title: snRNA-seq from left cerebral cortex (ENCLB766ZBL)

description:
https://www.encodeproject.org/experiments/ENCSR632EIK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR632EIK
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB766ZBL
fragmentation methods: see document
size range: 300-600

value: left cerebral cortex

tag: biosample encode accession

value: Michael Snyder, Stanford

value: ENCBS940SLP at ENCODE; https://www.encodeproject.org/ENCBS940SLP/


title: B.fo.IL1b.Sp_1

status: Public on Jan 14 2025

type: SRA

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

country: USA

institute: Harvard Medical School

library_source: transcriptomic

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Peritoneal Cavity

extract_protocol:
At 2 hours post-injection, 1,000 cells of the 14 immune cell-types from spleen and peritoneal cavity were double-sorted in 5uL of TCL Buffer (QIAGEN) containing 1% 2-mercaptoethanol (Sigma) by BD FACS Aria
Library construction and sequencing and data processing were performed according to the standard Immunological Genome Project protocols (https://www.immgen.org/img/Protocols/ImmGenULI_RNAseq_methods.pdf)

treatment_protocol: 5-8 week old C57Bl/6J mice shipped from the Jackson Laboratory, Bar Harbor. Mice were injected intravenously with either a free cytokine (5ug of IL1b, IL6 or TNFa in 120uL of PBS)  or PBS (120uL).

tag: tissue

value: Peritoneal Cavity

tag: cell type

tag: strain

tag: treatment


title: snRNA-seq from lung (ENCLB814PUF)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR225OII/
***************
biological replicate number: 1
technical replicate number: 1
description: snRNA on human lung. Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR083HFN)
experiment encode accession: ENCSR225OII
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB814PUF
size range: 300-600
spikeins used: Illumina PhiX sequencing control

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

organism: Homo sapiens

source_name: Homo sapiens female adult (47 years) lung tissue, preserved by flash-freezing nuclear fraction

value: lung

value: tissue

tag: Sex

value: female

tag: health state

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

tag: dev stage

value: adult

tag: age

value: 47 year

tag: lab

tag: subcellular fraction term name

value: nucleus

tag: source

value: Yiing Lin, MD, PhD

tag: link

value: ENCBS709MGO at ENCODE; https://www.encodeproject.org/ENCBS709MGO/

value: Derived from ENCODE donor ENCDO528BHB; https://www.encodeproject.org/ENCDO528BHB/


title: snRNA-seq from adrenal gland (ENCLB442AMV)

description:
https://www.encodeproject.org/experiments/ENCSR749GDE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR749GDE
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB442AMV
fragmentation methods: see document
size range: 300-600

source_name: Mus musculus strain B6CASTF1/J adrenal gland tissue nuclear fraction

value: adrenal gland

value: not collected

value: The Jackson Laboratory

value: ENCBS277UYJ at ENCODE; https://www.encodeproject.org/ENCBS277UYJ/

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


title: snRNA-seq from left cerebral cortex (ENCLB063XDV)

description:
https://www.encodeproject.org/experiments/ENCSR624WDN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR624WDN
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB063XDV
fragmentation methods: see document
size range: 300-600

source_name: Mus musculus strain B6CASTF1/J cerebral cortex tissue nuclear fraction

value: left cerebral cortex

value: Michael Snyder, Stanford

value: ENCBS275KKA at ENCODE; https://www.encodeproject.org/ENCBS275KKA/


title: 701168541

city: Doha

first: Darawan

last: Rinchai

state: Qatar

address: Al Gharrafa St

department: Research

country: Qatar

institute: Sidra Medicine

data_processing:
All FASTQ passed QC and were aligned to the reference genome GRChg38 using STAR 2.7.9a. BAM files were converted to a raw count expression matrix using HTSeq-count
Assembly: GRChg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: blood

extract_protocol:
RNA was extracted using the Tempus Spin RNA Isolation Kit (ThermoFisher), which was adapted for the handling of small blood volumes. Contaminating DNA was removed using the TurboDNAse kit (ThermoFisher), and RNA was quantitated on a Qubit instrument (ThermoFisher) and QCed using an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, California, USA).
mRNA-sequencing was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (75 single-end)

tag: time

tag: vaccine dose

value: THIRD

value: Fingerstick

value: blood


title: snRNA-seq from heart left ventricle (ENCLB507KDD)

description:
https://www.encodeproject.org/experiments/ENCSR204RHR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR204RHR
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB507KDD
size range: 300-600

source_name: Homo sapiens male adult (68 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

tag: description

value: Homo sapiens heart left ventricle tissue

value: male

value: ischemic

value: adult

value: 68 year

value: Shin Lin

value: ENCBS623RZE at ENCODE; https://www.encodeproject.org/ENCBS623RZE/

value: Derived from ENCODE donor ENCDO239INK; https://www.encodeproject.org/ENCDO239INK/


title: Control eCLIP from K562 (ENCLB044CBL)

description:
https://www.encodeproject.org/experiments/ENCSR058PIY/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP control experiment on K562 against DDX47
experiment encode accession: ENCSR058PIY
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB044CBL
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 cell line

tag: line

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

tag: passage number

value: Gene Yeo, UCSD

value: ATCC

tag: collection date

value: not applicable

tag: geographic location

value: ENCBS177POD at ENCODE; https://www.encodeproject.org/ENCBS177POD/


title: snRNA-seq from heart (ENCLB807HIR)

description:
https://www.encodeproject.org/experiments/ENCSR568GGW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR568GGW
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB807HIR
fragmentation methods: see document
size range: 300-600

source_name: Mus musculus strain B6CASTF1/J heart tissue nuclear fraction

value: heart

value: tissue

tag: biosample encode accession

value: not collected

value: Michael Snyder, Stanford

value: nucleus

value: The Jackson Laboratory

value: ENCBS815YOH at ENCODE; https://www.encodeproject.org/ENCBS815YOH/

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


title: 701168531

value: THIRD

value: Fingerstick

tag: tissue

value: blood


title: B.fo.PBS.Sp_5

value: Peritoneal Cavity

tag: cell type

tag: strain

tag: treatment

value: PBS


title: snRNA-seq from heart left ventricle (ENCLB863YCR)

description:
https://www.encodeproject.org/experiments/ENCSR203YOV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR203YOV
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB863YCR
size range: 300-600

source_name: Homo sapiens male adult (69 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: Homo sapiens heart left ventricle tissue

tag: Sex

value: male

tag: health state

value: ischemic

tag: dev stage

value: adult

tag: age

value: 69 year

value: Shin Lin

value: ENCBS432XFE at ENCODE; https://www.encodeproject.org/ENCBS432XFE/

value: Derived from ENCODE donor ENCDO737TEG; https://www.encodeproject.org/ENCDO737TEG/


title: B.fo.PBS.Sp_4


title: 701168521

tag: source


title: snRNA-seq from layer of hippocampus (ENCLB320HXY)

description:
https://www.encodeproject.org/experiments/ENCSR539XHZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR539XHZ
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB320HXY
fragmentation methods: see document
size range: 300-600

source_name: Mus musculus strain B6CASTF1/J layer of hippocampus tissue nuclear fraction

value: layer of hippocampus

value: tissue

value: not collected

tag: lab

value: Michael Snyder, Stanford

tag: subcellular fraction term name

value: nucleus

value: The Jackson Laboratory

tag: link

value: ENCBS432HEQ at ENCODE; https://www.encodeproject.org/ENCBS432HEQ/


title: snRNA-seq from heart (ENCLB560GBC)

description:
https://www.encodeproject.org/experiments/ENCSR665HPR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR665HPR
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB560GBC
fragmentation methods: none
size range: 300-800

source_name: Mus musculus strain B6CASTF1/J female (2 months) heart tissue nuclear fraction

value: heart

tag: description

value: Encode B6CastF1 2 months female #1 Heart

value: female

value: 2 month

value: Barbara Wold, Caltech

value: ENCBS834GBM at ENCODE; https://www.encodeproject.org/ENCBS834GBM/

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


title: snRNA-seq from heart (ENCLB608YNH)

description:
https://www.encodeproject.org/experiments/ENCSR533IGQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR533IGQ
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB608YNH
fragmentation methods: see document
size range: 300-600

value: ENCBS799OFC at ENCODE; https://www.encodeproject.org/ENCBS799OFC/


title: B.fo.PBS.Sp_3

value: Peritoneal Cavity

value: PBS


title: snRNA-seq from mucosa of gallbladder (ENCLB802MGH)

description:
https://www.encodeproject.org/experiments/ENCSR201WJO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR201WJO
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB802MGH
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens female child (16 years) mucosa of gallbladder tissue, preserved by cryopreservation nuclear fraction

value: mucosa of gallbladder

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

value: child

value: 16 year

value: Yiing Lin, MD, PhD

value: not applicable

value: ENCBS456NHC at ENCODE; https://www.encodeproject.org/ENCBS456NHC/


title: snRNA-seq from gastrocnemius (ENCLB320ZLU)

description:
https://www.encodeproject.org/experiments/ENCSR478PUL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR478PUL
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB320ZLU
fragmentation methods: see document
size range: 300-600

source_name: Mus musculus strain B6CASTF1/J gastrocnemius tissue nuclear fraction

value: gastrocnemius

value: tissue

value: not collected

value: Michael Snyder, Stanford

value: nucleus

value: The Jackson Laboratory

value: ENCBS234LLL at ENCODE; https://www.encodeproject.org/ENCBS234LLL/


title: B.fo.PBS.Sp_1


title: 701168511

tag: time

tag: vaccine dose

value: THIRD

value: Fingerstick

value: blood


title: snRNA-seq from liver (ENCLB540OBF)

description:
https://www.encodeproject.org/experiments/ENCSR192UEL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR192UEL
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2023-03-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB540OBF
size range: 300-600

source_name: Homo sapiens male adult (41 years) liver tissue, preserved by flash-freezing nuclear fraction

value: liver

tag: note

value: Homo sapiens liver tissue?

value: male

value: healthy

value: adult

value: 41 year

tag: collection date

tag: geographic location

value: ENCBS227ZRJ at ENCODE; https://www.encodeproject.org/ENCBS227ZRJ/


title: snRNA-seq from psoas muscle (ENCLB592LXS)

description:
https://www.encodeproject.org/experiments/ENCSR203THX/
***************
biological replicate number: 1
technical replicate number: 1
description: Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR916EDP).
experiment encode accession: ENCSR203THX
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB592LXS
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens female adult (41 years) psoas muscle tissue, preserved by flash-freezing nuclear fraction

value: psoas muscle

tag: biosample encode accession

value: female

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

value: Yiing Lin, MD, PhD

value: ENCBS345CVS at ENCODE; https://www.encodeproject.org/ENCBS345CVS/

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


title: snRNA-seq from heart left ventricle (ENCLB529BXD)

description:
https://www.encodeproject.org/experiments/ENCSR190TRK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR190TRK
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB529BXD
size range: 300-600

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

value: heart left ventricle

value: tissue

value: Homo sapiens heart left ventricle tissue

value: non ischemic (EF 33%, LVEDD 6.8), familial

value: 59 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS578OEH at ENCODE; https://www.encodeproject.org/ENCBS578OEH/

value: Derived from ENCODE donor ENCDO522PCG; https://www.encodeproject.org/ENCDO522PCG/


title: 701168551

value: THIRD

value: Fingerstick

tag: tissue

value: blood


title: MZB.TNFa.Sp_3

value: Peritoneal Cavity

tag: cell type

value: MZB

tag: strain

tag: treatment

value: TNFa


title: 701168681


title: MZB.TNFa.Sp_2


title: snRNA-seq from heart left ventricle (ENCLB872TNB)

description:
https://www.encodeproject.org/experiments/ENCSR176WWW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR176WWW
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-08-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB872TNB
size range: 300-600

source_name: Homo sapiens female adult (25 years) heart left ventricle tissue, preserved by flash-freezing

tag: Sex

value: female

tag: dev stage

value: adult

value: 25 year

tag: health state

value: healthy

value: ENCBS186SQI at ENCODE; https://www.encodeproject.org/ENCBS186SQI/

value: Derived from ENCODE donor ENCDO607DMC; https://www.encodeproject.org/ENCDO607DMC/


title: snRNA-seq from gastrocnemius (ENCLB854VKF)

description:
https://www.encodeproject.org/experiments/ENCSR438FRT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR438FRT
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB854VKF
fragmentation methods: see document
size range: 300-600

value: gastrocnemius

value: tissue

value: not collected

tag: age

tag: lab

value: nucleus

tag: source

value: The Jackson Laboratory

value: ENCBS306WRP at ENCODE; https://www.encodeproject.org/ENCBS306WRP/

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


title: 701126251

value: THIRD

value: Fingerstick

value: blood


title: MZB.TNFa.Sp_1

source_name: Peritoneal Cavity

value: Peritoneal Cavity

value: MZB

value: TNFa


title: snRNA-seq from heart (ENCLB713ETA)

description:
https://www.encodeproject.org/experiments/ENCSR462HCD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR462HCD
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB713ETA
fragmentation methods: none
size range: 300-800

source_name: Mus musculus strain B6CASTF1/J male (2 months) heart tissue nuclear fraction

value: heart

tag: description

value: Encode B6CastF1 2 months male #1 Heart

value: male

value: 2 month

value: Barbara Wold, Caltech

tag: subcellular fraction term name

tag: link

value: ENCBS405XFL at ENCODE; https://www.encodeproject.org/ENCBS405XFL/


title: 701126241

tag: time

tag: vaccine dose


title: B.fo.PBS.Sp_2

value: PBS


title: snRNA-seq from left cerebral cortex (ENCLB432ZEQ)

description:
https://www.encodeproject.org/experiments/ENCSR421YXX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR421YXX
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB432ZEQ
fragmentation methods: see document
size range: 300-600

source_name: Mus musculus strain B6CASTF1/J male (2 months) left cerebral cortex tissue nuclear fraction

value: left cerebral cortex

value: tissue

value: Encode B6CastF1 2 months male #1 L. Cortex

value: not collected

value: nucleus

value: ENCBS180GAM at ENCODE; https://www.encodeproject.org/ENCBS180GAM/


title: MZB.IL6.Sp_3


title: snRNA-seq from heart (ENCLB119RYO)

description:
https://www.encodeproject.org/experiments/ENCSR170SFR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR170SFR
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2024-02-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB119RYO
size range: 300-600

source_name: Homo sapiens male embryo (103 days) heart tissue, preserved by flash-freezing nuclear fraction

tag: note

value: Homo sapiens heart tissue

value: embryonic

value: 103 day

value: Michael Snyder, Stanford

value: BDRL

tag: collection date

value: not applicable

tag: geographic location

value: ENCBS452UFQ at ENCODE; https://www.encodeproject.org/ENCBS452UFQ/


title: 701168691

source_name: blood

value: THIRD

value: Fingerstick

tag: tissue

value: blood


title: MZB.IL6.Sp_2

value: Peritoneal Cavity

tag: cell type

value: MZB

tag: strain


title: 701126221


title: snRNA-seq from heart left ventricle (ENCLB433LMI)

description:
https://www.encodeproject.org/experiments/ENCSR157FDD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR157FDD
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB433LMI
size range: 300-600

source_name: Homo sapiens male adult (30 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

value: Homo sapiens heart left ventricle tissue

tag: biosample encode accession

tag: Sex

value: male

value: healthy

value: adult

value: 30 year

value: Shin Lin

value: ENCBS397INF at ENCODE; https://www.encodeproject.org/ENCBS397INF/

value: Derived from ENCODE donor ENCDO751PQQ; https://www.encodeproject.org/ENCDO751PQQ/


title: snRNA-seq from heart left ventricle (ENCLB861GQS)

description:
https://www.encodeproject.org/experiments/ENCSR175TRJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR175TRJ
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB861GQS
size range: 300-600

source_name: Homo sapiens male adult (61 years) heart left ventricle tissue, preserved by flash-freezing

tag: health state

value: nonischemic (EF 23%, LVEDD 6.5)

tag: dev stage

value: 61 year

value: Michael Snyder, Stanford

value: ENCBS346JJG at ENCODE; https://www.encodeproject.org/ENCBS346JJG/

value: Derived from ENCODE donor ENCDO229CTV; https://www.encodeproject.org/ENCDO229CTV/


title: snRNA-seq from heart (ENCLB808STP)

description:
https://www.encodeproject.org/experiments/ENCSR415HEP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR415HEP
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB808STP
fragmentation methods: see document
size range: 300-600

source_name: Mus musculus strain B6CASTF1/J heart tissue nuclear fraction

value: heart

value: not collected

tag: age

tag: lab

value: nucleus

value: The Jackson Laboratory

value: ENCBS556ZMG at ENCODE; https://www.encodeproject.org/ENCBS556ZMG/

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


title: snRNA-seq from heart (ENCLB871PHY)

description:
https://www.encodeproject.org/experiments/ENCSR417FCM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR417FCM
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB871PHY
fragmentation methods: none
size range: 300-800

value: tissue

tag: description

value: Encode B6CastF1 2 months female #2 Heart

value: female

value: 2 month

value: Barbara Wold, Caltech

tag: source

value: ENCBS019YAH at ENCODE; https://www.encodeproject.org/ENCBS019YAH/


title: MZB.IL6.Sp_1

value: Peritoneal Cavity

value: MZB

tag: treatment


title: 701126211

tag: time

value: THIRD

value: Fingerstick

value: blood


title: MZB.IL1b.Sp_3


title: snRNA-seq from adrenal gland (ENCLB069PRB)

description:
https://www.encodeproject.org/experiments/ENCSR402PHR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR402PHR
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB069PRB
fragmentation methods: see document
size range: 300-600

source_name: Mus musculus strain B6CASTF1/J adrenal gland tissue, preserved by flash-freezing nuclear fraction

value: adrenal gland

value: Michael Snyder, Stanford

tag: subcellular fraction term name

tag: link

value: ENCBS577ZNJ at ENCODE; https://www.encodeproject.org/ENCBS577ZNJ/


title: snRNA-seq from upper lobe of right lung (ENCLB228GCE)

description:
https://www.encodeproject.org/experiments/ENCSR142RRV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR142RRV
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB228GCE
fragmentation methods: none
size range: 300-800

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

value: upper lobe of right lung

value: male

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

value: adult

value: 60 year

value: nucleus

value: Yiing Lin, MD, PhD

tag: collection date

value: not applicable

value: ENCBS046YEZ at ENCODE; https://www.encodeproject.org/ENCBS046YEZ/


title: 701126201

tag: vaccine dose


title: MZB.IL1b.Sp_2

tag: tissue

value: Peritoneal Cavity


title: snRNA-seq from Right ventricle myocardium inferior (ENCLB297FDO)

description:
https://www.encodeproject.org/experiments/ENCSR151ONW/
***************
biological replicate number: 1
technical replicate number: 1
description: snRNA on human right ventricle myocardium inferior. Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR628POB)
experiment encode accession: ENCSR151ONW
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB297FDO
size range: 300-600
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens male adult (60 years) Right ventricle myocardium inferior tissue, preserved by flash-freezing nuclear fraction

value: Right ventricle myocardium inferior

value: tissue

value: ENCBS397MLS at ENCODE; https://www.encodeproject.org/ENCBS397MLS/

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


title: snRNA-seq from left cerebral cortex (ENCLB807VEG)

description:
https://www.encodeproject.org/experiments/ENCSR467GGT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR467GGT
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB807VEG
fragmentation methods: see document
size range: 300-600

source_name: Mus musculus strain B6CASTF1/J female (2 months) left cerebral cortex tissue nuclear fraction

value: left cerebral cortex

value: Encode B6CastF1 2 months female #1 L. Cortex

value: female

value: not collected

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS680HBI at ENCODE; https://www.encodeproject.org/ENCBS680HBI/

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


title: MZB.IL1b.Sp_1

tag: cell type

value: MZB


title: 701126191

value: THIRD

value: Fingerstick

value: blood


title: snRNA-seq from heart (ENCLB866MAL)

description:
https://www.encodeproject.org/experiments/ENCSR333SLJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR333SLJ
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB866MAL
fragmentation methods: see document
size range: 300-600

value: heart

value: Michael Snyder, Stanford

value: nucleus

value: ENCBS008VIL at ENCODE; https://www.encodeproject.org/ENCBS008VIL/


title: 701126171


title: 701126181


title: snRNA-seq from heart left ventricle (ENCLB001JCO)

description:
https://www.encodeproject.org/experiments/ENCSR138JCM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR138JCM
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-09-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB001JCO
size range: 300-600

source_name: Homo sapiens female adult (69 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

value: Homo sapiens heart left ventricle tissue

value: adult

value: 69 year

value: Shin Lin

value: sarcoid (EF 24%, LVEDD 6.9, PWd 0.6)

value: ENCBS692UAY at ENCODE; https://www.encodeproject.org/ENCBS692UAY/

value: Derived from ENCODE donor ENCDO695LFW; https://www.encodeproject.org/ENCDO695LFW/


title: snRNA-seq from adrenal gland (ENCLB495DSX)

description:
https://www.encodeproject.org/experiments/ENCSR356VJZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR356VJZ
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB495DSX
fragmentation methods: see document
size range: 300-600

source_name: Mus musculus strain B6CASTF1/J adrenal gland tissue nuclear fraction

value: adrenal gland

value: not collected

value: The Jackson Laboratory

value: ENCBS941IRK at ENCODE; https://www.encodeproject.org/ENCBS941IRK/

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


title: snRNA-seq from adrenal gland (ENCLB607FDJ)

description:
https://www.encodeproject.org/experiments/ENCSR224OUG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR224OUG
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB607FDJ
fragmentation methods: see document
size range: 300-600

value: Michael Snyder, Stanford

value: ENCBS396SGF at ENCODE; https://www.encodeproject.org/ENCBS396SGF/


title: 701126231

value: THIRD

value: Fingerstick

value: blood


title: MZB.PBS.Sp_4

value: Peritoneal Cavity

value: MZB

tag: strain

value: PBS


title: snRNA-seq from heart left ventricle (ENCLB039CPV)

description:
https://www.encodeproject.org/experiments/ENCSR093GXF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR093GXF
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-09-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB039CPV
size range: 300-600

source_name: Homo sapiens male adult (62 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

value: Homo sapiens heart left ventricle tissue

tag: biosample encode accession

value: male

value: adult

value: 62 year

value: Shin Lin

value: familial (EF 27%, LVEDD 6.5, LVPWd 0.85)

value: ENCBS878QCW at ENCODE; https://www.encodeproject.org/ENCBS878QCW/

value: Derived from ENCODE donor ENCDO110LFV; https://www.encodeproject.org/ENCDO110LFV/


title: snRNA-seq from left cerebral cortex (ENCLB275OVJ)

description:
https://www.encodeproject.org/experiments/ENCSR224RWH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR224RWH
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB275OVJ
fragmentation methods: see document
size range: 300-600

value: left cerebral cortex

value: Encode B6CastF1 2 months female #2 L. Cortex

tag: Sex

value: female

value: not collected

value: 2 month

value: Barbara Wold, Caltech

value: nucleus

value: The Jackson Laboratory

value: ENCBS818JSY at ENCODE; https://www.encodeproject.org/ENCBS818JSY/

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


title: MZB.PBS.Sp_3

value: Peritoneal Cavity

value: MZB

value: PBS


title: snRNA-seq from liver (ENCLB401DAZ)

description:
https://www.encodeproject.org/experiments/ENCSR133IBO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR133IBO
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2023-03-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB401DAZ
size range: 300-600

source_name: Homo sapiens female adult (39 years) liver tissue, preserved by flash-freezing nuclear fraction

value: liver

value: tissue

tag: note

value: Homo sapiens liver tissue?

tag: health state

value: healthy

value: adult

value: 39 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: not applicable

tag: geographic location

value: ENCBS509PYF at ENCODE; https://www.encodeproject.org/ENCBS509PYF/


title: snRNA-seq from right cardiac atrium (ENCLB399EQG)

description:
https://www.encodeproject.org/experiments/ENCSR087YKG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR087YKG
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB399EQG
fragmentation methods: none
size range: 300-800

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

value: right cardiac atrium

value: male

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

tag: dev stage

tag: age

value: 60 year

tag: lab

value: nucleus

value: ENCBS137FZY at ENCODE; https://www.encodeproject.org/ENCBS137FZY/

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


title: MZB.PBS.Sp_2

source_name: Peritoneal Cavity

value: Peritoneal Cavity

value: MZB

tag: treatment

value: PBS


title: 701126151

tag: time

value: THIRD

tag: source

value: Fingerstick

value: blood


title: snRNA-seq from heart left ventricle (ENCLB008XGB)

description:
https://www.encodeproject.org/experiments/ENCSR085XEW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR085XEW
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-09-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB008XGB
size range: 300-600

source_name: Homo sapiens male adult (65 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

tag: description

value: Homo sapiens heart left ventricle tissue

value: adult

value: 65 year

value: Michael Snyder, Stanford

value: Shin Lin

value: sarcoid and CAD (EF 22%, LVEDD 6.4, LVPWd 0.81)

tag: link

value: ENCBS313XWX at ENCODE; https://www.encodeproject.org/ENCBS313XWX/

value: Derived from ENCODE donor ENCDO240MDH; https://www.encodeproject.org/ENCDO240MDH/


title: snRNA-seq from gastrocnemius (ENCLB786EOH)

description:
https://www.encodeproject.org/experiments/ENCSR163GJZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR163GJZ
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB786EOH
fragmentation methods: see document
size range: 300-600

source_name: Mus musculus strain B6CASTF1/J female (2 months) gastrocnemius tissue nuclear fraction

value: gastrocnemius

value: Encode B6CastF1 2 months female #2 Gastroc.

value: female

value: not collected

value: 2 month

value: Barbara Wold, Caltech

tag: subcellular fraction term name

value: nucleus

value: The Jackson Laboratory

value: ENCBS455FAA at ENCODE; https://www.encodeproject.org/ENCBS455FAA/

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


title: MZB.PBS.Sp_1

tag: tissue

value: Peritoneal Cavity

value: MZB

value: PBS


title: 701168661

tag: vaccine dose

value: THIRD

value: Fingerstick

value: blood


title: 701168651


title: T.8.IL6.Sp_2

tag: cell type

tag: strain


title: snRNA-seq from left ventricle myocardium superior (ENCLB971CVF)

description:
https://www.encodeproject.org/experiments/ENCSR079LVG/
***************
biological replicate number: 1
technical replicate number: 1
description: Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR425CZQ).
experiment encode accession: ENCSR079LVG
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB971CVF
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens male adult (60 years) left ventricle myocardium superior tissue, preserved by flash-freezing nuclear fraction

value: left ventricle myocardium superior

value: tissue

tag: biosample encode accession

tag: Sex

value: male

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

value: adult

value: 60 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS999XQG at ENCODE; https://www.encodeproject.org/ENCBS999XQG/

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


title: snRNA-seq from heart left ventricle (ENCLB155EAA)

description:
https://www.encodeproject.org/experiments/ENCSR076ZLE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR076ZLE
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB155EAA
size range: 300-600

source_name: Homo sapiens female adult (61 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: Homo sapiens heart left ventricle tissue

value: female

tag: health state

value: nonischemic (EF 18%, LVEDD 6.8)

value: 61 year

value: Shin Lin

value: ENCBS372CQB at ENCODE; https://www.encodeproject.org/ENCBS372CQB/

value: Derived from ENCODE donor ENCDO650FUH; https://www.encodeproject.org/ENCDO650FUH/


title: snRNA-seq from heart left ventricle (ENCLB849AUZ)

description:
https://www.encodeproject.org/experiments/ENCSR067BOK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR067BOK
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-08-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB849AUZ
size range: 300-600

source_name: Homo sapiens female adult (50 years) heart left ventricle tissue, preserved by flash-freezing

value: tissue

value: 50 year

value: healthy

value: ENCBS966QMB at ENCODE; https://www.encodeproject.org/ENCBS966QMB/

value: Derived from ENCODE donor ENCDO166SII; https://www.encodeproject.org/ENCDO166SII/


title: snRNA-seq from heart right ventricle (ENCLB761CFQ)

description:
https://www.encodeproject.org/experiments/ENCSR060ZXZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR588PEE).
experiment encode accession: ENCSR060ZXZ
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB761CFQ
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens female adult (46 years) heart right ventricle tissue, preserved by flash-freezing nuclear fraction

value: heart right ventricle

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

value: adult

value: 46 year

value: Michael Snyder, Stanford

value: nucleus

value: ENCBS717WTC at ENCODE; https://www.encodeproject.org/ENCBS717WTC/

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


title: 701168641

source_name: blood

value: THIRD

value: Fingerstick

value: blood


title: snRNA-seq from left cerebral cortex (ENCLB675MBI)

description:
https://www.encodeproject.org/experiments/ENCSR132MEW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR132MEW
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB675MBI
fragmentation methods: see document
size range: 300-600

source_name: Mus musculus strain B6CASTF1/J male (2 months) left cerebral cortex tissue nuclear fraction

value: left cerebral cortex

value: Encode B6CastF1 2 months male #2 L. Cortex

value: male

value: not collected

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS894POY at ENCODE; https://www.encodeproject.org/ENCBS894POY/

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


title: T.8.TNFa.Sp_1

value: Peritoneal Cavity

value: TNFa


title: snRNA-seq from layer of hippocampus (ENCLB349KYC)

description:
https://www.encodeproject.org/experiments/ENCSR075HVN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR075HVN
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB349KYC
fragmentation methods: see document
size range: 300-600

source_name: Mus musculus strain B6CASTF1/J layer of hippocampus tissue, preserved by flash-freezing nuclear fraction

value: layer of hippocampus

value: tissue

value: Michael Snyder, Stanford

value: nucleus

value: ENCBS545IYY at ENCODE; https://www.encodeproject.org/ENCBS545IYY/


title: snRNA-seq from gastrocnemius (ENCLB526RVS)

description:
https://www.encodeproject.org/experiments/ENCSR188GDL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR188GDL
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB526RVS
fragmentation methods: see document
size range: 300-600

value: gastrocnemius

value: Encode B6CastF1 2 months female #1 Gastroc.

value: female

value: ENCBS589EZL at ENCODE; https://www.encodeproject.org/ENCBS589EZL/


title: T.8.IL6.Sp_1


title: snRNA-seq from bile duct (ENCLB765JXX)

description:
https://www.encodeproject.org/experiments/ENCSR060SEA/
***************
biological replicate number: 1
technical replicate number: 1
description: Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR833BMK).
experiment encode accession: ENCSR060SEA
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB765JXX
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens female adult (41 years) bile duct tissue, preserved by flash-freezing nuclear fraction

value: bile duct

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

value: adult

value: 41 year

value: Yiing Lin, MD, PhD

value: ENCBS423NLA at ENCODE; https://www.encodeproject.org/ENCBS423NLA/

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


title: snRNA-seq from adrenal gland (ENCLB293BAX)

description:
https://www.encodeproject.org/experiments/ENCSR157YJO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR157YJO
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB293BAX
fragmentation methods: see document
size range: 300-600

source_name: Mus musculus strain B6CASTF1/J adrenal gland tissue, preserved by flash-freezing nuclear fraction

value: adrenal gland

value: not collected

value: The Jackson Laboratory

value: ENCBS084MKW at ENCODE; https://www.encodeproject.org/ENCBS084MKW/

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


title: 701168631

value: THIRD

value: Fingerstick

value: blood


title: T.8.IL6.Sp_3

value: Peritoneal Cavity


title: snRNA-seq from gastrocnemius (ENCLB794PMK)

description:
https://www.encodeproject.org/experiments/ENCSR125XUV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR125XUV
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB794PMK
fragmentation methods: see document
size range: 300-600

source_name: Mus musculus strain B6CASTF1/J male (2 months) gastrocnemius tissue nuclear fraction

value: gastrocnemius

value: tissue

value: Encode B6CastF1 2 months male #1 Gastroc

value: male

value: 2 month

value: Barbara Wold, Caltech

value: nucleus

value: ENCBS618FPS at ENCODE; https://www.encodeproject.org/ENCBS618FPS/


title: snRNA-seq from heart left ventricle (ENCLB150JOE)

description:
https://www.encodeproject.org/experiments/ENCSR084XKX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR084XKX
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB150JOE
size range: 300-600

source_name: Homo sapiens male adult (30 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: Homo sapiens heart left ventricle tissue

value: healthy

value: adult

value: 30 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS117SFS at ENCODE; https://www.encodeproject.org/ENCBS117SFS/

value: Derived from ENCODE donor ENCDO377SFB; https://www.encodeproject.org/ENCDO377SFB/


title: 701168671

value: THIRD

value: Fingerstick

value: blood


title: 701126161


title: T.8.TNFa.Sp_3

value: Peritoneal Cavity

value: TNFa


title: 701126031


title: snRNA-seq from adrenal gland (ENCLB663TUU)

description:
https://www.encodeproject.org/experiments/ENCSR021YYL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR021YYL
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB663TUU
fragmentation methods: see document
size range: 300-600

value: adrenal gland

value: tissue

value: not collected

value: The Jackson Laboratory

value: ENCBS825FEU at ENCODE; https://www.encodeproject.org/ENCBS825FEU/

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


title: snRNA-seq from left cerebral cortex (ENCLB983BCX)

description:
https://www.encodeproject.org/experiments/ENCSR133XJX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR133XJX
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB983BCX
fragmentation methods: see document
size range: 300-600

source_name: Mus musculus strain B6CASTF1/J cerebral cortex tissue nuclear fraction

value: left cerebral cortex

value: nucleus

value: ENCBS766VSB at ENCODE; https://www.encodeproject.org/ENCBS766VSB/


title: snRNA-seq from heart left ventricle (ENCLB950DIT)

description:
https://www.encodeproject.org/experiments/ENCSR056QLB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR056QLB
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB950DIT
size range: 300-600

source_name: Homo sapiens male adult (50 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: Homo sapiens heart left ventricle tissue

value: male

value: ischemic (EF 49%, LVEDD 4.7) w/ Impella

value: adult

value: 50 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS662JCB at ENCODE; https://www.encodeproject.org/ENCBS662JCB/

value: Derived from ENCODE donor ENCDO602PYC; https://www.encodeproject.org/ENCDO602PYC/


title: T.8.IL1b.Sp_3

value: Peritoneal Cavity


title: snRNA-seq from gastrocnemius (ENCLB673NZA)

description:
https://www.encodeproject.org/experiments/ENCSR021MHR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR021MHR
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB673NZA
fragmentation methods: see document
size range: 300-600

source_name: Mus musculus strain B6CASTF1/J gastrocnemius tissue nuclear fraction

value: gastrocnemius

value: tissue

value: not collected

value: The Jackson Laboratory

value: ENCBS342SAO at ENCODE; https://www.encodeproject.org/ENCBS342SAO/


title: 701126351

value: THIRD

value: Fingerstick

value: blood


title: 701126011


title: T.8.PBS.Sp_4

source_name: Peritoneal Cavity

value: PBS


title: 701125991


title: FFPE_decalcified_MousePaws_H3K27ac

city: Evry

first: Marco Antonio

last: MENDOZA-PARRA

address: 2 rue Gaston Crémieux

country: France

institute: CNRS UMR8030

description: Library name: FFPE_decalcified_MousePaws_H3K27ac_CMM_DV

library_source: genomic

data_processing:
Primary analysis has been performed with our in-house developped tool SysISTD (SysFate Illumina Spatial transcriptomics Demultiplexer: https://github.com/SysFate/SysISTD). SysISTD takes as entry paired-end sequenced reads (fastq or fastq.gz format), and two TSV files, the first one containing the sequence of the molecular barcodes associated to the rows or column in the printed arrays and the second file presenting the physical position architecture of the spatial barcodes. SysISTD search for the Gibson sequence (regex query), then for two neighboring barcodes. Paired-reads presenting these features were aligned to either the human (hg19) or the mouse (mm9) genome with Bowtie2. In this manner, SysISTD generates SAM files per spatial coordinate, which are reprocessed with the help of featureCounts 31 and an in-house script for detecting reads counts per gene promoter (+/-5kb) and per spatial coordinate (SysISPD (SysFate Illumina Spatial Promoters Demultiplexer: https://github.com/SysFate/SysISPD). As outcome, SysISPD generates a matrix presenting read counts associated to physical coordinates in columns and known transcripts ID associated to the evaluated promoters in rows. To focus the downstream analysis to the physical positions corresponding to the analyzed tissue, we used an in-house R script taking as entry an image of the DNA array scanned with the TRICT filter, releaving the presence of the fiducial borders. Specifically, we upload to R a croped image within the fiducials (imager package) and we use the “px.flood” function to retrieve the pixels associated to the tissue. Finally we applied a pixel to gexel coordinates conversion prior to cross this information with the outcome of SysISPD. In parallel, all SAM files per coordinate were merged into a single-file and processed with the peak caller Macs2 5. The obtained confident peaks (P-value < 1x10-5) were annotated to their proximal coding regions. Finally, the spatial coordinates/promoters matrix provided by SysISPD was filtered by selecting transcripts associated to promoter regions presenting confident peaks. The “confident promoter peaks tissue-focused” matrix was quantile normalized with our previously described tool MULTILAYER 4,32. Then, the normalized matrix was further processed for revealing cell/tissue density contrast information by integrating normalized counts with pixel value levels retrieved in either the DAPI or the histone modification immunostaining image. The obtained normalized and pixels intensity adjusted matrix was used for all downstream analysis.
Assembly: mm9
Supplementary files format and content: Normalized spatial matrices
Library strategy: Spatial Epigenomics

molecule: genomic DNA

source_name: paws

extract_protocol:
Tissue samples were cryosectionned (16 µm sections for mouse embryo tissue and  and 20 µm sections for mouse brain WT tissue), collected between -15°C and -12°C then deposited on the DNA-arrays defined regions. Tissue sections were fixed with 1% Para-formaldheyde (PFA) (Life technologies 28908) in 1X PBS (Life technologies 70011-036) at room temperature during 30 minutes, then washed three times with 1X PBS. for FFPE samples, Mouse paws have been collected and fixed in 4% Paraformaldehyde (PFA) in 1X PBS for 24 hours. Then paws have been decalcified for 7 consecutive days in  an +4°C refrigerated room on agitation. A maximum of 5 paws, each inside a cassette, are decalcified  in 1L solution of 8,5g NaCl, 10% formol and 100mL of 99-100% glacial acetic acid. At mid incubation time, decalcification solution has been renewed and paws have been cut in half and put back into the cassette. Once decalcification is finished, paws have been rinsed in ddH20 to then be dehydrated and infiltrated with paraffin using an automated device (Novalix facilities) following this standard protocol: 70% ethanol, 2 washes of 70% ethanol, 96% ethanol, 100% ethanol, half and half mix of 100% ethanol with 100% xylene, empty the incubation chamber and final step of 100% xylene. Once dehydrated, each half paw has been paraffine embedded. All blocks of mouse paw FFPE can be stored at room temperature. 4µM thick sections around the Talus bone have been collected from those FFPE mouse paw blocks using a microtome. Paw FFPE sections were deparaffined and rehydrated following standard protocols on an automated device (Novalix facilities). Tissue sections were permeabilized during 1 hour at room temperature with 1% Triton X-100 (Merck 93443) in 1X PBS solution, then washed three times with 1X PBS followed by 5 minutes incubation at room temperature with 0.1M HCl for chromatin loosening, and washed three times with 1X PBS. Afterwads, sections were covered during 1 hour at room temperature with a blocking and permeabilizing mix (10% Normal Donkey serum (NDS) (Merck D9663), 0.25% Triton X-100 (Merck 93443), 0.1% Bovine Serum Albumin (BSA) (Merck A9418), 2 mM EDTA (Life technologies AM9260G), 0.5 mM Spermidine (Life technologies 132740010), 1 tablet EDTA-free Protease Inibitor Cocktail (PIC) (Merck 11873580001)) prepared in 1X PBS. Then tissue were washed twice with 150 mM NaCl Buffer (20 mM Hepes-KOH 1M pH=7.2 (Merck 391338), 150 mM NaCl; 0.1 % BSA, 0.5 mM Spermidine, 1 tablet PIC). After that, sections were incubated with a solution containing 2 μg of a selected primary Antibody (anti-Histone H3 (tri methyl K4) antibody (Abcam ab213244); anti-Histone H3 (acethyl K27) antibody (Abcam ab177178); or anti-Histone H3 (tri methyl K27) antibody (Abcam ab 192985)), in 150 mM NaCl Buffer at room temperature during 1 hour, followed by washing twice with 150 mM NaCl Buffer. Then tissues were incubated at room temperature with a pre-incubated mix (2 hours) containing 1:1 molar ratio of unloaded fusion protein pA-Tn5 (in-house production (9.5 µM) prepared using the plasmid Addgene #124601 by following previous protocols 3,30, and the corresponding secondary Antibody (donkey anti-rabbit IgG antibody (Merck SAB3700932). The pre-incubated mix was complemented with either a conjugated Alexa-488 secondary Antibody (donkey anti-rabbit IgG antibody, Alexa Fluor 488 (Life technologies A-21206)) or a conjugated Alexa-555 secondary Antibody (donkey anti-rabbit IgG antibody, Alexa Fluor 555 (Abcam ab 150062)), added at 1/1,000 dilution. The pre-incubated mix was used in a 5 times molar excess relative to the number of moles of the MOS sequence deposited per DNA array: for 2,048 spots it corresponds to 2,56.10-12 moles; for 4,096 spots it corresponds to 5,12.10-12 moles. After 3 hours of incubation with the assembled mix, tissue sections were washed twice with 300 mM NaCl Buffer (20 mM Hepes-KOH 1M pH=7.2, 300 mM NaCl; 0.1 % BSA, 0.5 mM Spermidine, 1 tablet PIC) to remove PA-Tn5-antibodies in excess. Then, tissue sections were incubated during 5 minutes with DAPI (Life technologies 62248) 1/5,000 dilution in 1xPBS, then washed twice with PBS 1X. DNA arrays were scanned under the TRICT filter to reveal the presence of the fiducial borders as well as the physical position of tissue sections on top of the printed DNA arrays. In case of the use of the conjugated Alexa-488 secondary Antibody, an additionnal scanning using FITC filter was done to reveal the localisation of the studied modification of histone. Finally, an additional scanning of the tissue using DAPI filter was done to observe nuclear localisation and to get cell density information. After imaging, sections were incubated overnight at 37°C with 10 mM MgCl2 (Life technologies AM9530G) in 300 mM NaCl Buffer for in situ tagmentation. Next day, tissue sections were incubated with a mix containing 2.25 µL of EDTA 0.5 M, 2.75 µL of 10% Sodium dodecyl sulfate (SDS) (Merck 71736) and 0.5 µL of 20 mg/mL Proteinase K (Life technologies 25530049) in 50 µL of ddH2O overnight at 37 °C. The mix volume was ajusted depending of the slide printing area. Finally, slides were washed under agitation (300 rpm) in containers containing: 100 mL of preheated buffer 1 (2X SSC and 0.1% SDS) during 15 minutes at 50°C, then 10 minutes with buffer 2 (0.2X SSC) at room temperature and 10 minutres with buffer 3 (0.1X SSC) at room temperature. At last the slides were washed in ddH2O and spin-dried. After that, DNA arrays were incubated with 0.1 M NaOH solution during 10 minutes at room temperature and then neutralized after removing liquid with a mix containig 100 µL of 0.1 M NaOH, 11.8 µL of 10X TE and 6.5 µL of 1.25 M acetic acid during 2-3 minutes. Finally, slides were washed within a falcon containing buffer 3 (0.1X SSC), then into a falcon containing ddH2O and spin-dried.
DNA arrays were incubated with a poly-C tailing mix containing 0.6 U/µL terminal transferase (New England Biolabs M0315), 1X terminal transferase buffer (New England Biolabs BO315), 0.3X CoCl2 (New England Biolabs B0252), 0.2 mM dCTP and 0.01 mM ddCTP during 35 minutes at 37°C, then 20 minutes at 70°C, and cooled at 12°C. To avoid evaporation, each printing area was closed by using sealing chambers (Life technologies AB-0576 (size 25 μL) or AB-0577 (size 65 μL)). Finally, slides were washed within a falcon containing buffer 3, and a falcon containing ddH2O, prior spin-dry. DNA arrays were then incubated with a mix containing:  0.1 U/µL  Klenow exo- (New England Biolabs M0212), 0.2 mg/mL BSA, 1X NEB2 buffer (New England Biolabs B7002), 0.5 mM dNTPs and an oligonucleotide (1 µM) having a complementary sequence for the poly-C tailed sequence, as well as a 5’-extremity providing an adapter sequence (“GTTCAGACGTGTGCTCTTCCGATCTGGGGGGGGGH”). As in the preceding step to avoid evaporation, the reaction was performed by using sealing chambers.The following conditions were used: 47°C during 5 minutes (primer annealing), 37°C during 1 hour (extension), 10 minutes at 70°C (enzyme deactivation) and cooled et 12°C. In order to recover the synthesized complementary DNA strands, DNA arrays were incubated with 100 µL of 0.1 M NaOH solution during 10 minutes, then the liquid was collected and a second incubation with 0.1 M NaOH solution was repetead. The two fractions were collected together and neutralized (for 100 µL 0.1 M NaOH solution add 11.8 µL of 10X TE and 6.5 µL of 1.25 M acetic acid). DNA arrays were also neutralized with 100 µL 0.1 M NaOH solution mixed with 11.8 µL of 10X TE and 6.5µL of 1.25 M acetic acid, then washed with buffer 3 and ddH2O and stored at 4 °C  for eventual supplementary experiments. The neutralized collected solution were precipitated with cold 100% ethanol (2X volume),  200 mM NaCl and 1 µL of 20 mg/mL glycogen (Merck 10901393001) and conserved at -20°C for at least 1 hour, then centrifuged at 12,500 rpm during 30 minutes, washed once with cold 70% ethanol and resuspended (after 30 minutes air drying) in 23 µL of ddH2O. Half of the resuspended cDNA’s complementary-probe material (12ul) was adjusted to 23ul with water, then mixed with: 25 µL of Q5 hot start high fidelity 2X master mix (New England Biolabs M0464L), 1 µL of adapter seq1 primer (0.02 µM (GTTCAGACGTGTGCTCTTCCGATCT)) and 1 µL of adapter seq2 primer (0.02 µM, (TACACTCTTTCCCTACACGACGCTCTTCCGATCTGACTCGTAATAC, corresponding to a part of the T7-promoter sequence)). This mix was amplifyied by PCR  (98°C, 30 s; 15 cycles: 98°C 10 s; 65°C 75 s; then 65°C 5 min; 12°C hold) and then cleanned at 0.9X ratio with SPRIselect beads (Beckman Coulter B23318) and resuspended in 24 µL of ddH2O. A second PCR amplification was done by mixing the 24 µL of adaptors linked cDNA’s complementary-probe strand with: 25 µL of Q5 hot start high fidelity 2X master mix, 0.5 µL of universal primer and 0.5 µL of index primer (0.1 µM final concentration NEBNext multiplex oligos for Illumina index primers set 1 E7335) by using the following cycling conditions: 98°C for 30 s, 15 cycles of 98°C for 10 s and 65°C for 75 s; then final extension at 65°C for 5 min and hold at 12°C. Then sample was cleanned at 0.9X ratio with SPRIselect beads. At last the library was used for Illumina sequencing (150 nts paired-ends sequencing; NovaSeq).

value: paws

tag: developmental stage

value: Adult

tag: disease state

value: CIA (collagen-induced arthritis; 42 days)


title: Mouse_Embryo_E11.5_H3K27me3

description: Library name: Mouse_Embryo_E11.5_H3K27me3_CMM_HW

source_name: whole Embryo

value: whole Embryo

value: Wild-type


title: snRNA-seq from adrenal gland (ENCLB000QLP)

description:
https://www.encodeproject.org/experiments/ENCSR035BDI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR035BDI
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB000QLP
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens female adult (47 years) adrenal gland tissue, preserved by cryopreservation nuclear fraction

value: adrenal gland

value: female

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

tag: dev stage

value: adult

tag: age

value: 47 year

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

tag: collection date

value: not applicable

tag: geographic location

value: ENCBS999YCV at ENCODE; https://www.encodeproject.org/ENCBS999YCV/


title: Mouse_Embryo_E11.5_H3K4me3

description: Library name: Mouse_Embryo_E11.5_H3K4me3_CMM_HU


title: 701126021

tag: time

value: THIRD

tag: source

value: Fingerstick

value: blood


title: T.8.PBS.Sp_1

value: Peritoneal Cavity

tag: treatment

value: PBS


title: snRNA-seq from mucosa of descending colon (ENCLB673QFY)

description:
https://www.encodeproject.org/experiments/ENCSR028MBY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR028MBY
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB673QFY
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens male adult (26 years) mucosa of descending colon tissue, preserved by flash-freezing nuclear fraction

value: mucosa of descending colon

value: tissue

value: male

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

value: 26 year

tag: lab

tag: subcellular fraction term name

tag: link

value: ENCBS001KXB at ENCODE; https://www.encodeproject.org/ENCBS001KXB/


title: T.8.PBS.Sp_3

tag: tissue

tag: cell type


title: T.8.IL1b.Sp_1

tag: strain


title: MouseBrain_H3K4me3

description: Library name: MouseBrain_H3K4me3_CMM_GI

source_name: brain

value: brain

value: Adult

value: Wild-type


title: 701125971

tag: vaccine dose


title: snRNA-seq from heart left ventricle (ENCLB062TYC)

description:
https://www.encodeproject.org/experiments/ENCSR012APQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR668XPI).
experiment encode accession: ENCSR012APQ
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB062TYC
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens male adult (66 years) heart left ventricle tissue, preserved by flash-freezing nuclear fraction

value: heart left ventricle

tag: biosample encode accession

tag: Sex

tag: health state

value: ischemic

value: adult

value: 66 year

value: Michael Snyder, Stanford

value: nucleus

value: Shin Lin

value: ENCBS056RAF at ENCODE; https://www.encodeproject.org/ENCBS056RAF/

value: Derived from ENCODE donor ENCDO529CYH; https://www.encodeproject.org/ENCDO529CYH/


title: 701126001

source_name: blood

value: THIRD

value: Fingerstick

value: blood


title: Neuron, dKO mice 3

city: Homburg

first: Lipao

last: Fang

address: Kirrbergerstrasse 100

department: Molecular Physiology, CIPMM

country: Germany

institute: University of Saarland

description: Library name: Neuron_dKO_3

data_processing:
1 Data Quality Control. 2 Readsmapping to the reference genome. 3 Quantification of gene expression level.4 Differential expression analysis. 5 Enrichment analysis of differentially expressed genes.6 Gene Set Enrichment Analysis. 7 SNP analysis. 8 AS analysi. 9 PPI analysis of differentially expressed genes. 10 Fusion Analysis.
Assembly: mm39
Supplementary files format and content: csv file include FPKM values for each sample

source_name: Cortex

extract_protocol:
RNA was harvested using the RNeasy Mini Kit (Qiagen).100-200 ng of total RNA was used for sequencing libraries.
RNA library was prepared using the TruSeq RNA Library Prep Kit v2. Additional PCR cycles were used to accommodate the lower input.

value: Cortex

value: Neuron

tag: genotype

value: dko


title: snRNA-seq from psoas muscle (ENCLB549KAN)

description:
https://www.encodeproject.org/experiments/ENCSR005TCL/
***************
biological replicate number: 1
technical replicate number: 1
description: snRNA on human psoas muscle. Please note that this experiment is part of 10x multiome and has a correspoding scATAC experiment (ENCSR332XEW).
experiment encode accession: ENCSR005TCL
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB549KAN
size range: 300-600
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens female adult (47 years) psoas muscle tissue, preserved by flash-freezing nuclear fraction

value: psoas muscle

value: tissue

value: female

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

tag: dev stage

tag: age

value: 47 year

value: Yiing Lin, MD, PhD

value: ENCBS481BQH at ENCODE; https://www.encodeproject.org/ENCBS481BQH/

value: Derived from ENCODE donor ENCDO528BHB; https://www.encodeproject.org/ENCDO528BHB/


title: T.4.TNFa.Sp_3

value: Peritoneal Cavity

value: TNFa


title: snRNA-seq from heart left ventricle (ENCLB457YKG)

description:
https://www.encodeproject.org/experiments/ENCSR008CVR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR008CVR
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB457YKG
size range: 300-600

source_name: Homo sapiens male adult (67 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

tag: description

value: Homo sapiens heart left ventricle tissue

value: male

value: ischemic (EF 15%, LVEDD 5.9)

value: adult

value: 67 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS753VJH at ENCODE; https://www.encodeproject.org/ENCBS753VJH/

value: Derived from ENCODE donor ENCDO269PFV; https://www.encodeproject.org/ENCDO269PFV/


title: Neuron, dKO mice 2

description: Library name: Neuron_dKO_2

value: Cortex

value: Neuron

value: dko


title: T.8.IL1b.Sp_2


title: 701125961

tag: time

value: THIRD

value: Fingerstick

value: blood


title: T.4.TNFa.Sp_2

value: Peritoneal Cavity

value: TNFa


title: snRNA-seq from placenta (ENCLB129RYA)

description:
https://www.encodeproject.org/experiments/ENCSR021QIA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR021QIA
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB129RYA
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens male embryo placenta tissue nuclear fraction

value: placenta

value: tissue

value: embryonic

value: not collected

value: John Stamatoyannopoulos, UW

value: nucleus

tag: source

value: John Stamatoyannopoulos

value: ENCBS256AHV at ENCODE; https://www.encodeproject.org/ENCBS256AHV/

value: Derived from ENCODE donor ENCDO023YQQ; https://www.encodeproject.org/ENCDO023YQQ/


title: Mouse_Embryo_E11.5_H3K27ac

description: Library name: Mouse_Embryo_E11.5_H3K27ac_CMM_HV

value: whole Embryo

tag: developmental stage

tag: disease state

value: Wild-type


title: snRNA-seq from heart left ventricle (ENCLB213TAB)

description:
https://www.encodeproject.org/experiments/ENCSR002SMQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR002SMQ
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB213TAB
size range: 300-600

source_name: Homo sapiens male adult (68 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: Homo sapiens heart left ventricle tissue

value: male

value: nonischemic (EF 21%, LVEDD 7.5)

value: adult

value: 68 year

tag: lab

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS210THB at ENCODE; https://www.encodeproject.org/ENCBS210THB/

value: Derived from ENCODE donor ENCDO038QFX; https://www.encodeproject.org/ENCDO038QFX/


title: T.8.PBS.Sp_2

value: Peritoneal Cavity

tag: treatment

value: PBS


title: 701125981

value: THIRD

value: Fingerstick

tag: tissue

value: blood


title: snRNA-seq from fallopian tube (ENCLB846XMI)

description:
https://www.encodeproject.org/experiments/ENCSR011EDH/
***************
biological replicate number: 1
technical replicate number: 1
description: Please note that this experiment is part of 10x multiome and has a corresponding scATAC experiment (ENCSR815FGT).
experiment encode accession: ENCSR011EDH
assay title: snRNA-seq
assembly: GRCh38
encode release date: 2022-03-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB846XMI
fragmentation methods: none
size range: 300-800

source_name: Homo sapiens female adult (59 years) fallopian tube tissue, preserved by flash-freezing nuclear fraction

value: fallopian tube

value: tissue

value: female

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

value: 59 year

tag: subcellular fraction term name

value: nucleus

value: Yiing Lin, MD, PhD

tag: link

value: ENCBS994MYO at ENCODE; https://www.encodeproject.org/ENCBS994MYO/

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


title: 701125941

tag: vaccine dose


title: Neuron, dKO mice 1

description: Library name: Neuron_dKO_1

value: Cortex

tag: cell type

value: Neuron

value: dko


title: KR1 biol rep 1

city: Semenyih

first: Zhen Yun

last: Siew

state: Selangor

address: University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.

department: School of Pharmacy

country: Malaysia

institute: University of Nottingham Malaysia

description:
Library name: Sample 7
Each processed data has its respective file instead of a combined file

data_processing:
Demultiplexing was carried out using the Illumina DRAGEN Bio-IT Platform v3.9 (Illumina), which provides an RNA-seq (splicing-aware) aligner and RNA-specific analysis tools for gene expression quantification and gene fusion detection. For differential gene expression (DEG) analysis, transcript quantification files were imported into R using tximport, and DEGs were identified with DESeq2. Functional enrichment analysis was performed using clusterProfiler, and gene-gene interaction networks were generated with STRING v12.0.
Supplementary files format and content: SFV files including quantified and normalised gene count for each samples

molecule: polyA RNA

growth_protocol: THP-1 (ATCC TIB-202) and K562 (ATCC CCL-243) cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 Medium, and Iscove's Modified Dulbecco’s Medium (IMDM), respectively. All media were sourced from Nacalai Tesque Inc., Japan, and supplemented with 5% foetal bovine serum (FBS; Biosera, France) and 1% penicillin-streptomycin-amphotericin B antibiotics (Abcam, UK). Cell cultures were maintained in a humidified 5% CO₂ incubator at 37°C. Routine mycoplasma testing was performed, particularly if abnormalities were observed in the cultures (e.g., rapid pH or colour changes), using a mycoplasma PCR detection kit (SouthernBiotech, USA), with results confirmed by a mycoplasma staining detection kit (Solarbio, China).

extract_protocol:
Cells were harvested at 5 dpi, centrifuged at 1,000 rpm for 10 minutes to remove the supernatant, and subjected to at least one freeze-thaw cycle using a -80°C freezer. Nucleic acid extraction was then performed with the Quick-DNA/RNA Miniprep Plus Kit (Zymo Research, USA), following the manufacturer’s protocol. Genomic DNA was removed with DNase I (Zymo Research, USA).
After DNA degradation, RNA samples were assessed for purity and prepared using the Illumina Stranded mRNA Prep, Ligation Kit (Illumina, USA) according to the manufacturer’s instructions. Sequencing was conducted on the Illumina NovaSeq 6000 system (Illumina, USA) with paired-end 150 bp reads (PE150). Libraries were normalised to 0.5 nM, pooled, and loaded onto the NovaSeq platform.

treatment_protocol: MOI 0.1 of PRV7S was added into all the treatment groups (1.0 X 106 cells/replicate) and incubated for 5 days.

tag: cell line

value: Chronic myeloid leukaemia cells

value: WT

value: PRV7S infection

value: 5 Days Post-Infection


title: KR2 biol rep 2

description:
Library name: Sample 8
Each processed data has its respective file instead of a combined file


title: Neuron, ctl mice 1

description: Library name: Neuron_Ctl_1


title: KNC2 biol rep 2

description:
Library name: Sample 6
Each processed data has its respective file instead of a combined file

value: Negative control


title: T.4.IL6.Sp_2

value: Peritoneal Cavity

tag: strain


title: T.4.IL6.Sp_3


title: 701126551

value: THIRD

value: Fingerstick

value: blood


title: T.4.IL6.Sp_1


title: T.4.TNFa.Sp_1

value: TNFa


title: OPC, dKO mice 2

description: Library name: OPC_dko_2

value: OPC

tag: genotype


title: 701126561


title: Neuron, ctl mice 3

description: Library name: Neuron_Ctl_3


title: Neuron, ctl mice 2

description: Library name: Neuron_Ctl_2


title: T.4.IL1b.Sp_3


title: 701168621


title: OPC, dKO mice 3

description: Library name: OPC_dko_3


title: KNC1 biol rep 1

description:
Library name: Sample 5
Each processed data has its respective file instead of a combined file


title: TR2 biol rep 2

description:
Library name: Sample 4
Each processed data has its respective file instead of a combined file

source_name: THP1 (ATCC TIB-202)

value: THP1 (ATCC TIB-202)

value: Acute myeloid leukaemia cells


title: 701126541


title: 701125951


title: OPC, dKO mice 1

description: Library name: OPC_dko_1


title: T.4.IL1b.Sp_2


title: 701168611


title: T.4.IL1b.Sp_1


title: TNC2 biol rep 2

description:
Library name: Sample 2
Each processed data has its respective file instead of a combined file


title: 701168601


title: OPC, ctl mice 3

description: Library name: OPC_ctl_3


title: T.4.PBS.Sp_5

value: PBS


title: TNC1 biol rep 1

description:
Library name: Sample 1
Each processed data has its respective file instead of a combined file


title: OPC, ctl mice 2

description: Library name: OPC_ctl_2

value: Cortex


title: 701125821


title: OPC, ctl mice 1

description: Library name: OPC_ctl_1


title: T.4.PBS.Sp_4


title: T.4.PBS.Sp_3


title: NCIH226_JTE607

city: shanghai

first: Xiaolan

middle: Phenome

last: Zhou

state: State

address: Songhu road

country: China

institute: fudan

description: Library name: sample4

library_source: transcriptomic single cell

data_processing:
Raw scRNA-seq data were processed using Cell Ranger (v8.0.1) from 10x Genomics (with Count functionality) for read alignment to the prebuilt GRCh38 genome reference. The resulting gene-by-cell unique molecular identifier (UMI) count matrix was analyzed using R package Seurat. Aligned BAM files were used as input for transcript-level peak calling with the SCAPTURE pipeline. The high-confidence PASs were used to construct a PAS-based GTF annotation, which was subsequently quantified using UMI-tools (v1.1.6) protocol. The final PAS-by-cell count matrix represented the expression of transcripts with distinct PASs at single-cell resolution. To assess the impact of JTE-607 treatment on intra-cell-line transcriptomic heterogeneity, we calculated the diversity score for each treatment condition based on the PAS-based transcript expression profiles. We performed PCA to project the expression profiles of all cells, enabling the extraction of key features while minimizing noise. The top 30 PCs were selected. We performed 1,000 down-sampling analyses by randomly sampling 1,000 cells without replacement, and defined diversity as the average distance of the sampled cells to the centroid. To mitigate the influence of outliers on diversity score calculation, we excluded the cells with all the first three PCs exceeding 3 standard deviations from the mean.
Assembly: GRCh38
Supplementary files format and content: mtx file with raw UMI counts for every gene and cell

source_name: Lung cancer cell line

extract_protocol:
Samples were processed using the Chromium Single Cell 3′ (v2 Chemistry), platform with the target of ∼10,000 cells (10x Genomics) following manufacturer's instructions. Briefly, cells were added onto a chip to form Gel Bead-in-Emulsion (GEMs) in the Chromium instrument followed by cell lysis, barcoding, fragmentation, adaptor ligation and addition of sample index to the libraries before sequencing.
cDNA from GEMs was recovered and amplified by PCR. Subsequently, cDNA fragment length was optimized by enzymatic digestion and fragment screening. Finally, library construction was completed by end repair and addition of traditional second-generation sequencing junctions, and a standard sequencing DNA library was obtained by PCR amplification. High-throughput sequencing was performed on the constructed library using the double-end sequencing mode of Illumina sequencing platform.

value: Lung cancer cell line


title: NCIH226_DMSO

description: Library name: sample3

value: DMSO


title: NCIH1299_JTE607

description: Library name: sample2


title: 701125811


title: NCIH1299_DMSO

description: Library name: sample1


title: DNase-seq from liver (ENCLB800MNW)

description:
https://www.encodeproject.org/experiments/ENCSR961KOD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR961KOD
assay title: DNase-seq
assembly: mm10
encode release date: 2022-12-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB800MNW

source_name: Mus musculus strain C57BL/6N,129 (LCR deletion, HOM globin mutation, multiple YAC copy) embryo (13.50 days) liver tissue

value: liver

value: tissue

tag: biosample encode accession

tag: Sex

value: not collected

tag: dev stage

value: embryonic

value: John Stamatoyannopoulos, UW

value: Mark Groudine

tag: model organism mating status

value: virgin

tag: collection date

value: not applicable

tag: geographic location

value: ENCBS326CZJ at ENCODE; https://www.encodeproject.org/ENCBS326CZJ/


title: DNase-seq from liver (ENCLB847XCF)

description:
https://www.encodeproject.org/experiments/ENCSR961KOD/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR961KOD
assay title: DNase-seq
assembly: mm10
encode release date: 2022-12-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB847XCF

tag: age

tag: source

value: ENCBS946XYK at ENCODE; https://www.encodeproject.org/ENCBS946XYK/


title: 701125801

tag: time

value: THIRD

value: Fingerstick

value: blood


title: T.4.PBS.Sp_1

source_name: Peritoneal Cavity

tag: tissue

value: Peritoneal Cavity

tag: treatment

value: PBS


title: T.4.PBS.Sp_2


title: 701125791


title: DNase-seq from liver (ENCLB885HLW)

description:
https://www.encodeproject.org/experiments/ENCSR961KOD/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR961KOD
assay title: DNase-seq
assembly: mm10
encode release date: 2022-12-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB885HLW

tag: lab

tag: link

value: ENCBS436LAA at ENCODE; https://www.encodeproject.org/ENCBS436LAA/


title: 701125781

tag: vaccine dose


title: TR1 biol rep 1

description:
Library name: Sample 3
Each processed data has its respective file instead of a combined file

tag: cell line

value: THP1 (ATCC TIB-202)

tag: cell type

value: Acute myeloid leukaemia cells

value: WT

value: PRV7S infection

value: 5 Days Post-Infection


title: pDC.TNFa.Sp_3

value: pDC

tag: strain

value: TNFa


title: 701125761


title: RPE1-TP53KO-EIF2AKO biorep 3 flow cell 2

city: Groningen

first: Maurits

last: Roorda

address: Hanzeplein 1

country: Netherlands

institute: University Medical Center Groningen

description: Library name: HH33MDSX3_105010-001-006_GAATCGTG-TTCACGGA_L004

data_processing:
RNeasy Mini kit (Qiagen) according to manufacturer’s instructions. 25 * 106 paired-end reads of 75 bp per sample from a NovaSeq 6000 were aligned to the Hg19 genome build using STAR, to obtain gene-level counts
Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.
Assembly: Hg19
Supplementary files format and content: Ensembl Gene ID-level gene counts (HGNC symbol included) in rows and samples in columns

source_name: Eye

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS and antibiotics at 37C and 5% CO2

extract_protocol:
RNeasy Mini kit (Qiagen) according to manufacturer’s instructions. 25 * 106 paired-end reads of 75 bp per sample from a NovaSeq 6000 were aligned to the Hg19 genome build using STAR, to obtain gene-level counts
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the sample(s). The sample preparation was performed according to the protocol "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760S/L). Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplicification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer (see appendices). The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp).

value: Eye

value: Retinal pigment epithelium

tag: genotype

tag: batch


title: DNase-seq from liver (ENCLB010SXH)

description:
https://www.encodeproject.org/experiments/ENCSR961KOD/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR961KOD
assay title: DNase-seq
assembly: mm10
encode release date: 2022-12-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB010SXH

value: liver

value: tissue

tag: biosample encode accession

tag: Sex

value: not collected

tag: dev stage

value: embryonic

value: John Stamatoyannopoulos, UW

value: Mark Groudine

value: virgin

value: not applicable

value: ENCBS790QAS at ENCODE; https://www.encodeproject.org/ENCBS790QAS/


title: RPE1-TP53KO-EIF2AKO biorep 2 flow cell 2

description: Library name: HH33MDSX3_105010-001-005_TGTGAAGC-TCTAGGAG_L004


title: DNase-seq from liver (ENCLB895NXT)

description:
https://www.encodeproject.org/experiments/ENCSR961KOD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR961KOD
assay title: DNase-seq
assembly: mm10
encode release date: 2022-12-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB895NXT

tag: model organism mating status

tag: collection date

tag: geographic location

value: ENCBS981ZBF at ENCODE; https://www.encodeproject.org/ENCBS981ZBF/


title: pDC.TNFa.Sp_1

value: Peritoneal Cavity


title: RPE1-TP53KO-EIF2AKO biorep 1 flow cell 2

description: Library name: HH33MDSX3_105010-001-004_TAAGTGGC-ATCCGTTG_L004


title: 701125751

tag: time

value: THIRD

tag: source

value: Fingerstick

value: blood


title: 701125741

tag: tissue


title: RPE1-TP53KO biorep 3 flow cell 2

description: Library name: HH33MDSX3_105010-001-003_ACGTGATG-GATAGCCA_L004


title: pDC.IL6.Sp_3

value: pDC

tag: treatment


title: DNase-seq from liver (ENCLB206RTG)

description:
https://www.encodeproject.org/experiments/ENCSR638QBF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR638QBF
assay title: DNase-seq
assembly: mm10
encode release date: 2022-12-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB206RTG

source_name: Mus musculus strain C57BL/6N,129 (HS2 HS3 deletion, HOM globin mutation) embryo (13.50 days) liver tissue

tag: age

tag: lab

tag: link

value: ENCBS767ZID at ENCODE; https://www.encodeproject.org/ENCBS767ZID/


title: DNase-seq from liver (ENCLB556AON)

description:
https://www.encodeproject.org/experiments/ENCSR638QBF/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR638QBF
assay title: DNase-seq
assembly: mm10
encode release date: 2022-12-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB556AON

value: ENCBS913HLN at ENCODE; https://www.encodeproject.org/ENCBS913HLN/


title: RPE1-TP53KO biorep 2 flow cell 2

description: Library name: HH33MDSX3_105010-001-002_ATTCGAGG-ACAAGCTC_L004

value: Eye

tag: cell line

tag: cell type

value: Retinal pigment epithelium


title: pDC.IL6.Sp_2

tag: strain


title: RPE1-TP53KO biorep 1 flow cell 2

description: Library name: HH33MDSX3_105010-001-001_GATACTGG-GAACCTTC_L004

tag: genotype

tag: batch


title: 701125731

tag: vaccine dose


title: DNase-seq from liver (ENCLB029HCK)

description:
https://www.encodeproject.org/experiments/ENCSR638QBF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR638QBF
assay title: DNase-seq
assembly: mm10
encode release date: 2022-12-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB029HCK

value: liver

value: tissue

tag: biosample encode accession

tag: Sex

value: not collected

tag: dev stage

value: ENCBS488CEA at ENCODE; https://www.encodeproject.org/ENCBS488CEA/


title: pDC.IL6.Sp_1


title: 701125721


title: 701125771


title: pDC.TNFa.Sp_2

value: TNFa


title: RPE1-TP53KO biorep 1 flow cell 1

description: Library name: HH2HLDSX3_105010-001-001_GATACTGG-GAACCTTC_L002


title: DNase-seq from liver (ENCLB929TUR)

description:
https://www.encodeproject.org/experiments/ENCSR887EBS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR887EBS
assay title: DNase-seq
assembly: mm10
encode release date: 2022-12-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB929TUR

source_name: Mus musculus strain C57BL/6N,129 (WT with A85 YAC, multiple YAC copy) embryo (13.50 days) liver tissue

value: embryonic

value: John Stamatoyannopoulos, UW

value: Mark Groudine

tag: model organism mating status

value: virgin

tag: collection date

value: not applicable

tag: geographic location

value: ENCBS671LBQ at ENCODE; https://www.encodeproject.org/ENCBS671LBQ/


title: 701168591

tag: time

value: THIRD

tag: source

value: Fingerstick

tag: tissue

value: blood


title: DNase-seq from liver (ENCLB512WXL)

description:
https://www.encodeproject.org/experiments/ENCSR887EBS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR887EBS
assay title: DNase-seq
assembly: mm10
encode release date: 2022-12-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB512WXL

tag: age

tag: lab

value: ENCBS395FCE at ENCODE; https://www.encodeproject.org/ENCBS395FCE/


title: H9, AAV-GFP, biological replicate 3

city: Charlestown

first: Ryuji

last: Morizane

address: 149 13th Street

institute: Massachusetts General Hospital

description: Library name: H9_GFP_3

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 and X-Plus Sequencing Platform of 150 bp pair-ended reads (Novogene), alignment and reference genome indexed via STAR (v2.5), and data supplied as fastq files. Visualization of differentially expressed genes was performed using OmicsBox Transcriptomics module, employing HTSeq (v0.6.1) for read number.
Alignment and annotation were conducted with OmicxBox.
Assembly: hg19
Supplementary files format and content: Processed data contains raw expression values of genes.

source_name: Kidney organoids

growth_protocol: The directed differentiation of hPSCs into kidney organoids is covered in detail elsewhere (Morizane et al, Nature Biotech, 2015; Morizane et al, Nature Protocols, 2017). Briefly, hPSCs were differentiated into metanephric mesenchyme cells which include nephron progenitor cells, with approximately 80-90% efficiency, by a 3-step directed differentiation protocol. Metanephric mesenchyme cells, arising on day 8 of differentiation, were transferred into suspension culture in 96-well ultra-low adhesion plates (Corning) and further differentiated into kidney organoids through intermediate stages of pre-tubular aggregates (day 11) and renal vesicles (day 14) as previously reported. Quality control measures of SIX2 immunostaining on differentiation day 8 and CDH1, LTL, and PODXL immunostaining on day 17 were performed on all batches of kidney organoids to limit batch-to-batch heterogeneity.

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen #15596026, per the manufacturer’s protocol) from triplicate samples of 3-4 kidney organoids for each of CRISPR, AAV, and Control samples on differentiation day 28, following 7 days of treatment with AAV2-saCas9 + AAV2-gRNA, AAV2-GFP, or vehicle control, respectively.
RNA was quantified (Thermo Scientific Nanodrop One spectrophotometer) and its integrity assessed (RNA Nano 6000 Assay Kit, Bioanalyzer 2100, Agilent Technologies, CA). cDNA was synthesized from 500 ng of RNA using a High-capacity cDNA Reverse Transcription kit (Applied Biosystems).

treatment_protocol: In the AAV2-saCas9 plasmid, saCas9 is expressed under the control of the CMV promoter. In the AAV2-gRNA plasmid, each of the two gRNA2 is expressed under the U6 promoter, and mCherry is expressed under the CMV promoter. VectorBuilder has provided stored catalog numbers for re-ordering these vectors (AAV2-saCas9, VB180125-1089ffa; AAV2-gRNA, VB210506-1386zxe). During the co-infection of these vectors in samples denoted ‘CRISPR’, a cumulative MOI of 10^5 vg/cell was employed in 100uL total volume of media, similar to the AAV-GFP serotype testing.

value: Kidney organoids

tag: cell line

value: Kidney


title: 701168501


title: pDC.PBS.Sp_4

value: Peritoneal Cavity

tag: cell type

value: pDC

tag: treatment

value: PBS


title: H9, AAV-GFP, biological replicate 2

description: Library name: H9_GFP_2


title: DNase-seq from CD8-positive naive resting alpha-beta T cell (ENCLB200OZE)

description:
https://www.encodeproject.org/experiments/ENCSR383XSU/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR383XSU
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB200OZE

source_name: Mus musculus strain B6CASTF1/J female adult (2 months) CD8-positive naive resting alpha-beta T primary cell

value: primary cell

value: female

value: adult

value: 2 month

tag: link

value: ENCBS525MTG at ENCODE; https://www.encodeproject.org/ENCBS525MTG/


title: DNase-seq from CD8-positive naive resting alpha-beta T cell (ENCLB951UOG)

description:
https://www.encodeproject.org/experiments/ENCSR383XSU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR383XSU
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB951UOG

value: John Stamatoyannopoulos, UW

value: Mark Groudine

value: virgin

value: ENCBS548CVI at ENCODE; https://www.encodeproject.org/ENCBS548CVI/


title: pDC.PBS.Sp_2

tag: strain


title: 701126511

tag: vaccine dose

value: THIRD

value: Fingerstick


title: pDC.PBS.Sp_1


title: H9, AAV-CRISPR/Cas9, biological replicate 3

description: Library name: H9_Cas9_3


title: DNase-seq from CD8-positive naive resting alpha-beta T cell (ENCLB069YDH)

description:
https://www.encodeproject.org/experiments/ENCSR383XSU/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR383XSU
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB069YDH

tag: biosample encode accession

value: not applicable

value: ENCBS817RCV at ENCODE; https://www.encodeproject.org/ENCBS817RCV/


title: 701126501

value: blood


title: pDC.PBS.Sp_5

value: Peritoneal Cavity


title: DNase-seq from CD8-positive naive resting alpha-beta T cell (ENCLB277OEB)

description:
https://www.encodeproject.org/experiments/ENCSR383XSU/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR383XSU
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB277OEB

tag: Sex

value: ENCBS810MQI at ENCODE; https://www.encodeproject.org/ENCBS810MQI/


title: 701126491


title: GN.TNFa.Sp_3

value: GN

value: TNFa


title: DNase-seq from monocyte (ENCLB040CTR)

description:
https://www.encodeproject.org/experiments/ENCSR606KBX/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR606KBX
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB040CTR

source_name: Mus musculus strain B6CASTF1/J female adult (2 months) monocyte primary cell

value: monocyte

value: primary cell

value: female

tag: dev stage

value: ENCBS562ZBM at ENCODE; https://www.encodeproject.org/ENCBS562ZBM/


title: 701126481

source_name: blood


title: H9, untreated control, biological replicate 3

description: Library name: H9_0_3

value: Kidney organoids

value: Kidney


title: DNase-seq from monocyte (ENCLB709GKI)

description:
https://www.encodeproject.org/experiments/ENCSR606KBX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR606KBX
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB709GKI

value: adult

value: 2 month

value: John Stamatoyannopoulos, UW

value: Mark Groudine

tag: model organism mating status

value: virgin

value: ENCBS682KBI at ENCODE; https://www.encodeproject.org/ENCBS682KBI/


title: GN.TNFa.Sp_1


title: 701126471

value: THIRD

value: Fingerstick

value: blood


title: 701126521


title: H9, untreated control, biological replicate 2

description: Library name: H9_0_2


title: 701126461


title: GN.IL6.Sp_3

value: Peritoneal Cavity

value: GN


title: DNase-seq from monocyte (ENCLB596GOD)

description:
https://www.encodeproject.org/experiments/ENCSR606KBX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR606KBX
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB596GOD

value: monocyte

tag: collection date

value: not applicable

value: ENCBS000MCL at ENCODE; https://www.encodeproject.org/ENCBS000MCL/


title: H9, untreated control, biological replicate 1

description: Library name: H9_0_1


title: DNase-seq from spleen (ENCLB468CVG)

description:
https://www.encodeproject.org/experiments/ENCSR603SOS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR603SOS
assay title: DNase-seq
assembly: mm10
encode release date: 2022-12-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB468CVG

source_name: Mus musculus strain C57BL/6N,129 (LCR deletion, HOM globin mutation, multiple YAC copy) female adult (12.00 weeks) spleen tissue

value: spleen

value: tissue

value: female

tag: geographic location

value: ENCBS236LMV at ENCODE; https://www.encodeproject.org/ENCBS236LMV/


title: H9, AAV-GFP, biological replicate 1

description: Library name: H9_GFP_1

value: Kidney organoids

value: Kidney


title: GN.IL6.Sp_2


title: 701126451

tag: time


title: DNase-seq from liver (ENCLB456YZA)

description:
https://www.encodeproject.org/experiments/ENCSR809OXS/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR809OXS
assay title: DNase-seq
assembly: mm10
encode release date: 2022-12-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB456YZA

source_name: Mus musculus strain C57BL/6NJ embryo (13.50 days) liver tissue

value: liver

value: not collected

value: embryonic

value: John Stamatoyannopoulos, UW

tag: source

value: Mark Groudine

value: ENCBS147YXH at ENCODE; https://www.encodeproject.org/ENCBS147YXH/


title: pDC.PBS.Sp_3

tag: tissue

value: Peritoneal Cavity

value: pDC

value: PBS


title: BJFF, AAV-GFP, biological replicate 3

description: Library name: BJFF_GFP_3

value: BJFF


title: 701126341

value: THIRD

value: Fingerstick

value: blood


title: H9, AAV-CRISPR/Cas9, biological replicate 2

description: Library name: H9_Cas9_2


title: BJFF, AAV-GFP, biological replicate 2

description: Library name: BJFF_GFP_2