title: total RNA-seq from GM19457 (ENCLB527UVD)

description:
https://www.encodeproject.org/experiments/ENCSR916BPD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR916BPD
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB527UVD
nucleic acid starting quantity: 30
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19457 cell line

value: cell line

value: GM19457 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: ENCBS000KQU at ENCODE; https://www.encodeproject.org/ENCBS000KQU/


title: V370-CGND-HRA-00235-A

status: Public on Jul 24 2026

type: SRA

city: New York

first: Christopher

last: Jackson

state: NY

address: 101 Avenue of the Americas

department: Center for the Genomics of Neurodegenerative Disease

country: USA

institute: New York Genome Center

description: Library name: V370-CGND-HRA-00235-A

library_source: transcriptomic

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

molecule: polyA RNA

organism: Homo sapiens

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: tissue

tag: subject id

tag: diagnosis

value: ALS

tag: pmi

tag: Sex

value: F

tag: age

tag: rin


title: input ABA imbibed rep2

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

description:
Library name: inp_ABA_2
OK

data_processing:
In our sequencing strategy, the R1 reads of pooled libraries contain two parts of UMI split by the barcode. We rearrange UMI sequences to position them next to each other and remove additional low-quality nucleotides, including  the oligo(dT) fragment and those that follow it. For this, we utilise the awk command: awk 'NR%2==1 {print $0} NR%2==0 {print substr($1,16,5) substr($1,1,15)}'
Fastq files for read R2 of pooled libraries were demultiplexed into separate fastq files for each replicate using BRBseqTools (v 1.6) Demultiplex and R1 with parameters -p UB -UMI 14 -n 1. The resulting reads were trimmed to eliminate potential contamination with the poly(A) tail using BRBseqTools (v 1.6) Trim and parameters -polyA 10 -minLength 30. Then, they were mapped using STAR (v 2.7.8a) with parameters --sjdbOverhang 99 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1. Finally, the deduplicated counts for each gene were obtained using BRBseqTools (v 1.6) CreateDGEMatrix with parameters -p UB -UMI 14 -s yes.
Assembly: TAIR10
Supplementary files format and content: gene count text files

molecule: total RNA

organism: Arabidopsis thaliana

source_name: seed

growth_protocol: Plants were grown in a greenhouse under a long day-night cycle at 22°C. Seeds from 8 to 12 plants were combined to create a single biological replicate.

extract_protocol:
RNA was isolated according to a standard seed protocol (https://doi.org/10.1002/biot.200900211). For 4-SU labelled RNAs enrichment, biotinylation was performed for 15 μg of freshly isolated RNA in a 200 μl reaction mixture (10 mM Tris pH 7.5; 1 mM EDTA; 0.2 mg/ml EZ-Link Biotin-HPDP (ThermoFisher)) for 1.5 h at 22°C. A portion of the RNA (250 ng) was retained as an input. Unbound Biotin-HPDP was removed by chloroform/isoamyl alcohol (24:1) extraction. Subsequently, a 1/10 volume of 5 M NaCl and an equal volume of isopropanol were added, and RNA was precipitated by centrifugation at 20,000g for 20 minutes. The pellet was washed with 1 ml of 80% ethanol, and after drying, it was resuspended in 25 μl of RNase-free water. Biotinylated RNA was purified using 50 μl of streptavidin C1 Dynabeads (ThermoFisher). The beads were washed in binding buffer (0.2 M NaCl; 0.1 M sodium phosphate pH 6.8; 25 mM MgCl2; 0.4% Tween), blocked in the binding buffer with 1 μg/μl glycogen for 10 minutes, and washed again in binding buffer. RNA samples were denatured at 65°C for 5 minutes, followed by 5 minutes on ice. Then, 25 μl of 2x binding buffer and 50 μl of washed streptavidin beads were added, mixed, and incubated at 22°C with gentle shaking for 20 minutes. The beads were washed three times with 0.5 ml of washing buffer (100 mM Tris-HCl pH 7.5; 10 mM EDTA; 1 M NaCl; 0.1% Tween20) at 65°C, followed by three washes at room temperature. Biotinylated RNA was eluted from the beads by two incubations with 50 μl of 200 mM DTT. RNA from the combined eluates was purified using RNA Clean & Concentrator-5 columns (Zymo), following the protocol for long RNA purification with DNase treatment. The entire volume of the sample was used for reverse transcription.
Input and enriched RNA samples were used in reverse transcription with 50 mM of various barcoded oligo(dT) primers and SuperScript III. 0.4 of each input and whole enriched RNA RT reaction were pooled. cDNA pools were purified with Ampure beads (1.5x beads to sample volumes) and then eluted in 17 µl of water. 15 µl of the recovered cDNA pools were mixed by pipetting with 15 µl of the second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 30 µM dNTPs) and incubated overnight at 16°C. The reactions were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 µl of water. 3 µl of the recovered dsDNA samples were used for tagmentation with 3 µl of 5x diluted B-loaded Tn5 enzyme (homemade) and 6 µl of freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). The reactions were mixed by pipetting and incubated for 7 minutes at 55°C, followed by 5 minutes at 80°C. Water was added to a total volume of 36 µl; samples were purified with Ampure beads (0.85x beads to sample volumes) and eluted with 21 µl of water. Illumina indexing PCRs were performed using 20 µl of the tagmented DNA in a 50 µl reaction with Q5 2× PCR Master Mix (NEB) and a final concentration of 0.5 µM of primers. Libraries were sequenced on the Illumina Nova-seq to obtain two reads: R1 (containing barcode and UMI) and R2 (containing mRNA sequence).

treatment_protocol: Seeds were imbibed for 6h in the presence of 2 mM 4-thiouridine (Merck; from a 50 mM stock solution in 6% methanol), and 3 μM ABA (Merck; from a 1 mM stock solution in ethanol), 100 μM antabactin (Kerafst; from a 50 mM stock solution in DMSO), or the respective mock solution.

value: seed

tag: ecotype

tag: treatment

value: ABA

tag: treatment enrichment

value: input

tag: batch


title: total RNA-seq from HG02722 (ENCLB165IDX)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR914CLE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR914CLE
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB165IDX
nucleic acid starting quantity: 36
nucleic acid starting quantity units: µg

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

source_name: Homo sapiens HG02722 cell line

extract_protocol: not provided

tag: line

tag: biosample encode accession

tag: encode accession

tag: note

value: HG02722 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: female

tag: dev stage

value: adult

tag: lab

value: Stephen Montgomery, Stanford

tag: source

value: Coriell

tag: link

value: ENCBS939JSI at ENCODE; https://www.encodeproject.org/ENCBS939JSI/


title: V370-CGND-HRA-00235-B

description: Library name: V370-CGND-HRA-00235-B

tag: tissue

tag: subject id

tag: diagnosis


title: V366-CGND-HRA-03419-D

description: Library name: V366-CGND-HRA-03419-D

tag: pmi

tag: Sex

value: M

tag: age


title: V365-CGND-HRA-03441-B

description: Library name: V365-CGND-HRA-03441-B

tag: rin


title: total RNA-seq from GM21733 (ENCLB566ZOY)

description:
https://www.encodeproject.org/experiments/ENCSR913TLO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR913TLO
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB566ZOY
nucleic acid starting quantity: 43
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21733 cell line

value: GM21733 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: ENCBS257QXB at ENCODE; https://www.encodeproject.org/ENCBS257QXB/


title: total RNA-seq from GM21479 (ENCLB048LPU)

description:
https://www.encodeproject.org/experiments/ENCSR913FIO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR913FIO
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB048LPU
nucleic acid starting quantity: 28
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21479 cell line

value: cell line

value: GM21479 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: ENCBS346HFH at ENCODE; https://www.encodeproject.org/ENCBS346HFH/


title: total RNA-seq from HG03419 (ENCLB726GEX)

description:
https://www.encodeproject.org/experiments/ENCSR914JWB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR914JWB
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB726GEX
nucleic acid starting quantity: 37
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03419 cell line

value: HG03419 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: ENCBS478VNC at ENCODE; https://www.encodeproject.org/ENCBS478VNC/


title: Normal skin and keloid_Asian

type: RNA

city: Los Angeles

first: Min

last: Deng

address: 650 Charles E. Young Dr. S., CHS-52-139

department: Medicine

institute: University of California, Los Angeles

hyb_protocol: A total of 360 genes were included in the analysis. Gene panel probe hybridization occurred overnight for 18 hours at 50°C. Slides were washed the next day to remove unbound probes. Ligase was added to circularize the paired ends of bound probes (2 hours at 37°C) followed by enzymatic rolling circle amplification (2 hours at 30°C). Slides were washed in TE buffer before background fluorescence was chemically quenched.

scan_protocol: Imaging processing, decoding, quality score generation, and DAPI-based cell segmentation was automatically performed by the Xenium Analyzer system. Data was analyzed on version xenium-4.1.1

data_processing: Xenium Onboard Analysis: 4.4.0. R using Seurat v5.3.0 packages.

label: Xenium probe set

source_name: One normal skin and one keloid from Asian

label_protocol: Xenium probe set

growth_protocol: Not applicable; primary human tissue.

extract_protocol: tissue preparation protocol: Tissue sections were cut at a thickness of 10µM and placed onto a Xenium slide followed by fixation and permeabilization.

treatment_protocol: Human skin tissue was formalin-fixed and paraffin-embedded. Tissue sections were prepared according to the 10x Genomics Xenium In Situ tissue-preparation protocol and placed on Xenium slides.

value: Skin

tag: tissue preservation method

value: FFPE

tag: treatment

value: Normal Skin and Keloid


title: V365-CGND-HRA-03441-A

description: Library name: V365-CGND-HRA-03441-A

value: ALS

value: F


title: total RNA-seq from HG02943 (ENCLB687CSP)

description:
https://www.encodeproject.org/experiments/ENCSR911ZBO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR911ZBO
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB687CSP
nucleic acid starting quantity: 36
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02943 cell line

tag: line

tag: description

value: HG02943 LCLs; Donor from the Esan in Nigeria (ESN)

value: female

value: adult

value: unknown

value: ENCBS899YBP at ENCODE; https://www.encodeproject.org/ENCBS899YBP/

value: Derived from ENCODE donor ENCDO610AIZ; https://www.encodeproject.org/ENCDO610AIZ/


title: total RNA-seq from GM21512 (ENCLB378XAH)

description:
https://www.encodeproject.org/experiments/ENCSR911SHG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR911SHG
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB378XAH
nucleic acid starting quantity: 36
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21512 cell line

tag: biosample encode accession

tag: encode accession

value: GM21512 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: male

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS802KZR at ENCODE; https://www.encodeproject.org/ENCBS802KZR/


title: V364-CGND-HRA-03441-A

description: Library name: V364-CGND-HRA-03441-A


title: V364-CGND-HRA-03441-B

description: Library name: V364-CGND-HRA-03441-B


title: zuo1 S288C, MG132 45min, biol rep 2, flowcell 1

city: Baltimore

first: Jeff

last: Coller

state: MD

address: 725 N Wolfe St

institute: Johns Hopkins University

description:
Library name: zuo1-MG-2
flowcell 1

data_processing:
FASTQs were passed through FASTQC  to identify possible adapter contamination or sequencing biases prior to processing. Read ends below quality cutoffs of 30 were removed with cutadapt v4.9 with the following parameters: -q 30,30 -m 1. FASTQs were mapped to a noncoding gene reference pulled from the Saccharomyces Genome Database ‘rna_coding’, including rRNA, tRNA, snRNA, snoRNA, and other ncRNA sequences, using Bowtie2 v2.4.4  with the following parameters: -q -p 8 --local --quiet. Reads unmapped by Bowtie2 were subsequently mapped to the pre-compiled Hisat2 R64-1-1 genome reference using Hisat2 v2.2.1  with the following parameters: -q -p 8 --quiet --rna-strandedness F. Footprint length distributions were obtained from samtools v1.21, and mapped reads were subsetted to RPFs of 20-29 nucleotides for downstream analysis.
Assembly: NCBI Saccharomyces cerevisiae S288C Genome Assembly R64 (GCF_000146045.2)
Supplementary files format and content: The processed data is a data frame in tab-delimited format with reads as rows. Columns represent characteristics of the reads, with A,P, and E-site amino acids and codons annotated. Samples are indicated in the ‘sampleType’ column.
Library strategy: Ribo-Seq

molecule: cytoplasmic RNA

organism: Saccharomyces cerevisiae

growth_protocol: Cells were seeded at an OD600 of 0.1 in YPD media and grown at room temperature to an OD600 of 0.4, at which time treatment was performed.

extract_protocol:
Cell pellets were resuspended in 200 µL Phenol/LET (100 mM LiCl, 20 mM EDTA, 25 mM Tris-HCl pH 8) and approximately 200 µL of glass microbeads were added to lyse the cells. After vortexing for 5 minutes at room temperature, 300 µL of Phenol/Chloroform/LET and 300 µL DEPC-treated water was added. After 5 minutes of additional vortexing, and spinning down for 5 minutes at 16,000 x g at room temperature, aqueous phase was collected and added to 500 µL Phenol/Chloroform/LET, vortexed for 5 minutes and spun down. Aqueous phase was collected and added to 500 µL Chloroform, vortexed for 5 minutes, and spun down. Aqueous phase was collected, 40 µL of 3 M Sodium Acetate (final concentration 0.3 M), 1 mL 100% ethanol was added to precipitate RNA at -20°C for approximately 1 hour. RNA was pelleted by spinning at 16,000 x g for 20 minutes at room temperature, washed with 75% ethanol, air dried, and resuspended in DEPC-treated water.
or MG132 and AZC treatment, both wild-type and zuo1Δ strains carried a PDR5 deletion to enable MG132 treatment. Cells were grown to an OD600 of 0.5 to 0.7 in 100 mL YPD media, and two 50 mL aliquots of culture were each treated with 100 µM MG132 with or without 2 mg/mL AZC at 24°C for 45 minutes. Upon collection, cultures were filtered using a 0.45 µm Whatman membrane (GE Life Sciences, USA) using a vacuum filter apparatus. After filtration, Cells were immediately scraped from the filter with a straight-edge metal spatula and plunged into 50 mL liquid nitrogen. Next, samples were ground using a Spex 6775 freezing grinding mill (Spex sample prep, USA) in the presence of 10 mL lysis buffer (20 mM Tris (pH 7.4), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/mL cycloheximide, 1% Triton X-100, 25 U/mL DNase I). The RNA concentration of each cell lysate was determined using Qubit RNA HS Assay Kit (ThermoFisher Q32852) with the Qubit Fluorometer 2.0 (Invitrogen, USA). For the ribosome profiling experiments under heat and oxidative stress, 30 µg total RNA was diluted to 200 µL with polysome buffer (20 mM Tris (pH 7.4), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/mL cycloheximide) and digested using 15 U RNase I (EpiCentre, USA N6901K) for 45 minutes at room temperature. Then, 200 U SUPERase*In RNase inhibitor (Invitrogen, USA AM2694) was added to quench the digestion reaction. To pellet the ribosomes, samples were transferred to a 13 mm × 51 mm polycarbonate ultracentrifuge tube containing 0.9 mL sucrose cushion (1 M sucrose in polysome buffer) and centrifuged at 70,000 rpm for 2 hours. For the ribosome profiling experiments under AZC treatment, 73.2 µg total RNA was diluted to 300 µL with polysome buffer and digested using 2.93 U RNase I (EpiCentre, USA N6901K) for 10 minutes at room temperature. Then, 39.2 U SUPERase*In RNase inhibitor (Invitrogen, USA AM2694) was added to quench the digestion reaction. To pellet the ribosomes, samples were transferred to a 13 mm × 51 mm polycarbonate ultracentrifuge tube containing 0.7 mL sucrose cushion (1 M sucrose in polysome buffer) and centrifuged in Beckman TLA-120.2 rotor at 55,000 rpm for 1.5 hours. Translucent ribosome pellets were resuspended in 300 µL polysome buffer followed by RNA purification using TRIzol reagent (Invitrogen, USA 15596026), according to the manufacturer's instructions. Samples were size-separated by running on 15% polyacrylamide TBE-Urea gels for 60 minutes at 200 V followed by gel-purification of the approximately 20 - 40 nucleotide (nt) length ribosome protected fragments (RPFs) using 17 - 34 nt length oligonucleotides as size markers. RPFs were treated with T4 PNK (NEB M0201S) to heal the 2′-3′ cyclic phosphate that results from RNase I cleavage. After end-healing reaction, pre-adenylated adapter oligonucleotides (35 nt length) were ligated to RPFs using T4 Rnl2(tr) K227Q ligase (NEB M0351S). Excess adapter oligos in the reaction were depleted by adding yeast 5′-deadenylase (EpiCentre, USA DA11101K) and RecJ exonuclease (EpiCentre, USA RJ411250) enzymes directly to the ligase reaction and incubated at 30°C for 45 minutes. Samples were purified using Oligo Clean & Concentrator kit (Zymo Research D4060) followed by ribosomal RNA (rRNA) depletion using either yeast Ribo-Zero Gold rRNA removal kit (Illumina, MRZG12324) for heat and oxidative stress samples or QIAseq FastSelect rRNA Yeast kit (Qiagen 334215) for AZC treated samples according to the manufacturer's instructions. Ligated RNA samples were reverse transcribed using Protoscript II RT (NEB M0368). Reverse transcription products were separated from the unextended primer products by polyacrylamide TBE-Urea gel electrophoresis followed by gel purification of the full-length cDNAs (80-120 nt length). Size-selected cDNAs were circularized using CircLigase II (EpiCentre, USA CL9021K). 10-15 rounds of PCR enrichment of the libraries were performed with the proper forward and reverse primers. Enriched libraries were used for cluster generation and sequencing. Single-end (50 bp) sequencing was carried out for two cDNA libraries (two biological replicates of each sample) using the Illumina HiSeq 4000 sequencing platform (Illumina, USA).

treatment_protocol: Once samples reached an OD600 of 0.4, AZC (final 2mg/mL) and/or MG132 (final 100uM) was added, and cells were grown at room temperature for 45 minutes before pelleting via centrifugation, freezing, and RNA extraction.

tag: cell line

tag: genotype

tag: batch


title: total RNA-seq from GM21473 (ENCLB530CQI)

description:
https://www.encodeproject.org/experiments/ENCSR910GKE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR910GKE
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB530CQI
nucleic acid starting quantity: 32
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21473 cell line

value: cell line

tag: note

value: GM21473 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

tag: dev stage

tag: lab

tag: source

tag: link

value: ENCBS497OOE at ENCODE; https://www.encodeproject.org/ENCBS497OOE/


title: B. napus 4h new mRNAs rep4

description: Library name: napus_new_4h_4

data_processing:
In our sequencing strategy, the R1 reads of pooled libraries contain two parts of UMI split by the barcode. We rearrange UMI sequences to position them next to each other and remove additional low-quality nucleotides, including  the oligo(dT) fragment and those that follow it. For this, we utilise the awk command: awk 'NR%2==1 {print $0} NR%2==0 {print substr($1,16,5) substr($1,1,15)}'
Fastq files for read R2 of pooled libraries were demultiplexed into separate fastq files for each replicate using BRBseqTools (v 1.6) Demultiplex and R1 with parameters -p UB -UMI 14 -n 1. The resulting reads were trimmed to eliminate potential contamination with the poly(A) tail using BRBseqTools (v 1.6) Trim and parameters -polyA 10 -minLength 30. Then, they were mapped using STAR (v 2.7.8a) with parameters --sjdbOverhang 99 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1. Finally, the deduplicated counts for each gene were obtained using BRBseqTools (v 1.6) CreateDGEMatrix with parameters -p UB -UMI 14 -s yes.
Assembly: AST_PRJEB5043_v1
Supplementary files format and content: gene count text files

organism: Brassica napus

growth_protocol: Plants were grown in a greenhouse under a long day-night cycle at 22°C. Seeds from 2 plants were combined to create a single biological replicate.

extract_protocol:
RNA was isolated according to a standard seed protocol (https://doi.org/10.1002/biot.200900211). For 4-SU labelled RNAs enrichment, biotinylation was performed for 25 μg of freshly isolated RNA in a 200 μl reaction mixture (10 mM Tris pH 7.5; 1 mM EDTA; 0.2 mg/ml EZ-Link Biotin-HPDP (ThermoFisher)) for 1.5 h at 22°C. A portion of the RNA (500 ng) was retained as an input. Unbound Biotin-HPDP was removed by chloroform/isoamyl alcohol (24:1) extraction. Subsequently, a 1/10 volume of 5 M NaCl and an equal volume of isopropanol were added, and RNA was precipitated by centrifugation at 20,000g for 20 minutes. The pellet was washed with 1 ml of 80% ethanol, and after drying, it was resuspended in 25 μl of RNase-free water. Biotinylated RNA was purified using 50 μl of streptavidin C1 Dynabeads (ThermoFisher). The beads were washed in binding buffer (0.2 M NaCl; 0.1 M sodium phosphate pH 6.8; 25 mM MgCl2; 0.4% Tween), blocked in the binding buffer with 1 μg/μl glycogen for 10 minutes, and washed again in binding buffer. RNA samples were denatured at 65°C for 5 minutes, followed by 5 minutes on ice. Then, 25 μl of 2x binding buffer and 50 μl of washed streptavidin beads were added, mixed, and incubated at 22°C with gentle shaking for 20 minutes. The beads were washed three times with 0.5 ml of washing buffer (100 mM Tris-HCl pH 7.5; 10 mM EDTA; 1 M NaCl; 0.1% Tween20) at 65°C, followed by three washes at room temperature. Biotinylated RNA was eluted from the beads by two incubations with 50 μl of 200 mM DTT. RNA from the combined eluates was purified using RNA Clean & Concentrator-5 columns (Zymo), following the protocol for long RNA purification with DNase treatment. The entire volume of the sample was used for reverse transcription.
Dry seed, input and enriched RNA samples were used in reverse transcription with 50 mM of various barcoded oligo(dT) primers and SuperScript III. 0.25 of each input/dry and whole enriched RNA RT reaction were pooled. cDNA pools were purified with Ampure beads (1.5x beads to sample volumes) and then eluted in 17 µl of water. 15 µl of the recovered cDNA pools were mixed by pipetting with 15 µl of the second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 30 µM dNTPs) and incubated overnight at 16°C. The reactions were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 µl of water. 3 µl of the recovered dsDNA samples were used for tagmentation with 3 µl of 5x diluted B-loaded Tn5 enzyme (homemade) and 6 µl of freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). The reactions were mixed by pipetting and incubated for 7 minutes at 55°C, followed by 5 minutes at 80°C. Water was added to a total volume of 36 µl; samples were purified with Ampure beads (0.85x beads to sample volumes) and eluted with 21 µl of water. Illumina indexing PCRs were performed using 20 µl of the tagmented DNA in a 50 µl reaction with Q5 2× PCR Master Mix (NEB) and a final concentration of 0.5 µM of primers. Libraries were sequenced on the Illumina Nova-seq to obtain two reads: R1 (containing barcode and UMI) and R2 (containing mRNA sequence).

treatment_protocol: Seeds were imbibed for 4h and 8h in the presence of 2 mM 4-thiouridine (Merck; from a 50 mM stock solution in 6% methanol).

tag: tissue

value: seed

tag: cultivar

value: Bazyl

value: 4h imbibed

tag: treatment enrichment

value: enriched


title: total RNA-seq from GM19379 (ENCLB336WYZ)

description:
https://www.encodeproject.org/experiments/ENCSR909EGF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR909EGF
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB336WYZ
nucleic acid starting quantity: 24
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19379 cell line

value: GM19379 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

tag: Sex

value: female

value: ENCBS782ERA at ENCODE; https://www.encodeproject.org/ENCBS782ERA/


title: V361-CGND-HRA-03375-B

description: Library name: V361-CGND-HRA-03375-B

tag: subject id

tag: diagnosis

value: ALS

tag: pmi

value: F

tag: age


title: V362-CGND-HRA-03375-A

description: Library name: V362-CGND-HRA-03375-A


title: total RNA-seq from GM19375 (ENCLB248UUJ)

description:
https://www.encodeproject.org/experiments/ENCSR908UDN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR908UDN
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB248UUJ
nucleic acid starting quantity: 51
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19375 cell line

tag: line

tag: biosample encode accession

tag: encode accession

value: GM19375 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: adult

value: ENCBS481SHR at ENCODE; https://www.encodeproject.org/ENCBS481SHR/


title: V361-CGND-HRA-03375-A

description: Library name: V361-CGND-HRA-03375-A


title: total RNA-seq from HG03072 (ENCLB038PCG)

description:
https://www.encodeproject.org/experiments/ENCSR908KTG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR908KTG
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB038PCG
nucleic acid starting quantity: 41
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03072 cell line

value: HG03072 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: male

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS038FOS at ENCODE; https://www.encodeproject.org/ENCBS038FOS/


title: V346-CGND-HRA-03049-2-D

description: Library name: V346-CGND-HRA-03049-2-D

value: M


title: V346-CGND-HRA-03049-2-C

description: Library name: V346-CGND-HRA-03049-2-C


title: V345-CGND-HRA-03049-2-D

description: Library name: V345-CGND-HRA-03049-2-D


title: total RNA-seq from HG03342 (ENCLB481SOY)

description:
https://www.encodeproject.org/experiments/ENCSR906CBF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR906CBF
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB481SOY
nucleic acid starting quantity: 34
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03342 cell line

value: cell line

tag: description

value: HG03342 LCLs; Donor from the Esan in Nigeria (ESN)

value: unknown

value: ENCBS335OWZ at ENCODE; https://www.encodeproject.org/ENCBS335OWZ/

value: Derived from ENCODE donor ENCDO573NZN; https://www.encodeproject.org/ENCDO573NZN/


title: total RNA-seq from HG03057 (ENCLB026PWP)

description:
https://www.encodeproject.org/experiments/ENCSR907GXX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR907GXX
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB026PWP
nucleic acid starting quantity: 34
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03057 cell line

tag: note

value: HG03057 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: ENCBS699JGG at ENCODE; https://www.encodeproject.org/ENCBS699JGG/


title: total RNA-seq from GM19452 (ENCLB034AZX)

description:
https://www.encodeproject.org/experiments/ENCSR905MYA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR905MYA
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB034AZX
nucleic acid starting quantity: 20
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19452 cell line

value: GM19452 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

tag: dev stage

value: ENCBS806OYT at ENCODE; https://www.encodeproject.org/ENCBS806OYT/

value: Derived from ENCODE donor ENCDO876QML; https://www.encodeproject.org/ENCDO876QML/


title: total RNA-seq from GM21381 (ENCLB692GUI)

description:
https://www.encodeproject.org/experiments/ENCSR901WQE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR901WQE
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB692GUI
nucleic acid starting quantity: 20
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21381 cell line

value: GM21381 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: adult

tag: lab

value: ENCBS295WIH at ENCODE; https://www.encodeproject.org/ENCBS295WIH/

value: Derived from ENCODE donor ENCDO740GUO; https://www.encodeproject.org/ENCDO740GUO/


title: V344-CGND-HRA-02179-2-D

description: Library name: V344-CGND-HRA-02179-2-D

value: Non-neurological control

tag: rin


title: V345-CGND-HRA-03049-2-C

description: Library name: V345-CGND-HRA-03049-2-C

value: ALS


title: total RNA-seq from GM21378 (ENCLB537HSJ)

description:
https://www.encodeproject.org/experiments/ENCSR899TLB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR899TLB
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB537HSJ
nucleic acid starting quantity: 22
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21378 cell line

value: GM21378 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: male

value: Stephen Montgomery, Stanford

tag: source

value: Coriell

tag: link

value: ENCBS205DMD at ENCODE; https://www.encodeproject.org/ENCBS205DMD/


title: total RNA-seq from HG02807 (ENCLB419KEI)

description:
https://www.encodeproject.org/experiments/ENCSR896WTR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR896WTR
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB419KEI
nucleic acid starting quantity: 19
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02807 cell line

value: cell line

value: HG02807 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: ENCBS718DPZ at ENCODE; https://www.encodeproject.org/ENCBS718DPZ/


title: V344-CGND-HRA-02179-2-C

description: Library name: V344-CGND-HRA-02179-2-C

tag: tissue

value: M


title: V343-CGND-HRA-02179-2-C

description: Library name: V343-CGND-HRA-02179-2-C


title: total RNA-seq from HG03297 (ENCLB367XSL)

description:
https://www.encodeproject.org/experiments/ENCSR889ALH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR889ALH
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB367XSL
nucleic acid starting quantity: 24
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03297 cell line

value: HG03297 LCLs; Donor from the Esan in Nigeria (ESN)

value: female

value: ENCBS550YMA at ENCODE; https://www.encodeproject.org/ENCBS550YMA/


title: V342-CGND-HRA-03055-2-D

description: Library name: V342-CGND-HRA-03055-2-D

value: F


title: HEK293T transfected 250ng HSP90AA1 bicistronic reporter, 4h with DMSO biol rep 2

city: Kansas City

first: Ariel

middle: Alejandro

last: Bazzini

state: Missouri

institute: Stowers Institute for Medical Research

description:
Library name: Sample 34
Row name in splice_junctions_All_Samples.csv: HSP90AA1_4h_DMSO

data_processing:
Paired-end RNA-seq reads (75 bp) were aligned to a custom reference genome consisting of the human genome assembly (hg38) supplemented with a gene-specific reporter construct sequence (bicistronic minigene) for each target gene (BCAP, CANX, HOXB7, CTDSP2, PHIP, HSP90AA1). Separate STAR indices were built for each gene using STAR v2.7.11b with --sjdbOverhang 74. Reads were aligned in two-pass mode (--twopassMode Basic) with the following parameters: end-to-end alignment (--alignEndsType EndToEnd), only uniquely mapping reads retained (-- outFilterMultimapNmax 1), zero mismatches permitted (--outFilterMismatchNmax 0), minimum splice junction overhang of 6 nt for both novel and annotated junctions (--alignSJoverhangMin 6, --alignSJDBoverhangMin 6), and non-canonical intron motifs removed (--outFilterIntronMotifs RemoveNoncanonical). The strand of each alignment was inferred from the intron motif (-- outSAMstrandField intronMotif). Output BAM files were coordinate-sorted and indexed with SAMtools.
Splice junction quantification was performed using a custom Python script (pysam v0.23.3). Only primary, uniquely mapped, non-supplementary alignments were considered. A read was classified as supporting a specific splice junction if its CIGAR string contained an N operation flanked by at least 6 matched bases (M/=/X) on each side. The donor coordinate was defined as the last exonic base before the intron (1-based), and the acceptor coordinate as the first exonic base after the intron. The number of reads supporting an exact donor–acceptor pair is reported as exact junction reads. For each splice site, unspliced reads were counted within a 12-nt window centred on the splice site boundary (half-window = 6 nt): for a donor site at position d, the window spans [d − 5, d + 6]; for an acceptor site at position a, the window spans [a − 6, a + 5]. A read was counted as unspliced if: (i) its CIGAR string contained no N operations (indicating no spliced alignment across an intron) and no D operations (indicating no deletion relative to the reference genome); and (ii) it continuously covered the entire 12-nt window without interruption. Duplicate alignments sharing the same read name, FLAG, reference start, and CIGAR string were counted only once.
Assembly: hg38
Supplementary files format and content: .csv file contains the splice junctions identified for each transfected construct in the corresponding sample

growth_protocol: HEK293T cells were grown in DMEM media supplemented with 10% FBS, 2mM L-Glutamine and Penstrep in humidified atmosphere at % CO2 at 37C

extract_protocol:
RNA was isolated by mixing cells with Trizol Reagent, adding choloroform, and isolating the aqueous layer after centrifugation and purified using the Zymo Direct-zol RNA MicroPrep kit. 100ng of total RNA was used as input for library prep.
RNA libraries for RNA-seq were prepared using the Watchmaker mRNA Library Prep Kit at 1/5 reaction volume.

treatment_protocol: When cells were treated with DMSO or PladB, the treatment was added at the indicated concentration just prior to transfetion

tag: cell line

tag: cell type

value: human embryonic kidney

tag: genotype

value: WT

tag: treatment

value: DMSO

tag: time

value: 4 hours


title: V343-CGND-HRA-02179-2-D

description: Library name: V343-CGND-HRA-02179-2-D

tag: subject id

tag: diagnosis

value: Non-neurological control

tag: pmi

tag: Sex

tag: age


title: total RNA-seq from GM21685 (ENCLB359ZZX)

description:
https://www.encodeproject.org/experiments/ENCSR890BUJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR890BUJ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB359ZZX
nucleic acid starting quantity: 33
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21685 cell line

tag: line

tag: biosample encode accession

tag: encode accession

tag: note

value: GM21685 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: male

value: adult

value: ENCBS822JYI at ENCODE; https://www.encodeproject.org/ENCBS822JYI/


title: total RNA-seq from inflammatory macrophage (ENCLB624HRZ)

description:
https://www.encodeproject.org/experiments/ENCSR894RTM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR894RTM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB624HRZ

library_source: genomic

molecule: genomic DNA

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

value: inflammatory macrophage

value: primary cell

tag: dev stage

value: 21 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: Shelly Heimfeld

value: ENCBS636KVO at ENCODE; https://www.encodeproject.org/ENCBS636KVO/


title: total RNA-seq from GM21523 (ENCLB700DSY)

description:
https://www.encodeproject.org/experiments/ENCSR886FYI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR886FYI
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB700DSY
nucleic acid starting quantity: 22
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21523 cell line

value: cell line

value: GM21523 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: Stephen Montgomery, Stanford

value: Coriell

tag: link

value: ENCBS951CGU at ENCODE; https://www.encodeproject.org/ENCBS951CGU/


title: V342-CGND-HRA-03055-2-C

description: Library name: V342-CGND-HRA-03055-2-C

tag: tissue

value: ALS

value: F


title: V342-CGND-HRA-02513-2-B

description: Library name: V342-CGND-HRA-02513-2-B

value: ALS Spectrum MND, Other Neurological Disorders

value: M

tag: rin


title: total RNA-seq from GM19454 (ENCLB369VZD)

description:
https://www.encodeproject.org/experiments/ENCSR880BTX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR880BTX
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB369VZD
nucleic acid starting quantity: 28
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19454 cell line

value: GM19454 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: male

value: adult

value: ENCBS708VOL at ENCODE; https://www.encodeproject.org/ENCBS708VOL/


title: total RNA-seq from HG02703 (ENCLB522TMF)

description:
https://www.encodeproject.org/experiments/ENCSR878HUP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR878HUP
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB522TMF
nucleic acid starting quantity: 34
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02703 cell line

value: HG02703 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: female

value: ENCBS506IXA at ENCODE; https://www.encodeproject.org/ENCBS506IXA/


title: V341-CGND-HRA-02513-2-B

description: Library name: V341-CGND-HRA-02513-2-B


title: V341-CGND-HRA-03055-2-C

description: Library name: V341-CGND-HRA-03055-2-C


title: total RNA-seq from GM19399 (ENCLB287JLJ)

description:
https://www.encodeproject.org/experiments/ENCSR875USR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR875USR
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB287JLJ
nucleic acid starting quantity: 34
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19399 cell line

value: GM19399 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: ENCBS638GLB at ENCODE; https://www.encodeproject.org/ENCBS638GLB/


title: total RNA-seq from HG03195 (ENCLB517TKW)

description:
https://www.encodeproject.org/experiments/ENCSR874LLG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR874LLG
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB517TKW
nucleic acid starting quantity: 31
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03195 cell line

value: cell line

value: HG03195 LCLs; Donor from the Esan in Nigeria (ESN)

value: ENCBS495KQB at ENCODE; https://www.encodeproject.org/ENCBS495KQB/


title: V330-CGND-HRA-03483-B

description: Library name: V330-CGND-HRA-03483-B


title: total RNA-seq from GM19309 (ENCLB154WGI)

description:
https://www.encodeproject.org/experiments/ENCSR875LVT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR875LVT
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB154WGI
nucleic acid starting quantity: 41
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19309 cell line

value: GM19309 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS777VDM at ENCODE; https://www.encodeproject.org/ENCBS777VDM/


title: V330-CGND-HRA-03483-A

description: Library name: V330-CGND-HRA-03483-A

value: ALS

value: M


title: V341-CGND-HRA-02513-2-A

description: Library name: V341-CGND-HRA-02513-2-A

value: ALS Spectrum MND, Other Neurological Disorders


title: total RNA-seq from GM21620 (ENCLB023GOE)

description:
https://www.encodeproject.org/experiments/ENCSR867IMW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR867IMW
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB023GOE
nucleic acid starting quantity: 28
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21620 cell line

value: GM21620 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: adult

value: ENCBS434FDH at ENCODE; https://www.encodeproject.org/ENCBS434FDH/


title: V329-CGND-HRA-03483-A

description: Library name: V329-CGND-HRA-03483-A


title: V328-CGND-HRA-03443-B

description: Library name: V328-CGND-HRA-03443-B


title: V328-CGND-HRA-03443-A

description: Library name: V328-CGND-HRA-03443-A


title: A50_2

status: Public on Jul 26 2026

city: Guangzhou

first: Yang

last: Ziqi

address: Jinsui Road

country: China

institute: Zhongshan opythalmic center

description: Library name: Sample14

data_processing:
Raw sequencing reads were processed to remove adaptor sequences and low-quality reads.Clean reads were aligned to the human reference genome using HISAT2 (v2.0.5).Gene expression levels were quantified as fragments per kilobase per million mapped reads (FPKM) using featureCounts.Differential gene expression analysis was performed using DESeq2 with adjusted P < 0.05 considered statistically significant.Gene Ontology (GO) and pathway enrichment analyses were conducted using clusterProfiler R package.
Assembly: hg38
Supplementary files format and content: csv files include FPKM values for each Sample

growth_protocol: HMC3 cells were cultured in MEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. RNA quality and integrity were assessed by agarose gel electrophoresis and an Agilent 2100 Bioanalyzer system.
RNA sequencing libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer’s protocol. Briefly, mRNA was enriched using poly-T oligo-attached magnetic beads, fragmented, and reverse-transcribed to synthesize first- and second-strand cDNA. After end repair, adaptor ligation, and PCR amplification, libraries with insert sizes of approximately 250–300 bp were generated and sequenced on an Illumina NovaSeq platform to obtain paired-end 150-bp reads.

treatment_protocol: HMC3 cells were treated with oxidized low-density lipoprotein (oxLDL) at concentrations of 0, 1, 2.5, 10, 50, or 100 μg/mL for 24 hours.

tag: cell line

tag: cell type

value: microglial cell line

tag: genotype

value: wild type

tag: treatment

value: oxLDL 50 μg/ml, 24h

tag: batch


title: total RNA-seq from GM21486 (ENCLB484YTI)

description:
https://www.encodeproject.org/experiments/ENCSR863NTY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR863NTY
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB484YTI
nucleic acid starting quantity: 24
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21486 cell line

value: GM21486 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

tag: Sex

value: female

value: ENCBS153TET at ENCODE; https://www.encodeproject.org/ENCBS153TET/


title: total RNA-seq from GM21689 (ENCLB815YRD)

description:
https://www.encodeproject.org/experiments/ENCSR865CQJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR865CQJ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB815YRD
nucleic acid starting quantity: 32
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21689 cell line

value: cell line

value: GM21689 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: male

value: ENCBS948XEH at ENCODE; https://www.encodeproject.org/ENCBS948XEH/


title: V328-CGND-HRA-03447-D

description: Library name: V328-CGND-HRA-03447-D

tag: subject id

tag: diagnosis

tag: pmi

tag: age


title: V328-CGND-HRA-03447-C

description: Library name: V328-CGND-HRA-03447-C


title: V327-CGND-HRA-03443-B

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


title: total RNA-seq from HG02614 (ENCLB781TIF)

description:
https://www.encodeproject.org/experiments/ENCSR861ROC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR861ROC
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB781TIF
nucleic acid starting quantity: 28
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02614 cell line

tag: line

tag: biosample encode accession

tag: encode accession

tag: note

value: HG02614 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS108AXA at ENCODE; https://www.encodeproject.org/ENCBS108AXA/


title: total RNA-seq from GM21385 (ENCLB517FQP)

description:
https://www.encodeproject.org/experiments/ENCSR860JQH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR860JQH
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB517FQP
nucleic acid starting quantity: 33
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21385 cell line

value: GM21385 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

tag: dev stage

tag: lab

tag: source

tag: link

value: ENCBS687UOA at ENCODE; https://www.encodeproject.org/ENCBS687UOA/


title: total RNA-seq from HG03117 (ENCLB973BSF)

description:
https://www.encodeproject.org/experiments/ENCSR857HDM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR857HDM
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB973BSF
nucleic acid starting quantity: 31
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03117 cell line

value: HG03117 LCLs; Donor from the Esan in Nigeria (ESN)

value: adult

value: ENCBS284TXM at ENCODE; https://www.encodeproject.org/ENCBS284TXM/


title: V327-CGND-HRA-03447-D

description: Library name: V327-CGND-HRA-03447-D

tag: tissue

value: ALS

value: M

tag: rin


title: V327-CGND-HRA-03447-C

description: Library name: V327-CGND-HRA-03447-C


title: V312-CGND-HRA-03531-D

description: Library name: V312-CGND-HRA-03531-D


title: V312-CGND-HRA-03531-C

description: Library name: V312-CGND-HRA-03531-C


title: total RNA-seq from HG03298 (ENCLB382ZDV)

description:
https://www.encodeproject.org/experiments/ENCSR851JLM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR851JLM
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB382ZDV
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03298 cell line

value: HG03298 LCLs; Donor from the Esan in Nigeria (ESN)

value: ENCBS571GEN at ENCODE; https://www.encodeproject.org/ENCBS571GEN/


title: V312-CGND-HRA-03369-B

description: Library name: V312-CGND-HRA-03369-B

value: F


title: total RNA-seq from HG03428 (ENCLB732WWD)

description:
https://www.encodeproject.org/experiments/ENCSR851YSK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR851YSK
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB732WWD
nucleic acid starting quantity: 26
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03428 cell line

value: cell line

value: HG03428 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: female

value: ENCBS240QYU at ENCODE; https://www.encodeproject.org/ENCBS240QYU/


title: V312-CGND-HRA-03369-A

description: Library name: V312-CGND-HRA-03369-A


title: total RNA-seq from GM21582 (ENCLB530FXP)

description:
https://www.encodeproject.org/experiments/ENCSR848SDO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR848SDO
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB530FXP
nucleic acid starting quantity: 29
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21582 cell line

value: GM21582 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: male

value: Stephen Montgomery, Stanford

value: ENCBS601VSG at ENCODE; https://www.encodeproject.org/ENCBS601VSG/


title: total RNA-seq from HG03539 (ENCLB329UJV)

description:
https://www.encodeproject.org/experiments/ENCSR842QJZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR842QJZ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB329UJV
nucleic acid starting quantity: 29
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03539 cell line

value: HG03539 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: Coriell

value: ENCBS727FMZ at ENCODE; https://www.encodeproject.org/ENCBS727FMZ/


title: V311-CGND-HRA-03369-B

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


title: total RNA-seq from GM19376 (ENCLB621UGL)

description:
https://www.encodeproject.org/experiments/ENCSR841IRK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR841IRK
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB621UGL
nucleic acid starting quantity: 40
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19376 cell line

value: GM19376 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: adult

value: ENCBS577MAD at ENCODE; https://www.encodeproject.org/ENCBS577MAD/


title: V293-U54-HRA-139-D

description: Library name: V293-U54-HRA-139-D

value: Non-neurological control


title: total RNA-seq from HG02816 (ENCLB534WHA)

description:
https://www.encodeproject.org/experiments/ENCSR840JAN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR840JAN
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB534WHA
nucleic acid starting quantity: 37
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02816 cell line

value: HG02816 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: ENCBS876OOK at ENCODE; https://www.encodeproject.org/ENCBS876OOK/


title: total RNA-seq from HG02715 (ENCLB155SLX)

description:
https://www.encodeproject.org/experiments/ENCSR840GAJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR840GAJ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB155SLX
nucleic acid starting quantity: 37
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02715 cell line

value: cell line

value: HG02715 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: ENCBS548QWP at ENCODE; https://www.encodeproject.org/ENCBS548QWP/


title: V293-U54-HRA-139-C

description: Library name: V293-U54-HRA-139-C

value: F


title: V293-U54-HRA-138-B

description: Library name: V293-U54-HRA-138-B


title: total RNA-seq from GM21723 (ENCLB276XTN)

description:
https://www.encodeproject.org/experiments/ENCSR836GCO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR836GCO
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB276XTN
nucleic acid starting quantity: 24
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21723 cell line

tag: description

value: GM21723 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: female

value: unknown

value: ENCBS510ZRZ at ENCODE; https://www.encodeproject.org/ENCBS510ZRZ/

value: Derived from ENCODE donor ENCDO468IXT; https://www.encodeproject.org/ENCDO468IXT/


title: total RNA-seq from GM19351 (ENCLB269GST)

description:
https://www.encodeproject.org/experiments/ENCSR838MLK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR838MLK
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB269GST
nucleic acid starting quantity: 43
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19351 cell line

value: GM19351 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS872TWA at ENCODE; https://www.encodeproject.org/ENCBS872TWA/

value: Derived from ENCODE donor ENCDO806NFB; https://www.encodeproject.org/ENCDO806NFB/


title: V293-U54-HRA-138-A

description: Library name: V293-U54-HRA-138-A

value: Non-neurological control


title: V292-U54-HRA-139-D

description: Library name: V292-U54-HRA-139-D


title: total RNA-seq from inflammatory macrophage (ENCLB272MAS)

description:
https://www.encodeproject.org/experiments/ENCSR835ZHL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR835ZHL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB272MAS

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

value: inflammatory macrophage

value: primary cell

value: male

value: adult

value: 21 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: ENCBS472QWK at ENCODE; https://www.encodeproject.org/ENCBS472QWK/


title: total RNA-seq from GM19042 (ENCLB643OQZ)

description:
https://www.encodeproject.org/experiments/ENCSR835EWA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR835EWA
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB643OQZ
nucleic acid starting quantity: 28
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19042 cell line

value: cell line

value: GM19042 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: female

value: ENCBS356GAK at ENCODE; https://www.encodeproject.org/ENCBS356GAK/


title: V292-U54-HRA-139-C

description: Library name: V292-U54-HRA-139-C

value: F


title: total RNA-seq from HG02870 (ENCLB954MVR)

description:
https://www.encodeproject.org/experiments/ENCSR833RNK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR833RNK
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB954MVR
nucleic acid starting quantity: 20
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02870 cell line

value: HG02870 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: unknown

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS983PPJ at ENCODE; https://www.encodeproject.org/ENCBS983PPJ/

value: Derived from ENCODE donor ENCDO921ZBU; https://www.encodeproject.org/ENCDO921ZBU/


title: total RNA-seq from HG02666 (ENCLB079FNR)

description:
https://www.encodeproject.org/experiments/ENCSR833GYF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR833GYF
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB079FNR
nucleic acid starting quantity: 31
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02666 cell line

value: HG02666 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: male

value: ENCBS890TVY at ENCODE; https://www.encodeproject.org/ENCBS890TVY/


title: V292-U54-HRA-138-B

description: Library name: V292-U54-HRA-138-B

value: Non-neurological control


title: V292-U54-HRA-138-A

description: Library name: V292-U54-HRA-138-A


title: total RNA-seq from GM21353 (ENCLB549ZRV)

description:
https://www.encodeproject.org/experiments/ENCSR833FBP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR833FBP
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB549ZRV
nucleic acid starting quantity: 27
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21353 cell line

value: GM21353 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: adult

value: ENCBS347YUC at ENCODE; https://www.encodeproject.org/ENCBS347YUC/


title: total RNA-seq from GM21409 (ENCLB043OCC)

description:
https://www.encodeproject.org/experiments/ENCSR830BZO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR830BZO
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB043OCC
nucleic acid starting quantity: 33
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21409 cell line

value: cell line

value: GM21409 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: ENCBS329QOK at ENCODE; https://www.encodeproject.org/ENCBS329QOK/


title: V285-CGND-HRA-03528-A

description: Library name: V285-CGND-HRA-03528-A

value: ALS

value: M


title: V285-CGND-HRA-03519-D

description: Library name: V285-CGND-HRA-03519-D


title: total RNA-seq from HG03135 (ENCLB013LJP)

description:
https://www.encodeproject.org/experiments/ENCSR829SDI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR829SDI
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB013LJP
nucleic acid starting quantity: 29
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03135 cell line

value: HG03135 LCLs; Donor from the Esan in Nigeria (ESN)

value: female

value: unknown

value: ENCBS987JML at ENCODE; https://www.encodeproject.org/ENCBS987JML/

value: Derived from ENCODE donor ENCDO279WUI; https://www.encodeproject.org/ENCDO279WUI/


title: V285-CGND-HRA-03519-C

description: Library name: V285-CGND-HRA-03519-C


title: total RNA-seq from HG02976 (ENCLB043UVO)

description:
https://www.encodeproject.org/experiments/ENCSR829JXN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR829JXN
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB043UVO
nucleic acid starting quantity: 26
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02976 cell line

value: HG02976 LCLs; Donor from the Esan in Nigeria (ESN)

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS894RTN at ENCODE; https://www.encodeproject.org/ENCBS894RTN/


title: V284-CGND-HRA-03528-B

description: Library name: V284-CGND-HRA-03528-B


title: total RNA-seq from GM21338 (ENCLB916IXO)

description:
https://www.encodeproject.org/experiments/ENCSR828IRM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR828IRM
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB916IXO
nucleic acid starting quantity: 46
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21338 cell line

value: GM21338 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: male

value: ENCBS455DSQ at ENCODE; https://www.encodeproject.org/ENCBS455DSQ/


title: V284-CGND-HRA-03519-D

description: Library name: V284-CGND-HRA-03519-D


title: total RNA-seq from GM19308 (ENCLB194KUG)

description:
https://www.encodeproject.org/experiments/ENCSR827CFV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR827CFV
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB194KUG
nucleic acid starting quantity: 30
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19308 cell line

value: cell line

value: GM19308 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: adult

value: ENCBS396ABA at ENCODE; https://www.encodeproject.org/ENCBS396ABA/


title: V284-CGND-HRA-03519-C

description: Library name: V284-CGND-HRA-03519-C

value: ALS

value: M


title: total RNA-seq from inflammatory macrophage (ENCLB330FNJ)

description:
https://www.encodeproject.org/experiments/ENCSR823VKN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR823VKN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB330FNJ

value: inflammatory macrophage

value: primary cell

value: 21 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: ENCBS100CWS at ENCODE; https://www.encodeproject.org/ENCBS100CWS/


title: total RNA-seq from HG03484 (ENCLB683YFO)

description:
https://www.encodeproject.org/experiments/ENCSR819LXM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR819LXM
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB683YFO
nucleic acid starting quantity: 19
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03484 cell line

value: HG03484 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS670WIM at ENCODE; https://www.encodeproject.org/ENCBS670WIM/


title: V283-CGND-HRA-03516-D

description: Library name: V283-CGND-HRA-03516-D


title: V283-CGND-HRA-03516-C

description: Library name: V283-CGND-HRA-03516-C


title: total RNA-seq from HG03112 (ENCLB055DWV)

description:
https://www.encodeproject.org/experiments/ENCSR818OVU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR818OVU
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB055DWV
nucleic acid starting quantity: 30
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03112 cell line

value: HG03112 LCLs; Donor from the Esan in Nigeria (ESN)

value: male

value: ENCBS002FPI at ENCODE; https://www.encodeproject.org/ENCBS002FPI/


title: V282-CGND-HRA-03516-D

description: Library name: V282-CGND-HRA-03516-D


title: total RNA-seq from HG03190 (ENCLB589UFD)

description:
https://www.encodeproject.org/experiments/ENCSR817XKF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR817XKF
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB589UFD
nucleic acid starting quantity: 28
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03190 cell line

value: cell line

value: HG03190 LCLs; Donor from the Esan in Nigeria (ESN)

value: adult

value: ENCBS068BIL at ENCODE; https://www.encodeproject.org/ENCBS068BIL/


title: V282-CGND-HRA-03516-C

description: Library name: V282-CGND-HRA-03516-C

value: ALS

value: M


title: total RNA-seq from HG02855 (ENCLB978ZZE)

description:
https://www.encodeproject.org/experiments/ENCSR814OFI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR814OFI
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB978ZZE
nucleic acid starting quantity: 32
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02855 cell line

value: HG02855 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: female

value: ENCBS715MUR at ENCODE; https://www.encodeproject.org/ENCBS715MUR/


title: V278-CGND-HRA-03436-C

description: Library name: V278-CGND-HRA-03436-C

value: F


title: total RNA-seq from HG03054 (ENCLB367UOT)

description:
https://www.encodeproject.org/experiments/ENCSR813PJF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR813PJF
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB367UOT
nucleic acid starting quantity: 43
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03054 cell line

value: HG03054 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: ENCBS856PWL at ENCODE; https://www.encodeproject.org/ENCBS856PWL/


title: V278-CGND-HRA-03419-B

description: Library name: V278-CGND-HRA-03419-B


title: total RNA-seq from HG03048 (ENCLB698AQO)

description:
https://www.encodeproject.org/experiments/ENCSR812FNH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR812FNH
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB698AQO
nucleic acid starting quantity: 25
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03048 cell line

value: HG03048 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS282ZLM at ENCODE; https://www.encodeproject.org/ENCBS282ZLM/


title: total RNA-seq from GM19026 (ENCLB255QQO)

description:
https://www.encodeproject.org/experiments/ENCSR810WKR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR810WKR
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB255QQO
nucleic acid starting quantity: 40
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19026 cell line

value: GM19026 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: male

value: ENCBS570FPO at ENCODE; https://www.encodeproject.org/ENCBS570FPO/


title: total RNA-seq from GM21364 (ENCLB443GFB)

description:
https://www.encodeproject.org/experiments/ENCSR810GEA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR810GEA
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB443GFB
nucleic acid starting quantity: 63
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21364 cell line

value: cell line

value: GM21364 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: adult

value: ENCBS732OSU at ENCODE; https://www.encodeproject.org/ENCBS732OSU/


title: total RNA-seq from GM19378 (ENCLB417MKI)

description:
https://www.encodeproject.org/experiments/ENCSR812EFD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR812EFD
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB417MKI
nucleic acid starting quantity: 32
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19378 cell line

value: GM19378 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: ENCBS180NEH at ENCODE; https://www.encodeproject.org/ENCBS180NEH/


title: V278-CGND-HRA-03419-A

description: Library name: V278-CGND-HRA-03419-A

value: ALS

value: M


title: V279-CGND-HRA-03436-C

description: Library name: V279-CGND-HRA-03436-C

value: F


title: V279-CGND-HRA-03419-B

description: Library name: V279-CGND-HRA-03419-B


title: V279-CGND-HRA-03419-A

description: Library name: V279-CGND-HRA-03419-A


title: total RNA-seq from GM21784 (ENCLB930KQH)

description:
https://www.encodeproject.org/experiments/ENCSR808WEZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR808WEZ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB930KQH
nucleic acid starting quantity: 22
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21784 cell line

value: GM21784 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: female

value: ENCBS212RNX at ENCODE; https://www.encodeproject.org/ENCBS212RNX/


title: V271-CGND-HRA-02412-D

description: Library name: V271-CGND-HRA-02412-D


title: total RNA-seq from GM21456 (ENCLB532DTJ)

description:
https://www.encodeproject.org/experiments/ENCSR807DNU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR807DNU
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB532DTJ
nucleic acid starting quantity: 25
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21456 cell line

value: GM21456 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS034WTI at ENCODE; https://www.encodeproject.org/ENCBS034WTI/


title: CasTuner sgZfp280c ctrl Day2 Rep1

status: Public on Jul 25 2026

city: Berlin

first: Edda

middle: G.

last: Schulz

state: Berlin

address: Ihnestrasse 63

department: Otto-Warburg-Laboratory

country: Germany

institute: Max Planck Institute for Molecular Genetics

description:
Library name: sgZfp280c_ctrl_D2_Rep1
500nM dTAG

data_processing:
Sequencing reads were trimmed with Trim Galore, with [--clip_R1 10 --three_prime_clip_R1 5 --clip_R2 15 --three_prime_clip_R2 5 --paired].
They were mapped using bsmapz with settings -m 0 -g 3 -n 1 -v 0.1 -w 10 to the reference fasta file that contains the amplicon sequences.
bam files were sorted and indexed with samtools, and merged if the sample was sequenced multiple times.
bam files were used for methylation calling by mcall command of MOABS package (Sun et al, 2014) [--trimWGBSEndRepairPE2Seq 0 --trimWGBSEndRepairPE1Seq 0 --reportCHX 0].
Assembly: mm10
Supplementary files format and content: bed files with MOABS methylation calls.

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: TX1072 mouse ES cells and all derived cell lines were cultured in feeder-free 2i/FBS/LIF conditions (DMEM (Sigma-Aldrich D6429), 15% ES cell-grade foetal bovine serum (FBS, Pan Biotech P30-2602), 0.1 mM β-mercaptoethanol, 1000 U/mL LIF (Millipore), 3 mM GSK3 inhibitor CT-99021 (Axon Medchem) and 1 mM MEK inhibitor PD0325901 (Axon Medchem)). For CasTuner lines, 500nM dTAG-13 was added to the medium. They were plated at a density of 3.2 × 10^4 cells per cm^2 on gelatin-coated T25 flasks (Corning). The medium was changed daily, and the cells were split every two days.  WT F121.9 mouse ESCs and the derived deletion cell lines Rnf12-/- and Rnf12 -/- Rex1 -/- (DKO) were adapted to feeder-free 2i/LIF conditions (DMEM (GIBCO 11995065), 15% ES cell-grade foetal bovine serum (FBS, Pan Biotech P30-2602), 100 U/mL penicillin/streptomycin (Thermo Fisher Scientifc), 1x NEAA (Gibco 11140035), 0.1 mM β-mercaptoethanol, 1000 U/mL LIF (Millipore), 3 mM GSK3 inhibitor CT-99021 (Axon Medchem) and 1 mM MEK inhibitor PD0325901 (Axon Medchem)) for 5 passages. They were plated at a density of 3.2 × 10^4 cells per cm^2 on gelatin-coated T25 plates (Corning). The medium was changed daily, and the cells were split every two days.

extract_protocol:
Genomic DNA was extracted from harvested cells using the DNeasy Blood & Tissue kit (Qiagen). 1μg of DNA were bisulfite-converted with EZ DNA Methylation-Gold kit (Zymo). One fifth of the eluted DNA was used per amplicon PCR. Primers for bisulfite-converted DNA targeting the Xist-promoter proximal CpG island (chrX:103,482,090-103,482,350 mm10 from UCSC Genome Browser) were designed with MethPrimer2.0 (Li & Dahiya, 2002). PCR was performed with EpiTaq polymerase (Takara), using 25mM MgCl2. DNA was amplified for 27 cycles, at an annealing temperature of 53oC. PCR reactions of each sample were pooled (total volume for Xist amplicons) and cleaned with MinElute Reaction Cleanup kit (Qiagen) (2 columns per sample).
Libraries were prepared with NEBNext Ultra II DNA Library Prep kit (New England Biolabs), indexed with NEBNext Multiplex Oligos for Illumina Dual Index Set 1 (New England Biolabs) and cleaned with AMPure XP beads (Beckman Coulter). Concentration and size distribution of libraries were analyzed with Qubit 1x dsDNA HS (Thermo Fisher Scientific) and HS DNA D1000 Tapestation (Agilent), respectively. Libraries were sequenced 2x150bp paired-end with MiSeq, DNBSEQ G400 or Aviti sequencers.

treatment_protocol: Differentiation of all cell lines was induced by 2i/LIF withdrawal (DMEM (Sigma-Aldrich), 10% FBS (Gibco) and 0.1 mM β-mercaptoethanol). The cells were plated at a density of 2.1 × 10^4 cells per cm^2, on 6-well plates coated with 10 μg/mL fibronectin (Corning 356008 or Serva 21370.03) in PBS for 1 hour. Once seeded for differentiation, the medium was changed every day and the cells were not split until harvesting.  For the knock-down of Zfp36l1 and Zfp280c, the CasTuner system was induced with dTAG-13 removal for 6 days in total, the last 4 of which differentiation was also induced. The control condition was cultured with dTAG-13 and differentiated for 4 days. To knock-down the transcription of Rex1 and Zfp281, the dCas9-KRAB system was induced with ABA for 5 days in total, the last 4 of which differentiation was also induced. The safe-targeting control line with “STC” guides was cultured in the same conditions as the knock-down cell lines. To knock-down the transcription of Rnf12 and Zic3, the CasTuner system was induced by dTAG-13 removal for 7 days in total, and during the last 3 days differentiation was induced. The control condition was cultured with dTAG-13 and differentiated for 3 days.

value: Embryonic stem cells

tag: cell line

tag: cell type

tag: genotype

value: CAST x C57BL/6

tag: treatment

value: Differentiation by 2i/LIF withdrawal, dTAG-13 for CasTuner degradation

tag: timepoint

value: Differentiation Day 2


title: CasTuner sgZfp280c KD Day4 Rep1

description:
Library name: sgZfp280c_KD_D4_Rep1
0nM dTAG

value: Differentiation by 2i/LIF withdrawal, KD by dTAG-13 removal

value: Differentiation Day 4


title: total RNA-seq from GM19391 (ENCLB257ZWZ)

description:
https://www.encodeproject.org/experiments/ENCSR806ZNR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR806ZNR
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB257ZWZ
nucleic acid starting quantity: 33
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19391 cell line

value: cell line

value: GM19391 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

tag: Sex

value: adult

value: ENCBS943QQQ at ENCODE; https://www.encodeproject.org/ENCBS943QQQ/


title: V271-CGND-HRA-02412-B

description: Library name: V271-CGND-HRA-02412-B

tag: subject id

tag: diagnosis

value: ALS

tag: pmi

value: M

tag: age


title: total RNA-seq from HG03304 (ENCLB497LQF)

description:
https://www.encodeproject.org/experiments/ENCSR806PZJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR806PZJ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB497LQF
nucleic acid starting quantity: 32
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03304 cell line

tag: line

tag: biosample encode accession

tag: encode accession

tag: note

value: HG03304 LCLs; Donor from the Esan in Nigeria (ESN)

value: male

tag: dev stage

value: ENCBS054NIH at ENCODE; https://www.encodeproject.org/ENCBS054NIH/


title: V269-CGND-HRA-03041-D

description: Library name: V269-CGND-HRA-03041-D

tag: tissue

value: F


title: total RNA-seq from HG03133 (ENCLB559QZV)

description:
https://www.encodeproject.org/experiments/ENCSR806NMB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR806NMB
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB559QZV
nucleic acid starting quantity: 36
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03133 cell line

value: HG03133 LCLs; Donor from the Esan in Nigeria (ESN)

tag: lab

value: Stephen Montgomery, Stanford

tag: source

value: Coriell

tag: link

value: ENCBS484LJD at ENCODE; https://www.encodeproject.org/ENCBS484LJD/


title: V269-CGND-HRA-03041-C

description: Library name: V269-CGND-HRA-03041-C


title: total RNA-seq from GM19312 (ENCLB208IKS)

description:
https://www.encodeproject.org/experiments/ENCSR805EHG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR805EHG
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB208IKS
nucleic acid starting quantity: 36
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19312 cell line

value: GM19312 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: ENCBS376OJV at ENCODE; https://www.encodeproject.org/ENCBS376OJV/


title: Split dCas9-KRAB sgRex1 ABA KD Day2 Rep3

description: Library name: sgRex1_ABA_KD_D2_Rep3

value: Embryonic stem cells

tag: cell line

tag: cell type

tag: genotype

value: CAST x C57BL/6

value: Differentiation by 2i/LIF withdrawal, 100μM ABA for CRISPR KD

value: Differentiation Day 2


title: V269-CGND-HRA-03041-A

description: Library name: V269-CGND-HRA-03041-A

tag: Sex


title: total RNA-seq from HG02561 (ENCLB930JCD)

description:
https://www.encodeproject.org/experiments/ENCSR802PYO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR802PYO
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB930JCD
nucleic acid starting quantity: 41
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02561 cell line

value: cell line

value: HG02561 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: adult

value: ENCBS961QEF at ENCODE; https://www.encodeproject.org/ENCBS961QEF/


title: total RNA-seq from GM19315 (ENCLB668YGK)

description:
https://www.encodeproject.org/experiments/ENCSR800DDH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR800DDH
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB668YGK
nucleic acid starting quantity: 37
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19315 cell line

value: GM19315 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: female

value: ENCBS710REG at ENCODE; https://www.encodeproject.org/ENCBS710REG/


title: V259-CGND-HRA-02470-D

description: Library name: V259-CGND-HRA-02470-D

tag: subject id

value: ALS

value: M

tag: rin


title: total RNA-seq from GM18516 (ENCLB668ROV)

description:
https://www.encodeproject.org/experiments/ENCSR786ALR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR786ALR
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB668ROV
nucleic acid starting quantity: 33
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM18516 cell line

value: GM18516 LCLs; Donor from the Yoruba in Ibadan, Nigeria (YRI)

value: male

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS671TME at ENCODE; https://www.encodeproject.org/ENCBS671TME/


title: XX 96h Rep3

description: Library name: XX_T96_Rep3

growth_protocol: TX1072 mouse ES cells were cultured in feeder-free 2i/FBS/LIF conditions (DMEM (Sigma-Aldrich), 15% ES cell-grade foetal bovine serum (FBS, Pan Biotech P30-2602), 0.1  mM β-mercaptoethanol, 1000 U/mL LIF (Millipore), 3 mM GSK3 inhibitor CT-99021 (Axon Medchem) and 1 mM MEK inhibitor PD0325901 (Axon Medchem)). They were plated at a density of 3.2 × 10^4 cells per cm^2 on gelatin-coated T25 plates (Corning). The medium was changed daily, and the cells were split every two days.

treatment_protocol: Differentiation was induced by 2i/LIF withdrawal (DMEM (Sigma-Aldrich), 10% FBS (Gibco) and 0.1 mM β-mercaptoethanol). The cells were plated at a density of 2.1 × 10^4 cells per cm^2, on 6-well plates coated with 10 μg/mL fibronectin (Corning 356008 or Serva 21370.03) in PBS for 1 hour. Once seeded in differentiation conditions, the medium was changed daily and the cells were not split until harvesting.

value: Embryonic stem cells

value: TX1072 XX

value: CAST x C57BL/6

tag: treatment

value: Differentiation by 2i/LIF withdrawal

tag: timepoint

value: 96 hours


title: total RNA-seq from HG02804 (ENCLB434TXA)

description:
https://www.encodeproject.org/experiments/ENCSR783CUF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR783CUF
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB434TXA
nucleic acid starting quantity: 25
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02804 cell line

tag: line

value: cell line

value: HG02804 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: adult

value: ENCBS861DYM at ENCODE; https://www.encodeproject.org/ENCBS861DYM/


title: V259-CGND-HRA-02470-C

description: Library name: V259-CGND-HRA-02470-C

tag: diagnosis

tag: pmi

tag: age


title: V258-CGND-HRA-02470-D

description: Library name: V258-CGND-HRA-02470-D


title: total RNA-seq from GM18499 (ENCLB086MFQ)

description:
https://www.encodeproject.org/experiments/ENCSR780HOX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR780HOX
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB086MFQ
nucleic acid starting quantity: 32
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM18499 cell line

tag: description

value: GM18499 LCLs; Donor from the Yoruba in Ibadan, Nigeria (YRI)

tag: biosample encode accession

value: female

tag: dev stage

value: unknown

value: ENCBS470OKU at ENCODE; https://www.encodeproject.org/ENCBS470OKU/

value: Derived from ENCODE donor ENCDO239IFC; https://www.encodeproject.org/ENCDO239IFC/


title: V258-CGND-HRA-02470-C

description: Library name: V258-CGND-HRA-02470-C

tag: tissue

value: ALS

value: M


title: total RNA-seq from GM21418 (ENCLB894TKW)

description:
https://www.encodeproject.org/experiments/ENCSR776FHJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR776FHJ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB894TKW
nucleic acid starting quantity: 47
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21418 cell line

tag: encode accession

tag: note

value: GM21418 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

tag: lab

value: Stephen Montgomery, Stanford

tag: source

value: Coriell

tag: link

value: ENCBS859YTS at ENCODE; https://www.encodeproject.org/ENCBS859YTS/


title: V257-CGND-HRA-03195-D

description: Library name: V257-CGND-HRA-03195-D

tag: subject id

tag: Sex


title: CasTuner sgZfp280c ctrl Day4 Rep2

description:
Library name: sgZfp280c_ctrl_D4_Rep2
500nM dTAG

value: Embryonic stem cells

tag: cell line

tag: cell type

tag: genotype

value: CAST x C57BL/6

tag: treatment

value: Differentiation by 2i/LIF withdrawal, dTAG-13 for CasTuner degradation

value: Differentiation Day 4


title: CasTuner sgZfp280c KD Day4 Rep3

description:
Library name: sgZfp280c_KD_D4_Rep3
0nM dTAG

value: Differentiation by 2i/LIF withdrawal, KD by dTAG-13 removal

tag: timepoint


title: V257-CGND-HRA-03195-C

description: Library name: V257-CGND-HRA-03195-C

tag: diagnosis

tag: pmi

tag: age

tag: rin


title: total RNA-seq from HG03198 (ENCLB961BJQ)

description:
https://www.encodeproject.org/experiments/ENCSR775YXT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR775YXT
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB961BJQ
nucleic acid starting quantity: 29
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03198 cell line

tag: line

value: cell line

tag: biosample encode accession

value: HG03198 LCLs; Donor from the Esan in Nigeria (ESN)

tag: dev stage

value: adult

value: ENCBS738UKF at ENCODE; https://www.encodeproject.org/ENCBS738UKF/


title: CasTuner sgZfp36l1 ctrl Day2 Rep1

description:
Library name: sgZfp36l1_ctrl_D2_Rep1
500nM dTAG

tag: tissue

value: Differentiation Day 2


title: total RNA-seq from HG03391 (ENCLB140EDV)

description:
https://www.encodeproject.org/experiments/ENCSR775MWA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR775MWA
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB140EDV
nucleic acid starting quantity: 28
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03391 cell line

tag: encode accession

tag: note

value: HG03391 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: male

tag: lab

tag: source

value: ENCBS198XXH at ENCODE; https://www.encodeproject.org/ENCBS198XXH/


title: V257-CGND-HRA-02451-B

description: Library name: V257-CGND-HRA-02451-B

tag: subject id

value: ALS-FTD

tag: Sex

value: F


title: V279-CGND-HRA-03436-D

description: Library name: V279-CGND-HRA-03436-D

value: ALS


title: V257-CGND-HRA-02451-A

description: Library name: V257-CGND-HRA-02451-A


title: total RNA-seq from inflammatory macrophage (ENCLB028NLI)

description:
https://www.encodeproject.org/experiments/ENCSR774WVH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR774WVH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB028NLI

source_name: Homo sapiens male adult (24 years) inflammatory macrophage primary cell

value: inflammatory macrophage

value: primary cell

value: 24 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

tag: link

value: ENCBS706WNW at ENCODE; https://www.encodeproject.org/ENCBS706WNW/


title: V251-CGND-HRA-03192-D

description: Library name: V251-CGND-HRA-03192-D


title: total RNA-seq from GM21513 (ENCLB556QJL)

description:
https://www.encodeproject.org/experiments/ENCSR775CYX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR775CYX
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB556QJL
nucleic acid starting quantity: 37
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21513 cell line

value: cell line

value: GM21513 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: female

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS224UEZ at ENCODE; https://www.encodeproject.org/ENCBS224UEZ/


title: V251-CGND-HRA-03192-C

description: Library name: V251-CGND-HRA-03192-C


title: total RNA-seq from GM19327 (ENCLB954PYF)

description:
https://www.encodeproject.org/experiments/ENCSR769PNT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR769PNT
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB954PYF
nucleic acid starting quantity: 27
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19327 cell line

value: GM19327 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: adult

value: ENCBS434BWA at ENCODE; https://www.encodeproject.org/ENCBS434BWA/


title: total RNA-seq from HG03240 (ENCLB833MQQ)

description:
https://www.encodeproject.org/experiments/ENCSR771GMU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR771GMU
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB833MQQ
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03240 cell line

value: HG03240 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: male

value: ENCBS163NLL at ENCODE; https://www.encodeproject.org/ENCBS163NLL/


title: V251-CGND-HRA-03189-B

description: Library name: V251-CGND-HRA-03189-B

value: ALS

value: F


title: V251-CGND-HRA-03189-A

description: Library name: V251-CGND-HRA-03189-A


title: total RNA-seq from GM19463 (ENCLB833DCR)

description:
https://www.encodeproject.org/experiments/ENCSR767WJT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR767WJT
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB833DCR
nucleic acid starting quantity: 29
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19463 cell line

tag: description

value: GM19463 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: unknown

value: ENCBS017DSU at ENCODE; https://www.encodeproject.org/ENCBS017DSU/

value: Derived from ENCODE donor ENCDO917QAZ; https://www.encodeproject.org/ENCDO917QAZ/


title: total RNA-seq from CD14-positive monocyte (ENCLB631HYK)

description:
https://www.encodeproject.org/experiments/ENCSR769FIE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR769FIE
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB631HYK

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: ENCBS232LID at ENCODE; https://www.encodeproject.org/ENCBS232LID/


title: V250-CGND-HRA-03192-D

description: Library name: V250-CGND-HRA-03192-D


title: V342-CGND-HRA-02513-2-A

description: Library name: V342-CGND-HRA-02513-2-A

value: ALS Spectrum MND, Other Neurological Disorders

value: M


title: V250-CGND-HRA-03192-C

description: Library name: V250-CGND-HRA-03192-C


title: total RNA-seq from HG02583 (ENCLB142OZK)

description:
https://www.encodeproject.org/experiments/ENCSR884LIM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR884LIM
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB142OZK
nucleic acid starting quantity: 38
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02583 cell line

value: cell line

value: HG02583 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: female

value: adult

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS035IPM at ENCODE; https://www.encodeproject.org/ENCBS035IPM/