession: ENCSR839HSB
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB063CSZ
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: Alexander Hoffmann

value: ENCBS040DQH at ENCODE; https://www.encodeproject.org/ENCBS040DQH/


title: polyA plus RNA-seq from macrophage (ENCLB458MCW)

description:
https://www.encodeproject.org/experiments/ENCSR917CGF/
***************
biological replicate number: 4
technical replicate number: 1
description: mRNA-seq on whole cell extract RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 0 minutes.
experiment encode accession: ENCSR917CGF
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB458MCW
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Mus musculus strain C57BL/6J macrophage primary cell originated from bone marrow treated with 100 ng/mL lipoprotein A for 12 hours

value: treatment_term_name:lipoprotein A; treatment_type:protein; duration:12; duration_units:hour;

value: ENCBS280UUC at ENCODE; https://www.encodeproject.org/ENCBS280UUC/

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


title: polyA plus RNA-seq from macrophage (ENCLB056LYP)

description:
https://www.encodeproject.org/experiments/ENCSR938LWT/
***************
biological replicate number: 1
technical replicate number: 1
description: mRNA-seq on whole cell extract RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for120 minutes.
experiment encode accession: ENCSR938LWT
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB056LYP
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: treatment_term_name:lipoprotein A; treatment_type:protein; duration:120; duration_units:minute;

value: ENCBS669BBL at ENCODE; https://www.encodeproject.org/ENCBS669BBL/


title: total RNA-seq from macrophage (ENCLB220SWT)

description:
https://www.encodeproject.org/experiments/ENCSR803TDA/
***************
biological replicate number: 2
technical replicate number: 1
description: Ribo depletion RNA-seq on nucleoplasmic fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 40 minute.
experiment encode accession: ENCSR803TDA
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB220SWT
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: macrophage

value: nucleus

value: ENCBS908DCM at ENCODE; https://www.encodeproject.org/ENCBS908DCM/


title: microRNA-seq from upper lobe of right lung (ENCLB475IUW)

description:
https://www.encodeproject.org/experiments/ENCSR637DRN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W78 upper lobe of right lung microRNA-seq from Mortazavi
experiment encode accession: ENCSR637DRN
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB475IUW
size range: <30

source_name: Homo sapiens male adult (60 years) upper lobe of right lung tissue, preserved by flash-freezing

value: upper lobe of right lung

value: tissue

value: male

value: adult

value: 60 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: ENCBS496CPG at ENCODE; https://www.encodeproject.org/ENCBS496CPG/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: polyA plus RNA-seq from macrophage (ENCLB570ZCO)

description:
https://www.encodeproject.org/experiments/ENCSR906KGC/
***************
biological replicate number: 3
technical replicate number: 1
description: mRNA-seq on whole cell extract RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 180 minutes.
experiment encode accession: ENCSR906KGC
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB570ZCO
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Mus musculus strain C57BL/6J macrophage primary cell originated from bone marrow treated with 100 ng/mL lipoprotein A for 12 hours, 100 ng/mL lipoprotein A for 180 minutes

value: primary cell

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: treatment_term_name:lipoprotein A; treatment_type:protein; duration:12; duration_units:hour; treatment_term_name:lipoprotein A; treatment_type:protein; duration:180; duration_units:minute;

value: ENCBS467QKW at ENCODE; https://www.encodeproject.org/ENCBS467QKW/


title: total RNA-seq from macrophage (ENCLB695NRK)

description:
https://www.encodeproject.org/experiments/ENCSR820OHO/
***************
biological replicate number: 3
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 60 minute.
experiment encode accession: ENCSR820OHO
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB695NRK
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: macrophage

value: chromatin

value: ENCBS559STN at ENCODE; https://www.encodeproject.org/ENCBS559STN/

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


title: total RNA-seq from macrophage (ENCLB106MTV)

description:
https://www.encodeproject.org/experiments/ENCSR811YTU/
***************
biological replicate number: 2
technical replicate number: 1
description: Ribo depletion RNA-seq on nucleoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 60 minute.
experiment encode accession: ENCSR811YTU
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB106MTV
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: nucleus

value: ENCBS936WOG at ENCODE; https://www.encodeproject.org/ENCBS936WOG/


title: total RNA-seq from macrophage (ENCLB889NXL)

description:
https://www.encodeproject.org/experiments/ENCSR911EZW/
***************
biological replicate number: 2
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 15 minute.
experiment encode accession: ENCSR911EZW
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB889NXL
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 250
nucleic acid starting quantity units: ng

value: ENCBS648UTP at ENCODE; https://www.encodeproject.org/ENCBS648UTP/


title: polyA plus RNA-seq from macrophage (ENCLB624GYW)

description:
https://www.encodeproject.org/experiments/ENCSR906KGC/
***************
biological replicate number: 2
technical replicate number: 1
description: mRNA-seq on whole cell extract RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 180 minutes.
experiment encode accession: ENCSR906KGC
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB624GYW
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS349BCN at ENCODE; https://www.encodeproject.org/ENCBS349BCN/


title: microRNA-seq from type B pancreatic cell (ENCLB498OYJ)

description:
https://www.encodeproject.org/experiments/ENCSR630APF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation H9 derived beta-like cells microRNA-seq from Mortazavi
experiment encode accession: ENCSR630APF
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-03-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB498OYJ
size range: <30

source_name: Homo sapiens female embryo (5 days) type B pancreatic in vitro differentiated cells originated from type B pancreatic cell

value: type B pancreatic cell

value: in vitro differentiated cells

value: WA09 derived insulin producing beta-like cells

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS779FCS at ENCODE; https://www.encodeproject.org/ENCBS779FCS/

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


title: total RNA-seq from macrophage (ENCLB706UKT)

description:
https://www.encodeproject.org/experiments/ENCSR820OHO/
***************
biological replicate number: 2
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 60 minute.
experiment encode accession: ENCSR820OHO
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB706UKT
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 250
nucleic acid starting quantity units: ng

value: macrophage

value: primary cell

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: chromatin

value: ENCBS491JUM at ENCODE; https://www.encodeproject.org/ENCBS491JUM/


title: total RNA-seq from macrophage (ENCLB054NLF)

description:
https://www.encodeproject.org/experiments/ENCSR664IMK/
***************
biological replicate number: 3
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 30 minute.
experiment encode accession: ENCSR664IMK
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB054NLF
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: ENCBS143SFG at ENCODE; https://www.encodeproject.org/ENCBS143SFG/

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


title: total RNA-seq from macrophage (ENCLB051MNC)

description:
https://www.encodeproject.org/experiments/ENCSR671DQW/
***************
biological replicate number: 2
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 90 minute.
experiment encode accession: ENCSR671DQW
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB051MNC
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: cytosol

value: ENCBS550WSN at ENCODE; https://www.encodeproject.org/ENCBS550WSN/


title: polyA plus RNA-seq from macrophage (ENCLB840GYI)

description:
https://www.encodeproject.org/experiments/ENCSR917CGF/
***************
biological replicate number: 3
technical replicate number: 1
description: mRNA-seq on whole cell extract RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 0 minutes.
experiment encode accession: ENCSR917CGF
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB840GYI
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: treatment_term_name:lipoprotein A; treatment_type:protein; duration:12; duration_units:hour;

value: ENCBS508ZMR at ENCODE; https://www.encodeproject.org/ENCBS508ZMR/


title: total RNA-seq from macrophage (ENCLB161MPD)

description:
https://www.encodeproject.org/experiments/ENCSR671DQW/
***************
biological replicate number: 3
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 90 minute.
experiment encode accession: ENCSR671DQW
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB161MPD
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS243DVV at ENCODE; https://www.encodeproject.org/ENCBS243DVV/


title: total RNA-seq from macrophage (ENCLB736ENJ)

description:
https://www.encodeproject.org/experiments/ENCSR771ODD/
***************
biological replicate number: 3
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 20 minute.
experiment encode accession: ENCSR771ODD
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB736ENJ
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: ENCBS009DUZ at ENCODE; https://www.encodeproject.org/ENCBS009DUZ/


title: total RNA-seq from macrophage (ENCLB299EXW)

description:
https://www.encodeproject.org/experiments/ENCSR814INP/
***************
biological replicate number: 2
technical replicate number: 1
description: Ribo depletion RNA-seq on nucleoplasmic fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 20 minute.
experiment encode accession: ENCSR814INP
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB299EXW
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: nucleus

value: ENCBS186WMB at ENCODE; https://www.encodeproject.org/ENCBS186WMB/


title: microRNA-seq from CD4-positive, alpha-beta T cell (ENCLB658KLO)

description:
https://www.encodeproject.org/experiments/ENCSR621NPL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation human CD4+ T cells microRNA-seq from Mortazavi
experiment encode accession: ENCSR621NPL
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2021-06-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB658KLO
size range: <30

source_name: Homo sapiens male adult (20 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: primary cell

value: male

value: adult

value: 20 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS075SKQ at ENCODE; https://www.encodeproject.org/ENCBS075SKQ/

value: Derived from ENCODE donor ENCDO394DKX; https://www.encodeproject.org/ENCDO394DKX/


title: total RNA-seq from macrophage (ENCLB589UZI)

description:
https://www.encodeproject.org/experiments/ENCSR771BCK/
***************
biological replicate number: 2
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 60 minute.
experiment encode accession: ENCSR771BCK
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB589UZI
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 250
nucleic acid starting quantity units: ng

source_name: Mus musculus strain C57BL/6J macrophage primary cell chromatin fraction

value: macrophage

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: chromatin

value: ENCBS127QRJ at ENCODE; https://www.encodeproject.org/ENCBS127QRJ/

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


title: microRNA-seq from K562 (ENCLB423FXU)

description:
https://www.encodeproject.org/experiments/ENCSR638BGL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation K562 microRNA-seq from Mortazavi
experiment encode accession: ENCSR638BGL
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-06-11
lab: Ali Mortazavi, UCI
library encode accession: ENCLB423FXU
size range: <30

source_name: Homo sapiens K562 cell line

value: cell line

value: female

value: 53 year

value: Mats Ljungman, UMichigan

value: ATCC

value: chronic myelogenous leukemia (CML)

value: ENCBS206PUV at ENCODE; https://www.encodeproject.org/ENCBS206PUV/

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


title: microRNA-seq from lower lobe of right lung (ENCLB741TXH)

description:
https://www.encodeproject.org/experiments/ENCSR763RNR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W78 lower lobe of right lung microRNA-seq from Mortazavi
experiment encode accession: ENCSR763RNR
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB741TXH
size range: <30

source_name: Homo sapiens male adult (60 years) lower lobe of right lung tissue, preserved by flash-freezing

value: lower lobe of right lung

value: tissue

value: male

value: adult

value: 60 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: ENCBS870VUM at ENCODE; https://www.encodeproject.org/ENCBS870VUM/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: microRNA-seq from type B pancreatic cell (ENCLB307NUY)

description:
https://www.encodeproject.org/experiments/ENCSR630APF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation H9 derived beta-like cells microRNA-seq from Mortazavi
experiment encode accession: ENCSR630APF
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-03-03
lab: Ali Mortazavi, UCI
library encode accession: ENCLB307NUY
size range: <30

value: type B pancreatic cell

value: in vitro differentiated cells

value: WA09 derived insulin producing beta-like cells

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS251SEQ at ENCODE; https://www.encodeproject.org/ENCBS251SEQ/

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


title: polyA plus RNA-seq from macrophage (ENCLB222CPW)

description:
https://www.encodeproject.org/experiments/ENCSR627RCT/
***************
biological replicate number: 2
technical replicate number: 1
description: mRNA-seq on whole cell extract RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 300 minutes.
experiment encode accession: ENCSR627RCT
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB222CPW
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Mus musculus strain C57BL/6J macrophage primary cell originated from bone marrow treated with 100 ng/mL lipoprotein A for 12 hours, 100 ng/mL lipoprotein A for 300 minutes

value: macrophage

value: primary cell

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: treatment_term_name:lipoprotein A; treatment_type:protein; duration:12; duration_units:hour; treatment_term_name:lipoprotein A; treatment_type:protein; duration:300; duration_units:minute;

value: ENCBS907XPS at ENCODE; https://www.encodeproject.org/ENCBS907XPS/

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


title: total RNA-seq from macrophage (ENCLB591GYS)

description:
https://www.encodeproject.org/experiments/ENCSR664IMK/
***************
biological replicate number: 2
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 30 minute.
experiment encode accession: ENCSR664IMK
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB591GYS
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 250
nucleic acid starting quantity units: ng

value: chromatin

value: ENCBS438TIY at ENCODE; https://www.encodeproject.org/ENCBS438TIY/


title: CRISPR RNA-seq from HepG2 (ENCLB865GAI)

description:
https://www.encodeproject.org/experiments/ENCSR733MVT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with a CRISPR gRNA against EIF3H. (EIF3H-BGHcLV05-D)
experiment encode accession: ENCSR733MVT
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR805TIZ
encode release date: 2020-11-03
lab: Brenton Graveley, UConn
library encode accession: ENCLB865GAI
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 EIF3H

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4bd3dc94-f3df-406f-8b4e-1a33d828a101/@@download/attachment/L-EIF3H-BGHcLV05-15D.pdf

value: cell line

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

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

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

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


title: total RNA-seq from macrophage (ENCLB875HWI)

description:
https://www.encodeproject.org/experiments/ENCSR726YJC/
***************
biological replicate number: 2
technical replicate number: 1
description: Ribo depletion RNA-seq on nucleoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 90 minute.
experiment encode accession: ENCSR726YJC
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB875HWI
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: macrophage

value: primary cell

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: nucleus

value: ENCBS121LFT at ENCODE; https://www.encodeproject.org/ENCBS121LFT/


title: total RNA-seq from macrophage (ENCLB848VFF)

description:
https://www.encodeproject.org/experiments/ENCSR739SJI/
***************
biological replicate number: 2
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 75 minute.
experiment encode accession: ENCSR739SJI
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB848VFF
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: Alexander Hoffmann

value: chromatin

value: ENCBS201FHH at ENCODE; https://www.encodeproject.org/ENCBS201FHH/

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


title: total RNA-seq from macrophage (ENCLB338CNW)

description:
https://www.encodeproject.org/experiments/ENCSR771BCK/
***************
biological replicate number: 3
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 60 minute.
experiment encode accession: ENCSR771BCK
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB338CNW
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: ENCBS978NDW at ENCODE; https://www.encodeproject.org/ENCBS978NDW/


title: total RNA-seq from macrophage (ENCLB002NJE)

description:
https://www.encodeproject.org/experiments/ENCSR731TGN/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on nucleoplasmic fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 35 minute.
experiment encode accession: ENCSR731TGN
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB002NJE
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS451YLM at ENCODE; https://www.encodeproject.org/ENCBS451YLM/


title: total RNA-seq from macrophage (ENCLB004FVB)

description:
https://www.encodeproject.org/experiments/ENCSR616IPE/
***************
biological replicate number: 2
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 20 minute.
experiment encode accession: ENCSR616IPE
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB004FVB
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Mus musculus strain C57BL/6J macrophage primary cell cytosolic fraction

value: cytosol

value: ENCBS627UTJ at ENCODE; https://www.encodeproject.org/ENCBS627UTJ/


title: microRNA-seq from HepG2 (ENCLB877ZDQ)

description:
https://www.encodeproject.org/experiments/ENCSR730NEO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation HepG2 microRNA-seq from Mortazavi
experiment encode accession: ENCSR730NEO
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-06-11
lab: Ali Mortazavi, UCI
library encode accession: ENCLB877ZDQ
size range: <30
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

source_name: Homo sapiens HepG2 immortalized cell line

value: cell line

value: hepatocellular carcinoma

value: 15 year

value: child

value: male

value: Barbara Wold, Caltech

value: ENCBS644SVK at ENCODE; https://www.encodeproject.org/ENCBS644SVK/

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

value: ENCODE dbxrefs HepG2; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HepG2


title: polyA plus RNA-seq from macrophage (ENCLB772JKS)

description:
https://www.encodeproject.org/experiments/ENCSR754DFU/
***************
biological replicate number: 2
technical replicate number: 1
description: mRNA-seq on whole cell extract RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 30 minutes.
experiment encode accession: ENCSR754DFU
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB772JKS
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Mus musculus strain C57BL/6J macrophage primary cell originated from bone marrow treated with 100 ng/mL lipoprotein A for 12 hours, 100 ng/mL lipoprotein A for 30 minutes

value: macrophage

value: primary cell

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: treatment_term_name:lipoprotein A; treatment_type:protein; duration:12; duration_units:hour; treatment_term_name:lipoprotein A; treatment_type:protein; duration:30; duration_units:minute;

value: ENCBS296VBP at ENCODE; https://www.encodeproject.org/ENCBS296VBP/


title: polyA plus RNA-seq from macrophage (ENCLB113SFA)

description:
https://www.encodeproject.org/experiments/ENCSR614DLJ/
***************
biological replicate number: 3
technical replicate number: 1
description: mRNA-seq on whole cell extract RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for0 minutes.
experiment encode accession: ENCSR614DLJ
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB113SFA
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Mus musculus strain C57BL/6J macrophage primary cell originated from bone marrow

value: ENCBS053FVJ at ENCODE; https://www.encodeproject.org/ENCBS053FVJ/

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


title: polyA plus RNA-seq from macrophage (ENCLB690ZFI)

description:
https://www.encodeproject.org/experiments/ENCSR627RCT/
***************
biological replicate number: 1
technical replicate number: 1
description: mRNA-seq on whole cell extract RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 300 minutes.
experiment encode accession: ENCSR627RCT
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB690ZFI
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: treatment_term_name:lipoprotein A; treatment_type:protein; duration:12; duration_units:hour; treatment_term_name:lipoprotein A; treatment_type:protein; duration:300; duration_units:minute;

value: ENCBS075ASQ at ENCODE; https://www.encodeproject.org/ENCBS075ASQ/


title: microRNA-seq from CD4-positive, alpha-beta T cell (ENCLB069BYZ)

description:
https://www.encodeproject.org/experiments/ENCSR621NPL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human CD4+ T cells microRNA-seq from Mortazavi
experiment encode accession: ENCSR621NPL
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2021-06-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB069BYZ
size range: <30

value: CD4-positive, alpha-beta T cell

value: male

value: adult

value: 20 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS984FMU at ENCODE; https://www.encodeproject.org/ENCBS984FMU/

value: Derived from ENCODE donor ENCDO394DKX; https://www.encodeproject.org/ENCDO394DKX/


title: total RNA-seq from macrophage (ENCLB711FMO)

description:
https://www.encodeproject.org/experiments/ENCSR911EZW/
***************
biological replicate number: 3
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 15 minute.
experiment encode accession: ENCSR911EZW
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB711FMO
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: macrophage

value: primary cell

value: not collected

value: unknown

value: chromatin

value: ENCBS388LAX at ENCODE; https://www.encodeproject.org/ENCBS388LAX/


title: polyA plus RNA-seq from macrophage (ENCLB107ECQ)

description:
https://www.encodeproject.org/experiments/ENCSR590GUK/
***************
biological replicate number: 2
technical replicate number: 1
description: mRNA-seq on whole cell extract RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 480 minutes.
experiment encode accession: ENCSR590GUK
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB107ECQ
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Mus musculus strain C57BL/6J macrophage primary cell originated from bone marrow treated with 100 ng/mL lipoprotein A for 12 hours, 100 ng/mL lipoprotein A for 480 minutes

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: treatment_term_name:lipoprotein A; treatment_type:protein; duration:12; duration_units:hour; treatment_term_name:lipoprotein A; treatment_type:protein; duration:480; duration_units:minute;

value: ENCBS968XQG at ENCODE; https://www.encodeproject.org/ENCBS968XQG/

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


title: total RNA-seq from macrophage (ENCLB838OFP)

description:
https://www.encodeproject.org/experiments/ENCSR616IPE/
***************
biological replicate number: 3
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 20 minute.
experiment encode accession: ENCSR616IPE
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB838OFP
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: cytosol

value: ENCBS551WYA at ENCODE; https://www.encodeproject.org/ENCBS551WYA/


title: total RNA-seq from macrophage (ENCLB202LSV)

description:
https://www.encodeproject.org/experiments/ENCSR737BTH/
***************
biological replicate number: 3
technical replicate number: 1
description: Ribo depletion RNA-seq on cytoplasmic fraction RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for 40 minute.
experiment encode accession: ENCSR737BTH
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB202LSV
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS519JGY at ENCODE; https://www.encodeproject.org/ENCBS519JGY/


title: polyA plus RNA-seq from macrophage (ENCLB860IBY)

description:
https://www.encodeproject.org/experiments/ENCSR614KOV/
***************
biological replicate number: 3
technical replicate number: 1
description: mRNA-seq on whole cell extract RNA which is part of BMDM cell, stimulated with 100 ng/ml Lipid A for480 minutes.
experiment encode accession: ENCSR614KOV
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB860IBY
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Mus musculus strain C57BL/6J macrophage primary cell originated from bone marrow treated with 100 ng/mL lipoprotein A for 480 minutes

value: treatment_term_name:lipoprotein A; treatment_type:protein; duration:480; duration_units:minute;

value: ENCBS065RKX at ENCODE; https://www.encodeproject.org/ENCBS065RKX/