title: Primary HGSOC patients 048

description: Library name: SS2014931


title: Primary HGSOC patients 049

status: Public on Dec 23 2025

type: SRA

city: Incheon

first: Mi-Ryung

last: Han

address: 265, Harmony-ro, Yeonsu-gu, Incheon, Republic of Korea

country: South Korea

institute: Incheon National University

description: Library name: SS2014056

library_source: transcriptomic

data_processing:
The quality of raw data was ensured using the FastQC v0.11.9.
Adapter sequences were trimmed using Trimfastq from Fabio v2.1.0, then trimmed FASTQ files were aligned to GRCh37.p13 using STAR v2.7.10.
Assembly: GRCh37.p13
Supplementary files format and content: TXT file containing detected gene fusions.
Supplementary files format and content: TXT file containing detected gene fusions.

molecule: total RNA

organism: Homo sapiens

source_name: Tumor tissue

extract_protocol:
RNA was extracted from formalin-fixed, paraffin-embedded (FFPE) tissue sections of HGSOC patients RNeasy Plus Kits (Qiagen, NY, USA).
Library preparation was performed using the TruSight Oncology 500 (TSO500) panel (Illumina, San Diego, CA, USA).

tag: disease status

value: Primary

tag: tumor stage

value: IIIB

tag: Sex

value: Female

tag: tissue

value: Tumor tissue


title: Primary HGSOC patients 045

description: Library name: SS2017747

value: IVB


title: Primary HGSOC patients 050

description: Library name: SS2010279


title: Recurrent HGSOC patients 057

description: Library name: SR2103368

value: Recurrent

value: IIIC


title: Primary HGSOC patients 065

description: Library name: OBGY0128


title: Recurrent HGSOC patients 053

description: Library name: SR2201037

value: IVA


title: Recurrent HGSOC patients 055

description: Library name: SR2105700


title: Primary HGSOC patients 066

description: Library name: OBGY0125

value: IB


title: Recurrent HGSOC patients 061

description: Library name: SR2004995


title: Primary HGSOC patients 071

description: Library name: OBGY0114


title: Recurrent HGSOC patients 054

description: Library name: SR2110185


title: Recurrent HGSOC patients 051

description: Library name: SR2203699


title: Primary HGSOC patients 038

description: Library name: SS2038942


title: Primary HGSOC patients 069

description: Library name: OBGY0121

value: IIB


title: Primary HGSOC patients 052

description: Library name: SR2201768


title: Primary HGSOC patients 070

description: Library name: OBGY0116


title: Recurrent HGSOC patients 058

description: Library name: SR2102216


title: Primary HGSOC patients 059

description: Library name: SR2012308


title: Primary HGSOC patients 067

description: Library name: OBGY0123


title: Recurrent HGSOC patients 062

description: Library name: SR2002963


title: Primary HGSOC patients 043

description: Library name: SS2026250


title: Primary HGSOC patients 063

description: Library name: SF2003515


title: Recurrent HGSOC patients 060

description: Library name: SR2006079


title: Recurrent HGSOC patients 064

description: Library name: OBGY0129


title: Primary HGSOC patients 080

description: Library name: OBGY0099


title: Recurrent HGSOC patients 068

description: Library name: OBGY0122


title: Recurrent HGSOC patients 079

description: Library name: OBGY0101


title: Primary HGSOC patients 072

description: Library name: OBGY0113


title: Recurrent HGSOC patients 056

description: Library name: SR2105061

value: R


title: Primary HGSOC patients 074

description: Library name: OBGY0110


title: Recurrent HGSOC patients 073

description: Library name: OBGY0111


title: Primary HGSOC patients 077

description: Library name: OBGY0105


title: Primary HGSOC patients 076

description: Library name: OBGY0106


title: Primary HGSOC patients 087

description: Library name: OBGY0076


title: Primary HGSOC patients 090

description: Library name: OBGY0051


title: Recurrent HGSOC patients 092

description: Library name: OBGY0043


title: Primary HGSOC patients 095

description: Library name: OBGY0038


title: Primary HGSOC patients 093

description: Library name: OBGY0041

value: III


title: Primary HGSOC patients 078

description: Library name: OBGY0103


title: Primary HGSOC patients 094

description: Library name: OBGY0039

value: IIIA


title: Primary HGSOC patients 081

description: Library name: OBGY0096


title: Primary HGSOC patients 082

description: Library name: OBGY0089


title: Primary HGSOC patients 075

description: Library name: OBGY0108


title: Primary HGSOC patients 083

description: Library name: OBGY0084


title: Primary HGSOC patients 097

description: Library name: OBGY0031


title: Primary HGSOC patients 100

description: Library name: OBGY0026


title: Primary HGSOC patients 084

description: Library name: OBGY0083

value: IC


title: Primary HGSOC patients 086

description: Library name: OBGY0077


title: Primary HGSOC patients 089

description: Library name: OBGY0053


title: Primary HGSOC patients 101

description: Library name: OBGY0025


title: Primary HGSOC patients 099

description: Library name: OBGY0027

value: IIA


title: Primary HGSOC patients 104

description: Library name: OBGY0020


title: Recurrent HGSOC patients 102

description: Library name: OBGY0023


title: Primary HGSOC patients 106

description: Library name: OBGY0011


title: Primary HGSOC patients 107

description: Library name: OBGY0008


title: Primary HGSOC patients 108

description: Library name: OBGY0007


title: Primary HGSOC patients 091

description: Library name: OBGY0049

value: IA


title: Recurrent HGSOC patients 096

description: Library name: OBGY0033


title: Primary HGSOC patients 098

description: Library name: OBGY0030


title: Recurrent HGSOC patients 103

description: Library name: OBGY0021


title: Primary HGSOC patients 088

description: Library name: OBGY0070


title: Primary HGSOC patients 085

description: Library name: OBGY0081


title: Zebra finch embryo 28 medial hypothalamus E14 heat call female

status: Public on Dec 22 2025

city: Clemson

first: Prakrit

last: Subba

state: SC

address: 132 Long Hall, 230 Parkway Drive

department: Biological Sciences

country: USA

institute: Clemson University

description:
Library name: sample_28
Medial coronal punch from E14 zebra finch embryo exposed to chronic heat call playback (E10-E13, 9h/day); female

data_processing:
Trimmomatic v0.39 was used for quality control and adapter trimming.
Quality-trimmed reads were mapped to the zebra finch reference transcriptome (bTaeGut1.4.pri) and quantified using Salmon v1.5.2 in quasi-mapping mode.
Transcript-level counts were imported and aggregated to gene-level using tximport, with tx2gene mapping derived from the reference GTF file.
Gene-level differential expression analysis was performed using DESeq2 v1.30.1 with negative binomial generalized linear models, adjusting for sex as a covariate. P-values were adjusted using the Benjamini-Hochberg FDR method.
Variance-stabilizing transformation (VST) was applied for downstream analyses including principal component analysis and weighted gene co-expression network analysis (WGCNA).
Assembly: bTaeGut1.4.pri
Supplementary files format and content: CSV file includes raw gene-level counts for each sample (19 columns: gene_id + 19 samples).
Supplementary files format and content: CSV file includes normalized counts (DESeq2 size-factor normalized) for each sample.
Supplementary files format and content: CSV file includes variance-stabilized expression values (VST) for each sample.

organism: Taeniopygia guttata

source_name: hypothalamus

growth_protocol: Zebra finch eggs were incubated at 37.5°C in experimental incubators and exposed to either heat call or control call playback (9 hours/day) from embryonic day 10 to embryonic day 13.

extract_protocol:
On embryonic day 14, embryos were decapitated and medial hypothalamic punches (1 mm diameter) were collected from 100 Œºm coronal cryosections (10 sections per brain) using a micro-punching technique. Total RNA was extracted using the Zymo Quick-RNA Microprep Kit (cat #R1050). RNA quality and concentration were assessed using NanoDrop spectrophotometry and Agilent 2100 Bioanalyzer.
The Genome Centre and Queen Mary University of London prepared mRNA stranded libraries from total RNA using a custom method. Libraries were sequenced on an Illumina NextSeq 500 platform (75 bp paired-end).

treatment_protocol:
Heat call playback group (n=10): Eggs exposed to whine + heat call audio stimuli for 9 hours per day from E10-E13 via speakers attached to incubators.
Control call playback group (n=9): Eggs exposed to whine + tet call audio stimuli for 9 hours per day from E10-E13 via speakers attached to incubators.

value: hypothalamus

value: female

tag: genotype

value: wild type

tag: treatment

value: Heat call playback E10-E13


title: Zebra finch embryo 24 medial hypothalamus E14 heat call male

description:
Library name: sample_24
Medial coronal punch from E14 zebra finch embryo exposed to chronic heat call playback (E10-E13, 9h/day); male

value: male


title: Zebra finch embryo 13 medial hypothalamus E14 control male

description:
Library name: sample_13
Medial coronal punch from E14 zebra finch embryo exposed to control call playback (E10-E13, 9h/day); male

value: Control call playback E10-E13


title: Zebra finch embryo 22 medial hypothalamus E14 heat call female

description:
Library name: sample_22
Medial coronal punch from E14 zebra finch embryo exposed to chronic heat call playback (E10-E13, 9h/day); female


title: Zebra finch embryo 33 medial hypothalamus E14 control male

description:
Library name: sample_33
Medial coronal punch from E14 zebra finch embryo exposed to control call playback (E10-E13, 9h/day); male


title: Zebra finch embryo 12 medial hypothalamus E14 control male

description:
Library name: sample_12
Medial coronal punch from E14 zebra finch embryo exposed to control call playback (E10-E13, 9h/day); male


title: Zebra finch embryo 32 medial hypothalamus E14 control female

description:
Library name: sample_32
Medial coronal punch from E14 zebra finch embryo exposed to control call playback (E10-E13, 9h/day); female


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 10um baricitinib, Replicate 3

status: Public on Dec 18 2025

city: Philadelphia

first: Frederick

middle: Chris

last: Bennett

state: PA

address: 3501 Civic Center Blvd

department: Neurology

institute: University of Pennsylvania

description: Library name: A11

data_processing:
All pre-processing steps were run using Terminal. FastQ files were downloaded from BaseSpace (Illumina) and concatenated across lanes using the “cat” function. All files were processed using FastP (Chen et al., 2018; Chen, 2023) to filter reads and trim Illumina adaptors, as well as FastQC (Andrews, 2014) to assess quality. All files were determined to be of sufficient quality for subsequent downstream processing. Reads were pseudoaligned to the mouse GRCm39 cDNA transcriptome (Ensembl release 99; Schneider et al., 2017; Zerbino et al., 2018) using Kallisto (version 0.46.0; Bray et al., 2016) and run through MultiQC (Ewels et al., 2016) for a final quality check after mapping.
All post-processing steps were run using RStudio (R Core Team, 2022). Transcripts were summarized to the gene level through tximport (version 1.14.2; Soneson et al., 2015) with abundance counts calculated via TPM and then normalized using TMM via edgeR (Robinson et al., 2010; McCarthy et al., 2012; Chen et al., 2016). Hierarchical cluster dendrograms were created using the “dist” function (method = euclidean) and “hclust” function (method = complete) and were visualized with the plot function. PCA plots were created using the “prcomp” function. Differential gene expression analysis was performed using linear modeling via limma (Ritchie et al., 2015), and differentially expressed genes (DEGs) were decided by applying an FDR cutoff of 0.05, a counts per million (CPM) cutoff of +1, and a Log2(FC) cutoff of +/- 2. Linear models and R2 values were created using the “lm” function. All output plots were visualized with ggplot2 (Wickham, 2016).
Assembly: mouse GRCm39 cDNA transcriptome
Supplementary files format and content: normalized_counts.tsv file contains transcript abundance counts calculated as described above for all samples

organism: Mus musculus

growth_protocol: Hoxb8s grown in RPMI media (Invitrogen, 7240047) supplemented with 1 mM Na-Pyruvate (Invitrogen, 11360070), 0.0005 mM beta-estradiol (Sigma Aldrich, E2758), and 10 ng/mL GM-CSF (Peprotech, 315-03). All cells were differentiated in DMEM media (ThermoFisher, 10569010), 10% FBS (VWR, 89510-186), 1% Penn/Strep (Invitrogen, 15140122), supplemented with 30 ng/mL murine M-CSF (Peprotech, 315-02) for 7 days unless noted otherwise. All cells kept at 5% C02 at 37C with media changes every 2-3 days.

extract_protocol:
For in vitro populations, RNA was extracted using the Qiagen RNeasy Mini Kit (74104) according to manufacturer’s instructions. For in vivo populations, cells were isolated and FACS sorted into TRIZol LS reagent.  Cells were briefly vortexed and 0.2 volumes of chloroform (Sigma, C2432-500ML) were added. Cells were again vortexed, incubated for 3 m at RT, and then centrifuged at 12,000xg for 15 m at 4c. The upper aqueous phase was then collected and 1 volume of fresh 70% EtOH was added. Cells were again vortexed and then run through the Qiagen RNeasy Micro Kit (74004) according to manufacturer’s instructions. Isolated RNA was stored at -80.
Sequencing libraries were prepared in-house using either 40 ng or 8ul RNA per sample, depending on if RIN scores and concentrations were able to be calculated, using the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB, E6420) according to manufacturer’s instructions.

treatment_protocol: Cells were treated with 0uM, 0.00064uM, 0.16uM, 0.4uM, or 10uM Baricitinib (Selleck Chemicals, S2851) with each media change.

tag: cell line

tag: cell type

value: Cas9 het; Adar KO

value: 10um baricitinib


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 0.4um baricitinib, Replicate 2

description: Library name: A12

value: 0.4um baricitinib


title: Zebra finch embryo 27 medial hypothalamus E14 control female

description:
Library name: sample_27
Medial coronal punch from E14 zebra finch embryo exposed to control call playback (E10-E13, 9h/day); female


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 0.4um baricitinib, Replicate 3

description: Library name: A17


title: Zebra finch embryo 20 medial hypothalamus E14 heat call female

description:
Library name: sample_20
Medial coronal punch from E14 zebra finch embryo exposed to chronic heat call playback (E10-E13, 9h/day); female


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 0.4um baricitinib, Replicate 1

description: Library name: A7


title: Zebra finch embryo 31 medial hypothalamus E14 heat call male

description:
Library name: sample_31
Medial coronal punch from E14 zebra finch embryo exposed to chronic heat call playback (E10-E13, 9h/day); male


title: Zebra finch embryo 16 medial hypothalamus E14 heat call male

description:
Library name: sample_16
Medial coronal punch from E14 zebra finch embryo exposed to chronic heat call playback (E10-E13, 9h/day); male


title: Zebra finch embryo 30 medial hypothalamus E14 control male

description:
Library name: sample_30
Medial coronal punch from E14 zebra finch embryo exposed to control call playback (E10-E13, 9h/day); male


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 0um baricitinib, Replicate 3

description: Library name: A15

value: 0um baricitinib


title: Zebra finch embryo 21 medial hypothalamus E14 control male

description:
Library name: sample_21
Medial coronal punch from E14 zebra finch embryo exposed to control call playback (E10-E13, 9h/day); male


title: Zebra finch embryo 26 medial hypothalamus E14 heat call female

description:
Library name: sample_26
Medial coronal punch from E14 zebra finch embryo exposed to chronic heat call playback (E10-E13, 9h/day); female


title: Zebra finch embryo 25 medial hypothalamus E14 control male

description:
Library name: sample_25
Medial coronal punch from E14 zebra finch embryo exposed to control call playback (E10-E13, 9h/day); male


title: Zebra finch embryo 14 medial hypothalamus E14 control male

description:
Library name: sample_14
Medial coronal punch from E14 zebra finch embryo exposed to control call playback (E10-E13, 9h/day); male


title: Zebra finch embryo 15 medial hypothalamus E14 heat call female

description:
Library name: sample_15
Medial coronal punch from E14 zebra finch embryo exposed to chronic heat call playback (E10-E13, 9h/day); female


title: Zebra finch embryo 10 medial hypothalamus E14 heat call female

description:
Library name: sample_10
Medial coronal punch from E14 zebra finch embryo exposed to chronic heat call playback (E10-E13, 9h/day); female


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 10um baricitinib, Replicate 1

description: Library name: A1


title: Zebra finch embryo 08 medial hypothalamus E14 heat call female

description:
Library name: sample_08
Medial coronal punch from E14 zebra finch embryo exposed to chronic heat call playback (E10-E13, 9h/day); female


title: Primary HGSOC patients 105

description: Library name: OBGY0018

value: Primary

value: Female

value: Tumor tissue


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 0.016um baricitinib, Replicate 2

description: Library name: A13

value: 0.016um baricitinib


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 0.0006um baricitinib, Replicate 3

description: Library name: A19

value: 0.0006um baricitinib


title: NTC ER-Hoxb8 macrophages grown for 7div with 0.4um baricitinib, Replicate 3

description: Library name: N12

value: Cas9 het; NTC


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 0.0006um baricitinib, Replicate 2

description: Library name: A9


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 10um baricitinib, Replicate 4

description: Library name: A16


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 0.016um baricitinib, Replicate 1

description: Library name: A8


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 0.016um baricitinib, Replicate 3

description: Library name: A18


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 0um baricitinib, Replicate 1

description: Library name: A5


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 0um baricitinib, Replicate 2

description: Library name: A10


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 10um baricitinib, Replicate 2

description: Library name: A6


title: NTC ER-Hoxb8 macrophages grown for 7div with 0.0006um baricitinib, Replicate 3

description: Library name: N14


title: NTC ER-Hoxb8 macrophages grown for 7div with 10um baricitinib, Replicate 1

description: Library name: N1


title: NTC ER-Hoxb8 macrophages grown for 7div with 0.016um baricitinib, Replicate 3

description: Library name: N13


title: NTC ER-Hoxb8 macrophages grown for 7div with 0.016um baricitinib, Replicate 4

description: Library name: N18


title: NTC ER-Hoxb8 macrophages grown for 7div with 0.4um baricitinib, Replicate 4

description: Library name: N17


title: NTC ER-Hoxb8 macrophages grown for 7div with 0um baricitinib, Replicate 3

description: Library name: N20


title: Adar KO (sgRNA #2) macrophages after 7div, Replicate 5

description: Library name: A2-Mac-5


title: NTC ER-Hoxb8 macrophages grown for 7div with 0um baricitinib, Replicate 1

description: Library name: N5


title: Adar KO (sgRNA #2) macrophages after 7div, Replicate 3

description: Library name: A2-Mac-3


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 0.0006um baricitinib, Replicate 1

description: Library name: A4


title: Adar KO (sgRNA #2) progenitors made from transducing Cas9 het ER-Hoxb8s, Replicate 3

description: Library name: A2-Prog-3


title: Adar KO (sgRNA #2) progenitors made from transducing Cas9 het ER-Hoxb8s, Replicate 2

description: Library name: A2-Prog-2


title: NTC macrophages after 7div, Replicate 3

description: Library name: NTC-3


title: NTC ER-Hoxb8 macrophages grown for 7div with 10um baricitinib, Replicate 3

description: Library name: N16


title: Adar KO (sgRNA #1) macrophages after 7div, Replicate 2

description: Library name: Adar1-2


title: NTC ER-Hoxb8 macrophages grown for 7div with 0.4um baricitinib, Replicate 1

description: Library name: N2


title: NTC ER-Hoxb8 macrophages grown for 7div with 0.0006um baricitinib, Replicate 1

description: Library name: N4


title: NTC ER-Hoxb8 macrophages grown for 7div with 10um baricitinib, Replicate 2

description: Library name: N11


title: NTC ER-Hoxb8 macrophages grown for 7div with 0.016um baricitinib, Replicate 2

description: Library name: N8


title: NTC ER-Hoxb8 macrophages grown for 7div with 0.0006um baricitinib, Replicate 2

description: Library name: N9


title: Adar KO (sgRNA #1) macrophages after 7div, Replicate 3

description: Library name: Adar1-3


title: NTC progenitors made from transducing Cas9 het ER-Hoxb8s, Replicate 3

description: Library name: NTC2Prog3


title: NTC ER-Hoxb8 macrophages grown for 7div with 0.016um baricitinib, Replicate 1

description: Library name: N3


title: Adar KO (sgRNA #2) macrophages after 7div, Replicate 2

description: Library name: A2-Mac-2


title: NTC ER-Hoxb8 macrophages grown for 7div with 0um baricitinib, Replicate 2

description: Library name: N10


title: NTC ER-Hoxb8 macrophages grown for 7div with 0.4um baricitinib, Replicate 2

description: Library name: N7


title: Unmanipulated microglia isolated from FVB WT mouse; no injection, Replicate 7

description: Library name: WT7

source_name: Mg

value: brain

value: Mg

value: WT


title: Unmanipulated microglia isolated from FVB WT mouse; no injection, Replicate 4

description: Library name: WT4


title: Unmanipulated microglia isolated from FVB WT mouse; no injection, Replicate 8

description: Library name: YSWT1


title: Adar KO (sgRNA #2) macrophages after 7div, Replicate 4

description: Library name: A2-Mac-4


title: Unmanipulated microglia isolated from FVB WT mouse; no injection, Replicate 6

description: Library name: WT6


title: Adar KO (sgRNA #2) macrophages after 7div, Replicate 1

description: Library name: A2-Mac-1


title: ER-Hoxb8 ICT inj. into CSF1R KO brain; re-isolated back out, Replicate 6

description: Library name: WTHox4Lo


title: ER-Hoxb8 ICT inj. into CSF1R KO brain; re-isolated back out, Replicate 5

description: Library name: WTHox2Lo


title: ER-Hoxb8 ICT inj. into CSF1R KO brain; re-isolated back out, Replicate 2

description: Library name: GFPHox2


title: ER-Hoxb8 ICT inj. into CSF1R KO brain; re-isolated back out, Replicate 4

description: Library name: WTHox1Lo


title: Adar KO (sgRNA #2) progenitors made from transducing Cas9 het ER-Hoxb8s, Replicate 1

description: Library name: A2-Prog-1


title: BM ICT inj. into CSF1R KO brain; re-isolated back out, Replicate 5

description: Library name: BM6

source_name: BM

value: BM


title: BM ICT inj. into CSF1R KO brain; re-isolated back out, Replicate 6

description: Library name: BM7


title: NTC macrophages after 7div, Replicate 1

description: Library name: NTC-1


title: NTC macrophages after 7div, Replicate 2

description: Library name: NTC2-2-Redo


title: Adar KO (sgRNA #1) macrophages after 7div, Replicate 1

description: Library name: Adar1-1


title: NTC progenitors made from transducing Cas9 het ER-Hoxb8s, Replicate 2

description: Library name: NTC2Prog2


title: BM ICT inj. into CSF1R KO brain; re-isolated back out, Replicate 2

description: Library name: BM2


title: ER-Hoxb8 macrophages grown for 7div from FVB Cas9 Mouse, Replicate 3

description: Library name: d7Hox3

value: Cas9 het


title: NTC progenitors made from transducing Cas9 het ER-Hoxb8s, Replicate 1

description: Library name: NTC2Prog1


title: ER-Hoxb8 macrophages grown for 7div from FVB Cas9 Mouse, Replicate 2

description: Library name: d7Hox2


title: Adar KO (sgRNA #1) progenitors made from transducing Cas9 het ER-Hoxb8s, Replicate 3

description: Library name: AdarProg3


title: ER-Hoxb8 cells grown for 4div from FVB Cas9 Mouse, Replicate 3

description: Library name: d4Hox3


title: ER-Hoxb8 macrophages grown for 7div from FVB Cas9 Mouse, Replicate 1

description: Library name: d7Hox1


title: Unmanipulated microglia isolated from FVB WT mouse; no injection, Replicate 9

description: Library name: YSWT2


title: ER-Hoxb8 Progenitors from FVB Cas9 Mouse, Replicate 3

description: Library name: d0Hox3


title: Adar KO (sgRNA #1) progenitors made from transducing Cas9 het ER-Hoxb8s, Replicate 2

description: Library name: AdarProg2


title: Unmanipulated microglia isolated from FVB WT mouse; no injection, Replicate 5

description: Library name: WT5


title: Unmanipulated microglia isolated from FVB WT mouse; no injection, Replicate 2

description: Library name: WT2


title: Monocytes isolated from FVB WT BM, Replicate 1

description: Library name: Mono1


title: Progenitors isolated from FVB WT BM, Replicate 1

description: Library name: Prog1


title: Progenitors isolated from FVB WT BM, Replicate 2

description: Library name: Prog2


title: Adar KO (sgRNA #1) progenitors made from transducing Cas9 het ER-Hoxb8s, Replicate 1

description: Library name: AdarProg1


title: L5_ET_CTX_Glut.male.9mo

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
Library name: sample 32
read length: 151

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Hisat3n.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

molecule: genomic DNA

source_name: brain

extract_protocol:
Mouse brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

treatment_protocol: The nuclei were isolated and sorted into 384-well plates using previous methods21. Briefly, single-nuclei were stained with AlexaFluor488-conjugated anti-NeuN antibody (MAB377X, Millipore) and Hoechst 33342 (62249, ThermoFisher) followed by FANS using a BD Influx sorter with single-cell (1 drop single) mode.

value: male


title: Macrophages grown for 7div from FVB WT BM, Replicate 1

description: Library name: Mac1


title: L5_ET_CTX_Glut.male.18mo

description:
Library name: sample 30
read length: 151


title: Unmanipulated microglia isolated from FVB WT mouse; no injection, Replicate 3

description: Library name: WT3


title: BM ICT inj. into CSF1R KO brain; re-isolated back out, Replicate 3

description: Library name: BM3


title: L45_IT_CTX_Glut.male.8wk

description:
Library name: sample 28
read length: 151


title: ER-Hoxb8 ICT inj. into CSF1R KO brain; re-isolated back out, Replicate 1

description: Library name: GFPHox1


title: BM ICT inj. into CSF1R KO brain; re-isolated back out, Replicate 4

description: Library name: BM5


title: L23_IT_PPP_Glut.male.8wk

description:
Library name: sample 25
read length: 151


title: ER-Hoxb8 cells grown for 4div from FVB Cas9 Mouse, Replicate 1

description: Library name: d4Hox1


title: ER-Hoxb8 Progenitors from FVB Cas9 Mouse, Replicate 2

description: Library name: d0Hox2


title: Macrophages grown for 7div from FVB WT BM, Replicate 3

description: Library name: wBM_1


title: ER-Hoxb8 cells grown for 4div from FVB Cas9 Mouse, Replicate 2

description: Library name: d4Hox2


title: L23_IT_PPP_Glut.male.9mo

description:
Library name: sample 26
read length: 151


title: Unmanipulated microglia isolated from FVB WT mouse; no injection, Replicate 1

description: Library name: WT1


title: L23_IT_ENT_Glut.male.9mo

description:
Library name: sample 23
read length: 151


title: ER-Hoxb8 ICT inj. into CSF1R KO brain; re-isolated back out, Replicate 3

description: Library name: GFPHox4


title: L23_IT_ENT_Glut.male.8wk

description:
Library name: sample 22
read length: 151


title: BM ICT inj. into CSF1R KO brain; re-isolated back out, Replicate 1

description: Library name: BM1


title: ER-Hoxb8 Progenitors from FVB Cas9 Mouse, Replicate 1

description: Library name: d0Hox1


title: Macrophages grown for 7div from FVB WT BM, Replicate 2

description: Library name: Mac3


title: Monocytes isolated from FVB WT BM, Replicate 3

description: Library name: Mono3


title: DG_Glut.male.9mo

description:
Library name: sample 17
read length: 151


title: L5_IT_CTX_Glut.male.8wk

description:
Library name: sample 34
read length: 151


title: Monocytes isolated from FVB WT BM, Replicate 2

description: Library name: Mono2


title: Progenitors isolated from FVB WT BM, Replicate 3

description: Library name: Prog3


title: CEA-BST_Gaba.male.9mo

description:
Library name: sample 14
read length: 151


title: L5_IT_CTX_Glut.male.9mo

description:
Library name: sample 35
read length: 151


title: CA1-ProS_Glut.male.9mo

description:
Library name: sample 8
read length: 151


title: CA3_Glut.male.9mo

description:
Library name: sample 11
read length: 151


title: CEA-BST_Gaba.male.18mo

description:
Library name: sample 12
read length: 151


title: L5_IT_CTX_Glut.male.18mo

description:
Library name: sample 33
read length: 151


title: L45_IT_CTX_Glut.male.9mo

description:
Library name: sample 29
read length: 151


title: L45_IT_CTX_Glut.male.18mo

description:
Library name: sample 27
read length: 151


title: CA1-ProS_Glut.male.18mo

description:
Library name: sample 6
read length: 151


title: Astro-TE_NN.male.9mo

description:
Library name: sample 5
read length: 151


title: L5_ET_CTX_Glut.male.8wk

description:
Library name: sample 31
read length: 151


title: CA3_Glut.male.8wk

description:
Library name: sample 10
read length: 151


title: L23_IT_ENT_Glut.male.18mo

description:
Library name: sample 21
read length: 151


title: L23_IT_PPP_Glut.male.18mo

description:
Library name: sample 24
read length: 151


title: L23_IT_CTX_Glut.male.9mo

description:
Library name: sample 20
read length: 151


title: PostFFX, Pt_F2

status: Public on Dec 13 2025

city: Los Angeles

first: Jason

middle: Michael

last: Link

address: 650 Charles E Young Dr S

department: Surgery

institute: University of California, Los Angeles

description: Library name: Pt_F2

data_processing:
The reads were mapped by STAR 2.7.9a and read counts per gene were quantified using the human genome GRCh38. In Partek Flow, read counts were normalized by CPM +1.0E-4
Assembly: GRCh38
Supplementary files format and content: txt file of normalized counts

source_name: Pancreatic Ductal Adenocarcinoma

extract_protocol:
Pre-treatment tumor biopsy or post-treatment tumor resection specimens were formalin fixed and embedded in paraffin. Tissue sections were cut to slides and pathologist-guided, tumor-enriched regions were macroscopically scraped.
Libraries for RNA-Seq were prepared with KAPA stranded RNA HyperPrep Kit with RiboErase (HMR)
Sequencing was performed on Illumina NovaSeq6000 for a PE 2x50 run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software

value: Pancreatic Ductal Adenocarcinoma

value: FOLFIRINOX


title: PostFFX+nivolumab, Pt_3

description: Library name: Pt_3

value: FOLFIRINOX+nivolumab


title: PostFFX, Pt_F3

description: Library name: Pt_F3


title: PostFFX, Pt_F1

description: Library name: Pt_F1


title: L23_IT_CTX_Glut.male.8wk

description:
Library name: sample 19
read length: 151


title: PostFFX+nivolumab, Pt_4

description: Library name: Pt_4


title: DG_Glut.male.8wk

description:
Library name: sample 16
read length: 151


title: PostFFX, Pt_F9

description: Library name: Pt_F9


title: DG_Glut.male.18mo

description:
Library name: sample 15
read length: 151


title: PostFFX, Pt_F4

description: Library name: Pt_F4


title: CA1-ProS_Glut.male.8wk

description:
Library name: sample 7
read length: 151


title: PostFFX, Pt_F8

description: Library name: Pt_F8


title: PostFFX, Pt_F7

description: Library name: Pt_F7


title: PostFFX+nivolumab, Pt_18

description: Library name: Pt_18


title: CEA-BST_Gaba.male.8wk

description:
Library name: sample 13
read length: 151


title: Astro-TE_NN.male.8wk

description:
Library name: sample 4
read length: 151


title: L23_IT_CTX_Glut.male.18mo

description:
Library name: sample 18
read length: 151


title: PostFFX+nivolumab, Pt_1

description: Library name: Pt_1


title: RNA_18m_rep1

status: Public on Dec 03 2025

city: San Diego

first: Kangli

last: Wang

address: 9500 Gilman Drive

institute: University of California San Diego

description: snRNA-seq

library_source: transcriptomic single cell

data_processing:
The sequencing reads were aligned to mm10 (GRCm38) reference genome and the feature-barcode matrix and fragments was generated using cellranger-arc (v2.0.0).
Assembly: mm10
Supplementary files format and content: Filtered H5 matrix files output from Cell Ranger software.
Supplementary files format and content: Fragments files output from Cell Ranger software.

molecule: nuclear RNA

extract_protocol:
C57BL/6 mice were purchased from Jackson Laboratories. Brains were extracted from mice and substantia nigra regions were dissected according to the Allen Brain Reference Atlas. For each sample, dissected brain tissues were pooled from 4-5 C57BL/6 mice to obtain enough nuclei for single nucleus multiome for each biological replicate, and two biological replicates were performed for each age stage.
Nucleus were isolated from the directions using the protocol suggested for use with the chromium Next GEM Single Cell Multiome ATAC+Gene Expression protocol (CG000338). Libraries were performed immediately for each sample as per Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide (CG000338).
Chromium Single Cell Multiome ATAC + Gene Expression

tag: tissue region

value: Substantia nigra

tag: strain

tag: number of_animals_pooled

tag: age

value: 18 months old


title: RNA_18m_rep2

description: snRNA-seq


title: ATAC_12m_rep2

description: snATC-seq

library_source: genomic single cell

value: 12 months old


title: CA3_Glut.male.18mo

description:
Library name: sample 9
read length: 151


title: Astro-TE_NN.male.18mo

description:
Library name: sample 3
read length: 151


title: ATAC_6m_rep2

description: snATC-seq

value: 6 months old


title: Astro-NT_NN.male.18mo

description:
Library name: sample 0
read length: 151


title: RNA_2m_rep2

description: snRNA-seq

value: 2 months old


title: PostFFX+nivolumab, Pt_9

description: Library name: Pt_9


title: RNA_2m_rep1

description: snRNA-seq


title: ATAC_2m_rep2

description: snATC-seq


title: PostFFX+nivolumab, Pt_15

description: Library name: Pt_15


title: PostFFX+nivolumab, Pt_6

description: Library name: Pt_6


title: Astro-NT_NN.male.9mo

description:
Library name: sample 2
read length: 151


title: PreFFX+nivolumab, Pt_2P

description: Library name: Pt_2P


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, Nutlin, 3hr, rep2

status: Public on Nov 26 2025

city: Daejeon

first: Wonki

last: Cho

address: 291 Daehak-ro Yuseong-gu

institute: KAIST

description: Library name: DMSO_Nutlin_rep2

data_processing:
Sequence reads were mapped to hg38 using STAR version 2.7.10b with default parameters. For differential gene expression analysis, we analyzed raw read counts using RSEM (Li et al., 2011), and then calculated statistics of differential expression via DESeq2 version 1.48.1 (Love et al., 2014) with default parameters.
Assembly: GRCh38
Supplementary files format and content: Tap-delimited text files include gene id, transcript id, length, effective length, expected count, TPM and FPKM for each replicates.

extract_protocol:
Total RNA was extracted by Trizol extraction. 0.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded Total RNA Library Prep Gold Kit following manufacture's protocols.


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, 5-Ph-IAA, control, 3hr, rep1

description: Library name: IAA_3hr_control_rep1


title: PostFFX, Pt_F5

description: Library name: Pt_F5


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, Nutlin, 3hr, rep1

description: Library name: DMSO_Nutlin_rep1


title: healthy donor 1_Control-FB

status: Public on Nov 21 2025

description:
Library name: 8674-TK-1-Control-FB
10X Genomics Chromium Single Cell 3′ v3.1 platform, Raw files are gene expression files and feature barcode (FB) files.

data_processing:
Library quality was assessed using a bioanalyzer and quantified using a qPCR-based method equipped with the KAPA Library Quantification Kit (P/N: KK4873) and the QuantStudio 12K instrument. The prepared libraries were pooled in equimolar ratios, and the resulting pool was subjected to cluster generation using the NovaSeq 6000 System, in accordance with the manufacturer’s protocols. 150-bp paired-end sequencing was performed on the NovaSeq 6000 platform targeting 50,000 reads per cell. Raw sequencing data (FASTQ files) obtained from the NovaSeq 6000 were subjected to quality control analysis, including read quality assessment. Real Time Analysis Software and NovaSeq Control Software v1.8.0 (Illumina, San Diego, CA, USA) were used for base calling. MultiQC v1.7 (Illumina, San Diego, CA, USA) was used for data quality assessments.
10x Genomics Cell Ranger v5.0.0 was used to perform single-cell gene counting based on the human genome GRCh38.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: barcodes.tsv.gz: list of cell barcodes, features.tsv.gz: list of gene IDs, matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format

source_name: Blood

extract_protocol:
Peripheral blood mononuclear cells (PBMC) of female mTNBC were obtained from a clinical study approved by the institutional review board of the Korea University Medical Center Anam Hospital, Seoul, the Republic of Korea (no. ED17183). PBMCs of two healthy donors with no known medical history of cancer or other general conditions such as hypertension, diabetes, hyperlipidemia, and cardiovascular and inflammatory diseases were collected for comparison. In brief, whole blood samples were collected, and PBMCs were isolated by Ficoll–Paque™ density-gradient centrifugation.
ScRNA-seq libraries were prepared using the Chromium Single Cell 3′ v3.1 platform (10X Genomics) according to the manufacturer’s protocol. In brief, 10,000 cells were loaded into each channel of the Chromium X controller to achieve the target cell recovery of 5,000 cells. The cells were partitioned into gel bead emulsions, where cell lysis and barcoded reverse transcription of RNA were performed, followed by cDNA amplification. The amplified cDNA was purified using SPRI beads, and dual-indexed libraries were constructed by fragmentation, end repair, A-tailing, adapter ligation, and PCR amplification.

value: Blood

tag: subject status

value: healthy donor

value: Peripheral blood mononuclear cells


title: E67_knee_spatial01

city: Boston

first: April

last: Craft

address: 300 Longwood Ave

institute: Boston Children's Hospital

description:
Library name: D1_k67_spatialHD
10X Genomics Visium HD

data_processing:
The raw files were mapped to the Human genome Hg38 using the Space Ranger v.4.0 software, available via the 10X Genomics website.
Assembly: hg38
Supplementary files format and content: space ranger output files: fragments, matrix and barcodes are provided.
Supplementary files format and content: Loupe file.
Library strategy: Spatial Transcriptomics

source_name: knee

extract_protocol:
Fresh knee tissues were dissected, flash frozen in OCT, sectioned at 10um, permeabalized, and follwed the 10X Genomics spatial Visium HD manufactureres protocol. cDNA was made, amplified and the DNA was purified using Ampure beads.
Libraries were constructed following 10X Genomics visium manufactures protocols. Quality was checked using the tapestation, libraries were pooled and eventually sequenced using the NovaSeq X.

value: knee


title: PostFFX, Pt_F6

description: Library name: Pt_F6


title: PostFFX+nivolumab, Pt_5

description: Library name: Pt_5


title: healthy donor 2_Control

description:
Library name: 8674-TK-2-Control
10X Genomics Chromium Single Cell 3′ v3.1 platform, Raw files are gene expression files and feature barcode (FB) files.


title: healthy donor 2_Control-FB

description:
Library name: 8674-TK-2-Control-FB
10X Genomics Chromium Single Cell 3′ v3.1 platform, Raw files are gene expression files and feature barcode (FB) files.


title: ATAC_18m_rep2

description: snATC-seq

value: brain


title: PostFFX+nivolumab, Pt_13

description: Library name: Pt_13


title: PostFFX+nivolumab, Pt_11

description: Library name: Pt_11


title: ATAC_18m_rep1

description: snATC-seq


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, DMSO, control, rep1

description: Library name: DMSO_control_rep1


title: PostFFX+nivolumab, Pt_12

description: Library name: Pt_12


title: R255X-WT_CO3, R255X-MUT_CO3, R255X-WT_TA3, R255X-MUT_TA3

status: Public on Nov 07 2025

first: Alysson

middle: R.

last: Muotri

address: 2880 Torrey Pines Scenic Drive - Room 3005

institute: UCSD

description:
Library name: Pool 4
10x Genomics

data_processing:
ScRNA-seq reads were processed with Cell Ranger multi v8.0.1 using the prebuilt 10X GRCh38 reference refdata-gex-GRCh38-2024-A and including introns. Further processing, such as demultiplexing, dimensionality reduction, clustering, and visualization, was performed in R v4.4.2 with Seurat v5.0.0. Demultiplexed datasets were filtered to retain high-quality cells. Only cells containing between 800 and 10,000 sequenced genes, a UMI count below 40,000, and a proportion of mitochondrial and ribosomal genes less than 15% and 30%, respectively, were retained. The Gruffi algorithm (v.1.5.6) (Vértesy et al., 2022) was used to identify and remove cells with a transcriptional signature of cellular stress (thresholds: GO:0006096, 1.124; GO:0034976, 0.464; GO:0042063, 0.948). Expression matrices were log-normalized and scaled, and dimensionality reduction was performed using principal component analysis (PCA) on the top 2,000 genes with the highest standardized variance (vst selection method). The top 40 principal components were used to batch correct libraries using Harmony v1.2.3, and the top 25 Harmony embeddings were used for UMAP visualization (for hTAs, the top 18 Harmony embeddings were used).
The first 12 harmony embeddings were used to identify telencephalic clusters, with clustering at resolution 0.7 and 1 yielding the most reliable cell type identification. hCO clusters were annotated using known marker genes expressed on the developing human neocortex 57: aRG (clusters 11 and 12 at resolution 0.7, and cluster 14 at resolution 1), oRG (cluster 10 at resolution 0.7), cycling NPCs (cluster 15 at resolution 0.7, and cluster 17 at resolution 1), IPs (cluster 4 at resolution 0.7, and cluster 2 at resolution 1), excitatory immature neurons (clusters 1, 13, and 14 at resolution 0.7, and clusters 0, 10, and 16 at resolution 1), excitatory infragranular neurons (cluster 3, 6, 8, 9, and 11 at resolution 1), excitatory supragranular neurons (clusters 1, 4, 5, 7, and 15 at resolution 1), and CGE interneurons (cluster 16 at resolution 0.7, and cluster 18 at resolution 1). hTA clusters were annotated similarly, but clustering was only performed at resolution 0.7: RG (cluster 9), cycling NPCs (clusters 10, 15, and 16), IPs (cluster 2), excitatory immature neurons (clusters 0, 1, and 14), excitatory infragranular neurons (cluster 5 and 11), excitatory supragranular neurons (clusters 3, 4, 6, 7, and 8), MGE interneurons (cluster 13), and OPCs (cluster 12).
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz are provided for each multiplexed pool
TA_Seuratobj.rds (Seurat object containing metadata information for the telencephalic assembloid (TA) dataset)

source_name: brain organoid

growth_protocol: Human cerebral organoids and telencephalic assembloids.

extract_protocol:
Multiplexing was performed with antibody-based cell hashing. Library preparation was performed according to the manufacter’s instructions (GEM-X Single Cell 3’ Kit v.4 protocol, 10x Genomics).
Antibody-based cell hashing was performed using 0.5 µg of TotalSeqTM-B anti-human antibodies against β2-microglobulin and CD298 (BioLegend: 394631, 394633, 394635, and 394637), according to the manufacturer’s instructions. To generate single-cell GEMs (Gel Beads in Emulsion), 40,000 live cells of the multiplexed pool were loaded per channel (to give an estimated recovery of 10,000 cells per channel) onto a Chromium GEM-X Single Cell Chip (10X Genomics, PN-1000690). The gene expression library was prepared with the GEM-X Single Cell 3' Kit v.4 (10X Genomics, PN-1000691), and the hashtag-oligo library was prepared with the GEM-X Single Cell 3' Feature Barcode Kit (10X Genomics, PN-1000702). ScRNA-seq libraries were then pooled and pair-end sequenced in a NovaSeq X flowcell (Illumina) with a targeted sequencing depth per cell of 50,000 gene expression reads and 5,000 surface barcode reads.

value: brain organoid

value: Neural progenitors and neurons

value: Patient 2042

value: week 17 of differentiation


title: R255X-WT_CO2, R255X-MUT_CO2, R255X-WT_TA2, R255X-MUT_TA2

description:
Library name: Pool 3
10x Genomics


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, 5-Ph-IAA, Nutlin, 3hr, rep1

description: Library name: IAA_3hr_Nutlin_rep1


title: RNA_12m_rep1

description: snRNA-seq


title: mTNBC patient 1_Case-FB

description:
Library name: 8674-TK-1-Case-FB
10X Genomics Chromium Single Cell 3′ v3.1 platform, Raw files are gene expression files and feature barcode (FB) files.

value: mTNBC patient

value: chemo, radiation therapy


title: ATAC_2m_rep1

description: snATC-seq


title: ATAC_6m_rep1

description: snATC-seq


title: RNA_6m_rep2

description: snRNA-seq


title: RNA_12m_rep2

description: snRNA-seq


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, 5-Ph-IAA, Nutlin, 3hr, rep2

description: Library name: IAA_3hr_Nutlin_rep2


title: RNA_6m_rep1

description: snRNA-seq


title: ATAC_12m_rep1

description: snATC-seq


title: rna_si3d_hypoxia_a

status: Public on Nov 06 2025

city: Aurora

first: Neelanjan

last: Mukherjee

state: Colorado

address: Research Complex 1 South, 12801 E 17th Ave

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

description: Library name: NM2023_0102

data_processing:
Adapters were trimmed with Cutadapt (Martin et al, 2011). UMIs were trimmed and collapsed using UMI-tools (Smith et al, 2017). Salmon (Patro et al, 2017) was used for quantifying transcript levels from RNA-seq and Ribo-seq libraries using GENCODEv26 transcriptome assembly. Briefly, Salmon data were imported using the tximport (Soneson et al, 2015).  Transcript expression was quantified using Salmon v1.6 (12). Quality of ribosome sequencing data, including ribosome footprint length, p-site positioning, and three-nucleotide periodicity, was assessed using Ribowaltz (Lauria et al, 2018).
Assembly: GRCh38
Supplementary files format and content: tabular file containing salmon quantification (raw reads and TPMs) for all samples

growth_protocol: Cells were cultured in incubators at 37 ℃ with 5% CO2 and ~21% O2 (atmospheric). MCF7SIX1 cells (Clone A13) (derived from human female breast cancer cells) were generated as previously described (Ford et al, 1998). The MCF7SIX1 cells were cultured Dulbecco’s High Glucose Modified Eagle Medium (DMEM, Hyclone SH30022.01), with which 10% fetal bovine serum (FBS, Corning 35-010-CV), and 2 mM L-glutamine (L-glut, Hyclone SH30034.02) were supplemented. The MDA-MB-231 cells were cultured with Dulbecco’s High Glucose Modified Eagle Medium (DMEM, Hyclone SH30022.01), with which 5% fetal bovine serum (FBS, Corning 35-010-CV), 2 mM L-glutamine (L-glut, Hyclone SH30034.02), were supplemented.

extract_protocol:
Ribosome profiling was performed as described previously with a few modifications (Calviello et al, 2016). The lysis buffer contained 100 ug/mL cycloheximide. Following lysis and clarification by centrifugation, total RNA was quantified using the Qubit RNA BR assay kit. A portion of the lysate was reserved as input sample for RNASeq preparation. Total RNA was extracted using the DirectZol RNA Microprep kit (ZYMO Research) following the manufacturer’s instructions with on-column DNase I treatment.  Ribosomal RNA was depleted from total RNA using our previously described RNaseH-based method (Baldwin et al, 2021), then input into the KAPA RNA Hyper prep RNAseq library prep kit (Roche) according to manufacturer’s instructions with dual-index adapters, followed by quality check of the final libraries by Qubit dsDNA HS assay and Tapestation High Sensitivity D1000 screentape. Libraries were pooled and submitted for paired-end 150 bp sequencing on the Illumina NovaSeq6000 platform to a depth of 40 million paired end reads per library.
The remaining lysate was used as input into the ribosome footprinting reaction with 750 U RNase I (Invitrogen Ambion). The digestion was stopped with SUPERaseIN followed by recovery of monosomes with equilibrated Microspin S-400 HR (GE) columns. Trizol LS was added to the monosome-containing elution and RNA isolated with the ZYMO Directzol microprep kit with on-column DNase I treatment. The isolated RNA was depleted of rRNA using the siTOOLs riboPOOLs kit for ribosome profiling. The samples were resolved on a 15% TBE-Urea PAGE gel and ribosome protected fragments (RPFs) 28-29 nt in size were extracted and recovered. RPFs were treated with T4-PNK then used as input into the Qiagen QIAseq miRNA library prep kit with provided single index adapters. Libraries were pooled and submitted for paired-end 150 bp sequencing on the Illumina NovaSeq 6000 S4 platform to a depth of 50 million paired end reads per library (Novogene Corporation Inc.).

treatment_protocol: To provide a hypoxic environment, cells were placed in either a modular hypoxic chamber and filled with a premixed gas comprised of 1% O2, or the cells were placed in a BioSpherix hypoxic chamber flushed with N2 and CO2 gas. The O2 and CO2 concentrations in the BioSpherix chamber were maintained at 1% and 5%, respectively, using a carbon dioxide & oxygen controller (BioSpherix). These conditions were maintained constant throughout the course of the experiments. After hypoxic incubation was completed, quick lysis (<3 min) of the cells was necessary to prevent reoxygenation from affecting our results. ON-TARGETplus siRNA SMARTPools were ordered specifically for eIF3e (cat #: L-010518-00-0010) and eIF3d (cat #: L-017556-00-0010) from Horizon Discovery. ON-TARGETplus non-targeting pool (cat # D-001810-10) was always used as a control. siRNA transfections occurred in 25% OPTIMEM Reduced serum media and 75% full growth media (cat # 31985062). siRNAs were added to the media mixture at a concentration of 7.5 nM for 5 minutes prior to the addition of 1.875 mL Lipofectamine RNAI MAX transfection reagent (cat # 13778150) per 1 mL of media. siRNA:lipofectamine mixtures were incubated for 20 minutes before adding it directly onto the cell culture overnight. siRNA knockdowns were assessed 48-72 hours after the addition of the siRNAs.  8430 and 209 were resuspended in DMSO to a working solution concentration of 20 mM. All experiments with 8430 and 209 were used at 20 mM (1:1000 dilution) with DMSO as a vehicle control.

value: breast cancer

value: SIX1 OE

value: eIF3d siRNA and hypoxia


title: rna_sictrl_normoxia_a

description: Library name: NM2023_0104

value: scramble siRNA


title: rna_sictrl_hypoxia_a

description: Library name: NM2023_0101

value: scramble siRNA and hypoxia


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, 5-Ph-IAA, control, 3hr, rep2

description: Library name: IAA_3hr_control_rep2


title: ribo_si3d_normoxia_a

description: Library name: NM2023_0045

data_processing:
Adapters were trimmed with Cutadapt (Martin et al, 2011). UMIs were trimmed and collapsed using UMI-tools (Smith et al, 2017). Salmon (Patro et al, 2017) was used for quantifying transcript levels from RNA-seq and Ribo-seq libraries using GENCODEv26 transcriptome assembly. Briefly, Salmon data were imported using the tximport (Soneson et al, 2015).  Transcript expression was quantified using Salmon v1.6 (12). Quality of ribosome sequencing data, including ribosome footprint length, p-site positioning, and three-nucleotide periodicity, was assessed using Ribowaltz (Lauria et al, 2018).
Assembly: GRCh38
Supplementary files format and content: tabular file containing salmon quantification (raw reads and TPMs) for all samples
Library strategy: Ribo-Seq

value: eIF3d siRNA


title: mTNBC patient 1_Case

description:
Library name: 8674-TK-1-Case
10X Genomics Chromium Single Cell 3′ v3.1 platform, Raw files are gene expression files and feature barcode (FB) files.

value: Blood


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, DMSO, control, rep2

description: Library name: DMSO_control_rep2


title: mTNBC patient 2_Case-FB

description:
Library name: 8674-TK-2-Case-FB
10X Genomics Chromium Single Cell 3′ v3.1 platform, Raw files are gene expression files and feature barcode (FB) files.


title: healthy donor 1_Control

description:
Library name: 8674-TK-1-Control
10X Genomics Chromium Single Cell 3′ v3.1 platform, Raw files are gene expression files and feature barcode (FB) files.

value: healthy donor


title: ribo_si3e_hypoxia_a

description: Library name: NM2023_0043

value: eIF3e siRNA and hypoxia


title: 230712_Flex_HC_1

status: Public on Oct 29 2025

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

description: Library name: 8911-JF-13

data_processing:
The CellRanger Pipeline (10X Genomics) was used to align reads and generate count matrices.”
Assembly: GRCm38
Supplementary files format and content: count matrix

source_name: skin

extract_protocol:
Protocol Overview: gentleMACS Octo Dissociator for Isolation of Cells from FFPE [https://cdn.10xgenomics.com/image/upload/v1721078231/support-documents/CG000632_DemonstratedProtocol_SamplePrep_from__FFPETissueSections_RevD.pdf]
Tissue Sections;  https://cdn.10xgenomics.com/image/upload/v1722287750/support-documents/CG000527_Chromium_FixedRNAProfiling_MultiplexedSamples_UserGuide_Rev_F.pdf

value: skin

tag: disease state

value: healthy control


title: R133C-WT_CO1, R133C-WT_CO2, R133C-MUT_CO1

description:
Library name: Pool 1
10x Genomics

data_processing:
ScRNA-seq reads were processed with Cell Ranger multi v8.0.1 using the prebuilt 10X GRCh38 reference refdata-gex-GRCh38-2024-A and including introns. Further processing, such as demultiplexing, dimensionality reduction, clustering, and visualization, was performed in R v4.4.2 with Seurat v5.0.0. Demultiplexed datasets were filtered to retain high-quality cells. Only cells containing between 800 and 10,000 sequenced genes, a UMI count below 40,000, and a proportion of mitochondrial and ribosomal genes less than 15% and 30%, respectively, were retained. The Gruffi algorithm (v.1.5.6) (Vértesy et al., 2022) was used to identify and remove cells with a transcriptional signature of cellular stress (thresholds: GO:0006096, 1.124; GO:0034976, 0.464; GO:0042063, 0.948). Expression matrices were log-normalized and scaled, and dimensionality reduction was performed using principal component analysis (PCA) on the top 2,000 genes with the highest standardized variance (vst selection method). The top 40 principal components were used to batch correct libraries using Harmony v1.2.3, and the top 25 Harmony embeddings were used for UMAP visualization (for hTAs, the top 18 Harmony embeddings were used).
The first 12 harmony embeddings were used to identify telencephalic clusters, with clustering at resolution 0.7 and 1 yielding the most reliable cell type identification. hCO clusters were annotated using known marker genes expressed on the developing human neocortex 57: aRG (clusters 11 and 12 at resolution 0.7, and cluster 14 at resolution 1), oRG (cluster 10 at resolution 0.7), cycling NPCs (cluster 15 at resolution 0.7, and cluster 17 at resolution 1), IPs (cluster 4 at resolution 0.7, and cluster 2 at resolution 1), excitatory immature neurons (clusters 1, 13, and 14 at resolution 0.7, and clusters 0, 10, and 16 at resolution 1), excitatory infragranular neurons (cluster 3, 6, 8, 9, and 11 at resolution 1), excitatory supragranular neurons (clusters 1, 4, 5, 7, and 15 at resolution 1), and CGE interneurons (cluster 16 at resolution 0.7, and cluster 18 at resolution 1). hTA clusters were annotated similarly, but clustering was only performed at resolution 0.7: RG (cluster 9), cycling NPCs (clusters 10, 15, and 16), IPs (cluster 2), excitatory immature neurons (clusters 0, 1, and 14), excitatory infragranular neurons (cluster 5 and 11), excitatory supragranular neurons (clusters 3, 4, 6, 7, and 8), MGE interneurons (cluster 13), and OPCs (cluster 12).
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz are provided for each multiplexed pool
CO_Seuratobj.rds (Seurat object containing metadata information for the cerebral organoid (CO) dataset)

value: brain organoid

value: Patient 2036


title: 230712_Flex_HC_2

description: Library name: 8911-JF-14


title: 230628_Flex_GPP_6

description: Library name: 8821-JF-6

value: GPP


title: 230628_Flex_GPP_7

description: Library name: 8821-JF-7


title: R255X-WT_CO1, R255X-MUT_CO1, R255X-WT_TA1, R255X-MUT_TA1

description:
Library name: Pool 2
10x Genomics

value: Neural progenitors and neurons

value: Patient 2042

value: week 17 of differentiation


title: rna_si3d_normoxia_a

description: Library name: NM2023_0105

value: breast cancer


title: 230628_Flex_GPP_4

description: Library name: 8821-JF-4


title: 230628_Flex_GPP_9

description: Library name: 8821-JF-9


title: 230628_Flex_GPP_8

description: Library name: 8821-JF-8


title: rna_si3e_hypoxia_a

description: Library name: NM2023_0103

value: SIX1 OE


title: 230712_Flex_HC_4

description: Library name: 8911-JF-16


title: 230628_Flex_GPP_11

description: Library name: 8821-JF-11


title: ribo_si3e_normoxia_a

description: Library name: NM2023_0046

value: eIF3e siRNA


title: mTNBC patient 2_Case

description:
Library name: 8674-TK-2-Case
10X Genomics Chromium Single Cell 3′ v3.1 platform, Raw files are gene expression files and feature barcode (FB) files.

value: mTNBC patient

value: Peripheral blood mononuclear cells

value: chemo, radiation therapy


title: ribo_sictrl_normoxia_a

description: Library name: NM2023_0044

value: scramble siRNA


title: Hi-C S-phase, Scc1-depleted

status: Public on Oct 23 2025

city: Lyon

first: Aurele

last: Piazza

address: 46 Allee d'Italie

country: France

institute: ENS Lyon

description: Library name: AD561

data_processing:
Reads alignement, contact filtering and PCR duplicate removal was performed using the hicstuff (v3.1.2) pipeline function in cutsite mode with mapping quality set to 20. Hi-C contact matrices in sparse format were binned at 1 kb using hicstuff rebin function and converted to cooler format using hicstuff convert function. Cooler zoomify function was used to generate balanced cooler at 1, 2, 5, 10, and 20 kb resolution.
Assembly: S. cerevisiae S288c-R64-2-1 (http://sgd-archive.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-2-1_20150113.tgz)
Supplementary files format and content: Hi-C in mcool format, containing balanced contact data at 1, 2, 5, 10, and 20 kb resolution.

organism: Saccharomyces cerevisiae

growth_protocol: Cells arrested in G1 with alpha-factor in YPD medium (1% yeast extract, 2% peptone, 2% glucose) at 30°C were washed 3 times with 200 mL of YPD and released in S-phase at 30°C for 20 minutes prior to crosslinking. In all cultures, 2 mM indole-3-acetic acid (aka auxin) was added 2 hours prior to, and in all following wash and culture media post G1 release.

extract_protocol:
Cells were spheroplasted with 0.25 mg/mL Zymolyase 100T at 37°C for 30 minutes, crosslinked with 3 mM EGS (ethylene glycol bis(succinimidyl succinate)) at 30°C for 40 minutes at 100 rpm, and quenched with 400 mM glycine for 5 minutes at 100 rpm.
Hi-C library were generated using the Arima Hi-C+ kit following manufacturer instructions starting from 2-5x10^7 cells. DNA was fragmented in 300-400 bp DNA fragments using Covaris M220 sonicator. Illumina sequencing libraries were prepared using the Thermofisher Collibri ES DNA Library Prep Kit for Illumina Systems with UD indexes following manufacturer's instructions.

treatment_protocol: ~1.5x10^9 cells were crosslinked with 3% formaldehyde for 30 minutes at 120 rpm at room temperature, followed by quenching with 330 mM glycine for 30 minutes at 120 rpm.

value: MATa-inc, ura3::LY-HOcs, lys2::LY, trp1::GAL-HO-hphMX, can1-100, ade2-1, leu2-3,112, his3::OsTIR1-9Myc::HIS3, SCC1-Pk3-AID::KMX, RAD5

value: Auxin


title: Hi-C S-phase,  WT, replicate 2

description: Library name: AD560

value: MATa-inc, ura3::LY-HOcs, lys2::LY, can1::HIS3-LY-Pad, trp1::GAL-HO-hphMX, his3::OsTIR1-9Myc::HIS3, ade2-1, leu2-3,112, RAD5


title: Hi-C S-phase,  Cdc45-depleted, replicate 1

description: Library name: AD559

value: MATa-inc, ura3::LY-Hocs, lys2::LY, trp1::GAL-HO-hphMX,can1::HIS3-L0.6kb, his3::pADH1-OsTIR1-9Myc::HIS3, ade2-1, leu2-3,112, RAD5, CDC45-FlagX5-mini-AID::KanMx4


title: Human spinal cord donor H35 central canal Vderived cell culture

status: Public on Oct 02 2025

city: Ottawa

first: Sasi Kumar

last: Jagadeesan

state: ON

address: 1053 Carling Avenue,

department: Neuroscience

country: Canada

institute: Ottawa Hospital Research Institute

description:
Library name: H35
Human spinal cord NSPCs, female donor, neuro+

data_processing:
Raw FASTQ files were quality-checked with FastQC and summarized with MultiQC.
Adapters/low-quality bases were trimmed (e.g., fastp/Trim Galore; default stringency).
Transcript quantification was performed with Salmon (v1.x) in selective-alignment/quasi-mapping mode against GENCODE v35 transcripts (GRCh38), with bias correction enabled. data processing step
Per-sample output files (quant.sf) were retained as processed data; downstream gene-level summarization (tximport to DESeq2) was used for analyses in the manuscript and is described there.
Quality and mapping summaries were inspected to confirm expected depth and consistency across samples.
Assembly: Human reference GRCh38, transcript annotation GENCODE v35.
Supplementary files format and content: Processed files are Salmon quant.sf (tab-delimited) for each sample, containing columns Name, Length, EffectiveLength, TPM, NumReads; reference transcripts: GENCODE v35 (GRCh38). File names: H17_primary_quant.sf, H18_primary_quant.sf, H25_primary_quant.sf, H35_quant.sf, H38_quant.sf, H39_quant.sf.
Supplementary files format and content: No alignment (BAM/SAM) files are deposited; quantitative transcript-level abundances are provided as the primary processed outputs.

molecule: polyA RNA

source_name: Spinal cord (lumbar)

growth_protocol: Primary neural stem/progenitor cells (NSPCs) were derived from adult human spinal cord tissue obtained from deceased organ donors under institutional REB approval. Cells were expanded as adherent cultures on matrix-coated plates in serum-free NSPC medium (DMEM/F12 + N2/B27 + heparin) supplemented with EGF and FGF2 (“EFH”) until sufficient biomass for RNA extraction.

extract_protocol:
Total RNA was isolated from NSPC cultures using a column-based kit with on-column DNase digestion (e.g., Qiagen RNeasy Plus Mini with RNase-Free DNase). RNA integrity was assessed by Bioanalyzer/TapeStation (RIN ≥ 7) and quantity by Qubit/Nanodrop.
mRNA was enriched by poly(A) selection, and strand-specific libraries were prepared using the Illumina TruSeq Stranded mRNA workflow with unique sample barcodes, following the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq 6000 (150-bp reads; single-end)

treatment_protocol: No experimental treatment was applied in culture. Donor-level attributes (neurological condition yes/no; substance use yes/no; spinal cord region) are recorded in the sample metadata.

value: Spinal cord (lumbar)

value: Neural stem/progenitor cells


title: Hi-C S-phase,  WT, replicate 3

description: Library name: AD681


title: Hi-C S-phase,  WT, replicate 1

description: Library name: AD436


title: ribo_sictrl_hypoxia_a

description: Library name: NM2023_0041

value: scramble siRNA and hypoxia


title: Human spinal cord donor H38 central canal Vderived cell culture

description:
Library name: H38
Human spinal cord NSPCs, male donor, neuro–, substance use+

value: substance use+


title: 230628_Flex_GPP_5

description: Library name: 8821-JF-5

value: skin

value: GPP


title: 230628_Flex_GPP_10

description: Library name: 8821-JF-10


title: 230628_Flex_GPP_3

description: Library name: 8821-JF-3


title: ribo_si3d_hypoxia_a

description: Library name: NM2023_0042

value: breast cancer

value: eIF3d siRNA and hypoxia


title: 230628_Flex_GPP_1

description: Library name: 8821-JF-1


title: 230628_Flex_GPP_13

description: Library name: 8821-JF-13


title: Hi-C S-phase,  Cdc45-depleted, replicate 2

description: Library name: AD680

value: MATa, leu2-3,112, trp1-1, can1-100, ura3-1, ade2-1, his3::ADH1promoter-OsTIR1-9myc::HIS3,  CDC45-Flagx5-aid::KanMX4, RAD5


title: Sample 13

status: Public on Aug 06 2025

city: Redwood City

first: Susanna

last: Rosi

address: 2200 Island Dr

institute: Altos Labs

description: Library name: Sample 13

data_processing:
Sample demultiplexing, barcode processing, and single-cell counting were performed using the Cell Ranger Single-Cell Software Suite (10x Genomics). The cellranger count command was used to align reads to the human reference genome (hg38).
Raw sequencing reads were aligned to the GRCh38 human reference genome using the Cell Ranger pipeline (v.8.0.0) to generate the raw RNA count matrix. The resulting count matrix was further processed using the Seurat R package (v5.2.0) for downstream quality control, normalization, and dimensionality reduction. To ensure high data quality, filtering was performed using PopsicleR (v0.2.1) with strict thresholds. The criteria included: 1) A minimum of 500 and maximum 12000 detected genes per cell (G_RNA_low=500, G_RNA_hi=12000). 2) The number of unique molecules per cell was required to fall within a reasonable range (U_RNA_low=1500, U_RNA_hi=37000). 3) Cells exceeding the upper limits for mitochondrial, ribosomal, and dissociation gene percentages (percent_mt_hi=5, percent_ribo_hi=100, percent_disso_hi=100)vwere removed. After filtering, 98,492 cells met the inclusion criteria for analysis. The dataset had an average read depth of 9,226 unique RNA molecules per cell, with an average of 3,312 unique genes detected per cell. Doublets were detected and removed using the CalculateDoublets function within PopsicleR. RNA normalization was performed using the log-normalization method within Seurat’s NormalizeData function, followed by scaling using ScaleData. This was followed by Principal Component Analysis (PCA), on the top 2,000 highly variable features, retaining the first 30 principal components for downstream clustering and visualization. For cell type annotation, we utilized Azimuth (v0.5.0) for reference-based mapping, using the humancortexref reference dataset to assign cell identities. The classification was performed at two hierarchical levels: Level 1: Broad categorization into GABAergic neurons, Glutamatergic neurons, and non-neuronal populations. Level 2: Further refinement into specific neuronal and non-neuronal subtypes.
Assembly: GRCh38
Supplementary files format and content: Counts, barcodes, and metadata for all samples in 10X format.

source_name: Brain

extract_protocol:
Frozen human brain tissues were homogenized in a Dounce homogenizer using Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.025% NP-40) and incubated on ice for 15 minutes. The homogenate was filtered through a 30-μm mesh to remove debris and centrifuged at 500g for 5 minutes at 4°C to pellet the nuclei. Nuclei were then washed and filtered twice using Nuclei Wash Buffer (1% BSA in PBS with 0.2 U/μl RNasin, Promega). For myelin debris removal, the nuclei were resuspended in 500 μl of Nuclei Wash Buffer, mixed with 900 μl of 1.8 M sucrose, and carefully layered over 500 μl of 1.8 M sucrose. This gradient was centrifuged at 13,000g for 45 minutes at 4°C.
The isolated nuclei were then resuspended in Nuclei Wash Buffer at a final concentration of 1,000 nuclei/μl and passed through a 40-μm FlowMi Cell Strainer for further purification. Isolated human nuclei were processed using the Chromium Single Cell 5′ Reagent Kits (10x Genomics) for droplet-based 5′ end massively parallel single-cell RNA sequencing. Sequencing libraries were generated and run on Illumina sequencers at the McDonnell Genome Institute.

value: Brain

tag: tbi

value: No

value: Male

tag: age at_death

value: 50 years


title: 230628_Flex_GPP_2

description: Library name: 8821-JF-2


title: rna_si3e_normoxia_a

description: Library name: NM2023_0106

value: SIX1 OE

value: eIF3e siRNA


title: Sample 6

description: Library name: Sample 6

value: Yes

value: 40 years


title: Human spinal cord donor H39 central canal Vderived cell culture

description:
Library name: H39
Human spinal cord NSPCs, female donor, neuro–

source_name: Spinal cord (thoracic)

value: Spinal cord (thoracic)


title: 230712_Flex_HC_3

description: Library name: 8911-JF-15

value: healthy control


title: Sample 5

description: Library name: Sample 5

value: 55 years


title: 230628_Flex_GPP_12

description: Library name: 8821-JF-12


title: Human spinal cord donor H25 central canal Vderived cell culture

description:
Library name: H25_primary
Human spinal cord NSPCs, female donor, neuro–, substance use+

value: Neural stem/progenitor cells

value: substance use+


title: Sample 3

description: Library name: Sample 3

value: 29 years


title: Human spinal cord donor H18 central canal Vderived cell culture

description:
Library name: H18_primary
Human spinal cord NSPCs, male donor, neuro–

source_name: Spinal cord (conus)

value: Spinal cord (conus)


title: Sample 11

description: Library name: Sample 11

value: 59 years


title: Sample 7

description: Library name: Sample 7

value: 38 years


title: Sample 14

description: Library name: Sample 14

value: Brain

value: 52 years


title: Sample 4

description: Library name: Sample 4

value: Male

value: 66 years


title: Sample 10

description: Library name: Sample 10

value: No

value: 54 years


title: 30days,Rep5

description: Library name: m-30dpi-8_S53_L006_R1_001_T1

data_processing:
RNA-seq FASTQ files were trimmed, aligned to the mouse reference genome (GRCm39, v108), and quantified using the nf-core/rnaseq pipeline with the star_salmon option (v3.12.0). Gene-level length-scaled counts were used for all downstream analyses.
Assembly: GRCm39
Supplementary files format and content: quant.sf files from salmon quantification.

source_name: Whole Brain

extract_protocol:
CD11b+ CD45+ tdTomato+ cells (MDMs) were sorted from whole brains of Ccr2-creERT2::Ai14D mice at 7 and 30 days after TBI.
cDNAs were generated using the SMART-Seq v4 Ultra Low input RNA kit for sequencing (Takara bio, 634891), according to the vendor protocol with 14 cycles of cDNA amplification. At the last step, the cDNA was eluted in 30ul of RNase/DNase free water. Subsequently 30ul of cDNA was used as a starting material with Illumina DNA Prep library kit (Illumina, 20018705) according to the vendor protocol, with final library PCR amplification of 10 cycles. After library completion, individual libraries were pooled equally by volume, and quantified on Fragment Analyzer (Agilent, DNF-474). Quantified library pool was diluted to 1nM and sequenced on MiniSeq (Illumina, FC-420-1001) to check for quality of reads. Finally, individual libraries were normalized according to MiniSeq output reads, specifically by % protein coding genes and were sequenced on two lanes of HiSeq4000 SE50 for a total of ~30M reads per sample.

value: Whole Brain

value: Monocyte-derived Macrophages

value: TBI

tag: time

tag: lane


title: Human spinal cord donor H17 central canal Vderived cell culture

description:
Library name: H17_primary
Human spinal cord NSPCs, male donor, neuro+

value: Spinal cord (thoracic)


title: 30days,Rep6

description: Library name: m-30dpi-9_S54_L006_R1_001_T1


title: 7days,Rep3

description: Library name: f-7dpi-6_S62_L007_R1_001_T1


title: 30days,Rep4

description: Library name: m-30dpi-7_S58_L006_R1_001_T1


title: Sample 1

description: Library name: Sample 1

value: Yes

value: 24 years


title: Sample 12

description: Library name: Sample 12

value: 49 years


title: 7days,Rep1

description: Library name: f-7dpi-4_S64_L007_R1_001_T1


title: 30days,Rep1

description: Library name: f-30dpi-10_S60_L007_R1_001_T1


title: 7days,Rep5

description: Library name: m-7dpi-2_S61_L007_R1_001_T1


title: Macrophages,Naive,0dpi,Rep6

description: Library name: F029493_E5-7

extract_protocol:
MDMs (tdTomato+), microglia (CD11b+, CD45mid/low, tdTomato-) and “classical” monocytes (Ly6G-,Ly6Chi) were sorted from brain and blood of female and male Ms4a3-cre::Ai14D mice at 7 and 30 days with and without TBI. Naïve samples were collected from untreated mice.
cDNAs were generated using the SMART-Seq® mRNA LP (with UMIs) kit for sequencing (Takara bio,634765), according to the vendor protocol. cDNA amplification cycle was adjusted to 19 cycles. PCR-amplified cDNA was purified by immobilization on NucleoMag NGS Clean-up and Size Select beads. The beads were then washed with 80% ethanol, and cDNA is eluted with ~15ul of Elution Buffer. Subsequently, 8 ul of cDNA 0.125 ng/μL was used as a starting material for library preparation using the the Unique Dual Index (UDI) kits (Takara bio, 634752-5) according to the vendor protocol, with final library PCR amplification of 14 cycles. PCR-amplified library was purified individually by immobilization on NucleoMag NGS Clean-up and Size Select beads. The beads were then washed with 80% ethanol and the library eluted with nuclease-free water.
Quality control and quantification was performed using the Qubit dsDNA HS Assay Kit (Thermofisher, 32854) and TapeStation D5000 Reagents (Agilent, 5067-5589) and Screentape (Agilent, 5067-5588). Samples were normalized and pooled individually for sequencing. An additional double-sided SPRI selection was performed on the pool prior to sequencing. Libraries were sequenced using the NextSeq 2000 P3, 300 cycles kit (Illumina, 20040561).

value: Naive

tag: mouse id

tag: library prep_date

tag: lysis plate_id


title: Microglia,Naive,0dpi,Rep6

description: Library name: F029493_E1-3

tag: tissue

value: Microglia

tag: genotype


title: Microglia,Naive,0dpi,Rep5

description: Library name: F029488_E1-3

tag: treatment


title: 7days,Rep6

description: Library name: m-7dpi-3_S59_L007_R1_001_T1

tag: cell type


title: Macrophages,TBI,7dpi,Rep8

description: Library name: F029532_D5-7


title: Monocytes,Naive,0dpi,Rep5

description: Library name: F029487_E1-3

value: Blood

value: Monocytes


title: 30days,Rep3

description: Library name: f-30dpi-12_S56_L006_R1_001_T1


title: Sample 8

description: Library name: Sample 8

value: Brain

tag: Sex

value: 47 years


title: Microglia,TBI,7dpi,Rep8

description: Library name: F029532_D1-3


title: 30days,Rep2

description: Library name: f-30dpi-11_S63_L007_R1_001_T1


title: Microglia,SHAM,7dpi,Rep3

description: Library name: F029533_D1-3

value: SHAM


title: Macrophages,Naive,0dpi,Rep5

description: Library name: F029488_E5-7


title: 7days,Rep2

description: Library name: f-7dpi-5_S57_L006_R1_001_T1


title: Monocytes,Naive,0dpi,Rep4

description: Library name: F029492_D1-3


title: Microglia,Naive,0dpi,Rep4

description: Library name: F029493_D1-3


title: Sample 2

description: Library name: Sample 2

value: Male

value: 46 years


title: Monocytes,SHAM,30dpi,Rep2

description: Library name: F029490_E1-3


title: Macrophages,SHAM,7dpi,Rep3

description: Library name: F029533_D5-7


title: Macrophages,SHAM,7dpi,Rep1

description: Library name: F029488_C5-7


title: Microglia,Naive,0dpi,Rep3

description: Library name: F029488_D1-3


title: Macrophages,Naive,0dpi,Rep4

description: Library name: F029493_D5-7


title: Monocytes,TBI,7dpi,Rep8

description: Library name: F029495_D1-3


title: Monocytes,Naive,0dpi,Rep6

description: Library name: F029492_E1-3


title: Monocytes,SHAM,7dpi,Rep3

description: Library name: F029494_D1-3


title: Macrophages,TBI,7dpi,Rep7

description: Library name: F029532_C5-7


title: 7days,Rep4

description: Library name: m-7dpi-1_S55_L006_R1_001_T1


title: Monocytes,Naive,0dpi,Rep3

description: Library name: F029487_D1-3


title: Macrophages,Naive,0dpi,Rep3

description: Library name: F029488_D5-7


title: Monocytes,SHAM,30dpi,Rep1

description: Library name: F029490_D1-3


title: Monocytes,TBI,7dpi,Rep7

description: Library name: F029495_C1-3


title: Monocytes,SHAM,7dpi,Rep2

description: Library name: F029494_C1-3


title: Monocytes,TBI,30dpi,Rep5

description: Library name: F029490_C1-3


title: Monocytes,SHAM,7dpi,Rep1

description: Library name: F029487_C1-3


title: Macrophages,TBI,7dpi,Rep5

description: Library name: F029532_B5-7


title: Macrophages,TBI,30dpi,Rep2

description: Library name: F029493_B5-7


title: Sample 9

description: Library name: Sample 9

value: No

value: 60 years


title: Microglia,TBI,7dpi,Rep5

description: Library name: F029532_B1-3

value: Whole Brain


title: Macrophages,TBI,7dpi,Rep4

description: Library name: F029489_B5-7

value: Monocyte-derived Macrophages

value: TBI


title: Microglia,TBI,7dpi,Rep6

description: Library name: F029533_B1-3


title: Macrophages,SHAM,7dpi,Rep2

description: Library name: F029533_C5-7


title: Macrophages,TBI,30dpi,Rep3

description: Library name: F029493_C5-7


title: Monocytes,TBI,30dpi,Rep6

description: Library name: F029492_C1-3


title: Monocytes,TBI,7dpi,Rep5

description: Library name: F029495_B1-3


title: Monocytes,TBI,7dpi,Rep6

description: Library name: F029489_B9-11


title: Macrophages,TBI,7dpi,Rep6

description: Library name: F029533_B5-7


title: Microglia,TBI,7dpi,Rep7

description: Library name: F029532_C1-3


title: Microglia,TBI,30dpi,Rep2

description: Library name: F029493_B1-3


title: Microglia,SHAM,7dpi,Rep1

description: Library name: F029488_C1-3


title: Macrophages,TBI,7dpi,Rep3

description: Library name: F029533_A5-7


title: Monocytes,TBI,30dpi,Rep4

description: Library name: F029492_B1-3


title: Macrophages,Naive,0dpi,Rep2

description: Library name: F029488_B5-7


title: Microglia,TBI,7dpi,Rep4

description: Library name: F029489_B1-3


title: Microglia,TBI,30dpi,Rep3

description: Library name: F029493_C1-3


title: Monocytes,Naive,0dpi,Rep2

description: Library name: F029487_B1-3


title: Macrophages,TBI,7dpi,Rep2

description: Library name: F029532_A5-7


title: Macrophages,TBI,30dpi,Rep1

description: Library name: F029493_A5-7


title: Microglia,Naive,0dpi,Rep2

description: Library name: F029488_B1-3


title: Macrophages,Naive,0dpi,Rep1

description: Library name: F029488_A5-7


title: Monocytes,TBI,30dpi,Rep3

description: Library name: F029490_B1-3


title: Microglia,SHAM,7dpi,Rep2

description: Library name: F029533_C1-3


title: Microglia,TBI,7dpi,Rep2

description: Library name: F029532_A1-3


title: Monocytes,TBI,7dpi,Rep4

description: Library name: F029494_B1-3


title: Monocytes,TBI,7dpi,Rep3

description: Library name: F029489_A9-11


title: Microglia,TBI,7dpi,Rep3

description: Library name: F029533_A1-3


title: Monocytes,TBI,7dpi,Rep1

description: Library name: F029494_A1-3


title: Monocytes,TBI,30dpi,Rep1

description: Library name: F029490_A1-3


title: Microglia,TBI,30dpi,Rep1

description: Library name: F029493_A1-3


title: Microglia,Naive,0dpi,Rep1

description: Library name: F029488_A1-3


title: Monocytes,TBI,7dpi,Rep2

description: Library name: F029495_A1-3


title: Microglia,SHAM,8months,Rep12

description: Library name: J189323_F1.J189323_F2.J189323_F3

extract_protocol:
CD11b+ CD45+ tdTomato+ cells (MDMs) and CD11b+, CD45mid/low, tdTomato- cells (microglia) were sorted from whole brains of Ccr2-creERT2::Ai14D mice at 8 months after TBI.
cDNAs were generated using the SMART-Seq® mRNA LP (with UMIs) kit for sequencing (Takara bio,634765), according to the vendor protocol. cDNA amplification cycle was adjusted to 19 cycles. PCR-amplified cDNA was purified by immobilization on NucleoMag NGS Clean-up and Size Select beads. The beads were then washed with 80% ethanol, and cDNA is eluted with ~15ul of Elution Buffer. Subsequently, 8 ul of cDNA 0.125 ng/μL was used as a starting material for library preparation using the the Unique Dual Index (UDI) kits (Takara bio, 634752-5) according to the vendor protocol, with final library PCR amplification of 14 cycles. PCR-amplified library was purified individually by immobilization on NucleoMag NGS Clean-up and Size Select beads. The beads were then washed with 80% ethanol and the library eluted with nuclease-free water.
Quality control and quantification was performed using the Qubit dsDNA HS Assay Kit (Thermofisher, 32854) and TapeStation D5000 Reagents (Agilent, 5067-5589) and Screentape (Agilent, 5067-5588). Samples were normalized and pooled individually for sequencing. An additional double-sided SPRI selection was performed on the pool prior to sequencing. Libraries were sequenced using the NextSeq 2000 P3, 300 cycles kit (Illumina, 20040561).

tag: library prep_plate_id


title: Microglia,TBI,7dpi,Rep1

description: Library name: F029489_A1-3


title: Macrophages,TBI,7dpi,Rep1

description: Library name: F029489_A5-7


title: Microglia,TBI,8months,Rep9

description: Library name: J189322_C1.J189322_C2.J189322_C3


title: Microglia,SHAM,8months,Rep10

description: Library name: J189323_D1.J189323_D2.J189323_D3


title: Microglia,SHAM,8months,Rep8

description: Library name: J189322_E1.J189322_E2.J189322_E3


title: Monocytes,Naive,0dpi,Rep1

description: Library name: F029487_A1-3


title: Microglia,TBI,8months,Rep12

description: Library name: J189323_C1.J189323_C2.J189323_C3


title: Microglia,SHAM,8months,Rep9

description: Library name: J189322_F1.J189322_F2.J189322_F3


title: Macrophages,TBI,8months,Rep10

description: Library name: J189323_A5.J189323_A6


title: Microglia,TBI,8months,Rep10

description: Library name: J189323_A1.J189323_A2.J189323_A3


title: Macrophages,TBI,8months,Rep9

description: Library name: J189322_C5.J189322_C6


title: Microglia,TBI,8months,Rep11

description: Library name: J189323_B1.J189323_B2.J189323_B3


title: Monocytes,TBI,30dpi,Rep2

description: Library name: F029492_A1-3


title: Macrophages,TBI,8months,Rep8

description: Library name: J189322_B5.J189322_B6


title: Microglia,SHAM,8months,Rep7

description: Library name: J189322_D1.J189322_D2.J189322_D3


title: Macrophages,TBI,8months,Rep11

description: Library name: J189323_C5.J189323_C6


title: Microglia,TBI,8months,Rep4

description: Library name: J189321_A1.J189321_A2.J189321_A3


title: Microglia,SHAM,8months,Rep11

description: Library name: J189323_E1.J189323_E2.J189323_E3


title: Macrophages,TBI,8months,Rep4

description: Library name: J189321_A5.J189321_A6


title: Macrophages,TBI,8months,Rep7

description: Library name: J189322_A5.J189322_A6


title: Microglia,SHAM,8months,Rep4

description: Library name: J189321_D1.J189321_D2.J189321_D3


title: Macrophages,TBI,8months,Rep6

description: Library name: J189321_C5.J189321_C6


title: Macrophages,TBI,8months,Rep5

description: Library name: J189321_B5.J189321_B6


title: Microglia,TBI,8months,Rep7

description: Library name: J189322_A1.J189322_A2.J189322_A3


title: Microglia,SHAM,8months,Rep5

description: Library name: J189321_E1.J189321_E2.J189321_E3


title: Microglia,TBI,8months,Rep5

description: Library name: J189321_B1.J189321_B2.J189321_B3


title: Microglia,TBI,8months,Rep6

description: Library name: J189321_C1.J189321_C2.J189321_C3


title: Macrophages,TBI,8months,Rep3

description: Library name: J189319_C5.J189319_C6


title: Microglia,SHAM,8months,Rep6

description: Library name: J189321_F1.J189321_F2.J189321_F3


title: Microglia,SHAM,8months,Rep2

description: Library name: J189319_E1.J189319_E2.J189319_E3


title: Macrophages,TBI,8months,Rep2

description: Library name: J189319_B5.J189319_B6


title: Microglia,TBI,8months,Rep8

description: Library name: J189322_B1.J189322_B2.J189322_B3


title: Microglia,SHAM,8months,Rep1

description: Library name: J189319_D1.J189319_D2.J189319_D3


title: Microglia,SHAM,8months,Rep3

description: Library name: J189319_F1.J189319_F2.J189319_F3


title: Microglia,TBI,8months,Rep2

description: Library name: J189319_B1.J189319_B2.J189319_B3


title: Microglia,TBI,8months,Rep1

description: Library name: J189319_A1.J189319_A2.J189319_A3


title: iPSC derived human organoids, 8week, treatment

status: Public on Jul 28 2025

city: Parkville

first: Samantha

last: Barton

address: Parkville Campus 30 Royal Parade

country: Australia

institute: The Florey

description:
Library name: 18a_8week_LPC
10x Genomics

data_processing:
The Fastq files were processed using cellrnager multi (cellranger-6.1.2).  Per sample fastq files were generated using bamtofastq on the sample_alignments.bam.
Assembly: GRCh38-2020-A
Supplementary files format and content: The Fastq files were processed using cellrnager multi (cellranger-6.1.2).  Per sample fastq files were generated using bamtofastq on the sample_alignments.bam.

source_name: iPSC derived human organoids

extract_protocol:
Single cells were fixed overnight at 4 °C using 4 % PFA (ProSciTech) diluted in Concentrated Fix & Permealisation buffer. After fixation, cells were pelleted at 850 x g for 5 min. Cell pellets were quenched with Quenching and Enhancer buffer (from Chromium Gene Expression Flex Library Prep kit). Glycerol was added to each sample to a final concentration of 25 % prior to storing in -80 °C.  RNA was released and captured in‑GEM using the Chromium Gene Expression Flex Library Prep Kit (10x Genomics PN‑1000414) following the Fixed RNA Profiling Demonstrated Protocol CG000478 and User Guide CG000527; this includes in‑droplet lysis of fixed cells and on‑bead reverse transcription.
Chromium Gene Expression Flex Library Prep Kit  following Fixed RNA Profiling Demonstrated Protocol CG000478 and User Guide CG000527; includes in‑GEM lysis, on‑bead reverse transcription, and cDNA amplification.

value: iPSC derived human organoids

tag: cell line

value: iPSC derived organoids cells enriched for mature myelinating olig. and funcitonally reactive microglia


title: Passage 4 Basal cell isolates in PEX media -Repliate 2

status: Public on Jun 20 2025

city: Glendale

first: Crystal

last: Marconett

address: 1856 Kirkby Rd

department: Translational Genomics

institute: Keck School of Medicine

data_processing:
Paired end FASTQ read files were assessed for quality using FastQC [Andrews, S. (2010) FastQC: A Quality Control Tool for High Throughput Sequence Data]. Reads were cleaned by filtering out those with less than 90% of the read having a quality score of < Q30 and were subsequently aligned to the Homo.Sapiens.GRCh38.96 transcriptome using Kallisto (version 0.46.0) [N. L. Bray, H. Pimentel, and P. M. &. L. Pachter. 2016. Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology. 34(5): 525-527.].
To account for the wide range of raw sequencing depth between samples (35M to 135M), total read numbers were adjusted to ~42M per sample [aligned read range: ~31 - 45M] prior to calculation of read count per transcript (Supplemental Table 1). Kallisto count tables were filtered to include transcripts with counts per million > 50 (Supplemental Table 2) and were subsequently input into R (v 4.0.2 GUI 1.72 Catalina build 7847) and EdgeR [Robinson MD, McCarthy DJ, Smyth GK (2010). “edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.” Bioinformatics, 26(1), 139-140. doi:10.1093/bioinformatics/btp616.] was used to calculate differential expression and FDR correction of significance.
Assembly: Homo.Sapiens.GRCh38.96 transcriptome
Supplementary files format and content: Bigwig density files showing read alignment in human hg38 genome
Supplementary files format and content: Kallisto-aligned pseudocount tables were filtered to include transcripts with counts per million > 50

source_name: Lung proximal basal cells

growth_protocol: Basal cells were isolated from donors using established protocols ().

extract_protocol:
Total bulk RNA (2ug/sample) was sent to Azenta (formerly Genewiz) for poly-A tail library construction and sequencing.
Libraries were constructed with unique adapters that allowed for all samples to be run on one Illunima HiSeq 2500 run.

treatment_protocol: Basal cells were grown in 2D culture using the indicated media.

value: Lung proximal basal cells

tag: passages

value: Purified Basal Cells in Culture

value: Pneumacult EX (PEX) media


title: iPSC derived human organoids, 24hr,  control

description:
Library name: 18a_24hr_EtOH
10x Genomics


title: Microglia,TBI,8months,Rep3

description: Library name: J189319_C1.J189319_C2.J189319_C3

value: Microglia


title: Passage 4 Basal cell isolates in DSI media -Repliate 2

value: Dual Smad Inhibitor (DSI) media


title: Macrophages,TBI,8months,Rep1

description: Library name: J189319_A5.J189319_A6


title: Passage 4 Basal cell isolates in AECGM media -Repliate 1

value: AECGM media


title: Passage 4 Basal cell isolates in PEX media -Repliate 1


title: Passage 4 Basal cell isolates in DSI media -Repliate 1


title: Passage 1 Basal cell isolates in PEX media -Repliate 1


title: embryo E7.75 rep2

status: Public on Jun 19 2025

city: nanjing

first: yi

last: yang

address: sipailou 2

country: China

institute: southeast university

description: Library name: Sample 4

data_processing:
Sequencing reads were processed with the SAW workflow (https://github.com/BGIResearch/SAW), which encompasses several critical steps: mRNA spatial location restoration, data filtering, mRNA genome alignment, gene region annotation, MID correction, expression matrix generation, and tissue region extraction. These Clean Reads were mapped to the NCBI-referenced genome using STAR (v2.5.3).
Assembly: GRCm38
Supplementary files format and content: h5ad; gene expression matrix where the rows are genes and columns are single cells

source_name: Whole embryo

extract_protocol:
Stereo-seq
Briefly, following cryosection, tissue sections are mounted on Stereo-seq chips, incubated at 37°C, and fixed with 20°C methanol. The chips underwent ssDNA staining and imaging with a Nikon Ti-7 Eclipse microscope. Tissue permeabilization was performed with 0.1% pepsin in HCl buffer, followed by washing with SSC buffer containing RNAase Inhibitor. Captured mRNA was reverse transcribed at 42°C. Post in situ reverse transcription, the chips were treated with tissue removal buffer and then washed. cDNA was released from the chips using a cDNA Release Mix at 55°C, followed by fragmentation, amplification, and purification to produce a DNBs library.

value: Whole embryo

value: WT


title: iPSC derived human organoids, 24hr, treatment

description:
Library name: 18a_24hr_LPC
10x Genomics


title: Passage 1 Basal cell isolates in PEX media -Repliate 2


title: Passage 1 Basal cell isolates in AECGM media -Repliate 1


title: iPSC derived human organoids, 8week, control

description:
Library name: 18a_8week_EtOH
10x Genomics


title: Passage 4 Basal cell isolates in AECGM media -Repliate 2


title: NRF2-RNAi-2

status: Public on Jun 17 2025

city: Nantong City

first: Lili

last: Ji

address: No.1 Build 19 Qixiu Road, Nantong City Jiangsu Province, China

institute: Medical School of Nantong University

description:
Library name: Sample 5
Column name in all.genes.expression.annot.xls: NRF2-RNAi-2

data_processing:
The resulting cDNA library was sequenced on an Illumina Novaseq6000 platform by Gene Denovo Biotechnology Co. (Guangzhou, China).
To obtain high-quality clean reads, the reads were further filtered using fastp (version 0.18.0).
Differential expression analysis of RNAs was conducted between two different groups using DESeq2 software.
Pathway enrichment analysis was carried out using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database (http://www.genome.jp/kegg).
Gene set enrichment analysis (GSEA) was conducted using GSEA software and MSigDB software to determine whether two groups exhibited significant differences in regard to a set of genes in specific KEGG pathways.
Assembly: Ensembl release 106
Supplementary files format and content: all.genes.expression.annot.xls file includes raw counts for each Sample
Supplementary files format and content: all.genes.expression.annot.xls include FPKM values for each Sample

source_name: lung

growth_protocol: The NSCLC cisplatin-resistant cell line A549/DDP (CL-0519) were purchased from Procell Life Science & Technology Co, Ltd. Cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, 5 mg/mL penicillin-streptomycin, and 1–2 µg/ml DDP specific for A549/DDP cells at 37˚C under 5% CO2.

extract_protocol:
Total RNA was isolated using the Trizol reagent kit (15596026, Invitrogen, Carlsbad, CA, USA) in accordance with the manufacturer’s protocol. The quality of the RNA was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and verified by RNase free agarose gel electrophoresis.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530, New England Biolabs, Ipswich, MA, USA).

value: lung

value: tumor-cell line from a human lung carcinoma

value: Nrf2 knockdown


title: embryo E8.0 rep1

description: Library name: Sample 5


title: NRF2-RNAi-3

description:
Library name: Sample 6
Column name in all.genes.expression.annot.xls: NRF2-RNAi-3


title: embryo E8.0 rep2

description: Library name: Sample 6


title: NRF2-RNAi-1

description:
Library name: Sample 4
Column name in all.genes.expression.annot.xls: NRF2-RNAi-1


title: Con-RNAi-3

description:
Library name: Sample 3
Column name in all.genes.expression.annot.xls: Con-RNAi-3


title: Con-RNAi-2

description:
Library name: Sample 2
Column name in all.genes.expression.annot.xls: Con-RNAi-2


title: Con-RNAi-1

description:
Library name: Sample 1
Column name in all.genes.expression.annot.xls: Con-RNAi-1


title: Passage 1 Basal cell isolates in DSI media -Repliate 2


title: Passage 1 Basal cell isolates in AECGM media -Repliate 2


title: embryo E7.75 rep1

description: Library name: Sample 3


title: Passage 1 Basal cell isolates in DSI media -Repliate 1


title: EAE Perampanel 03

status: Public on Jun 12 2025

city: Mainz

first: Neuroimmunology

last: Mainz

address: Langenbeckstr. 1

country: Germany

institute: University Medical Center of the Johannes Gutenberg University Mainz

data_processing:
The raw sequencing reads (30 mio 150 PE reads per sample) of Illumina’s NovaSeq 6000 (Novogene; Cambridge, UK) were preprocessed according to the Illumina standard protocol.
Sequence reads were trimmed for adapter sequences and further processed using Qiagen’s software CLC Genomics Workbench (v21.0.5 with CLC’s default settings for RNA-Seq analysis).
Reads were aligned to GRCm38 genome. Unique gene counts from the CLC workbench were used to perform statistical differential expression analysis with DESeq2 (Love et al., 2014). Gene ontology analysis was performed for genes with adjusted p-values under 0.05 using clusterProfiler and DOSE (Yu et al., 2015). Network plots were generated with Enrichplot (Yu et al., 2015). Heatmaps were generated using the pheatmap R package (Kolde, 2019). Volcano plots were created with the ggplot2 (Wickham, 2016) and ggrepel (Slowikowski, 2021) R packages. The database org.Mm.eg.db was used for annotating genes (Carlson, 2019).
Unique gene counts from the CLC workbench were used to perform statistical differential expression analysis with DESeq2 (Love et al., 2014). Gene ontology analysis was performed for genes with adjusted p-values under 0.05 using clusterProfiler and DOSE (Yu et al., 2015).
Network plots were generated with Enrichplot (Yu et al., 2015). Heatmaps were generated using the pheatmap R package (Kolde, 2019). Volcano plots were created with the ggplot2 (Wickham, 2016) and ggrepel (Slowikowski, 2021) R packages. The database org.Mm.eg.db was used for annotating genes (Carlson, 2019).
Assembly: GRCm38
Supplementary files format and content: DESeq 2 output

source_name: inguinal lymph node

extract_protocol:
RNA was purified immediately after with the RNeasy Plus Micro Kit according to the manufacturer’s protocol (Qiagen). RNA was quantified with a Qubit 2.0 fluorometer (Invitrogen) and the quality was assessed on a Bioanalyzer 2100 (Agilent) using a RNA 6000 Pico chip (Agilent). Samples with an RNA integrity number (RIN) of > 9 were used for library preparation.
Barcoded mRNA-seq cDNA libraries were prepared from 100 ng of total RNA using NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® according to the manual with a final amplification of 12 PCR cycles. Quantity was assessed using Invitrogen’s Qubit HS assay kit and library size was determined using Agilent’s 2100 Bioanalyzer HS DNA assay.

treatment_protocol: Inguinal lymph nodes were isolated on day 3 after EAE induction from 3 SJL mice therapeutically treated with perampanel as well as 3 control mice. Lymph nodes were meshed through a 100-µm cell strainer in order to create a single-cell suspension.

value: inguinal lymph node

value: primary tissue

value: Lymphocytes

value: SJL

value: Perampanel


title: EAE Perampanel 02


title: EAE Perampanel 01


title: embryo E7.5 rep2

description: Library name: Sample 2