title: polyA plus RNA-seq from macrophage (ENCLB904AIY)

description:
https://www.encodeproject.org/experiments/ENCSR614KOV/
***************
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 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: ENCLB904AIY
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS416HYC at ENCODE; https://www.encodeproject.org/ENCBS416HYC/


title: total RNA-seq from macrophage (ENCLB078TZO)

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/ENCSR499CRL/
***************
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 120 minute.
experiment encode accession: ENCSR499CRL
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB078TZO
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 250
nucleic acid starting quantity units: ng

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

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

value: macrophage

value: primary cell

tag: biosample encode accession

tag: Sex

value: not collected

tag: dev stage

value: unknown

tag: age

tag: lab

value: Alexander Hoffmann, UCLA

tag: source

value: Alexander Hoffmann

tag: subcellular fraction term name

value: chromatin

tag: link

value: ENCBS595KGY at ENCODE; https://www.encodeproject.org/ENCBS595KGY/

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


title: polyA plus RNA-seq from macrophage (ENCLB973XYM)

description:
https://www.encodeproject.org/experiments/ENCSR754DFU/
***************
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 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: ENCLB973XYM
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

tag: treatments

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: ENCBS903WXU at ENCODE; https://www.encodeproject.org/ENCBS903WXU/


title: total RNA-seq from macrophage (ENCLB787IIG)

description:
https://www.encodeproject.org/experiments/ENCSR739SJI/
***************
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 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: ENCLB787IIG
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 250
nucleic acid starting quantity units: ng

value: ENCBS798ZWE at ENCODE; https://www.encodeproject.org/ENCBS798ZWE/


title: total RNA-seq from macrophage (ENCLB017QHY)

description:
https://www.encodeproject.org/experiments/ENCSR737BTH/
***************
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 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: ENCLB017QHY
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: ENCBS763WNC at ENCODE; https://www.encodeproject.org/ENCBS763WNC/


title: CRISPR RNA-seq from HepG2 (ENCLB899QXE)

description:
https://www.encodeproject.org/experiments/ENCSR733MVT/
***************
biological replicate number: 2
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: ENCLB899QXE
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins

organism: Homo sapiens

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/337defc9-7fa6-43ed-8a0a-5afe43df5c25/@@download/attachment/L-EIF3H-BGHcLV05-16D.pdf

tag: antibody

tag: line

value: cell line

tag: description

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

value: male

tag: health state

value: hepatocellular carcinoma

value: child

value: 15 year

value: Brenton Graveley, UConn

value: ATCC

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

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


title: microRNA-seq from HepG2 (ENCLB152MAK)

description:
https://www.encodeproject.org/experiments/ENCSR730NEO/
***************
biological replicate number: 1
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: ENCLB152MAK
size range: <30
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

source_name: Homo sapiens HepG2 immortalized cell line

value: Barbara Wold, Caltech

value: ENCBS429YJD at ENCODE; https://www.encodeproject.org/ENCBS429YJD/

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: total RNA-seq from macrophage (ENCLB381HVY)

description:
https://www.encodeproject.org/experiments/ENCSR386FUR/
***************
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 75 minute.
experiment encode accession: ENCSR386FUR
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB381HVY
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: Alexander Hoffmann

value: chromatin

value: ENCBS473YGP at ENCODE; https://www.encodeproject.org/ENCBS473YGP/

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


title: total RNA-seq from macrophage (ENCLB512XHU)

description:
https://www.encodeproject.org/experiments/ENCSR719VAW/
***************
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 20 minute.
experiment encode accession: ENCSR719VAW
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB512XHU
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

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

value: nucleus

value: ENCBS118VOJ at ENCODE; https://www.encodeproject.org/ENCBS118VOJ/


title: total RNA-seq from macrophage (ENCLB485WML)

description:
https://www.encodeproject.org/experiments/ENCSR771ODD/
***************
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 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: ENCLB485WML
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 250
nucleic acid starting quantity units: ng

value: ENCBS866JPR at ENCODE; https://www.encodeproject.org/ENCBS866JPR/


title: total RNA-seq from macrophage (ENCLB383UCN)

description:
https://www.encodeproject.org/experiments/ENCSR599ZAL/
***************
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 35 minute.
experiment encode accession: ENCSR599ZAL
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB383UCN
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: cytosol

value: ENCBS912QKI at ENCODE; https://www.encodeproject.org/ENCBS912QKI/


title: polyA plus RNA-seq from macrophage (ENCLB635EZY)

description:
https://www.encodeproject.org/experiments/ENCSR590GUK/
***************
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 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: ENCLB635EZY
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: 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: ENCBS863XKB at ENCODE; https://www.encodeproject.org/ENCBS863XKB/


title: total RNA-seq from macrophage (ENCLB075TBO)

description:
https://www.encodeproject.org/experiments/ENCSR663YJQ/
***************
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 20 minute.
experiment encode accession: ENCSR663YJQ
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB075TBO
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: ENCBS993ROQ at ENCODE; https://www.encodeproject.org/ENCBS993ROQ/


title: total RNA-seq from macrophage (ENCLB968AWU)

description:
https://www.encodeproject.org/experiments/ENCSR386FUR/
***************
biological replicate number: 1
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 75 minute.
experiment encode accession: ENCSR386FUR
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB968AWU
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 250
nucleic acid starting quantity units: ng

value: macrophage

value: ENCBS970YKU at ENCODE; https://www.encodeproject.org/ENCBS970YKU/


title: total RNA-seq from macrophage (ENCLB913ZNU)

description:
https://www.encodeproject.org/experiments/ENCSR498KKO/
***************
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 90 minute.
experiment encode accession: ENCSR498KKO
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB913ZNU
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 250
nucleic acid starting quantity units: ng

value: primary cell

value: not collected

value: ENCBS432OMW at ENCODE; https://www.encodeproject.org/ENCBS432OMW/


title: total RNA-seq from macrophage (ENCLB430FRO)

description:
https://www.encodeproject.org/experiments/ENCSR663YJQ/
***************
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 20 minute.
experiment encode accession: ENCSR663YJQ
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB430FRO
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: ENCBS329YTI at ENCODE; https://www.encodeproject.org/ENCBS329YTI/


title: total RNA-seq from macrophage (ENCLB743QSR)

description:
https://www.encodeproject.org/experiments/ENCSR596SMN/
***************
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 60 minute.
experiment encode accession: ENCSR596SMN
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB743QSR
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: nucleus

value: ENCBS616WLF at ENCODE; https://www.encodeproject.org/ENCBS616WLF/

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


title: polyA plus RNA-seq from macrophage (ENCLB541JZY)

description:
https://www.encodeproject.org/experiments/ENCSR577EOP/
***************
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 60 minutes.
experiment encode accession: ENCSR577EOP
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB541JZY
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 60 minutes

value: treatment_term_name:lipoprotein A; treatment_type:protein; duration:12; duration_units:hour; treatment_term_name:lipoprotein A; treatment_type:protein; duration:60; duration_units:minute;

value: ENCBS489FED at ENCODE; https://www.encodeproject.org/ENCBS489FED/


title: total RNA-seq from macrophage (ENCLB277PML)

description:
https://www.encodeproject.org/experiments/ENCSR489JUY/
***************
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 35 minute.
experiment encode accession: ENCSR489JUY
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB277PML
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS442ZRO at ENCODE; https://www.encodeproject.org/ENCBS442ZRO/


title: total RNA-seq from macrophage (ENCLB149LGT)

description:
https://www.encodeproject.org/experiments/ENCSR489PYT/
***************
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 60 minute.
experiment encode accession: ENCSR489PYT
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB149LGT
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: cytosol

value: ENCBS028MVW at ENCODE; https://www.encodeproject.org/ENCBS028MVW/


title: total RNA-seq from macrophage (ENCLB600TZZ)

description:
https://www.encodeproject.org/experiments/ENCSR499CRL/
***************
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 120 minute.
experiment encode accession: ENCSR499CRL
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB600TZZ
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: macrophage

value: chromatin

value: ENCBS332PJP at ENCODE; https://www.encodeproject.org/ENCBS332PJP/


title: total RNA-seq from macrophage (ENCLB781JFQ)

description:
https://www.encodeproject.org/experiments/ENCSR498KKO/
***************
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 90 minute.
experiment encode accession: ENCSR498KKO
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB781JFQ
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: primary cell

value: not collected

value: ENCBS765WUH at ENCODE; https://www.encodeproject.org/ENCBS765WUH/


title: total RNA-seq from macrophage (ENCLB351VEZ)

description:
https://www.encodeproject.org/experiments/ENCSR584FVS/
***************
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 0 minute.
experiment encode accession: ENCSR584FVS
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB351VEZ
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: ENCBS949OVB at ENCODE; https://www.encodeproject.org/ENCBS949OVB/


title: total RNA-seq from macrophage (ENCLB643YPB)

description:
https://www.encodeproject.org/experiments/ENCSR584FVS/
***************
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 0 minute.
experiment encode accession: ENCSR584FVS
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB643YPB
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: Alexander Hoffmann

value: ENCBS636JAH at ENCODE; https://www.encodeproject.org/ENCBS636JAH/


title: polyA plus RNA-seq from macrophage (ENCLB684IBN)

description:
https://www.encodeproject.org/experiments/ENCSR535SFV/
***************
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 for300 minutes.
experiment encode accession: ENCSR535SFV
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB684IBN
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 300 minutes

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

value: ENCBS477RIQ at ENCODE; https://www.encodeproject.org/ENCBS477RIQ/

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


title: total RNA-seq from macrophage (ENCLB841NJD)

description:
https://www.encodeproject.org/experiments/ENCSR568GJM/
***************
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 75 minute.
experiment encode accession: ENCSR568GJM
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB841NJD
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: nucleus

value: ENCBS959LQW at ENCODE; https://www.encodeproject.org/ENCBS959LQW/


title: total RNA-seq from macrophage (ENCLB364ZSD)

description:
https://www.encodeproject.org/experiments/ENCSR465TWT/
***************
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 25 minute.
experiment encode accession: ENCSR465TWT
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB364ZSD
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: ENCBS261IQY at ENCODE; https://www.encodeproject.org/ENCBS261IQY/


title: total RNA-seq from macrophage (ENCLB386RFZ)

description:
https://www.encodeproject.org/experiments/ENCSR542BJQ/
***************
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 30 minute.
experiment encode accession: ENCSR542BJQ
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB386RFZ
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: macrophage

value: cytosol

value: ENCBS646SGP at ENCODE; https://www.encodeproject.org/ENCBS646SGP/


title: total RNA-seq from macrophage (ENCLB482COM)

description:
https://www.encodeproject.org/experiments/ENCSR489PYT/
***************
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 60 minute.
experiment encode accession: ENCSR489PYT
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB482COM
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: primary cell

value: ENCBS879PJQ at ENCODE; https://www.encodeproject.org/ENCBS879PJQ/


title: total RNA-seq from macrophage (ENCLB776VYZ)

description:
https://www.encodeproject.org/experiments/ENCSR434TXU/
***************
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 40 minute.
experiment encode accession: ENCSR434TXU
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB776VYZ
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 250
nucleic acid starting quantity units: ng

value: not collected

value: chromatin

value: ENCBS594XRU at ENCODE; https://www.encodeproject.org/ENCBS594XRU/


title: total RNA-seq from macrophage (ENCLB881CZE)

description:
https://www.encodeproject.org/experiments/ENCSR460HQN/
***************
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 120 minute.
experiment encode accession: ENCSR460HQN
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB881CZE
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: unknown

value: Alexander Hoffmann, UCLA

value: ENCBS894TBQ at ENCODE; https://www.encodeproject.org/ENCBS894TBQ/


title: polyA plus RNA-seq from macrophage (ENCLB991KSI)

description:
https://www.encodeproject.org/experiments/ENCSR577EOP/
***************
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 60 minutes.
experiment encode accession: ENCSR577EOP
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB991KSI
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

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:60; duration_units:minute;

value: ENCBS568ACL at ENCODE; https://www.encodeproject.org/ENCBS568ACL/


title: total RNA-seq from macrophage (ENCLB819QZP)

description:
https://www.encodeproject.org/experiments/ENCSR434TXU/
***************
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 40 minute.
experiment encode accession: ENCSR434TXU
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB819QZP
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: ENCBS009RPZ at ENCODE; https://www.encodeproject.org/ENCBS009RPZ/

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


title: polyA plus RNA-seq from macrophage (ENCLB117RQW)

description:
https://www.encodeproject.org/experiments/ENCSR535SFV/
***************
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 for300 minutes.
experiment encode accession: ENCSR535SFV
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB117RQW
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:300; duration_units:minute;

value: ENCBS295WII at ENCODE; https://www.encodeproject.org/ENCBS295WII/


title: total RNA-seq from macrophage (ENCLB486UXD)

description:
https://www.encodeproject.org/experiments/ENCSR464OLG/
***************
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 25 minute.
experiment encode accession: ENCSR464OLG
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB486UXD
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: macrophage

value: nucleus

value: ENCBS747UQO at ENCODE; https://www.encodeproject.org/ENCBS747UQO/


title: total RNA-seq from macrophage (ENCLB694KPX)

description:
https://www.encodeproject.org/experiments/ENCSR426AUD/
***************
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 120 minute.
experiment encode accession: ENCSR426AUD
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB694KPX
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: primary cell

value: cytosol

value: ENCBS326CJQ at ENCODE; https://www.encodeproject.org/ENCBS326CJQ/


title: total RNA-seq from macrophage (ENCLB244UYJ)

description:
https://www.encodeproject.org/experiments/ENCSR460RCF/
***************
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 90 minute.
experiment encode accession: ENCSR460RCF
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB244UYJ
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: not collected

value: ENCBS997DWZ at ENCODE; https://www.encodeproject.org/ENCBS997DWZ/


title: total RNA-seq from macrophage (ENCLB216TWH)

description:
https://www.encodeproject.org/experiments/ENCSR542BJQ/
***************
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 30 minute.
experiment encode accession: ENCSR542BJQ
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB216TWH
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: ENCBS626INT at ENCODE; https://www.encodeproject.org/ENCBS626INT/


title: total RNA-seq from macrophage (ENCLB690ZCA)

description:
https://www.encodeproject.org/experiments/ENCSR465TWT/
***************
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 25 minute.
experiment encode accession: ENCSR465TWT
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB690ZCA
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 250
nucleic acid starting quantity units: ng

value: Alexander Hoffmann

value: chromatin

value: ENCBS604QGP at ENCODE; https://www.encodeproject.org/ENCBS604QGP/


title: total RNA-seq from macrophage (ENCLB303DSR)

description:
https://www.encodeproject.org/experiments/ENCSR460RCF/
***************
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 90 minute.
experiment encode accession: ENCSR460RCF
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB303DSR
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS425HRT at ENCODE; https://www.encodeproject.org/ENCBS425HRT/

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


title: total RNA-seq from macrophage (ENCLB818MPQ)

description:
https://www.encodeproject.org/experiments/ENCSR426AUD/
***************
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 120 minute.
experiment encode accession: ENCSR426AUD
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB818MPQ
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS400XVF at ENCODE; https://www.encodeproject.org/ENCBS400XVF/


title: total RNA-seq from macrophage (ENCLB283KRY)

description:
https://www.encodeproject.org/experiments/ENCSR515LYM/
***************
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 25 minute.
experiment encode accession: ENCSR515LYM
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB283KRY
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 250
nucleic acid starting quantity units: ng

value: macrophage

value: ENCBS674FBI at ENCODE; https://www.encodeproject.org/ENCBS674FBI/


title: total RNA-seq from macrophage (ENCLB245YKS)

description:
https://www.encodeproject.org/experiments/ENCSR330ILI/
***************
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 30 minute.
experiment encode accession: ENCSR330ILI
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB245YKS
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: ENCBS345MVS at ENCODE; https://www.encodeproject.org/ENCBS345MVS/


title: total RNA-seq from macrophage (ENCLB769UQR)

description:
https://www.encodeproject.org/experiments/ENCSR311OMP/
***************
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 10 minute.
experiment encode accession: ENCSR311OMP
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB769UQR
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: primary cell

value: nucleus

value: ENCBS636ZHP at ENCODE; https://www.encodeproject.org/ENCBS636ZHP/


title: total RNA-seq from macrophage (ENCLB169DAE)

description:
https://www.encodeproject.org/experiments/ENCSR464OLG/
***************
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 25 minute.
experiment encode accession: ENCSR464OLG
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB169DAE
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: not collected

value: ENCBS711KQD at ENCODE; https://www.encodeproject.org/ENCBS711KQD/


title: total RNA-seq from macrophage (ENCLB408AKL)

description:
https://www.encodeproject.org/experiments/ENCSR507OWX/
***************
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 15 minute.
experiment encode accession: ENCSR507OWX
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB408AKL
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: unknown

value: ENCBS349NKD at ENCODE; https://www.encodeproject.org/ENCBS349NKD/


title: total RNA-seq from macrophage (ENCLB147SBV)

description:
https://www.encodeproject.org/experiments/ENCSR507OWX/
***************
biological replicate number: 3
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 15 minute.
experiment encode accession: ENCSR507OWX
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB147SBV
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: Alexander Hoffmann, UCLA

value: ENCBS204MMP at ENCODE; https://www.encodeproject.org/ENCBS204MMP/


title: total RNA-seq from macrophage (ENCLB962TZG)

description:
https://www.encodeproject.org/experiments/ENCSR295PZT/
***************
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 40 minute.
experiment encode accession: ENCSR295PZT
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB962TZG
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: Alexander Hoffmann

value: ENCBS933JVU at ENCODE; https://www.encodeproject.org/ENCBS933JVU/


title: total RNA-seq from macrophage (ENCLB727WFQ)

description:
https://www.encodeproject.org/experiments/ENCSR403ING/
***************
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 20 minute.
experiment encode accession: ENCSR403ING
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB727WFQ
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: cytosol

value: ENCBS094WPV at ENCODE; https://www.encodeproject.org/ENCBS094WPV/


title: microRNA-seq from H1 (ENCLB004BYK)

description:
https://www.encodeproject.org/experiments/ENCSR588ZRK/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA Evaluation H1 hESC microRNA-seq from Mortazavi
experiment encode accession: ENCSR588ZRK
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB004BYK
size range: <30

source_name: Homo sapiens H1 cell line, preserved by flash-freezing

value: cell line

value: male

value: embryonic

value: Job Dekker, UMass

value: René Maehr

value: healthy

value: ENCBS719XQC at ENCODE; https://www.encodeproject.org/ENCBS719XQC/

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


title: total RNA-seq from macrophage (ENCLB037LDH)

description:
https://www.encodeproject.org/experiments/ENCSR330ILI/
***************
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 30 minute.
experiment encode accession: ENCSR330ILI
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB037LDH
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: chromatin

value: ENCBS128YRK at ENCODE; https://www.encodeproject.org/ENCBS128YRK/

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


title: total RNA-seq from macrophage (ENCLB598WPV)

description:
https://www.encodeproject.org/experiments/ENCSR504QOC/
***************
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 30 minute.
experiment encode accession: ENCSR504QOC
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB598WPV
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: nucleus

value: ENCBS155NRA at ENCODE; https://www.encodeproject.org/ENCBS155NRA/


title: total RNA-seq from macrophage (ENCLB010WVR)

description:
https://www.encodeproject.org/experiments/ENCSR515LYM/
***************
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 25 minute.
experiment encode accession: ENCSR515LYM
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB010WVR
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: ENCBS783TAE at ENCODE; https://www.encodeproject.org/ENCBS783TAE/


title: total RNA-seq from macrophage (ENCLB935HZH)

description:
https://www.encodeproject.org/experiments/ENCSR403ING/
***************
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 20 minute.
experiment encode accession: ENCSR403ING
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB935HZH
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: cytosol

value: ENCBS996NSP at ENCODE; https://www.encodeproject.org/ENCBS996NSP/


title: total RNA-seq from macrophage (ENCLB739JPH)

description:
https://www.encodeproject.org/experiments/ENCSR278PZG/
***************
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 50 minute.
experiment encode accession: ENCSR278PZG
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB739JPH
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS496FCB at ENCODE; https://www.encodeproject.org/ENCBS496FCB/


title: microRNA-seq from H1 (ENCLB498EYU)

description:
https://www.encodeproject.org/experiments/ENCSR588ZRK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation H1 hESC microRNA-seq from Mortazavi
experiment encode accession: ENCSR588ZRK
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB498EYU
size range: <30

value: cell line

value: male

value: embryonic

value: Job Dekker, UMass

value: René Maehr

value: healthy

value: ENCBS287SWH at ENCODE; https://www.encodeproject.org/ENCBS287SWH/


title: total RNA-seq from macrophage (ENCLB497HOQ)

description:
https://www.encodeproject.org/experiments/ENCSR272OBW/
***************
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 75 minute.
experiment encode accession: ENCSR272OBW
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB497HOQ
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: ENCBS191DWM at ENCODE; https://www.encodeproject.org/ENCBS191DWM/

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


title: total RNA-seq from macrophage (ENCLB945KQF)

description:
https://www.encodeproject.org/experiments/ENCSR278PZG/
***************
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 50 minute.
experiment encode accession: ENCSR278PZG
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB945KQF
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: nucleus

value: ENCBS069TWE at ENCODE; https://www.encodeproject.org/ENCBS069TWE/


title: total RNA-seq from macrophage (ENCLB269XJP)

description:
https://www.encodeproject.org/experiments/ENCSR282JJC/
***************
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 40 minute.
experiment encode accession: ENCSR282JJC
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB269XJP
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: cytosol

value: ENCBS277HRD at ENCODE; https://www.encodeproject.org/ENCBS277HRD/


title: total RNA-seq from macrophage (ENCLB624ABL)

description:
https://www.encodeproject.org/experiments/ENCSR247QSE/
***************
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 120 minute.
experiment encode accession: ENCSR247QSE
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB624ABL
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 250
nucleic acid starting quantity units: ng

value: chromatin

value: ENCBS946RSA at ENCODE; https://www.encodeproject.org/ENCBS946RSA/


title: polyA plus RNA-seq from macrophage (ENCLB392MKM)

description:
https://www.encodeproject.org/experiments/ENCSR164XXE/
***************
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 120 minutes.
experiment encode accession: ENCSR164XXE
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB392MKM
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 120 minutes

value: treatment_term_name:lipoprotein A; treatment_type:protein; duration:12; duration_units:hour; treatment_term_name:lipoprotein A; treatment_type:protein; duration:120; duration_units:minute;

value: ENCBS465YVX at ENCODE; https://www.encodeproject.org/ENCBS465YVX/


title: total RNA-seq from macrophage (ENCLB414STF)

description:
https://www.encodeproject.org/experiments/ENCSR269GXO/
***************
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 0 minute.
experiment encode accession: ENCSR269GXO
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB414STF
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: ENCBS630GLO at ENCODE; https://www.encodeproject.org/ENCBS630GLO/


title: total RNA-seq from macrophage (ENCLB882OJA)

description:
https://www.encodeproject.org/experiments/ENCSR294OOK/
***************
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 120 minute.
experiment encode accession: ENCSR294OOK
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB882OJA
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: macrophage

value: ENCBS013YIU at ENCODE; https://www.encodeproject.org/ENCBS013YIU/


title: total RNA-seq from macrophage (ENCLB439IYA)

description:
https://www.encodeproject.org/experiments/ENCSR272OBW/
***************
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 75 minute.
experiment encode accession: ENCSR272OBW
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB439IYA
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: primary cell

value: not collected

value: ENCBS285QEX at ENCODE; https://www.encodeproject.org/ENCBS285QEX/


title: total RNA-seq from macrophage (ENCLB281IKW)

description:
https://www.encodeproject.org/experiments/ENCSR282JJC/
***************
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 40 minute.
experiment encode accession: ENCSR282JJC
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB281IKW
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: unknown

value: ENCBS019YLT at ENCODE; https://www.encodeproject.org/ENCBS019YLT/

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


title: polyA plus RNA-seq from macrophage (ENCLB410INE)

description:
https://www.encodeproject.org/experiments/ENCSR195JXZ/
***************
biological replicate number: 4
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 for60 minutes.
experiment encode accession: ENCSR195JXZ
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB410INE
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 60 minutes

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: treatment_term_name:lipoprotein A; treatment_type:protein; duration:60; duration_units:minute;

value: ENCBS238LBZ at ENCODE; https://www.encodeproject.org/ENCBS238LBZ/


title: total RNA-seq from macrophage (ENCLB665LWF)

description:
https://www.encodeproject.org/experiments/ENCSR080COL/
***************
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 0 minute.
experiment encode accession: ENCSR080COL
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB665LWF
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: nucleus

value: ENCBS497MYE at ENCODE; https://www.encodeproject.org/ENCBS497MYE/


title: polyA plus RNA-seq from macrophage (ENCLB653TFM)

description:
https://www.encodeproject.org/experiments/ENCSR195JXZ/
***************
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 for60 minutes.
experiment encode accession: ENCSR195JXZ
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB653TFM
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS090IRO at ENCODE; https://www.encodeproject.org/ENCBS090IRO/


title: microRNA-seq from aorta (ENCLB905SXI)

description:
https://www.encodeproject.org/experiments/ENCSR586WVD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W73 aorta microRNA-seq from Mortazavi
experiment encode accession: ENCSR586WVD
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB905SXI
size range: <30

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

value: aorta

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: ENCBS759AII at ENCODE; https://www.encodeproject.org/ENCBS759AII/

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


title: total RNA-seq from macrophage (ENCLB028MWG)

description:
https://www.encodeproject.org/experiments/ENCSR156DUX/
***************
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 50 minute.
experiment encode accession: ENCSR156DUX
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB028MWG
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: ENCBS805ZZT at ENCODE; https://www.encodeproject.org/ENCBS805ZZT/

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


title: total RNA-seq from macrophage (ENCLB088WMN)

description:
https://www.encodeproject.org/experiments/ENCSR247QSE/
***************
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 120 minute.
experiment encode accession: ENCSR247QSE
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB088WMN
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: ENCBS379TSG at ENCODE; https://www.encodeproject.org/ENCBS379TSG/


title: total RNA-seq from macrophage (ENCLB293OTM)

description:
https://www.encodeproject.org/experiments/ENCSR314GIF/
***************
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 30 minute.
experiment encode accession: ENCSR314GIF
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB293OTM
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: nucleus

value: ENCBS835JMB at ENCODE; https://www.encodeproject.org/ENCBS835JMB/


title: total RNA-seq from macrophage (ENCLB295FGR)

description:
https://www.encodeproject.org/experiments/ENCSR159CPE/
***************
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 10 minute.
experiment encode accession: ENCSR159CPE
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB295FGR
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: ENCBS283IHP at ENCODE; https://www.encodeproject.org/ENCBS283IHP/


title: microRNA-seq from PC-3 (ENCLB666POM)

description:
https://www.encodeproject.org/experiments/ENCSR387TQN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation PC-3 microRNA-seq from Mortazavi
experiment encode accession: ENCSR387TQN
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-10-12
lab: Ali Mortazavi, UCI
library encode accession: ENCLB666POM
size range: <30

source_name: Homo sapiens PC-3 cell line

value: cell line

value: male

value: adult

value: 62 year

value: Mats Ljungman, UMichigan

value: ATCC

value: grade IV, adenocarcinoma

value: ENCBS555BGE at ENCODE; https://www.encodeproject.org/ENCBS555BGE/

value: Derived from ENCODE donor ENCDO349AAA; https://www.encodeproject.org/ENCDO349AAA/


title: total RNA-seq from macrophage (ENCLB842BWW)

description:
https://www.encodeproject.org/experiments/ENCSR159CPE/
***************
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 10 minute.
experiment encode accession: ENCSR159CPE
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB842BWW
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: ENCBS927FGX at ENCODE; https://www.encodeproject.org/ENCBS927FGX/


title: total RNA-seq from macrophage (ENCLB217IGD)

description:
https://www.encodeproject.org/experiments/ENCSR156DUX/
***************
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 50 minute.
experiment encode accession: ENCSR156DUX
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB217IGD
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: Alexander Hoffmann

value: nucleus

value: ENCBS983SIA at ENCODE; https://www.encodeproject.org/ENCBS983SIA/

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


title: polyA plus RNA-seq from macrophage (ENCLB031QAA)

description:
https://www.encodeproject.org/experiments/ENCSR164XXE/
***************
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 120 minutes.
experiment encode accession: ENCSR164XXE
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB031QAA
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:120; duration_units:minute;

value: ENCBS783NSH at ENCODE; https://www.encodeproject.org/ENCBS783NSH/


title: total RNA-seq from macrophage (ENCLB486NPI)

description:
https://www.encodeproject.org/experiments/ENCSR060ATH/
***************
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 50 minute.
experiment encode accession: ENCSR060ATH
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB486NPI
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: cytosol

value: ENCBS820SJO at ENCODE; https://www.encodeproject.org/ENCBS820SJO/


title: microRNA-seq from H1 (ENCLB806VWW)

description:
https://www.encodeproject.org/experiments/ENCSR588ZRK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation H1 hESC microRNA-seq from Mortazavi
experiment encode accession: ENCSR588ZRK
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB806VWW
size range: <30

value: cell line

value: male

value: embryonic

value: Job Dekker, UMass

value: René Maehr

value: healthy

value: ENCBS584QDY at ENCODE; https://www.encodeproject.org/ENCBS584QDY/

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


title: microRNA-seq from right cardiac atrium (ENCLB914VDL)

description:
https://www.encodeproject.org/experiments/ENCSR495VFH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W78 right cardiac atrium microRNA-seq from Mortazavi
experiment encode accession: ENCSR495VFH
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-10-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB914VDL
size range: <30

source_name: Homo sapiens male adult (60 years) right cardiac atrium tissue, preserved by flash-freezing

value: right cardiac atrium

value: tissue

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: ENCBS271WJL at ENCODE; https://www.encodeproject.org/ENCBS271WJL/

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


title: total RNA-seq from macrophage (ENCLB283WZX)

description:
https://www.encodeproject.org/experiments/ENCSR153YLH/
***************
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 50 minute.
experiment encode accession: ENCSR153YLH
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB283WZX
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: Alexander Hoffmann

value: chromatin

value: ENCBS261TAC at ENCODE; https://www.encodeproject.org/ENCBS261TAC/

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


title: total RNA-seq from macrophage (ENCLB906QOL)

description:
https://www.encodeproject.org/experiments/ENCSR153YLH/
***************
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 50 minute.
experiment encode accession: ENCSR153YLH
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB906QOL
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 250
nucleic acid starting quantity units: ng

value: ENCBS979ZGH at ENCODE; https://www.encodeproject.org/ENCBS979ZGH/


title: total RNA-seq from macrophage (ENCLB921ZQO)

description:
https://www.encodeproject.org/experiments/ENCSR060ATH/
***************
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 50 minute.
experiment encode accession: ENCSR060ATH
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB921ZQO
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: cytosol

value: ENCBS771RMW at ENCODE; https://www.encodeproject.org/ENCBS771RMW/


title: total RNA-seq from macrophage (ENCLB674XSY)

description:
https://www.encodeproject.org/experiments/ENCSR059NPM/
***************
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 0 minute.
experiment encode accession: ENCSR059NPM
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB674XSY
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS013RHI at ENCODE; https://www.encodeproject.org/ENCBS013RHI/


title: total RNA-seq from macrophage (ENCLB214CKQ)

description:
https://www.encodeproject.org/experiments/ENCSR060ATH/
***************
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 50 minute.
experiment encode accession: ENCSR060ATH
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB214CKQ
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS089KWK at ENCODE; https://www.encodeproject.org/ENCBS089KWK/


title: total RNA-seq from macrophage (ENCLB780SRK)

description:
https://www.encodeproject.org/experiments/ENCSR232TFT/
***************
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 15 minute.
experiment encode accession: ENCSR232TFT
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB780SRK
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS066TKM at ENCODE; https://www.encodeproject.org/ENCBS066TKM/


title: total RNA-seq from macrophage (ENCLB102ZZA)

description:
https://www.encodeproject.org/experiments/ENCSR059NPM/
***************
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 0 minute.
experiment encode accession: ENCSR059NPM
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB102ZZA
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS677ANR at ENCODE; https://www.encodeproject.org/ENCBS677ANR/


title: total RNA-seq from macrophage (ENCLB343XPP)

description:
https://www.encodeproject.org/experiments/ENCSR140QWR/
***************
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 50 minute.
experiment encode accession: ENCSR140QWR
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB343XPP
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 250
nucleic acid starting quantity units: ng

value: ENCBS349KMF at ENCODE; https://www.encodeproject.org/ENCBS349KMF/


title: total RNA-seq from macrophage (ENCLB746QPZ)

description:
https://www.encodeproject.org/experiments/ENCSR224FMP/
***************
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 25 minute.
experiment encode accession: ENCSR224FMP
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB746QPZ
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: macrophage

value: ENCBS608FQO at ENCODE; https://www.encodeproject.org/ENCBS608FQO/


title: total RNA-seq from macrophage (ENCLB495WJS)

description:
https://www.encodeproject.org/experiments/ENCSR232TFT/
***************
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 15 minute.
experiment encode accession: ENCSR232TFT
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB495WJS
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: primary cell

value: not collected

value: ENCBS186SVJ at ENCODE; https://www.encodeproject.org/ENCBS186SVJ/


title: total RNA-seq from macrophage (ENCLB916DNN)

description:
https://www.encodeproject.org/experiments/ENCSR140QWR/
***************
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 50 minute.
experiment encode accession: ENCSR140QWR
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB916DNN
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: ENCBS297NWF at ENCODE; https://www.encodeproject.org/ENCBS297NWF/


title: microRNA-seq from left colon (ENCLB460RFP)

description:
https://www.encodeproject.org/experiments/ENCSR591GQG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W72 left colon microRNA-seq from Mortazavi
experiment encode accession: ENCSR591GQG
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-10-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB460RFP
size range: <30

source_name: Homo sapiens female adult (46 years) left colon tissue, preserved by flash-freezing

value: left colon

value: tissue

value: female

value: adult

value: 46 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

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

value: ENCBS009KPO at ENCODE; https://www.encodeproject.org/ENCBS009KPO/

value: Derived from ENCODE donor ENCDO411EVD; https://www.encodeproject.org/ENCDO411EVD/


title: total RNA-seq from macrophage (ENCLB408FNM)

description:
https://www.encodeproject.org/experiments/ENCSR112SFD/
***************
biological replicate number: 3
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 15 minute.
experiment encode accession: ENCSR112SFD
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB408FNM
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: nucleus

value: ENCBS575SMT at ENCODE; https://www.encodeproject.org/ENCBS575SMT/

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


title: total RNA-seq from macrophage (ENCLB871JRA)

description:
https://www.encodeproject.org/experiments/ENCSR029TSM/
***************
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 10 minute.
experiment encode accession: ENCSR029TSM
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB871JRA
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: cytosol

value: ENCBS584PXA at ENCODE; https://www.encodeproject.org/ENCBS584PXA/


title: total RNA-seq from macrophage (ENCLB693HZY)

description:
https://www.encodeproject.org/experiments/ENCSR219DFA/
***************
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 10 minute.
experiment encode accession: ENCSR219DFA
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB693HZY
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: ENCBS105BSR at ENCODE; https://www.encodeproject.org/ENCBS105BSR/


title: total RNA-seq from macrophage (ENCLB473GND)

description:
https://www.encodeproject.org/experiments/ENCSR224FMP/
***************
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 25 minute.
experiment encode accession: ENCSR224FMP
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB473GND
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS331CTN at ENCODE; https://www.encodeproject.org/ENCBS331CTN/


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB607NYP)

description:
https://www.encodeproject.org/experiments/ENCSR469QEM/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR469QEM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR934ZBY
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB607NYP
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: 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: total RNA-seq from macrophage (ENCLB786FGA)

description:
https://www.encodeproject.org/experiments/ENCSR040LSC/
***************
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 15 minute.
experiment encode accession: ENCSR040LSC
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB786FGA
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: primary cell

value: chromatin

value: ENCBS970MAG at ENCODE; https://www.encodeproject.org/ENCBS970MAG/


title: total RNA-seq from macrophage (ENCLB134BEE)

description:
https://www.encodeproject.org/experiments/ENCSR008YAY/
***************
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 30 minute.
experiment encode accession: ENCSR008YAY
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB134BEE
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: ENCBS407PJC at ENCODE; https://www.encodeproject.org/ENCBS407PJC/

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


title: total RNA-seq from macrophage (ENCLB715WNV)

description:
https://www.encodeproject.org/experiments/ENCSR029TSM/
***************
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 10 minute.
experiment encode accession: ENCSR029TSM
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB715WNV
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: ENCBS151SFV at ENCODE; https://www.encodeproject.org/ENCBS151SFV/


title: microRNA-seq from heart left ventricle (ENCLB843RZV)

description:
https://www.encodeproject.org/experiments/ENCSR482MHU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W73 heart left ventricle microRNA-seq from Mortazavi
experiment encode accession: ENCSR482MHU
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-10-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB843RZV
size range: <30

source_name: Homo sapiens female adult (59 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

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: ENCBS692CKU at ENCODE; https://www.encodeproject.org/ENCBS692CKU/

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


title: total RNA-seq from macrophage (ENCLB502MVP)

description:
https://www.encodeproject.org/experiments/ENCSR224FMP/
***************
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 25 minute.
experiment encode accession: ENCSR224FMP
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB502MVP
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: ENCBS592ZLF at ENCODE; https://www.encodeproject.org/ENCBS592ZLF/


title: total RNA-seq from macrophage (ENCLB031TCF)

description:
https://www.encodeproject.org/experiments/ENCSR125BYY/
***************
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 50 minute.
experiment encode accession: ENCSR125BYY
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB031TCF
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: cytosol

value: ENCBS166IQB at ENCODE; https://www.encodeproject.org/ENCBS166IQB/

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


title: total RNA-seq from macrophage (ENCLB853WJT)

description:
https://www.encodeproject.org/experiments/ENCSR125BYY/
***************
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 50 minute.
experiment encode accession: ENCSR125BYY
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB853WJT
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS325SHO at ENCODE; https://www.encodeproject.org/ENCBS325SHO/


title: total RNA-seq from macrophage (ENCLB377VLG)

description:
https://www.encodeproject.org/experiments/ENCSR107TKJ/
***************
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 90 minute.
experiment encode accession: ENCSR107TKJ
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB377VLG
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: nucleus

value: ENCBS617VHE at ENCODE; https://www.encodeproject.org/ENCBS617VHE/


title: microRNA-seq from GM12878 (ENCLB416JYO)

description:
https://www.encodeproject.org/experiments/ENCSR466AZX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation GM12878 microRNA-seq from Mortazavi
experiment encode accession: ENCSR466AZX
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-06-11
lab: Ali Mortazavi, UCI
library encode accession: ENCLB416JYO
size range: <30

source_name: Homo sapiens GM12878 cell line

value: cell line

value: female

value: adult

value: Mats Ljungman, UMichigan

value: Coriell

value: ENCBS975OUN at ENCODE; https://www.encodeproject.org/ENCBS975OUN/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: total RNA-seq from macrophage (ENCLB898VFY)

description:
https://www.encodeproject.org/experiments/ENCSR232TFT/
***************
biological replicate number: 4
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 15 minute.
experiment encode accession: ENCSR232TFT
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB898VFY
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: ENCBS403KZT at ENCODE; https://www.encodeproject.org/ENCBS403KZT/


title: total RNA-seq from macrophage (ENCLB823OJP)

description:
https://www.encodeproject.org/experiments/ENCSR008YAY/
***************
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 30 minute.
experiment encode accession: ENCSR008YAY
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB823OJP
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: cytosol

value: ENCBS222BJG at ENCODE; https://www.encodeproject.org/ENCBS222BJG/


title: eCLIP from K562 (ENCLB355VZJ)

description:
https://www.encodeproject.org/experiments/ENCSR999YGP/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against GRWD1
experiment encode accession: ENCSR999YGP
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR251FMT
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB355VZJ
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

value: 53 year

value: chronic myelogenous leukemia (CML)

tag: passage number

value: Gene Yeo, UCSD

value: ENCBS175JIH at ENCODE; https://www.encodeproject.org/ENCBS175JIH/

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

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

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: total RNA-seq from macrophage (ENCLB467VIB)

description:
https://www.encodeproject.org/experiments/ENCSR125BYY/
***************
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 50 minute.
experiment encode accession: ENCSR125BYY
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB467VIB
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS541PYB at ENCODE; https://www.encodeproject.org/ENCBS541PYB/

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


title: microRNA-seq from cardiac septum (ENCLB642MSL)

description:
https://www.encodeproject.org/experiments/ENCSR373HRP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W61 cardiac septum microRNA-seq from Mortazavi
experiment encode accession: ENCSR373HRP
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-10-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB642MSL
size range: <30

source_name: Homo sapiens female adult (41 years) cardiac septum tissue

value: cardiac septum

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: ENCBS731WFT at ENCODE; https://www.encodeproject.org/ENCBS731WFT/

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


title: eCLIP from K562 (ENCLB813LYA)

description:
https://www.encodeproject.org/experiments/ENCSR999YGP/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against GRWD1
experiment encode accession: ENCSR999YGP
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR251FMT
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB813LYA
fragmentation methods: see document
size range: 175-300

value: cell line

value: 53 year

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

value: ENCBS505ILK at ENCODE; https://www.encodeproject.org/ENCBS505ILK/


title: total RNA-seq from macrophage (ENCLB049ARI)

description:
https://www.encodeproject.org/experiments/ENCSR112SFD/
***************
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 15 minute.
experiment encode accession: ENCSR112SFD
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB049ARI
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

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

value: macrophage

value: primary cell

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: nucleus

value: ENCBS148CQJ at ENCODE; https://www.encodeproject.org/ENCBS148CQJ/


title: eCLIP from K562 (ENCLB303DXO)

description:
https://www.encodeproject.org/experiments/ENCSR891RIC/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against NIPBL
experiment encode accession: ENCSR891RIC
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR816NVJ
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB303DXO
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 cell line

value: NIPBL

value: female

value: adult

value: ATCC

value: ENCBS344MAK at ENCODE; https://www.encodeproject.org/ENCBS344MAK/

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


title: TF ChIP-seq from K562 (ENCLB129FDC)

description:
https://www.encodeproject.org/experiments/ENCSR987KYK/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF717 ChIP-seq on human K562
experiment encode accession: ENCSR987KYK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR501CEJ, ENCSR012KTG
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB129FDC
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ZNF717

value: cell line

value: 53 year

value: Michael Snyder, Stanford

value: ENCBS530DRM at ENCODE; https://www.encodeproject.org/ENCBS530DRM/


title: total RNA-seq from macrophage (ENCLB263DCH)

description:
https://www.encodeproject.org/experiments/ENCSR040LSC/
***************
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 15 minute.
experiment encode accession: ENCSR040LSC
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB263DCH
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: chromatin

value: ENCBS967FJT at ENCODE; https://www.encodeproject.org/ENCBS967FJT/

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


title: eCLIP from K562 (ENCLB434SDQ)

description:
https://www.encodeproject.org/experiments/ENCSR891RIC/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against NIPBL
experiment encode accession: ENCSR891RIC
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR816NVJ
encode release date: 2018-08-30
lab: Gene Yeo, UCSD
library encode accession: ENCLB434SDQ
fragmentation methods: see document
size range: 175-300

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

value: ENCBS839QBD at ENCODE; https://www.encodeproject.org/ENCBS839QBD/