title: MO113-CGND-HRA-02907-GEX

description: Library name: MO113-CGND-HRA-02907-GEX

value: F

value: Limb


title: total RNA-seq from HG03162 (ENCLB616FHW)

status: Public on Jul 24 2026

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR389UOP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR389UOP
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB616FHW
nucleic acid starting quantity: 34
nucleic acid starting quantity units: µg

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens HG03162 cell line

extract_protocol: not provided

tag: line

value: cell line

tag: biosample encode accession

tag: encode accession

tag: note

value: HG03162 LCLs; Donor from the Esan in Nigeria (ESN)

tag: Sex

value: female

tag: dev stage

value: adult

tag: lab

value: Stephen Montgomery, Stanford

tag: source

value: Coriell

tag: link

value: ENCBS757XFN at ENCODE; https://www.encodeproject.org/ENCBS757XFN/


title: MO112-CGND-HRA-02466-GEX

city: New York

first: Christopher

last: Jackson

state: NY

address: 101 Avenue of the Americas

department: Center for the Genomics of Neurodegenerative Disease

institute: New York Genome Center

description: Library name: MO112-CGND-HRA-02466-GEX

library_source: transcriptomic single cell

data_processing:
Sequenced 10x libraries were aligned to a standard reference genome (hg38; GENCODE v32/Ensembl98) and counted (Cellranger-ARC v2.0.2). ATAC peaks were aligned between samples for quantification (Cellranger-ARC aggr v2.0.2)
Assembly: hg38
Supplementary files format and content: atac_fragments.tsv
Supplementary files format and content: gex_molecule_info.h5
Supplementary files format and content: filtered_feature_bc_matrix.h5
Supplementary files format and content: per_barcode_metrics.csv

molecule: polyA RNA

extract_protocol:
Nuclei isolation protocol was adapted from previously described methods (PMID: 31042697; PMID: 36385529). All procedures were carried out on ice unless otherwise stated. Frozen post-mortem brain tissue was retrieved from storage at -80 °C and equilibrated on dry ice for 20–30 minutes before being transferred to a cryostat at -18 °C. Tissue samples were left for 15–20 minutes inside the cryostat before sectioning. We collected 20-50 mg of tissue per preparation, taking care to avoid excessive sampling of white matter. Tissue cuts were placed in a pre-chilled Dounce homogenizer containing 700 µL of ice-cold homogenization buffer (320 mM sucrose, 5 mM CaCl2 [#21115; Millipore Sigma], 3 mM magnesium acetate [#63052; Millipore Sigma], 10 mM Tris HCl [pH 7.8; prepared from Thermo Fisher’s #AM9850G and #AM9855G], 0.1 mM EDTA [pH 8.0; Thermo Fisher #AM9260G], 0.1% IGEPAL CA-630 [#I8896; Millipore Sigma], 1 mM DTT [#646563, Millipore Sigma], and 0.4 U/µl Protector RNase inhibitor [#03335402001, Millipore Sigma]). Homogenization was performed with 10 strokes of the loose pestle followed by 10 strokes of the tight pestle. After a 5-minute incubation on ice, the homogenized tissue was passed through a 70-µm Flowmi Cell Strainer (Bel-Art; H13680-0070) and combined with an equal volume of a solution made of 50% OptiPrep (#07820, STEMCELL Technologies), 5 mM CaCl2, 3 mM magnesium acetate, 10 mM Tris HCl (pH 7.8), 0.1 mM EDTA (pH 8.0), and 1 mM DTT. Using a 15-mL conical tube, this mixture was then layered onto a density gradient made up of 750 µL of a 30% OptiPrep solution supplemented with 134 mM sucrose, 5 mM CaCl2, 3 mM magnesium acetate, 10 mM Tris HCl (pH 7.8), 0.1 mM EDTA (pH 8.0), 1 mM DTT, 0.04% IGEPAL CA-630, and 0.17 U µl−1 RNase inhibitor) over 300 µL of 40% OptiPrep solution supplemented with 96 mM sucrose, 5 mM CaCl2, 3 mM magnesium acetate, 10 mM Tris HCl (pH 7.8), 0.1 mM EDTA (pH 8.0), 1 mM DTT, 0.03% IGEPAL CA-630, and 0.12 U µl−1 RNase inhibitor. Nuclei were separated by centrifugation at 3,000 × g for 20 minutes at 4 °C using a pre-chilled swinging-bucket rotor with the brake off. Approximately 150 µL of nuclei were collected from the 30%/40% gradient interphase and subsequently washed in PBS containing 1% BSA and 1 U µl-1 RNase inhibitor. Following a 5-minute incubation on ice, the nuclei were centrifuged at 450 × g for 3 minutes at 4 °C, and the pellet resuspended in 15 µL of diluted 10X Genomics Nuclei Buffer. Nuclei counting was performed using a Countess II FL instrument (Thermo Fisher) by staining with SYTOX Green (ThermoFisher; S7020). Additional quality control measures included Trypan Blue staining (#EBT-001, NanoEntek) to evaluate adequate permeabilization (cutoff: >95% of ‘dead cells’) and the assessment of nuclear morphology before proceeding with transposition.
Matched snRNA-seq and snATAC-seq libraries were prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit (#PN-1000283) according to the protocol provided by 10X Genomics. Nuclei (16,100 per reaction; targeted recovery: 10,000 nuclei) from a single donor were used for each library preparation. Partitioning of nuclei was performed on a Chromium X instrument (10X Genomics). Quality control of cDNAs and libraries was conducted using Agilent High Sensitivity DNA Kits and a BioAnalyzer instrument. Final library quantification prior to pooling utilized KAPA Biosystems’ Library Quantification Kit for Illumina Platforms (KK4824). Libraries were sequenced on a NovaSeq X system using a 2 × 100 bp configuration run on a 10B flow cell. BA44/45 and BA46 libraries (n = 48) were prepared and sequenced in independent batches.

tag: tissue

tag: genotype

value: ALS

tag: pmi

value: M

tag: age at_death

tag: age at_symptom_onset

tag: site of_motor_onset


title: MO111-CGND-HRA-02454-GEX

description: Library name: MO111-CGND-HRA-02454-GEX

value: Bulbar


title: total RNA-seq from GM19324 (ENCLB027ZVP)

description:
https://www.encodeproject.org/experiments/ENCSR388XWZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR388XWZ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB027ZVP
nucleic acid starting quantity: 34
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19324 cell line

tag: description

value: GM19324 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

tag: age

value: unknown

value: ENCBS122REB at ENCODE; https://www.encodeproject.org/ENCBS122REB/

value: Derived from ENCODE donor ENCDO057UPO; https://www.encodeproject.org/ENCDO057UPO/


title: total RNA-seq from GM21339 (ENCLB319CEZ)

description:
https://www.encodeproject.org/experiments/ENCSR388XYJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR388XYJ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB319CEZ
nucleic acid starting quantity: 37
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21339 cell line

tag: line

value: GM21339 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: ENCBS963YZF at ENCODE; https://www.encodeproject.org/ENCBS963YZF/


title: MO110-CGND-HRA-02636-GEX

description: Library name: MO110-CGND-HRA-02636-GEX

value: Control


title: total RNA-seq from GM21597 (ENCLB467SLS)

description:
https://www.encodeproject.org/experiments/ENCSR387DCM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR387DCM
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB467SLS
nucleic acid starting quantity: 26
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21597 cell line

value: cell line

tag: biosample encode accession

value: GM21597 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: ENCBS809OTZ at ENCODE; https://www.encodeproject.org/ENCBS809OTZ/


title: MO109-CGND-HRA-03519-GEX

description: Library name: MO109-CGND-HRA-03519-GEX

value: Limb


title: total RNA-seq from GM18864 (ENCLB649NHK)

description:
https://www.encodeproject.org/experiments/ENCSR386MVA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR386MVA
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB649NHK
nucleic acid starting quantity: 35
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM18864 cell line

tag: encode accession

value: GM18864 LCLs; Donor from the Yoruba in Ibadan, Nigeria (YRI)

value: female

value: adult

value: Stephen Montgomery, Stanford

value: ENCBS511QDU at ENCODE; https://www.encodeproject.org/ENCBS511QDU/


title: MO108-CGND-HRA-02472-GEX

description: Library name: MO108-CGND-HRA-02472-GEX

value: ALS

value: M

value: Bulbar


title: total RNA-seq from GM19397 (ENCLB589ZCV)

description:
https://www.encodeproject.org/experiments/ENCSR385YME/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR385YME
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB589ZCV
nucleic acid starting quantity: 36
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19397 cell line

value: GM19397 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: male

value: unknown

value: Coriell

value: ENCBS855ELP at ENCODE; https://www.encodeproject.org/ENCBS855ELP/

value: Derived from ENCODE donor ENCDO671BAY; https://www.encodeproject.org/ENCDO671BAY/


title: MO106-U54-HRA-187-GEX

description: Library name: MO106-U54-HRA-187-GEX

value: Control


title: total RNA-seq from GM21770 (ENCLB726KEB)

description:
https://www.encodeproject.org/experiments/ENCSR380MGB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR380MGB
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB726KEB
nucleic acid starting quantity: 32
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21770 cell line

value: cell line

tag: note

value: GM21770 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: ENCBS107HQL at ENCODE; https://www.encodeproject.org/ENCBS107HQL/


title: total RNA-seq from HG02977 (ENCLB805VAN)

description:
https://www.encodeproject.org/experiments/ENCSR378HSG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR378HSG
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB805VAN
nucleic acid starting quantity: 50
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02977 cell line

value: HG02977 LCLs; Donor from the Esan in Nigeria (ESN)

tag: Sex

value: ENCBS574OTU at ENCODE; https://www.encodeproject.org/ENCBS574OTU/


title: MO104-CGND-HRA-03436-GEX

description: Library name: MO104-CGND-HRA-03436-GEX

value: F

value: Limb


title: total RNA-seq from HG02968 (ENCLB263MSO)

description:
https://www.encodeproject.org/experiments/ENCSR381HHP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR381HHP
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB263MSO
nucleic acid starting quantity: 30
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02968 cell line

value: HG02968 LCLs; Donor from the Esan in Nigeria (ESN)

tag: dev stage

value: adult

value: Stephen Montgomery, Stanford

value: ENCBS019CQE at ENCODE; https://www.encodeproject.org/ENCBS019CQE/


title: MO107-U54-HRA-136-GEX

description: Library name: MO107-U54-HRA-136-GEX


title: total RNA-seq from GM21614 (ENCLB838OGX)

description:
https://www.encodeproject.org/experiments/ENCSR374LLP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR374LLP
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB838OGX
nucleic acid starting quantity: 30
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21614 cell line

value: GM21614 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: male

tag: lab

value: ENCBS338FQC at ENCODE; https://www.encodeproject.org/ENCBS338FQC/


title: total RNA-seq from HG03446 (ENCLB814SEX)

description:
https://www.encodeproject.org/experiments/ENCSR868HHH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR868HHH
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB814SEX
nucleic acid starting quantity: 27
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03446 cell line

value: HG03446 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: female

tag: source

value: Coriell

value: ENCBS837ZNA at ENCODE; https://www.encodeproject.org/ENCBS837ZNA/


title: MO103-CGND-HRA-02463-GEX

description: Library name: MO103-CGND-HRA-02463-GEX

value: ALS

value: M


title: total RNA-seq from GM21365 (ENCLB231BEW)

description:
https://www.encodeproject.org/experiments/ENCSR866TNS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR866TNS
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB231BEW
nucleic acid starting quantity: 34
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21365 cell line

value: cell line

value: GM21365 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

tag: link

value: ENCBS117XQY at ENCODE; https://www.encodeproject.org/ENCBS117XQY/


title: total RNA-seq from GM21716 (ENCLB087UNO)

description:
https://www.encodeproject.org/experiments/ENCSR374DLH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR374DLH
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB087UNO
nucleic acid starting quantity: 26
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21716 cell line

value: GM21716 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: ENCBS021YTS at ENCODE; https://www.encodeproject.org/ENCBS021YTS/


title: MO102-U54-HRA-139-GEX

description: Library name: MO102-U54-HRA-139-GEX

tag: tissue

value: Control

value: F


title: total RNA-seq from GM21379 (ENCLB786MXZ)

description:
https://www.encodeproject.org/experiments/ENCSR374DHS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR374DHS
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB786MXZ
nucleic acid starting quantity: 38
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21379 cell line

value: GM21379 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: adult

value: Stephen Montgomery, Stanford

value: ENCBS805NPH at ENCODE; https://www.encodeproject.org/ENCBS805NPH/


title: MO101-CGND-HRA-02905-GEX

description: Library name: MO101-CGND-HRA-02905-GEX

tag: genotype

value: Limb


title: total RNA-seq from HG03121 (ENCLB841FDZ)

description:
https://www.encodeproject.org/experiments/ENCSR373KYU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR373KYU
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB841FDZ
nucleic acid starting quantity: 39
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03121 cell line

value: HG03121 LCLs; Donor from the Esan in Nigeria (ESN)

value: female

value: ENCBS092CGM at ENCODE; https://www.encodeproject.org/ENCBS092CGM/


title: MO100-CGND-HRA-02982-GEX

description: Library name: MO100-CGND-HRA-02982-GEX

value: ALS

tag: pmi

value: Bulbar and Limb


title: total RNA-seq from HG03511 (ENCLB624FDW)

description:
https://www.encodeproject.org/experiments/ENCSR371ANC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR371ANC
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB624FDW
nucleic acid starting quantity: 33
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03511 cell line

value: cell line

value: HG03511 LCLs; Donor from the Esan in Nigeria (ESN)

value: Coriell

value: ENCBS733XVO at ENCODE; https://www.encodeproject.org/ENCBS733XVO/


title: total RNA-seq from HG03066 (ENCLB028PSP)

description:
https://www.encodeproject.org/experiments/ENCSR367JCF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR367JCF
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB028PSP
nucleic acid starting quantity: 31
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03066 cell line

value: HG03066 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: male

value: unknown

value: ENCBS293HQE at ENCODE; https://www.encodeproject.org/ENCBS293HQE/

value: Derived from ENCODE donor ENCDO033LJA; https://www.encodeproject.org/ENCDO033LJA/


title: MO099-CGND-HRA-00611-GEX

description: Library name: MO099-CGND-HRA-00611-GEX

value: F

tag: age at_death

value: Bulbar


title: MO098-CGND-HRA-03195-GEX

description: Library name: MO098-CGND-HRA-03195-GEX

value: M

tag: age at_symptom_onset


title: MO097-U54-HRA-138-GEX

description: Library name: MO097-U54-HRA-138-GEX

value: Control


title: total RNA-seq from GM19377 (ENCLB461DOH)

description:
https://www.encodeproject.org/experiments/ENCSR367CJH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR367CJH
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB461DOH
nucleic acid starting quantity: 46
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19377 cell line

value: GM19377 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: female

value: adult

value: Stephen Montgomery, Stanford

value: ENCBS148MBQ at ENCODE; https://www.encodeproject.org/ENCBS148MBQ/


title: total RNA-seq from HG02888 (ENCLB173VHE)

description:
https://www.encodeproject.org/experiments/ENCSR365RUM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR365RUM
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB173VHE
nucleic acid starting quantity: 27
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02888 cell line

value: cell line

value: HG02888 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: ENCBS928JBC at ENCODE; https://www.encodeproject.org/ENCBS928JBC/


title: total RNA-seq from HG03088 (ENCLB141EUT)

description:
https://www.encodeproject.org/experiments/ENCSR360IYN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR360IYN
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB141EUT
nucleic acid starting quantity: 26
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03088 cell line

value: HG03088 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: Coriell

value: ENCBS061OKQ at ENCODE; https://www.encodeproject.org/ENCBS061OKQ/


title: MO096-CGND-HRA-02402-GEX

description: Library name: MO096-CGND-HRA-02402-GEX

value: ALS

tag: site of_motor_onset

value: Limb


title: MO095-CGND-HRA-02980-GEX

description: Library name: MO095-CGND-HRA-02980-GEX

value: F


title: total RNA-seq from HG03583 (ENCLB603NZN)

description:
https://www.encodeproject.org/experiments/ENCSR360GOQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR360GOQ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB603NZN
nucleic acid starting quantity: 32
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03583 cell line

value: HG03583 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: ENCBS142BJC at ENCODE; https://www.encodeproject.org/ENCBS142BJC/


title: MO094-CGND-HRA-02633-GEX

description: Library name: MO094-CGND-HRA-02633-GEX

value: Control

value: M


title: MO093-CGND-HRA-03516-GEX

description: Library name: MO093-CGND-HRA-03516-GEX


title: total RNA-seq from GM19438 (ENCLB775ZGS)

description:
https://www.encodeproject.org/experiments/ENCSR359VLP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR359VLP
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB775ZGS
nucleic acid starting quantity: 45
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19438 cell line

tag: description

value: GM19438 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: female

value: unknown

value: ENCBS902ITG at ENCODE; https://www.encodeproject.org/ENCBS902ITG/

value: Derived from ENCODE donor ENCDO098MAZ; https://www.encodeproject.org/ENCDO098MAZ/


title: MO092-CGND-HRA-02427-GEX

description: Library name: MO092-CGND-HRA-02427-GEX

value: Bulbar


title: total RNA-seq from HG02810 (ENCLB048BQG)

description:
https://www.encodeproject.org/experiments/ENCSR360BWE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR360BWE
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB048BQG
nucleic acid starting quantity: 33
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02810 cell line

value: cell line

value: HG02810 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: male

value: adult

value: Stephen Montgomery, Stanford

value: ENCBS970IBN at ENCODE; https://www.encodeproject.org/ENCBS970IBN/


title: total RNA-seq from HG03095 (ENCLB002MZU)

description:
https://www.encodeproject.org/experiments/ENCSR359NAG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR359NAG
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB002MZU
nucleic acid starting quantity: 45
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03095 cell line

value: HG03095 LCLs; Donor from the Mende in Sierra Leone (MSL)

tag: age

value: Coriell

value: ENCBS751KFE at ENCODE; https://www.encodeproject.org/ENCBS751KFE/

value: Derived from ENCODE donor ENCDO701OVN; https://www.encodeproject.org/ENCDO701OVN/


title: total RNA-seq from GM21599 (ENCLB594TSP)

description:
https://www.encodeproject.org/experiments/ENCSR358ZQT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR358ZQT
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB594TSP
nucleic acid starting quantity: 35
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21599 cell line

tag: line

value: GM21599 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: ENCBS730IYY at ENCODE; https://www.encodeproject.org/ENCBS730IYY/


title: MO091-CGND-HRA-03040-GEX

description: Library name: MO091-CGND-HRA-03040-GEX

value: ALS

value: F


title: total RNA-seq from suppressor macrophage (ENCLB511QTZ)

description:
https://www.encodeproject.org/experiments/ENCSR358IQT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR358IQT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB511QTZ

library_source: genomic

molecule: genomic DNA

source_name: Homo sapiens male adult (21 years) suppressor macrophage primary cell

value: suppressor macrophage

value: primary cell

tag: biosample encode accession

value: 21 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: ENCBS852BYC at ENCODE; https://www.encodeproject.org/ENCBS852BYC/


title: MO090-CGND-HRA-02470-GEX

description: Library name: MO090-CGND-HRA-02470-GEX

value: M

value: Bulbar


title: MO089-CGND-HRA-02451-GEX

description: Library name: MO089-CGND-HRA-02451-GEX


title: U54-HRA-135-A1-GEX

description: Library name: U54-HRA-135-A1-GEX

value: Control


title: total RNA-seq from GM21449 (ENCLB319TPQ)

description:
https://www.encodeproject.org/experiments/ENCSR357YYW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR357YYW
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB319TPQ
nucleic acid starting quantity: 33
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21449 cell line

value: cell line

tag: encode accession

value: GM21449 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: female

value: adult

value: Stephen Montgomery, Stanford

value: ENCBS782ZJP at ENCODE; https://www.encodeproject.org/ENCBS782ZJP/


title: total RNA-seq from GM18924 (ENCLB350YNP)

description:
https://www.encodeproject.org/experiments/ENCSR356LOW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR356LOW
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB350YNP
nucleic acid starting quantity: 36
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM18924 cell line

tag: note

value: GM18924 LCLs; Donor from the Yoruba in Ibadan, Nigeria (YRI)

value: Coriell

value: ENCBS241CUQ at ENCODE; https://www.encodeproject.org/ENCBS241CUQ/


title: total RNA-seq from HG02642 (ENCLB393YWG)

description:
https://www.encodeproject.org/experiments/ENCSR356ESQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR356ESQ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB393YWG
nucleic acid starting quantity: 32
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02642 cell line

value: HG02642 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

tag: Sex

value: male

value: unknown

value: ENCBS622NKJ at ENCODE; https://www.encodeproject.org/ENCBS622NKJ/

value: Derived from ENCODE donor ENCDO480FPE; https://www.encodeproject.org/ENCDO480FPE/


title: MO131-U54-HRA-201-ATAC

description: Library name: MO131-U54-HRA-201-ATAC

library_source: genomic single cell

value: F


title: MO105-CGND-HRA-03443-GEX

description: Library name: MO105-CGND-HRA-03443-GEX

value: ALS

value: M

value: Limb


title: MO130-U54-HRA-229-ATAC

description: Library name: MO130-U54-HRA-229-ATAC

value: Control


title: total RNA-seq from HG03130 (ENCLB970QBJ)

description:
https://www.encodeproject.org/experiments/ENCSR852WYF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR852WYF
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB970QBJ
nucleic acid starting quantity: 22
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03130 cell line

value: cell line

value: HG03130 LCLs; Donor from the Esan in Nigeria (ESN)

tag: dev stage

value: ENCBS688HUW at ENCODE; https://www.encodeproject.org/ENCBS688HUW/


title: V327-CGND-HRA-03443-A

description: Library name: V327-CGND-HRA-03443-A

data_processing:
Each sequenced 10X Visium library was aligned to a standard reference genome (hg38; GENCODE v32/Ensembl98) and counted with spaceranger
Assembly: hg38
Supplementary files format and content: filtered_feature_bc_matrix.h5 file contains spaceranger counts in spaceranger h5 format
Supplementary files format and content: spatial.tar file contains slide images and spot & scaling metadata from spaceranger outs/spatial
Library strategy: Spatial Transcriptomics

extract_protocol:
Frozen tissue blocks, kept at -80°C prior to processing, were equilibrated to -16°C inside a Leica CM3050S cryostat, embedded in Tissue Plus OCT Compound (Fisher Healthcare, #4585), and sectioned in a perpendicular orientation with regard to the pial surface. Tissue sections (10 µm-thick) from quality controlled blocks (H&E staining and imaging) were collected onto prechilled Visium Spatial Gene Expression Slides (10X Genomics, #1000185) while briefly warming the back of the slide with a gloved finger to improve adherence and minimize artifacts.
Visium libraries were prepared using unique Illumina-compatible PCR primers with Dual Index Kit TT Set A (10X Genomics, #1000215). Size distribution profiles of the final libraries were assessed by running Agilent High Sensitivity DNA chips (#5067-4626) on a 2100 Bioanalyzer system (Agilent, #G2939BA). Libraries outside the expected range (450 ± 50 bp) or that contained adapter dimer contaminants were discarded and reprocessed. Total yields were initially measured on a Qubit 3.0 fluorometer before final qPCR quantification (KAPA Library Quantification Kit for Illumina Platforms, KAPA Biosystems, #KK4824).

tag: subject id

tag: diagnosis

tag: rin


title: total RNA-seq from GM21457 (ENCLB319TFL)

description:
https://www.encodeproject.org/experiments/ENCSR845YVK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR845YVK
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB319TFL
nucleic acid starting quantity: 16
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21457 cell line

value: GM21457 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: female

value: adult

tag: lab

value: Stephen Montgomery, Stanford

tag: source

tag: link

value: ENCBS134ICN at ENCODE; https://www.encodeproject.org/ENCBS134ICN/


title: V311-CGND-HRA-03531-C

description: Library name: V311-CGND-HRA-03531-C

tag: tissue


title: total RNA-seq from HG03097 (ENCLB213UMX)

description:
https://www.encodeproject.org/experiments/ENCSR861WHN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR861WHN
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB213UMX
nucleic acid starting quantity: 35
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03097 cell line

value: HG03097 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: Coriell

value: ENCBS554XES at ENCODE; https://www.encodeproject.org/ENCBS554XES/

value: Derived from ENCODE donor ENCDO742ZFH; https://www.encodeproject.org/ENCDO742ZFH/


title: total RNA-seq from HG03515 (ENCLB854ZYT)

description:
https://www.encodeproject.org/experiments/ENCSR353BNA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR353BNA
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB854ZYT
nucleic acid starting quantity: 25
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03515 cell line

value: HG03515 LCLs; Donor from the Esan in Nigeria (ESN)

value: male

value: ENCBS067SHB at ENCODE; https://www.encodeproject.org/ENCBS067SHB/


title: MO129-U54-HRA-223-ATAC

description: Library name: MO129-U54-HRA-223-ATAC

tag: genotype

tag: pmi

value: M

tag: age at_death


title: V311-CGND-HRA-03369-A

description: Library name: V311-CGND-HRA-03369-A

value: ALS

value: F

tag: age


title: MO128-U54-HRA-205-ATAC

description: Library name: MO128-U54-HRA-205-ATAC

value: Control


title: total RNA-seq from CD14-positive monocyte (ENCLB215QOH)

description:
https://www.encodeproject.org/experiments/ENCSR351BFL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR351BFL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB215QOH

source_name: Homo sapiens male adult (40 years) CD14-positive monocyte primary cell

value: CD14-positive monocyte

value: primary cell

value: 40 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: ENCBS075ZNY at ENCODE; https://www.encodeproject.org/ENCBS075ZNY/


title: total RNA-seq from HG02851 (ENCLB938USG)

description:
https://www.encodeproject.org/experiments/ENCSR348CLS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR348CLS
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB938USG
nucleic acid starting quantity: 37
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02851 cell line

tag: line

value: cell line

value: HG02851 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: adult

value: Stephen Montgomery, Stanford

value: ENCBS747JRL at ENCODE; https://www.encodeproject.org/ENCBS747JRL/


title: MO127-U54-HRA-216-ATAC

description: Library name: MO127-U54-HRA-216-ATAC


title: MO126-U54-HRA-108-ATAC

description: Library name: MO126-U54-HRA-108-ATAC


title: total RNA-seq from GM19027 (ENCLB600BNU)

description:
https://www.encodeproject.org/experiments/ENCSR347PFE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR347PFE
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB600BNU
nucleic acid starting quantity: 30
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19027 cell line

tag: biosample encode accession

value: GM19027 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: male

value: Coriell

value: ENCBS906CEH at ENCODE; https://www.encodeproject.org/ENCBS906CEH/


title: total RNA-seq from GM21356 (ENCLB436WYI)

description:
https://www.encodeproject.org/experiments/ENCSR345DTP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR345DTP
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB436WYI
nucleic acid starting quantity: 22
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21356 cell line

tag: encode accession

value: GM21356 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: ENCBS699IPL at ENCODE; https://www.encodeproject.org/ENCBS699IPL/


title: total RNA-seq from HG03367 (ENCLB341VRV)

description:
https://www.encodeproject.org/experiments/ENCSR342EIB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR342EIB
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB341VRV
nucleic acid starting quantity: 35
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03367 cell line

tag: note

value: HG03367 LCLs; Donor from the Esan in Nigeria (ESN)

value: ENCBS292SEZ at ENCODE; https://www.encodeproject.org/ENCBS292SEZ/


title: MO124-CGND-HRA-03419-ATAC

description: Library name: MO124-CGND-HRA-03419-ATAC

value: ALS

tag: Sex

value: M

tag: age at_symptom_onset

tag: site of_motor_onset

value: Bulbar


title: MO125-CGND-HRA-04082-ATAC

description: Library name: MO125-CGND-HRA-04082-ATAC

value: Control

value: F


title: total RNA-seq from inflammatory macrophage (ENCLB152KSZ)

description:
https://www.encodeproject.org/experiments/ENCSR341MGP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR341MGP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB152KSZ

source_name: Homo sapiens male adult (40 years) inflammatory macrophage primary cell

value: inflammatory macrophage

value: primary cell

tag: dev stage

value: 40 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: ENCBS067GDG at ENCODE; https://www.encodeproject.org/ENCBS067GDG/


title: MO122-CGND-HRA-04087-ATAC

description: Library name: MO122-CGND-HRA-04087-ATAC


title: total RNA-seq from GM21740 (ENCLB731RFY)

description:
https://www.encodeproject.org/experiments/ENCSR339YKD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR339YKD
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB731RFY
nucleic acid starting quantity: 24
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21740 cell line

value: cell line

value: GM21740 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: male

value: adult

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS303ZTP at ENCODE; https://www.encodeproject.org/ENCBS303ZTP/


title: total RNA-seq from HG02896 (ENCLB609XSL)

description:
https://www.encodeproject.org/experiments/ENCSR340WCM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR340WCM
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB609XSL
nucleic acid starting quantity: 22
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02896 cell line

value: HG02896 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: female

value: ENCBS202NBD at ENCODE; https://www.encodeproject.org/ENCBS202NBD/


title: MO121-CGND-HRA-00235-ATAC

description: Library name: MO121-CGND-HRA-00235-ATAC

value: ALS

value: F

value: Bulbar


title: MO119-U54-HRA-093-ATAC

description: Library name: MO119-U54-HRA-093-ATAC

value: Control

value: M


title: MO120-CGND-HRA-03423-ATAC

description: Library name: MO120-CGND-HRA-03423-ATAC


title: MO118-CGND-HRA-03447-ATAC

description: Library name: MO118-CGND-HRA-03447-ATAC

value: Limb


title: total RNA-seq from GM18871 (ENCLB503PPS)

description:
https://www.encodeproject.org/experiments/ENCSR336KOK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR336KOK
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB503PPS
nucleic acid starting quantity: 44
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM18871 cell line

value: GM18871 LCLs; Donor from the Yoruba in Ibadan, Nigeria (YRI)

value: ENCBS464SDR at ENCODE; https://www.encodeproject.org/ENCBS464SDR/


title: total RNA-seq from HG03514 (ENCLB635UCB)

description:
https://www.encodeproject.org/experiments/ENCSR337UDT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR337UDT
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB635UCB
nucleic acid starting quantity: 34
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03514 cell line

value: cell line

value: HG03514 LCLs; Donor from the Esan in Nigeria (ESN)

value: ENCBS170NTB at ENCODE; https://www.encodeproject.org/ENCBS170NTB/


title: total RNA-seq from HG03175 (ENCLB500NGO)

description:
https://www.encodeproject.org/experiments/ENCSR339SAH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR339SAH
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB500NGO
nucleic acid starting quantity: 34
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03175 cell line

tag: description

value: HG03175 LCLs; Donor from the Esan in Nigeria (ESN)

value: male

value: adult

value: unknown

value: Stephen Montgomery, Stanford

value: ENCBS883GAC at ENCODE; https://www.encodeproject.org/ENCBS883GAC/

value: Derived from ENCODE donor ENCDO756WCQ; https://www.encodeproject.org/ENCDO756WCQ/


title: total RNA-seq from GM21768 (ENCLB108ITF)

description:
https://www.encodeproject.org/experiments/ENCSR335GZY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR335GZY
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB108ITF
nucleic acid starting quantity: 49
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21768 cell line

value: GM21768 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: female

tag: lab

value: Coriell

value: ENCBS721CCF at ENCODE; https://www.encodeproject.org/ENCBS721CCF/


title: MO117-CGND-HRA-03441-ATAC

description: Library name: MO117-CGND-HRA-03441-ATAC

value: ALS

value: F

value: Limb


title: total RNA-seq from GM21510 (ENCLB063MCF)

description:
https://www.encodeproject.org/experiments/ENCSR330IHF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR330IHF
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB063MCF
nucleic acid starting quantity: 22
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21510 cell line

value: cell line

value: GM21510 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

tag: source

value: ENCBS567OTX at ENCODE; https://www.encodeproject.org/ENCBS567OTX/


title: total RNA-seq from HG03291 (ENCLB600ANV)

description:
https://www.encodeproject.org/experiments/ENCSR335AIJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR335AIJ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB600ANV
nucleic acid starting quantity: 34
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03291 cell line

value: HG03291 LCLs; Donor from the Esan in Nigeria (ESN)

tag: link

value: ENCBS188MCL at ENCODE; https://www.encodeproject.org/ENCBS188MCL/


title: MO115-CGND-HRA-03041-ATAC

description: Library name: MO115-CGND-HRA-03041-ATAC

tag: tissue

value: Bulbar


title: MO116-CGND-HRA-03369-ATAC

description: Library name: MO116-CGND-HRA-03369-ATAC

tag: genotype


title: total RNA-seq from GM21649 (ENCLB675XIE)

description:
https://www.encodeproject.org/experiments/ENCSR329BWL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR329BWL
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB675XIE
nucleic acid starting quantity: 34
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21649 cell line

value: GM21649 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: male

value: adult

value: ENCBS671JUB at ENCODE; https://www.encodeproject.org/ENCBS671JUB/


title: MO114-U54-HRA-185-ATAC

description: Library name: MO114-U54-HRA-185-ATAC

value: Control

tag: pmi

value: M


title: total RNA-seq from GM21420 (ENCLB875EOH)

description:
https://www.encodeproject.org/experiments/ENCSR328VZB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR328VZB
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB875EOH
nucleic acid starting quantity: 24
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21420 cell line

value: GM21420 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS565JOA at ENCODE; https://www.encodeproject.org/ENCBS565JOA/


title: total RNA-seq from HG02763 (ENCLB526RHK)

description:
https://www.encodeproject.org/experiments/ENCSR324GJH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR324GJH
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB526RHK
nucleic acid starting quantity: 23
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02763 cell line

value: HG02763 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: female

value: unknown

value: ENCBS645NZI at ENCODE; https://www.encodeproject.org/ENCBS645NZI/

value: Derived from ENCODE donor ENCDO095LOP; https://www.encodeproject.org/ENCDO095LOP/


title: MO112-CGND-HRA-02466-ATAC

description: Library name: MO112-CGND-HRA-02466-ATAC

value: ALS

tag: age at_death

value: Limb


title: total RNA-seq from HG03082 (ENCLB864XNZ)

description:
https://www.encodeproject.org/experiments/ENCSR323KRN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR323KRN
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB864XNZ
nucleic acid starting quantity: 35
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03082 cell line

value: cell line

value: HG03082 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: ENCBS213TDO at ENCODE; https://www.encodeproject.org/ENCBS213TDO/


title: MO107-U54-HRA-136-ATAC

description: Library name: MO107-U54-HRA-136-ATAC

value: F


title: total RNA-seq from HG03118 (ENCLB570KQG)

description:
https://www.encodeproject.org/experiments/ENCSR319FNG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR319FNG
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB570KQG
nucleic acid starting quantity: 41
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03118 cell line

value: HG03118 LCLs; Donor from the Esan in Nigeria (ESN)

value: male

value: adult

value: ENCBS120FPM at ENCODE; https://www.encodeproject.org/ENCBS120FPM/


title: MO110-CGND-HRA-02636-ATAC

description: Library name: MO110-CGND-HRA-02636-ATAC

value: Control

value: M


title: total RNA-seq from GM19360 (ENCLB537KNI)

description:
https://www.encodeproject.org/experiments/ENCSR318SAZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR318SAZ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB537KNI
nucleic acid starting quantity: 50
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19360 cell line

value: GM19360 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS395OSX at ENCODE; https://www.encodeproject.org/ENCBS395OSX/


title: total RNA-seq from GM21573 (ENCLB867STO)

description:
https://www.encodeproject.org/experiments/ENCSR318HAQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR318HAQ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB867STO
nucleic acid starting quantity: 38
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21573 cell line

value: GM21573 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: ENCBS852UFZ at ENCODE; https://www.encodeproject.org/ENCBS852UFZ/


title: total RNA-seq from HG02922 (ENCLB286DQQ)

description:
https://www.encodeproject.org/experiments/ENCSR316MUV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR316MUV
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB286DQQ
nucleic acid starting quantity: 25
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02922 cell line

value: HG02922 LCLs; Donor from the Esan in Nigeria (ESN)

value: female

value: ENCBS128LTF at ENCODE; https://www.encodeproject.org/ENCBS128LTF/


title: MO103-CGND-HRA-02463-ATAC

description: Library name: MO103-CGND-HRA-02463-ATAC

value: ALS

value: Limb


title: total RNA-seq from HG03189 (ENCLB386VMS)

description:
https://www.encodeproject.org/experiments/ENCSR308AAU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR308AAU
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB386VMS
nucleic acid starting quantity: 36
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03189 cell line

value: cell line

value: HG03189 LCLs; Donor from the Esan in Nigeria (ESN)

value: ENCBS933YPB at ENCODE; https://www.encodeproject.org/ENCBS933YPB/


title: MO106-U54-HRA-187-ATAC

description: Library name: MO106-U54-HRA-187-ATAC


title: MO104-CGND-HRA-03436-ATAC

description: Library name: MO104-CGND-HRA-03436-ATAC

value: F


title: total RNA-seq from HG03049 (ENCLB819NYW)

description:
https://www.encodeproject.org/experiments/ENCSR307SKY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR307SKY
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB819NYW
nucleic acid starting quantity: 27
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03049 cell line

value: HG03049 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: adult

value: ENCBS249QXP at ENCODE; https://www.encodeproject.org/ENCBS249QXP/


title: MO102-U54-HRA-139-ATAC

description: Library name: MO102-U54-HRA-139-ATAC

value: Control


title: MO101-CGND-HRA-02905-ATAC

description: Library name: MO101-CGND-HRA-02905-ATAC


title: MO123-CGND-HRA-00223-ATAC

description: Library name: MO123-CGND-HRA-00223-ATAC

value: Bulbar


title: MO099-CGND-HRA-00611-ATAC

description: Library name: MO099-CGND-HRA-00611-ATAC


title: total RNA-seq from GM21737 (ENCLB206TDH)

description:
https://www.encodeproject.org/experiments/ENCSR301GDF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR301GDF
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB206TDH
nucleic acid starting quantity: 23
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21737 cell line

value: GM21737 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: male

tag: age

value: unknown

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS411HVU at ENCODE; https://www.encodeproject.org/ENCBS411HVU/

value: Derived from ENCODE donor ENCDO381WTR; https://www.encodeproject.org/ENCDO381WTR/


title: total RNA-seq from GM21738 (ENCLB107DYL)

description:
https://www.encodeproject.org/experiments/ENCSR300UGR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR300UGR
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB107DYL
nucleic acid starting quantity: 32
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21738 cell line

tag: line

value: GM21738 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: ENCBS877ULO at ENCODE; https://www.encodeproject.org/ENCBS877ULO/


title: total RNA-seq from GM19430 (ENCLB642RXW)

description:
https://www.encodeproject.org/experiments/ENCSR297TFS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR297TFS
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB642RXW
nucleic acid starting quantity: 37
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19430 cell line

value: cell line

tag: biosample encode accession

value: GM19430 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: ENCBS361SYC at ENCODE; https://www.encodeproject.org/ENCBS361SYC/


title: MO098-CGND-HRA-03195-ATAC

description: Library name: MO098-CGND-HRA-03195-ATAC

value: ALS

value: M


title: MO096-CGND-HRA-02402-ATAC

description: Library name: MO096-CGND-HRA-02402-ATAC

value: Limb


title: total RNA-seq from HG03172 (ENCLB872ONH)

description:
https://www.encodeproject.org/experiments/ENCSR296IPK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR296IPK
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB872ONH
nucleic acid starting quantity: 41
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03172 cell line

tag: encode accession

value: HG03172 LCLs; Donor from the Esan in Nigeria (ESN)

value: adult

value: ENCBS323OHZ at ENCODE; https://www.encodeproject.org/ENCBS323OHZ/


title: total RNA-seq from HG02970 (ENCLB984WGH)

description:
https://www.encodeproject.org/experiments/ENCSR296FVA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR296FVA
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB984WGH
nucleic acid starting quantity: 34
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02970 cell line

value: HG02970 LCLs; Donor from the Esan in Nigeria (ESN)

value: female

value: ENCBS998ZPG at ENCODE; https://www.encodeproject.org/ENCBS998ZPG/

value: Derived from ENCODE donor ENCDO852FCI; https://www.encodeproject.org/ENCDO852FCI/


title: MO095-CGND-HRA-02980-ATAC

description: Library name: MO095-CGND-HRA-02980-ATAC

value: F

value: Bulbar


title: MO094-CGND-HRA-02633-ATAC

description: Library name: MO094-CGND-HRA-02633-ATAC

value: Control


title: total RNA-seq from HG03313 (ENCLB805GDB)

description:
https://www.encodeproject.org/experiments/ENCSR292FRI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR292FRI
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB805GDB
nucleic acid starting quantity: 27
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03313 cell line

tag: note

value: HG03313 LCLs; Donor from the Esan in Nigeria (ESN)

value: male

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS669TBG at ENCODE; https://www.encodeproject.org/ENCBS669TBG/


title: MO093-CGND-HRA-03516-ATAC

description: Library name: MO093-CGND-HRA-03516-ATAC

value: ALS

tag: Sex

value: M


title: total RNA-seq from GM21776 (ENCLB998ERN)

description:
https://www.encodeproject.org/experiments/ENCSR291JPP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR291JPP
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB998ERN
nucleic acid starting quantity: 29
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21776 cell line

value: cell line

value: GM21776 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: ENCBS775YPB at ENCODE; https://www.encodeproject.org/ENCBS775YPB/


title: MO092-CGND-HRA-02427-ATAC

description: Library name: MO092-CGND-HRA-02427-ATAC

tag: age at_symptom_onset


title: total RNA-seq from HG02721 (ENCLB002SZK)

description:
https://www.encodeproject.org/experiments/ENCSR291GAN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR291GAN
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB002SZK
nucleic acid starting quantity: 24
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02721 cell line

value: HG02721 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: adult

value: ENCBS993NXS at ENCODE; https://www.encodeproject.org/ENCBS993NXS/


title: MO091-CGND-HRA-03040-ATAC

description: Library name: MO091-CGND-HRA-03040-ATAC

tag: site of_motor_onset


title: total RNA-seq from HG03565 (ENCLB440ODJ)

description:
https://www.encodeproject.org/experiments/ENCSR290OZK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR290OZK
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB440ODJ
nucleic acid starting quantity: 34
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03565 cell line

value: HG03565 LCLs; Donor from the Mende in Sierra Leone (MSL)

tag: dev stage

value: unknown

value: ENCBS637OXR at ENCODE; https://www.encodeproject.org/ENCBS637OXR/

value: Derived from ENCODE donor ENCDO037SOF; https://www.encodeproject.org/ENCDO037SOF/


title: MO090-CGND-HRA-02470-ATAC

description: Library name: MO090-CGND-HRA-02470-ATAC

value: Bulbar


title: MO089-CGND-HRA-02451-ATAC

description: Library name: MO089-CGND-HRA-02451-ATAC

value: F


title: total RNA-seq from HG03472 (ENCLB839FOV)

description:
https://www.encodeproject.org/experiments/ENCSR287KOI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR287KOI
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB839FOV
nucleic acid starting quantity: 36
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03472 cell line

value: HG03472 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: male

value: Stephen Montgomery, Stanford

value: ENCBS796GSU at ENCODE; https://www.encodeproject.org/ENCBS796GSU/


title: total RNA-seq from GM18519 (ENCLB714YUD)

description:
https://www.encodeproject.org/experiments/ENCSR287BGD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR287BGD
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB714YUD
nucleic acid starting quantity: 45
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM18519 cell line

tag: description

value: GM18519 LCLs; Donor from the Yoruba in Ibadan, Nigeria (YRI)

value: Coriell

value: ENCBS725IOX at ENCODE; https://www.encodeproject.org/ENCBS725IOX/

value: Derived from ENCODE donor ENCDO531WGA; https://www.encodeproject.org/ENCDO531WGA/


title: total RNA-seq from GM21405 (ENCLB478GUR)

description:
https://www.encodeproject.org/experiments/ENCSR286VXU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR286VXU
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB478GUR
nucleic acid starting quantity: 39
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21405 cell line

value: cell line

value: GM21405 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

tag: lab

value: ENCBS022YVL at ENCODE; https://www.encodeproject.org/ENCBS022YVL/


title: MCF7 30 mg/kg SNX631-6-4

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

description:
Library name: S84
SNX_Rep4
202507_InVivo_Human_genes_TPM.xlsx
202507_InVivo_Mouse_genes_TPM.xlsx

data_processing:
Indexed sequences were checked quality by Fastqc
Indexed sequences were trimmed adaptor sequence by TrimGalore-0.4.5
Sequences were aligned to the GRCh38 using STAR v2.7.2b with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255
Read counts over annotated genes were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -B -M -O --fraction -T 10
Assembly: GRCh38 & GRCm39
Supplementary files format and content: 202507_InVitroCompiled_All_CPMTPM.xlsx file includes CPM/TPM values for each Samples, subsequent sheets include treatment group avarage CPM/TPM and DEG values.
Supplementary files format and content: 202507_InVivo_Human_genes_TPM file includes TPM values for each in vivo sample, subsequent sheets include treatment group avarage TPM and DEG values.

source_name: Xenograft

extract_protocol:
Total RNA was extracted using  Qiagen RNeasy Kits for RNA Purification kit as per manufacturer recommendations (Qiagen) and RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent) / 5200 Fragment Analyzer.
S01~S15 and S65~84 sequencing libraries were generated using NEBNext Ultra II Directional RNA Library prep Kit, S85~S96 sequencing libraries were generated using Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit FWD.

value: Xenograft

tag: cell line

tag: cell type

value: Estrogen Receptor-Positive Breast Cancer

value: WT

tag: treatment


title: total RNA-seq from GM18861 (ENCLB148MLJ)

description:
https://www.encodeproject.org/experiments/ENCSR284UWJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR284UWJ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB148MLJ
nucleic acid starting quantity: 34
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM18861 cell line

value: GM18861 LCLs; Donor from the Yoruba in Ibadan, Nigeria (YRI)

value: female

value: adult

value: unknown

tag: source

tag: link

value: ENCBS718CIS at ENCODE; https://www.encodeproject.org/ENCBS718CIS/

value: Derived from ENCODE donor ENCDO022XXF; https://www.encodeproject.org/ENCDO022XXF/


title: MCF7 30 mg/kg SNX631-6-3

description:
Library name: S83
SNX_Rep3
202507_InVivo_Human_genes_TPM.xlsx
202507_InVivo_Mouse_genes_TPM.xlsx

tag: tissue

tag: genotype


title: total RNA-seq from HG02973 (ENCLB994JUD)

description:
https://www.encodeproject.org/experiments/ENCSR283KGT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR283KGT
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB994JUD
nucleic acid starting quantity: 29
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02973 cell line

tag: line

value: HG02973 LCLs; Donor from the Esan in Nigeria (ESN)

value: male

tag: age

value: Stephen Montgomery, Stanford

value: ENCBS888IRD at ENCODE; https://www.encodeproject.org/ENCBS888IRD/

value: Derived from ENCODE donor ENCDO771VFC; https://www.encodeproject.org/ENCDO771VFC/


title: MCF7 30 mg/kg SNX631-6-2

description:
Library name: S82
SNX_Rep2
202507_InVivo_Human_genes_TPM.xlsx
202507_InVivo_Mouse_genes_TPM.xlsx


title: MCF7 50 mg/kg Palbo and 30 mg/kg SNX631-6-5

description:
Library name: S79
COMBO_Rep5
202507_InVivo_Human_genes_TPM.xlsx
202507_InVivo_Mouse_genes_TPM.xlsx

value: 50 mg/kg Palbociclib isethionate + 30 mg/kg SNX631-6


title: MCF7 50 mg/kg Palbo and 30 mg/kg SNX631-6-4

description:
Library name: S78
COMBO_Rep4
202507_InVivo_Human_genes_TPM.xlsx
202507_InVivo_Mouse_genes_TPM.xlsx


title: total RNA-seq from GM21785 (ENCLB982ZVW)

description:
https://www.encodeproject.org/experiments/ENCSR282JJL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR282JJL
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB982ZVW
nucleic acid starting quantity: 3
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21785 cell line

value: cell line

tag: biosample encode accession

tag: encode accession

value: GM21785 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: Coriell

value: ENCBS861CJQ at ENCODE; https://www.encodeproject.org/ENCBS861CJQ/


title: total RNA-seq from HG03280 (ENCLB817TCP)

description:
https://www.encodeproject.org/experiments/ENCSR280NHG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR280NHG
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB817TCP
nucleic acid starting quantity: 40
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03280 cell line

value: HG03280 LCLs; Donor from the Esan in Nigeria (ESN)

tag: Sex

value: ENCBS424WPI at ENCODE; https://www.encodeproject.org/ENCBS424WPI/

value: Derived from ENCODE donor ENCDO069UGQ; https://www.encodeproject.org/ENCDO069UGQ/


title: MCF7 50 mg/kg Palbo and 30 mg/kg SNX631-6-3

description:
Library name: S77
COMBO_Rep3
202507_InVivo_Human_genes_TPM.xlsx
202507_InVivo_Mouse_genes_TPM.xlsx

value: Xenograft

value: Estrogen Receptor-Positive Breast Cancer

value: WT


title: total RNA-seq from HG02944 (ENCLB414YOH)

description:
https://www.encodeproject.org/experiments/ENCSR279XCC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR279XCC
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB414YOH
nucleic acid starting quantity: 3
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02944 cell line

tag: note

value: HG02944 LCLs; Donor from the Esan in Nigeria (ESN)

value: adult

value: ENCBS563PZO at ENCODE; https://www.encodeproject.org/ENCBS563PZO/


title: MCF7 50 mg/kg Palbo and 30 mg/kg SNX631-6-2

description:
Library name: S76
COMBO_Rep2
202507_InVivo_Human_genes_TPM.xlsx
202507_InVivo_Mouse_genes_TPM.xlsx


title: total RNA-seq from GM21622 (ENCLB098USC)

description:
https://www.encodeproject.org/experiments/ENCSR277HKQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR277HKQ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB098USC
nucleic acid starting quantity: 17
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21622 cell line

value: GM21622 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: female

value: Stephen Montgomery, Stanford

value: ENCBS386ARM at ENCODE; https://www.encodeproject.org/ENCBS386ARM/


title: MCF7 50 mg/kg Palbo and 30 mg/kg SNX631-6-1

description:
Library name: S75
COMBO_Rep1
202507_InVivo_Human_genes_TPM.xlsx
202507_InVivo_Mouse_genes_TPM.xlsx

value: 50 mg/kg Palbociclib isethionate + 30 mg/kg SNX631-6


title: total RNA-seq from HG02891 (ENCLB337KPV)

description:
https://www.encodeproject.org/experiments/ENCSR273CUX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR273CUX
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB337KPV
nucleic acid starting quantity: 26
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02891 cell line

value: cell line

value: HG02891 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: ENCBS591CYW at ENCODE; https://www.encodeproject.org/ENCBS591CYW/


title: MCF7 50 mg/kg Palbo-4

description:
Library name: S74
PALBO_Rep4
202507_InVivo_Human_genes_TPM.xlsx
202507_InVivo_Mouse_genes_TPM.xlsx

value: 50 mg/kg Palbociclib isethionate


title: total RNA-seq from GM21596 (ENCLB605RHM)

description:
https://www.encodeproject.org/experiments/ENCSR273BGW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR273BGW
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB605RHM
nucleic acid starting quantity: 30
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21596 cell line

value: GM21596 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: male

value: Coriell

value: ENCBS951DAQ at ENCODE; https://www.encodeproject.org/ENCBS951DAQ/


title: MCF7 50 mg/kg Palbo-3

description:
Library name: S72
PALBO_Rep3
202507_InVivo_Human_genes_TPM.xlsx
202507_InVivo_Mouse_genes_TPM.xlsx

value: Xenograft

value: Estrogen Receptor-Positive Breast Cancer

value: WT


title: total RNA-seq from HG02562 (ENCLB530HCY)

description:
https://www.encodeproject.org/experiments/ENCSR272DJF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR272DJF
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB530HCY
nucleic acid starting quantity: 32
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02562 cell line

value: HG02562 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: adult

value: ENCBS106NLI at ENCODE; https://www.encodeproject.org/ENCBS106NLI/


title: total RNA-seq from GM21617 (ENCLB069WHA)

description:
https://www.encodeproject.org/experiments/ENCSR272BGX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR272BGX
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB069WHA
nucleic acid starting quantity: 27
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21617 cell line

value: GM21617 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: female

value: Stephen Montgomery, Stanford

value: ENCBS004DPX at ENCODE; https://www.encodeproject.org/ENCBS004DPX/


title: MCF7 50 mg/kg Palbo-1

description:
Library name: S70
PALBO_Rep1
202507_InVivo_Human_genes_TPM.xlsx
202507_InVivo_Mouse_genes_TPM.xlsx


title: total RNA-seq from HG02679 (ENCLB533QWQ)

description:
https://www.encodeproject.org/experiments/ENCSR270JED/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR270JED
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB533QWQ
nucleic acid starting quantity: 30
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02679 cell line

value: cell line

value: HG02679 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: ENCBS190HUG at ENCODE; https://www.encodeproject.org/ENCBS190HUG/


title: total RNA-seq from HG03091 (ENCLB878VPQ)

description:
https://www.encodeproject.org/experiments/ENCSR269JGO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR269JGO
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB878VPQ
nucleic acid starting quantity: 28
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03091 cell line

value: HG03091 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: ENCBS918YEL at ENCODE; https://www.encodeproject.org/ENCBS918YEL/


title: MCF7 Vehicle Control-4

description:
Library name: S69
Veh_Rep4
202507_InVivo_Human_genes_TPM.xlsx
202507_InVivo_Mouse_genes_TPM.xlsx

value: Vehicle 70% PEG400/ 30% Propylene Glycol


title: MCF7 Vehicle Control-3

description:
Library name: S67
Veh_Rep3
202507_InVivo_Human_genes_TPM.xlsx
202507_InVivo_Mouse_genes_TPM.xlsx


title: total RNA-seq from GM18487 (ENCLB837UUA)

description:
https://www.encodeproject.org/experiments/ENCSR267HYR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR267HYR
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB837UUA
nucleic acid starting quantity: 30
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM18487 cell line

value: GM18487 LCLs; Donor from the Yoruba in Ibadan, Nigeria (YRI)

value: male

value: Coriell

value: ENCBS145YVN at ENCODE; https://www.encodeproject.org/ENCBS145YVN/


title: MCF7 Vehicle Control-2

description:
Library name: S66
Veh_Rep2
202507_InVivo_Human_genes_TPM.xlsx
202507_InVivo_Mouse_genes_TPM.xlsx

value: Xenograft

value: Estrogen Receptor-Positive Breast Cancer

value: WT


title: MCF7 30 mg/kg SNX631-6-1

description:
Library name: S80
SNX_Rep1
202507_InVivo_Human_genes_TPM.xlsx
202507_InVivo_Mouse_genes_TPM.xlsx


title: total RNA-seq from HG03114 (ENCLB240XHX)

description:
https://www.encodeproject.org/experiments/ENCSR264ICG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR264ICG
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB240XHX
nucleic acid starting quantity: 26
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03114 cell line

value: HG03114 LCLs; Donor from the Esan in Nigeria (ESN)

value: adult

value: ENCBS459GSH at ENCODE; https://www.encodeproject.org/ENCBS459GSH/


title: MCF7 Vehicle Control-1

description:
Library name: S65
Veh_Rep1
202507_InVivo_Human_genes_TPM.xlsx
202507_InVivo_Mouse_genes_TPM.xlsx


title: total RNA-seq from GM19332 (ENCLB105YST)

description:
https://www.encodeproject.org/experiments/ENCSR264HRG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR264HRG
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB105YST
nucleic acid starting quantity: 23
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19332 cell line

value: GM19332 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: female

value: Stephen Montgomery, Stanford

value: ENCBS382WFT at ENCODE; https://www.encodeproject.org/ENCBS382WFT/


title: total RNA-seq from GM19372 (ENCLB492ORS)

description:
https://www.encodeproject.org/experiments/ENCSR262DEI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR262DEI
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB492ORS
nucleic acid starting quantity: 32
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19372 cell line

value: cell line

value: GM19372 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: unknown

value: ENCBS059VNF at ENCODE; https://www.encodeproject.org/ENCBS059VNF/

value: Derived from ENCODE donor ENCDO805VUT; https://www.encodeproject.org/ENCDO805VUT/


title: snATAC-seq from astrocyte (ENCLB587ZBU)

description:
https://www.encodeproject.org/experiments/ENCSR986YGY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR986YGY
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB587ZBU
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (53 years) astrocyte in vitro differentiated cells nuclear fraction

value: astrocyte

value: in vitro differentiated cells

value: PGP1 derived astrocytes

value: male

value: 53 year

value: Bradley Bernstein, Broad

tag: subcellular fraction term name

value: nucleus

value: George Church

value: ENCBS521QAI at ENCODE; https://www.encodeproject.org/ENCBS521QAI/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: total RNA-seq from GM21769 (ENCLB295GVH)

description:
https://www.encodeproject.org/experiments/ENCSR261LTY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR261LTY
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB295GVH
nucleic acid starting quantity: 38
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21769 cell line

value: GM21769 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: female

tag: dev stage

value: adult

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS155OYA at ENCODE; https://www.encodeproject.org/ENCBS155OYA/


title: TF ChIP-seq from K562 (ENCLB344HFT)

description:
https://www.encodeproject.org/experiments/ENCSR985RPY/
***************
biological replicate number: 1
technical replicate number: 1
description: TEAD4 ChIP-seq on K562 cells treated with shRNA targeting GATA1
experiment encode accession: ENCSR985RPY
assay title: TF ChIP-seq
possible controls: ENCSR562EHT
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB344HFT
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line expressing RNAi targeting H. sapiens GATA1

tag: antibody

value: cell line

tag: health state

value: chronic myelogenous leukemia (CML)

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS886MUY at ENCODE; https://www.encodeproject.org/ENCBS886MUY/


title: total RNA-seq from GM21615 (ENCLB326FWT)

description:
https://www.encodeproject.org/experiments/ENCSR257XFI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR257XFI
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB326FWT
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21615 cell line

value: GM21615 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

tag: lab

value: ENCBS092DRT at ENCODE; https://www.encodeproject.org/ENCBS092DRT/


title: TF ChIP-seq from K562 (ENCLB710VTG)

description:
https://www.encodeproject.org/experiments/ENCSR985RPY/
***************
biological replicate number: 2
technical replicate number: 1
description: TEAD4 ChIP-seq on K562 cells treated with shRNA targeting GATA1
experiment encode accession: ENCSR985RPY
assay title: TF ChIP-seq
possible controls: ENCSR562EHT
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB710VTG
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: 53 year

value: ENCBS282PEG at ENCODE; https://www.encodeproject.org/ENCBS282PEG/


title: total RNA-seq from HG03351 (ENCLB992JZT)

description:
https://www.encodeproject.org/experiments/ENCSR256ODN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR256ODN
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB992JZT
nucleic acid starting quantity: 22
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03351 cell line

value: HG03351 LCLs; Donor from the Esan in Nigeria (ESN)

value: ENCBS781WDB at ENCODE; https://www.encodeproject.org/ENCBS781WDB/


title: Control ChIP-seq from HepG2 (ENCLB689XNG)

description:
https://www.encodeproject.org/experiments/ENCSR981UIH/
***************
biological replicate number: 1
technical replicate number: 1
description: TEAD4 ChIP-seq on HepG2 cells treated with vector control shRNA
experiment encode accession: ENCSR981UIH
assay title: Control ChIP-seq
possible controls: ENCSR482BUK
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB689XNG
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens HepG2 cell line

value: Homo sapiens HepG2 cell line transduced with doxycycline-inducible shRNA targeting FOXA3. Cells were treated for 72 hours with 4ug/mL doxycycline prior to experiment harvest.

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS205EMK at ENCODE; https://www.encodeproject.org/ENCBS205EMK/


title: total RNA-seq from HG03303 (ENCLB049UFQ)

description:
https://www.encodeproject.org/experiments/ENCSR255NTN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR255NTN
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB049UFQ
nucleic acid starting quantity: 17
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03303 cell line

value: cell line

value: HG03303 LCLs; Donor from the Esan in Nigeria (ESN)

value: female

value: adult

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS814EUS at ENCODE; https://www.encodeproject.org/ENCBS814EUS/


title: total RNA-seq from HG02923 (ENCLB637MTB)

description:
https://www.encodeproject.org/experiments/ENCSR255EMJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR255EMJ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB637MTB
nucleic acid starting quantity: 29
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02923 cell line

value: HG02923 LCLs; Donor from the Esan in Nigeria (ESN)

value: ENCBS216ADO at ENCODE; https://www.encodeproject.org/ENCBS216ADO/


title: snATAC-seq from psoas muscle (ENCLB025AYB)

description:
https://www.encodeproject.org/experiments/ENCSR963HLE/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human psoas muscle
experiment encode accession: ENCSR963HLE
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB025AYB
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens female adult (61 years) psoas muscle tissue, preserved by flash-freezing nuclear fraction

value: psoas muscle

value: tissue

value: DM:no; HTN:no; CAD:no; lungs with moderate emphysema

value: 61 year

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS895JXQ at ENCODE; https://www.encodeproject.org/ENCBS895JXQ/

value: Derived from ENCODE donor ENCDO186XRB; https://www.encodeproject.org/ENCDO186XRB/


title: MCF7 50 mg/kg Palbo-2

description:
Library name: S71
PALBO_Rep2
202507_InVivo_Human_genes_TPM.xlsx
202507_InVivo_Mouse_genes_TPM.xlsx

source_name: Xenograft

value: Xenograft

tag: cell line

tag: cell type

value: Estrogen Receptor-Positive Breast Cancer

value: WT

value: 50 mg/kg Palbociclib isethionate


title: total RNA-seq from CD14-positive monocyte (ENCLB450BLO)

description:
https://www.encodeproject.org/experiments/ENCSR252NGG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR252NGG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB450BLO

source_name: Homo sapiens male adult (24 years) CD14-positive monocyte primary cell

value: CD14-positive monocyte

value: primary cell

value: male

value: adult

value: 24 year

value: John Stamatoyannopoulos, UW

tag: source

value: Shelly Heimfeld

value: ENCBS046EKV at ENCODE; https://www.encodeproject.org/ENCBS046EKV/


title: snATAC-seq from heart left ventricle (ENCLB071SWF)

description:
https://www.encodeproject.org/experiments/ENCSR960IDI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR960IDI
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB071SWF
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (69 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: ischemic

value: 69 year

value: Michael Snyder, Stanford

value: Shin Lin

tag: link

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

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


title: total RNA-seq from HG03157 (ENCLB415QFI)

description:
https://www.encodeproject.org/experiments/ENCSR251NJW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR251NJW
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB415QFI
nucleic acid starting quantity: 39
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03157 cell line

value: cell line

value: HG03157 LCLs; Donor from the Esan in Nigeria (ESN)

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS713OAJ at ENCODE; https://www.encodeproject.org/ENCBS713OAJ/


title: snATAC-seq from heart left ventricle (ENCLB057DFI)

description:
https://www.encodeproject.org/experiments/ENCSR958FFE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR958FFE
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB057DFI
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (37 years) heart left ventricle tissue, preserved by flash-freezing

value: male

value: healthy

value: adult

value: 37 year

value: ENCBS183VKV at ENCODE; https://www.encodeproject.org/ENCBS183VKV/

value: Derived from ENCODE donor ENCDO123GXG; https://www.encodeproject.org/ENCDO123GXG/


title: total RNA-seq from GM19461 (ENCLB147NGF)

description:
https://www.encodeproject.org/experiments/ENCSR247BNP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR247BNP
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB147NGF
nucleic acid starting quantity: 32
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19461 cell line

value: GM19461 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: ENCBS003FIP at ENCODE; https://www.encodeproject.org/ENCBS003FIP/


title: V242-CGND-HRA-02472-D

description: Library name: V242-CGND-HRA-02472-D

tag: tissue

tag: subject id

tag: diagnosis

value: ALS

tag: pmi

value: M

tag: rin


title: V242-CGND-HRA-02472-C

description: Library name: V242-CGND-HRA-02472-C

tag: Sex

tag: age


title: snATAC-seq from heart left ventricle (ENCLB376ALY)

description:
https://www.encodeproject.org/experiments/ENCSR951AID/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR951AID
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB376ALY
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (51 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: female

value: 51 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS303DQG at ENCODE; https://www.encodeproject.org/ENCBS303DQG/

value: Derived from ENCODE donor ENCDO068KYD; https://www.encodeproject.org/ENCDO068KYD/


title: snATAC-seq from SK-N-SH (ENCLB573OLH)

description:
https://www.encodeproject.org/experiments/ENCSR989MQQ/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human cell line SK-N-SH (RA treated)
experiment encode accession: ENCSR989MQQ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB573OLH
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens SK-N-SH cell line treated with 6 uM all-trans-retinoic acid for 48 hours nuclear fraction

tag: line

value: SK-N-SH

value: cell line

value: Metastatic neuroblastoma from bone marrow

tag: dev stage

value: child

value: 4 year

tag: subcellular fraction term name

value: nucleus

value: ATCC

tag: treatments

value: treatment_term_id:CHEBI:15367; treatment_term_name:all-trans-retinoic acid; treatment_type:chemical; duration:48; duration_units:hour;

value: ENCBS781UZE at ENCODE; https://www.encodeproject.org/ENCBS781UZE/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/


title: total RNA-seq from HG02678 (ENCLB455KUS)

description:
https://www.encodeproject.org/experiments/ENCSR263KTR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR263KTR
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB455KUS
nucleic acid starting quantity: 37
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02678 cell line

value: HG02678 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: male

value: adult

value: unknown

tag: lab

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS373UGJ at ENCODE; https://www.encodeproject.org/ENCBS373UGJ/

value: Derived from ENCODE donor ENCDO116OHH; https://www.encodeproject.org/ENCDO116OHH/


title: total RNA-seq from HG03363 (ENCLB948CSO)

description:
https://www.encodeproject.org/experiments/ENCSR245LXH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR245LXH
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB948CSO
nucleic acid starting quantity: 29
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03363 cell line

value: cell line

tag: encode accession

tag: note

value: HG03363 LCLs; Donor from the Esan in Nigeria (ESN)

value: female

value: ENCBS260TRB at ENCODE; https://www.encodeproject.org/ENCBS260TRB/


title: snATAC-seq from T-helper 2 cell (ENCLB692XUT)

description:
https://www.encodeproject.org/experiments/ENCSR932LAJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR932LAJ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB692XUT
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (35 years) T-helper 2 primary cell treated with 5 ug/mL Interferon-gamma antibody, 100 ng/mL Interleukin-4 nuclear fraction

value: T-helper 2 cell

value: primary cell

value: 35 year

value: Yijun Ruan, JAX

value: nucleus

tag: source

value: AllCells

value: treatment_term_name:Interferon-gamma antibody; treatment_type:antibody; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein;

value: ENCBS347BFK at ENCODE; https://www.encodeproject.org/ENCBS347BFK/

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


title: snATAC-seq from heart left ventricle (ENCLB714RNW)

description:
https://www.encodeproject.org/experiments/ENCSR987PQH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR987PQH
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-08-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB714RNW
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (32 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: adult

value: 32 year

value: Michael Snyder, Stanford

value: Shin Lin

tag: health state

value: healthy

tag: link

value: ENCBS684NAD at ENCODE; https://www.encodeproject.org/ENCBS684NAD/

value: Derived from ENCODE donor ENCDO212WIV; https://www.encodeproject.org/ENCDO212WIV/


title: total RNA-seq from HG03124 (ENCLB382BHX)

description:
https://www.encodeproject.org/experiments/ENCSR244TCU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR244TCU
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB382BHX
nucleic acid starting quantity: 33
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03124 cell line

value: cell line

value: HG03124 LCLs; Donor from the Esan in Nigeria (ESN)

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS854QDP at ENCODE; https://www.encodeproject.org/ENCBS854QDP/


title: snATAC-seq from mucosa of urinary bladder (ENCLB957NOS)

description:
https://www.encodeproject.org/experiments/ENCSR927MVL/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human mucosa of urinary bladder
experiment encode accession: ENCSR927MVL
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB957NOS
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

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

value: mucosa of urinary bladder

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

value: 26 year

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS867VLU at ENCODE; https://www.encodeproject.org/ENCBS867VLU/

value: Derived from ENCODE donor ENCDO221IPH; https://www.encodeproject.org/ENCDO221IPH/


title: snATAC-seq from mucosa of descending colon (ENCLB472WOW)

description:
https://www.encodeproject.org/experiments/ENCSR922FEK/
***************
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 (ENCSR460MGC).
experiment encode accession: ENCSR922FEK
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB472WOW
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens female adult (61 years) mucosa of descending colon tissue, preserved by flash-freezing nuclear fraction

value: mucosa of descending colon

value: tissue

value: female

value: DM:no; HTN:no; CAD:no; lungs with moderate emphysema

value: adult

value: 61 year

value: Michael Snyder, Stanford

value: ENCBS825JLE at ENCODE; https://www.encodeproject.org/ENCBS825JLE/

value: Derived from ENCODE donor ENCDO186XRB; https://www.encodeproject.org/ENCDO186XRB/


title: total RNA-seq from GM19334 (ENCLB970CBX)

description:
https://www.encodeproject.org/experiments/ENCSR243MXR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR243MXR
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB970CBX
nucleic acid starting quantity: 41
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19334 cell line

value: cell line

value: GM19334 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: male

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS457RIJ at ENCODE; https://www.encodeproject.org/ENCBS457RIJ/


title: total RNA-seq from GM21368 (ENCLB240RQQ)

description:
https://www.encodeproject.org/experiments/ENCSR240OYY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR240OYY
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB240RQQ
nucleic acid starting quantity: 31
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21368 cell line

value: GM21368 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: ENCBS030IBD at ENCODE; https://www.encodeproject.org/ENCBS030IBD/