title: Female_Placenta_Low_GenX_Rep_1

description: 21513_1226_Female_Placenta_Low_GenX_1_Rep_1

value: placenta

value: embryonic day 17.5

value: GenX

value: 2 mg/kg/day


title: Female_Placenta_High_GenX_Rep_4

status: Public on Jul 29 2026

type: RNA

city: Research Triangle Park

first: Suzanne

middle: E

last: Fenton

state: North Carolina

address: 111 TW ALEXANDER DR

department: Mechanistic Toxicology Branch

country: USA

institute: Division of the National Toxicology Program, National Institute of Environmental Health Sciences

description: 21521_1226_Female_Placenta_High_GenX_4_Rep_4

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Annotation was derived in R from the Affymetrix annotation file MTA-1_0.na36.mm10.transcript.csv. For each transcript, the raw intensities were background adjusted and RMA normalized.

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Total RNA (25 ng/sample) was first amplified and labeled using the Affymetrix WT Plus Reagent Kit (WT Plus Kit) per manufacturer’s instructions.

growth_protocol: On embryoinic day E 11.5 or E 17.5 pregnant dams were weighed and humanely euthanized by swift decapitation. The uterus was removed and the placentas from viable embryos were collected in succession within a uterine horn and immediately snap frozen in liquid nitrogen (n = 2-5 placentas/litter). For placentas collected at E 17.5, a portion of fetal tissue corresponding to each snap frozen placenta was reserved and genotyped by PCR amplification of the sex determining region-Y (SRY) gene. Sex determination was not conducted for placentas collected at E 11.5 as the embryo gametes are not yet fully developed.

extract_protocol: For placentas collected at E 11.5, three placentas per litter were pooled to achieve sufficient tissue mass for the RNA extraction protocol (> 0.5 mg). For placentas collected at E 17.5, no more than one placenta from each sex was used from a given litter. Snap frozen tissues were weighed then homogenized using a FastPrep-24™ 5G (MP Biomedicals, Valiant Co., Ltd, China) in Buffer RLT (Qiagen, Hilden, Germany) within 2mL, 2.4mm metal bead homogenization tubes (Thermo Fisher Scientific, Waltham, MA). Homogenized placenta samples were snap frozen and stored at -80°C prior to RNA extraction. RNA was extracted using RNeasy kits following manufacturer’s protocols (Qiagen, Hilden, Germany). Resulting purified RNA was subjected to quality control assessments using a NanoDrop™ 2000/2000c Spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and Bioanalyzer High Sensitivity RNA Analysis (Agilent, Santa Clara, CA). All RNA samples used for transcriptomics analysis had a 260/280 ratio > 2.0 and RIN > 5.0. RNA isolates were diluted to a standard concentration of 100 ng RNA/ 1 µL H2O.

treatment_protocol: Pregnant CD-1 mice were exposed via daily oral gavage from embryonic day (E) 1.5 to E 11.5 (early developmental gestation) or E 17.5 (mature gestation) to PFOA (0, 1, or 5 mg/kg) or GenX (0, 2, or 10 mg/kg). A total N = 4-5 per treatment group (exposure chemical, dose, and duration) were used in the current study.

tag: tissue

tag: strain

tag: age

tag: Sex

value: Female

tag: treatment

tag: dose

value: 10 mg/kg/day

tag: outlier

value: No


title: HDF cells, overexpressing OCT4 and EGFP, day 5, O-EGFP-1

type: SRA

city: changchun

first: songqin

last: yang

address: No. 5625, Renmin Street

country: China

institute: Changchun Institute of Applied Chemistry

description:
Library name: O_d5_1
O-EGFP-1

library_source: transcriptomic

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
The clean reads were mapped to the reference genome using HISAT2. After that, Ericscript (v0.5.5) and rMATS (V4.1.2)  were used to detect fusion genes and differential splicing genes (DSGs), respectively
owtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1). The heatmap was drawn by pheatmap (v1.0.12)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.34.0) (or DEGseq （v1.48.0）or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Assembly: GRCh38
Supplementary files format and content: xlsx file includes read count vlaues  for each Sample

organism: Homo sapiens

source_name: human dermal fibroblasts

extract_protocol:
Total RNA was isolated using the UNIQ-10 Silica-Matrix RNA Purification System (Sangon Biotech, China) following manufacturer-recommended protocols. 0.2 ug of total RNA was used for the construction of sequencing libraries
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China).

tag: cell type

value: human dermal fibroblasts


title: SH-SY5Y_BSJ_DMSO_rep2

city: Ghent

first: Sarah-Lee

last: Bekaert

state: No state

address: Corneel Heymanslaan 10

country: Belgium

institute: UGent

description:
Library name: SH-SY5Y_BSJ_DMSO_rep2
SH-SY5Y_BSJ_DMSO_rep2

data_processing:
Reads were quality checked with FastQC (v0.11.7) and aligned to the Homo sapiens reference genome (GRCh38.96) using STAR (v2.7.2b).
Post-alignment, read counts were generated and normalized with edgeR (v3.36.0).
After performing PCA plotting, certain replicates were removed from the analysis as they did not cluster with the other replicates, indicating potential outliers or inconsistencies.
Differential expression analysis was performed using the Limma-Voom pipeline (v3.50.3) with three or four replicates per condition.
Assembly: Homo sapiens GRCh38.96
Supplementary files format and content: Tab-delimited text file include STAR counts per experiment

molecule: polyA RNA

source_name: bone marrow

extract_protocol:
RNA was isolated as described in the ‘RNA isolation and RT-qPCR’ section. RNA quality was measured using the Fragment analyzer 12 capillary array prior to profiling
A total of 55ng of RNA was used as input for the library preparation with the Illumina Stranded mRNA prep (#20040534). During the library preparation 15 PCR cycles were used. qPCR quantification of the libraries was done using the Kapa Library Quantification Kit for the Illumina LightCycler 480 (Roche diagnostics #07960298001).
RNA-Seq libraries were sequenced on the Illumina NextSeq 2000 platform using the NextSeq 2000 P2 Reagents 100 Cycles single-end kit (Illumina #20100987).

value: bone marrow

tag: cell line

value: neuroblast

tag: genotype

value: WT

value: DMSO in BSJ-4-116 experiment


title: Female_Placenta_Low_PFOA_Rep_5

description: 21507_1226_Female_Placenta_Low_PFOA_5_Rep_5

value: PFOA

value: 1 mg/kg/day


title: Female_Placenta_High_GenX_Rep_3

description: 21520_1226_Female_Placenta_High_GenX_3_Rep_3


title: DiR-ID (DiR-ID, DMSO) - rep2

city: Illkirch-Graffenstaden

first: Maximiliano

middle: M.

last: Portal

state: Alsace

address: 1 rue Laurent Fries

department: Functional Genomics and Cancer

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 1.17.21.3 and CASAVA 1.8.2. Obtained data was further analyzed using fastQC and fastQScreen.
DiR-F, ChIP-seq and FAIRE-seq data was mapped to hg38 using Bowtie2. For peaks/broad region enrichment calling we used PePr pipeline in either sharp peaks (DiR-F, FAIRE, H3K4me1, H3K4me3, H3K9Ac and H3K27Ac) or broad (DiR-F, H3K9me3, H3K27me3 and H3K36me3) mode with 200 window size for DiR-F and FAIRE-seq data and 146 window size for ChiP-seq data with an FDR<0.05. DiR-F data was analyzed in both modes and peaks/regions were collapsed into a single file using intersectBed tool from BedTools. All data obtained from sharp peak detection was further refined using PePr-postprocess. DNAseI footprint analysis was performed over DiR-F detected peaks/regions using wellington_footprints.py from pyDNAse suite using and FDR<0.01 cutoff. mNET-Seq obtained reads were first stripped from adaptors using cutadapt pipeline and obtained reads were mapped to hg38 using Tophat2 under standard conditions for reads longer than 20 nucleotides. For reads smaller than 20 nucleotides reads were mapped using bowtie2 with the following parameters: bowtie2 –k 20 –end-to-end –D 20 –R 3 –N 0 –L 6 –I 5,1,0.50 to ensure that reads of 6-19 nucleotides were mapped at least 20 times when multiple alignment was possible. mNET-Seq datasets were further curated to remove rRNA and tRNA mapping reads using intersectBed from BedTools and 3’-ends position was recorded using bam2wig module from BioToolBox (https://github.com/tjparnell/biotoolbox). Nucleosome mapping was achieved by collapsing ChIP-seq data obtained from input material (mononucleosomes) and processed using Nucwave suite in single-end reads mode. All data analyzed in this section was processed through R (https://cran.r-project.org) and/or DeepTools for visualization purposes.
TARDIS obtained strand-specific RNA-Seq data was mapped to hg38 using HISAT2 and HeLa cells transcriptome reconstructed using Stringtie. Differential analysis was performed using Kallisto/Sleuth pipeline (FDR<0.05) to determine either differential recruitment or differential expression. Triplexator analysis was performed using the following parameters: –l 20 –e 5 –fr on –mrl 7 –mrp 3 –dc –1 using all detected DiR-F peaks/regions as targets and RNAseA treated DiR-ID RNA library as transcript source. For individual transcript analysis we used Triplex Domain Finder using and FDR<0.05, minimum length of 20, maximum error rate of 20, a tolerated number of consecutive events of 2 for 5000 randomization events. All data analyzed in this section was processed through R and/or DeepTools for visualization purposes.
Genome_build: hg38
Supplementary_files_format_and_content: bdg files were generated using bam2wig module from BioToolBox (https://github.com/tjparnell/biotoolbox).

source_name: HeLa cells

extract_protocol:
Input and immunoprecipitated DNA was recovered using Qiagen MinElute kits. mNET-Seq immunoprecipitated material was recovered using Qiagen MinElute kits. DiR-F derived samples were recovered using PAGE electrophoresis. RNA was recovered using Trizol.
DNA libraries were prepared following Diagenode MicroPlex kit instructions. RNA libraries were prepared following TARDIS protocol (Portal MM et al. Nature Protocols. 2016)
DNA or RNA molecules were end-repaired and ligated to DNA/RNA adaptors prior to PCR amplification and further sequencing.

tag: sample type

value: DiR-ID

value: HeLa


title: Female_Placenta_High_PFOA_Rep_1

description: 21508_1226_Female_Placenta_High_PFOA_1_Rep_1

value: 5 mg/kg/day


title: SH-SY5Y_BSJ_DMSO_rep1

description:
Library name: SH-SY5Y_BSJ_DMSO_rep1
SH-SY5Y_BSJ_DMSO_rep1


title: HDF cells, overexpressing KDM8, day 5, KDM8-3

description:
Library name: KDM8_3
KDM8-3

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
The clean reads were mapped to the reference genome using HISAT2. After that, Ericscript (v0.5.5) and rMATS (V4.1.2)  were used to detect fusion genes and differential splicing genes (DSGs), respectively
owtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1). The heatmap was drawn by pheatmap (v1.0.12)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.34.0) (or DEGseq （v1.48.0）or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Assembly: GRCh38
Supplementary files format and content: xlsx file includes read count values  for each Sample


title: Actively transcribed RNA (Tx, DMSO) - rep2

value: TARDIS RNA-seq


title: Female_Placenta_Low_PFOA_Rep_4

description: 21506_1226_Female_Placenta_Low_PFOA_4_Rep_4

value: placenta

value: embryonic day 17.5


title: DiR-ID (DiR-ID, DMSO) - rep1


title: SH-SY5Y_BSJ_rep4

description:
Library name: SH-SY5Y_BSJ_rep4
SH-SY5Y_BSJ_rep4


title: HDF cells, overexpressing KDM8, day 5, KDM8-2

description:
Library name: KDM8_2
KDM8-2


title: HDF cells, overexpressing KDM8, day 5, KDM8-1

description:
Library name: KDM8_1
KDM8-1


title: Female_Placenta_Low_PFOA_Rep_3

description: 21505_1226_Female_Placenta_Low_PFOA_3_Rep_3


title: SH-SY5Y_BSJ_rep3

description:
Library name: SH-SY5Y_BSJ_rep3
SH-SY5Y_BSJ_rep3


title: Actively transcribed RNA (Tx, DMSO) - rep1


title: SH-SY5Y_BSJ_rep2

description:
Library name: SH-SY5Y_BSJ_rep2
SH-SY5Y_BSJ_rep2


title: HDF cells, overexpressing EGFP, day 5, EGFP-3

description:
Library name: EGFP_3
EGFP-3


title: Female_Placenta_Low_PFOA_Rep_2

description: 21504_1226_Female_Placenta_Low_PFOA_2_Rep_2


title: Total RNA (SS, DMSO) - Rep2


title: S.cerevisae BY4741_empty vector, Gal24h, Biol Rep1

city: Vancouver

first: Marjan

last: Barazandeh

state: BC

address: 6622-2405 Wesbrook Mall

department: Pharmaceutical Sciences

country: Canada

institute: University of British Columbia

description:
Library name: RP_gal24_1
gal24_rep_avg.bw

library_source: genomic

data_processing:
Adapters and low-quality bases were removed from paired-end reads with Trimmomatic (v0.39).
The reads were then mapped to the S. cerevisiae R64 reference genome using BWA-MEM (v0.7.18).
Only primary alignments with MAPQ ≥30 were retained, and unmapped, secondary, QC-fail, and supplementary reads were excluded.
PCR/optical duplicates were removed to generate de-duplicated, coordinate-sorted BAM files, which were indexed and summarized with SAMtools (v1.19.2).
dyad-centered coverage tracks were generated from de-duplicated BAMs using a 147-bp fragment shift, normalized to the genome-wide mean (excluding zero bins), Gaussian-smoothed (window = 3), and converted to bigWig.
Assembly: R64 (SacCer3)
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: overnight in SC-Ura+2% raffinose+ 0.1% dextrose, SC-Ura+2% galactose for 24 hours, SC-Ura+2% glucose for 24 hours, SC-Ura+2% galactose for 6 hours, SC-Ura+2% galactose for 12 hours,  SC-Ura+2% galactose for 24 hours, SC complete+2% glucose for 24 hours

extract_protocol:
Qiagen MinElute column
NEBNext Ultra™ II DNA Library Prep Kit

treatment_protocol: Minimal media with Raffinose, Galactose, glucose

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0

value: BY4741+ empty URA3 vector grown in SC-Ura+2% galactose for 24 hours


title: Female_Placenta_Low_PFOA_Rep_1

description: 21503_1226_Female_Placenta_Low_PFOA_1_Rep_1

value: Female


title: HDF cells, overexpressing EGFP, day 5, EGFP-2

description:
Library name: EGFP_2
EGFP-2


title: SH-SY5Y_BSJ_rep1

description:
Library name: SH-SY5Y_BSJ_rep1
SH-SY5Y_BSJ_rep1


title: Total RNA (SS, DMSO) - Rep1


title: DiR_F_non_crosslinked

value: DiR-F non-crosslinked control


title: N206_BSJ_DMSO_rep3

description:
Library name: N206_BSJ_DMSO_rep3
N206_BSJ_DMSO_rep3

source_name: neuroblastoma cell line

value: neuroblastoma cell line


title: HDF cells, overexpressing EGFP, day 5, EGFP-1

description:
Library name: EGFP_1
EGFP-1

value: human dermal fibroblasts


title: Female_Placenta_Cont_Rep_5

value: Vehicle control

value: 0 mg/kg/day

value: No


title: DiR_F_RNAseH_rep2

value: DiR-F


title: HeLa cells, DisP 12A, bisox, rep2

city: Beijing

first: Qidong

last: Deng

address: No.5 Yiheyuan Road Haidian District, Beijing 100871 P.R. China

department: School of Life Sciences

institute: Peking university

description: Library name: Sample8

data_processing:
For DisP-seq analysis, paired sequenced reads were aligned to GRCh38/hg38 genome using Bowtie2 (v2.4.5). Duplicate reads were removed using Picard tools.MACS2 (2.2.7.1) was used for peak calling with parameter: --nomodel -B --SPMR -f BAMPE --broad -p 0.01 --broad-cutoff 0.01.Subsequently, featureCounts (v2.0.1) was employed to quantify DisP-seq signal across identified peaks using paired-end mode. Peaks with fold change greater than 1.5 (b-isox over DMSO) wertained for downstream analysis. We applied DISPbind (v1.0.2) under default settings to define DisP islands (https://github.com/rdong08/DISPbind)
Assembly: hg38
Supplementary files format and content: For DisP-seq, bigWig
Library strategy: DisP-seq

source_name: HeLa

growth_protocol: HeLa cell line was cultured in DMEM medium (Gibco) supplemented with 10% fetal bovine serum and 1% penicillin/ streptomycin at 37°C under 5% CO2.

extract_protocol:
Lysates were clarified from Mnase digested nuclei and protein-DNA complexes were isolated with biotinylated isoxazole.
Precipitated DNA samples were used to prepare sequencing libraries with JMDNA Bio-Medical Technology Corporation on an DNBSEQ-T7 platform.

value: Cervical cancer cells

value: bisox, 12A


title: N206_BSJ_DMSO_rep2

description:
Library name: N206_BSJ_DMSO_rep2
N206_BSJ_DMSO_rep2

value: neuroblast

value: WT

value: DMSO in BSJ-4-116 experiment


title: Female_Placenta_Cont_Rep_4

value: placenta


title: HeLa cells, DisP 12A, bisox, rep1

description: Library name: Sample7

value: HeLa


title: N206_BSJ_DMSO_rep1

description:
Library name: N206_BSJ_DMSO_rep1
N206_BSJ_DMSO_rep1


title: DiR_F_RNAseH_rep1


title: HeLa cells, DisP 12A, DMSO, rep2

description: Library name: Sample6

value: DMSO, 12A


title: N206_BSJ_rep4

description:
Library name: N206_BSJ_rep4
N206_BSJ_rep4


title: IL-1R1 gKO_F_sham_72h_A073

city: Lexington

first: Joshua

middle: M

last: Morganti

state: KY

address: 789 S. Limestone St

department: Sanders-Brown Center on Aging

institute: University of Kentucky

description:
Library name: A073
Bulk RNA-seq, IL-1R1 gKO, F, sham, 72h

data_processing:
Quality assessment of raw reads with FastQC
Read alignment with STAR to mouse genome
Transcript quantification with Salmon
Gene-level count aggregation with tximeta
Differential expression analysis with DESeq2
Assembly: GRCm39 (mm39)
Supplementary files format and content: Tab-delimited text file with Salmon-quantified gene-level read counts (salmon.merged.gene_counts.tsv). Columns are sample IDs, rows are Ensembl gene IDs with gene names.
Supplementary files format and content: Tab-delimited text file with Salmon-quantified gene-level TPM values (salmon.merged.gene_tpm.tsv). Columns are sample IDs, rows are Ensembl gene IDs with gene names.

source_name: mouse brain

growth_protocol: 14:10 (light:dark), ad lib food access

extract_protocol:
RNeasy Mini with genomic dna depletion
RNA library preparation was performed by Novogene (Project X202SC24077443-Z01-F001). [Add library prep kit info, e.g., Illumina Stranded mRNA Prep, polyA selection, etc.]

treatment_protocol: Mice underwent closed head injury (CHI) or sham surgery. Brain tissue was collected at 9h, 24h, or 72h post-injury.

value: mouse brain

value: IL-1R1 gKO

tag: surgery

value: sham

tag: timepoint

tag: age (months)

value: 5.8 months

tag: animal id

tag: experiment id


title: Female_Placenta_Cont_Rep_3

value: embryonic day 17.5

value: Female


title: DiR_F_rep2


title: HeLa cells, DisP 12A, DMSO, rep1

description: Library name: Sample5


title: Female_Placenta_Cont_Rep_2

value: Vehicle control

value: 0 mg/kg/day


title: Female_Placenta_Cont_Rep_1

value: No


title: E11.5_Placenta_High_GenX_Rep_5

description: 21497_1226_E11.5_Placenta_High_GenX_5_Rep_5

value: embryonic day 11.5

value: pooled M/F

value: GenX

value: 10 mg/kg/day


title: E11.5_Placenta_High_GenX_Rep_4

description: 21496_1226_E11.5_Placenta_High_GenX_4_Rep_4


title: N206_BSJ_rep3

description:
Library name: N206_BSJ_rep3
N206_BSJ_rep3

value: neuroblastoma cell line

value: neuroblast

value: WT


title: 203968030003_R03C01_C037_CNG

type: genomic

city: Exeter

last: Harvey

state: Devon

address: RILD Building, RD&E, Barrack Road

department: Clinical and Biomedical Sciences

country: United Kingdom

institute: University of Exeter

hyb_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the Zymo EZ 96 DNA methylation kit (Zymo Research) according to the manufacturer’s standard protocol.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) using a Illumina iScan System (Illumina)

data_processing:
Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions.
[ukbbn_betas_normalised.Rdata] wateRmelon processed beta values, dasen quantile normalised

label: Cy3 & Cy5

source_name: Anterior cingulate

label_protocol: Standard Illumina Protocol

extract_protocol: ~30mg of brain tissue was milled over liquid nitrogen and extracted following the Qiagen AllPrep DNA/RNA/miRNA Universal kit following standard protocol. Samples were pre-checked using nanodrop fluorometer prior to further processing.

value: Anterior cingulate

tag: regiondescription

tag: plate

tag: centre

value: Imperial Brain Bank

value: male

tag: thal

value: FALSE


title: N206_BSJ_rep1

description:
Library name: N206_BSJ_rep1
N206_BSJ_rep1

tag: tissue


title: DiR_F_rep1

value: DiR-F

value: HeLa


title: 203973690040_R08C01_20174926_CNG

value: Newcastle Brain Tissue Resource

tag: Sex


title: N206_BSJ_rep2

description:
Library name: N206_BSJ_rep2
N206_BSJ_rep2

tag: treatment


title: mNET-seq_rep1

value: mNET-seq


title: HeLa cells, DisP WT, bisox, rep2

description: Library name: Sample4

value: Cervical cancer cells

value: bisox, WT


title: mNET-seq_rep2


title: N206_OKI_single_rep4

description:
Library name: N206_OKI_single_rep4
N206_OKI_single_rep4


title: HeLa cells, DisP WT, bisox, rep1

description: Library name: Sample3


title: FAIRE_seq_Input

value: FAIRE-seq Input


title: HeLa cells, DisP WT, DMSO, rep2

description: Library name: Sample2

value: DMSO, WT


title: N206_OKI_single_rep3

description:
Library name: N206_OKI_single_rep3
N206_OKI_single_rep3


title: E11.5_Placenta_High_GenX_Rep_3

description: 21495_1226_E11.5_Placenta_High_GenX_3_Rep_3

value: placenta

tag: strain

tag: age

value: embryonic day 11.5

value: pooled M/F

value: GenX

tag: dose

tag: outlier

value: No


title: FAIRE_seq_rep2

tag: sample type

value: FAIRE-seq

tag: cell line


title: HeLa cells, DisP WT, DMSO, rep1

description: Library name: Sample1

tag: cell type

tag: genotype

value: WT


title: N206_OKI_single_rep2

description:
Library name: N206_OKI_single_rep2
N206_OKI_single_rep2

value: neuroblastoma cell line

value: neuroblast


title: E11.5_Placenta_High_GenX_Rep_2

description: 21494_1226_E11.5_Placenta_High_GenX_2_Rep_2

value: 10 mg/kg/day


title: E11.5_Placenta_High_GenX_Rep_1

description: 21493_1226_E11.5_Placenta_High_GenX_1_Rep_1


title: E11.5_Placenta_Low_GenX_Rep_4

description: 21491_1226_E11.5_Placenta_Low_GenX_4_Rep_4

value: 2 mg/kg/day


title: HeLa cells, ChIP 12A, rep2

data_processing:
For RNA-seq analysis, raw sequencing reads for shBRD4 HeLa rescued by EGFP-BRD4-WT and EGFP-BRD4-12A samples were trimmed for low-quality nucleotides and adapter sequences using Trim Galore! (v0.6.7). The reads were then aligned to human genome GRCh38/hg38 with HISAT2 (v2.2.1) using the ‘-rna-strandness RF’ parameter and an additional ‘-k 30’ parameter for chromatin RNA analysis. Gene annotation GTF format files for human were downloaded from the ENSEMBL database (https://www.ensembl.org/index.html). Reads counts for genes were obtained using featureCounts (v2.0.2) and then normalized to fragments per kilobase of transcript per million mapped reads (FPKM). Differential expression analysis was performed with the R/Bioconductor package DESeq2 (v1.36.0),using P value < 0.05 and log2 |fold change| > log2 (1.5) threshold.
For ChIP-seq analysis, raw reads were trimmed and aligned to the GRCh38/hg38 human reference genome using Bowtie2 (v2.4.5). Duplicate reads were removed using Picard tools (v.1.88, http://broadinstitute.github.io/picard) and BAM files were generated using Samtools (v1.2). Peak calling was performed using MACS2 (2.2.7.1) with ‘-q 0.01 --extsize 150 --keep-dup 5’ parameters to identify histone and transcription factor ChIP-seq enrichment regions over background. Robust BRD4 peaks intersected from two biological replicates were merged from both the 12A and WT treatments using Bedtools (v2.31.1).
Assembly: hg38
Supplementary files format and content: For RNA-seq, tab-delimited text file includes raw counts for each Sample. For ChIP-seq, bigWig

extract_protocol:
For RNA-seq, Total RNA and RNA associated with different cell fractions were extracted using TRIzol™ reagent (Invitrogen, 15596026) according to the manufacturer’s protocol and quantified using NanoDrop One spectrophotometer (Invitrogen). For ChIP-seq, HeLa cells were resuspended with growth medium into a density of 106 mL-1. Crosslinking was performed by adding 1% formaldehyde (Sigma-Aldrich, F1635) into the cells followed by rotation for 20 min at RT, which was ceased by glycine with a final concentration of 0.125 M followed by rotating for 5 min at RT. Supernatants were removed and cell pellets were rinsed with ice cold PBS twice, then the cells were resuspended with lysis buffer (50 mM HEPES, pH 7.9, 5 mM MgCl2, 0.2% Triton X-100, 20% glycerol, 300 mM NaCl, 1× protease inhibitor) on ice for 10 min. Cell pellets were collected by centrifugation at 4 °C, 500 g for 5 min, then resuspended with SDS lysis buffer (50 mM HEPES, pH 7.4, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 1× protease inhibitor) and kept on ice for 30 min. The lysates were sonicated utilizing a Bioruptor sonicator (Diagenode) at high power for 30 cycles, followed by centrifugation at 17000 × g for 10 min. Supernatants were collected into new tubes. The specified antibodies, BRD4 (E2A7X) Rabbit mAb (Cell Signaling Technology, 13440S) and HA-Tag (C29F4) Rabbit mAb (Cell Signaling Technology, 3724S), were diluted 1:50 in SDS lysis buffer and incubated with a pre-washed mixture of Protein A and G magnetic beads at 4 °C with continuous rotation for a minimum of 2 h. The beads were subsequently washed three times with SDS lysis buffer. Cell lysates were pre-cleaned with washed Protein A and G magnet beads mixture at 4 °C for 1 h with rotation, and 10% of the lysate were kept as the input control. Then, the remaining lysates and antibody-coated beads were incubated at 4 °C overnight with rotation. The beads were washed with rotation sequentially at 4 °C with the following buffers, 5 min for each: twice with SDS lysis buffer, twice with high salt wash buffer (50 mM HEPES, pH 7.5, 350 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS), twice with LiCl wash buffer (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate) and once with TE wash buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.2% Triton X-100), then eluted with 240 µL elution buffer (100 mM NaHCO3, 1% freshly added SDS) by shaking at 30 °C for 1 h. The eluent was then mixed with 14.4 µL 5 M NaCl and shaken at 65 °C for 4 h to reverse the crosslinks between proteins and DNA. Afterwards, the eluent was treated with 4 µL RNase A (Thermo Scientific, EN0531), shaken at 37 °C for 15 min, then 4 µL proteinase K (Thermo Scientific, 100005393), shaken at 65 °C overnight. The DNA was extracted by DNA clean & concentrator (Zymo Research, D4014) and set aside for subsequent qPCR assay or library preparation.
For RNA-seq, RNA-seq library preparation was performed utilizing VAHTS Universal V8 RNA-seq Library Prep Kit (Vazyme, NR605) following the manufacturer’s protocols with 1 µg initial amount of total RNA for each sample, and sequencing was performed at JMDNA Bio-Medical Technology Corporation on an Illumina NovaSeq 6000 platform. For ChIP-seq, library preparation was performed utilizing VAHTS Universal Pro DNA Library Prep Kit (Vazyme, ND608) following the manufacturer’s protocols with 10 ng initial amount of DNA for each sample, and sequencing was performed at JMDNA Bio-Medical Technology Corporation on an Illumina NovaSeq 6000 platform.

value: HeLa


title: FAIRE_seq_rep1


title: N206_OKI_single_rep1

description:
Library name: N206_OKI_single_rep1
N206_OKI_single_rep1


title: HeLa cells, ChIP 12A, rep1

value: BRD4 (E2A7X) Rabbit mAb (Cell Signaling Technology, 13440S)


title: Input_rep2

value: ChIP-Seq

tag: ChIP-seq Input


title: E11.5_Placenta_Low_GenX_Rep_5

description: 21492_1226_E11.5_Placenta_Low_GenX_5_Rep_5


title: N206_OKI_Mer_Combo_rep4

description:
Library name: N206_OKI_Mer_Combo_rep4
N206_OKI_Mer_Combo_rep4

value: Combi Merestinib & OKI-1546


title: E11.5_Placenta_Low_GenX_Rep_3

description: 21490_1226_E11.5_Placenta_Low_GenX_3_Rep_3


title: HeLa cells, ChIP WT, rep2

value: Cervical cancer cells


title: N206_OKI_Mer_Combo_rep3

description:
Library name: N206_OKI_Mer_Combo_rep3
N206_OKI_Mer_Combo_rep3


title: Input_rep1


title: H3K9me3_rep2

tag: chip-seq antibody


title: N206_OKI_Mer_Combo_rep2

description:
Library name: N206_OKI_Mer_Combo_rep2
N206_OKI_Mer_Combo_rep2


title: HeLa cells, Input


title: HeLa cells, ChIP WT, rep1


title: H3K9me3_rep1


title: E11.5_Placenta_Low_GenX_Rep_1

description: 21488_1226_E11.5_Placenta_Low_GenX_1_Rep_1


title: E11.5_Placenta_Low_GenX_Rep_2

description: 21489_1226_E11.5_Placenta_Low_GenX_2_Rep_2


title: N206_OKI_Mer_Combo_rep1

description:
Library name: N206_OKI_Mer_Combo_rep1
N206_OKI_Mer_Combo_rep1


title: E11.5_Placenta_High_PFOA_Rep_5

description: 21487_1226_E11.5_Placenta_High_PFOA_5_Rep_5

value: PFOA

value: 5 mg/kg/day


title: E11.5_Placenta_High_PFOA_Rep_4

description: 21486_1226_E11.5_Placenta_High_PFOA_4_Rep_4

value: placenta

value: embryonic day 11.5


title: E11.5_Placenta_High_PFOA_Rep_3

description: 21485_1226_E11.5_Placenta_High_PFOA_3_Rep_3

value: pooled M/F


title: N206_OKI_GI50_rep3

description:
Library name: N206_OKI_GI50_rep3
N206_OKI_GI50_rep3


title: HeLa cells, Cyto RNA-seq, WT, rep2

molecule: cytoplasmic RNA

value: Cytoplasm, WT


title: E11.5_Placenta_High_PFOA_Rep_2

description: 21484_1226_E11.5_Placenta_High_PFOA_2_Rep_2

value: No


title: N206_OKI_GI50_rep2

description:
Library name: N206_OKI_GI50_rep2
N206_OKI_GI50_rep2

value: WT


title: H3K4me3_rep1


title: HeLa cells, Cyto RNA-seq, WT, rep1


title: HeLa cells, Nuc RNA-seq, 12A, rep2

molecule: nuclear RNA

value: Nucleoplasm, 12A


title: N206_OKI_GI50_rep1

description:
Library name: N206_OKI_GI50_rep1
N206_OKI_GI50_rep1

value: neuroblastoma cell line

value: neuroblast


title: H3K4me1_rep2


title: N206_Mer_single_rep4

description:
Library name: N206_Mer_single_rep4
N206_Mer_single_rep4

value: Merestinib 9833.33nM


title: HeLa cells, Nuc RNA-seq, 12A, rep1

value: HeLa


title: H3K4me1_rep1


title: N206_Mer_single_rep3

description:
Library name: N206_Mer_single_rep3
N206_Mer_single_rep3


title: E11.5_Placenta_Low_PFOA_Rep_5

description: 21482_1226_E11.5_Placenta_Low_PFOA_5_Rep_5

value: 1 mg/kg/day


title: H3K36me3_rep2

value: ChIP-Seq


title: HeLa cells, Nuc RNA-seq, WT, rep1

value: Nucleoplasm, WT


title: N206_Mer_single_rep1

description:
Library name: N206_Mer_single_rep1
N206_Mer_single_rep1


title: H3K36me3_rep1


title: E11.5_Placenta_Low_PFOA_Rep_4

description: 21481_1226_E11.5_Placenta_Low_PFOA_4_Rep_4


title: E11.5_Placenta_High_PFOA_Rep_1

description: 21483_1226_E11.5_Placenta_High_PFOA_1_Rep_1


title: HeLa cells, Chr RNA-seq, 12A, rep2

value: Cervical cancer cells

value: Chromatin, 12A


title: HeLa cells, Chr RNA-seq, WT, rep2

value: Chromatin, WT


title: E11.5_Placenta_Cont_Rep_4

value: placenta

value: Vehicle control

value: 0 mg/kg/day


title: HeLa cells, Chr RNA-seq, WT, rep1


title: E11.5_Placenta_Cont_Rep_5

value: embryonic day 11.5

value: pooled M/F


title: H3K27Ac_rep1


title: E11.5_Placenta_Cont_Rep_2

value: No


title: Olfm4_Ogt_KO_1

status: Public on Jul 28 2026

city: Xin Xiang

first: xiwen

last: xiong

address: 602 Jinsui Road

department: School of Forensic Medicine

institute: Xinxiang Medical University

description: Library name: Sample4

data_processing:
CLC Genomics Workbenchv 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM39/mm39 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCm39.108
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKMvalues for each Sample

source_name: Ileum

growth_protocol: Mice were housed in a temperature (22 ± 2 °C) and humidity (40–60%)-controlled facility with regular 12:12 light/dark cycle and fed a rodent chow with free access to water.

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: To generate Olfm4∆Ogt mice, Ogt‑floxed mice were crossed with Olfm4‑CreER mice. At 2 months of age, the offspring received tamoxifen for three consecutive days to induce Ogt deletion, and tissues were collected on day 10, when the entire ileal epithelium of Olfm4∆Ogt mice was Ogt‑negative.

value: Ileum

value: primarily isolated Intestinal epithelial cells

value: Ogt intestinal stem cell-specific knockout

value: total RNA


title: Olfm4_Ogt_KO_3

description: Library name: Sample6


title: E11.5_Placenta_Cont_Rep_1


title: Olfm4Ctrl_3

description: Library name: Sample3

value: LoxP


title: Postnatal day 5 bio replicate 2 (Male)

city: Bethesda

first: Whitney

last: Heavner

state: MD

address: 35 Convent Drive

department: NINDS

institute: National Institutes of Health

description:
Library name: p5_R2
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using the Cell Ranger software v9.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest).
Assembly: mm10
Supplementary files format and content: tab separated values files and matrix files

source_name: main olfactory epithelium

growth_protocol: Olfactory epithelium (OE) was dissected from the nasal cavity of wild-type (C57Bl/6) mice at P1, P3, P5, P8, P15, or P22

extract_protocol:
The sensory OE was microdissected from the mouse nasal cavity at P1, P3, P5, P8, P15, and P22, dissociated in 2-3 mL pre-warmed dissociation medium (Worthington) (150 units papain, 100 units DNAse I, 2.5 mM cysteine, and 2.5 mM EDTA in 5 mL Neurobasal), and kept at 37°C for 25 min in a CO2 incubator. Samples were washed 3 times with 10% fetal bovine serum in phosphate-buffered saline (FBS-PBS), gently triturated 5-10 times using a fire-polished glass Pasteur pipette, and strained through a 35 μm nylon filter into a 5 mL polypropylene tube. DAPI, used to identify dead cells, was added at a final concentration of 0.1-1 μg/mL, and live cells (DAPI-low) were collected using a Sony LE-SH-800G cell sorter. At least two biological replicates and at least one female and one male per time point were used for all time points except P5, which only contained males.
Cells were pelleted in a swinging bucket centrifuge at 400g for 5 minutes at 4°C. The cell pellet was resuspended in 43.2 μl FBS-PBS, then 31.8 μl RT master mix was added to the cell pellet before loading the cells onto a Next GEM Chip G. A Chromium Next GEM Single Cell 3′ Kit v3.1 (10x Genomics, PN-1000268) and Dual Index Kit TT Set A (10x Genomics, PN-1000215) were used to generate single-cell whole-transcriptome libraries according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 Dual Index User Guide Rev E).

value: main olfactory epithelium

value: postnatal day 5

tag: cell types

value: multipotent progenitors and their progeny

value: wild-type

value: Male

tag: sequencing batch


title: Liver, EtOH-fed Ripk1-Con female mouse, S41

city: Nanjing

first: Dan

last: Weng

address: 200 Xiaolingwei Street

institute: Nanjing University of Science and Technology

description: Library name: S41

data_processing:
Adapter sequences and low-quality sequences at the 3' ends of reads were removed using Skewer v0.2.2. Quality control of the preprocessed reads and calculation of Q20 and Q30 base proportions were performed using FastQC v0.11.5. Clean paired-end reads were aligned to the Mus musculus GRCm38.p6 reference genome with Ensembl release 98 gene annotation using STAR v2.5.2b with the parameters --twopassMode Basic, --outSAMstrandField intronMotif, and --alignSJstitchMismatchNmax 5 -1 5 5; other parameters were left at default settings. Alignment quality statistics were assessed using RSeQC v2.6.4. Transcript assembly and gene-level expression quantification, including raw read counts and FPKM values, were performed using StringTie v2.2.1 guided by the reference annotation. Differential expression analysis was performed using DESeq2 v1.38.1.
Assembly: GRCm38.p6
Supplementary files format and content: Gzip-compressed, tab-delimited text file containing gene-level raw read counts for all eight libraries. The first column contains Ensembl Mus musculus gene identifiers, and the remaining columns contain non-negative integer raw counts for S28, S29, S32, S34, S37, S39, S40, and S41.

source_name: liver

extract_protocol:
Total RNA was extracted from mouse liver tissues using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. RNA concentration and purity were evaluated using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) by measuring the A260/A280 and A260/A230 ratios. Before library construction, RNA integrity was assessed by agarose gel electrophoresis and RNA quantity was further assessed using Qubit fluorometric quantification.
Polyadenylated mRNA was enriched from total RNA using Oligo(dT) magnetic beads and randomly fragmented into approximately 200-bp fragments. First-strand cDNA was synthesized using random primers. During second-strand cDNA synthesis, dTTP was replaced by dUTP to enable strand-specific library construction. Double-stranded cDNA was purified using AMPure XP beads, end-repaired, A-tailed, and ligated to sequencing adapters. The second cDNA strand was digested using USER enzyme, and the resulting strand-specific libraries were enriched by approximately 15 cycles of PCR. Libraries were quality assessed and quantified before paired-end 150-bp sequencing on an Illumina NovaSeq 6000 platform.

value: liver


title: Liver, EtOH-fed Ripk1-Con female mouse, S40

description: Library name: S40


title: Liver, EtOH-fed Ripk1-hepKO female mouse, S34

description: Library name: S34


title: N206_OKI_GI50_rep4

description:
Library name: N206_OKI_GI50_rep4
N206_OKI_GI50_rep4

value: neuroblastoma cell line

value: neuroblast

value: WT


title: H3K9Ac_rep2

value: ChIP-Seq

value: HeLa


title: HeLa cells, Cyto RNA-seq, 12A, rep1

value: Cervical cancer cells

value: Cytoplasm, 12A


title: HeLa cells, Cyto RNA-seq, 12A, rep2


title: H3K9Ac_rep1


title: H3K4me3_rep2


title: Liver, EtOH-fed Ripk1-Con female mouse, S32

description: Library name: S32


title: E11.5_Placenta_Low_PFOA_Rep_3

description: 21480_1226_E11.5_Placenta_Low_PFOA_3_Rep_3

value: placenta

value: embryonic day 11.5

value: pooled M/F

value: PFOA

value: 1 mg/kg/day

value: No


title: E11.5_Placenta_Low_PFOA_Rep_2

description: 21479_1226_E11.5_Placenta_Low_PFOA_2_Rep_2


title: HeLa cells, Nuc RNA-seq, WT, rep2

value: Nucleoplasm, WT


title: N206_Mer_single_rep2

description:
Library name: N206_Mer_single_rep2
N206_Mer_single_rep2

value: Merestinib 9833.33nM


title: Liver, EtOH-fed Ripk1-Con female mouse, S29

description: Library name: S29


title: Liver, EtOH-fed Ripk1-hepKO female mouse, S28

description: Library name: S28


title: cortex,P2_PKA,experiment

city: Shanghai

first: TongYe

last: Fu

address: 138 Yi Xue Yuan Road

institute: Fudan University

description:
Library name: sample6
10x Genomics

data_processing:
High quality sequences (clean reads) were obtained by removing low quality sequences and joints. The clean reads were then processed with Cell Ranger software to obtain quantitative information on gene expression.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: cortex

extract_protocol:
Briefly, mouse embryos were dissected out and immediately submerged in fresh ice-cold Hanks balanced salt solution (Gibco 12175-095). The cortex was then cut into pieces and dissociated into a single-cell suspension using a Papain Cell Dissociation Kit (Miltenyi Biotec, catalog no. 130-092-628) according to the manufacturer’s instructions.
The Chromium dropletbased sequencing platform (10X Genomics) was used to generate scRNA-Seq libraries, following the manufacturer’s instructions (manual document part number: CG00052 Rev C). The cDNA libraries were purified, quantified using an Agilent 2100 Bioanalyzer, and sequenced on an Illumina NovaSeq 6000.

value: cortex

value: PKA


title: cortex,P0,control

description:
Library name: sample7
10x Genomics


title: cortex,P2_PKA,control

description:
Library name: sample5
10x Genomics


title: E11.5_Placenta_Low_PFOA_Rep_1

description: 21478_1226_E11.5_Placenta_Low_PFOA_1_Rep_1


title: cortex,E17_PKA,experiment

description:
Library name: sample4
10x Genomics


title: N206_MER_OKI_DMSO_rep3

description:
Library name: N206_MER_OKI_DMSO_rep3
N206_MER_OKI_DMSO_rep3

value: neuroblastoma cell line

value: DMSO in MER+OKI experiment


title: N206_MER_OKI_DMSO_rep4

description:
Library name: N206_MER_OKI_DMSO_rep4
N206_MER_OKI_DMSO_rep4

value: neuroblast

value: WT


title: H3K27me3_rep2

value: ChIP-Seq

value: HeLa


title: H3K27me3_rep1


title: HeLa cells, Chr RNA-seq, 12A, rep1

value: Cervical cancer cells

value: Chromatin, 12A


title: cortex,E17_PKA,control

description:
Library name: sample3
10x Genomics


title: H3K27Ac_rep2


title: N206_MER_OKI_DMSO_rep2

description:
Library name: N206_MER_OKI_DMSO_rep2
N206_MER_OKI_DMSO_rep2


title: E11.5_Placenta_Cont_Rep_3

value: placenta

value: embryonic day 11.5

value: Vehicle control

value: 0 mg/kg/day


title: cortex,E12_Mek1dd,control

description:
Library name: sample1
10x Genomics


title: cortex,E12_Mek1dd,experiment

description:
Library name: sample2
10x Genomics


title: E2-30-8

first: sijia

last: liu

address: Xiannongtan Street, Xicheng District

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College

description: Library name: Sample 20

data_processing:
Raw fastq reads were quality-controlled by FastQC; low-quality reads and sequencing adapters were removed using Trimmomatic software to obtain clean reads. Clean reads were aligned to mouse reference genome mm10 via HISAT2 software.
Gene expression abundance was quantified and raw read counts of each gene were generated by StringTie software.
Differentially expressed genes (DEGs) were screened using DESeq2 R package with threshold |log2(fold change)| > 1 and adjusted q-value < 0.05.
GO biological process and KEGG pathway enrichment analysis of DEGs were performed using topGO and KOBAS R packages.
Transcriptome results were further validated by western blot and immunofluorescence assays to detect p38 MAPK, apoptosis-related protein expression in renal tissue.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Gene read count matrix file (readcount.xlsx): Excel spreadsheet containing raw read counts of all detected genes across 18 samples. Rows represent individual genes, columns correspond to each biological replicate sample.

source_name: kidney

growth_protocol: Male C57BL/6J mice aged 6–8 weeks were housed in a specific pathogen-free (SPF) animal facility with 12 h light/dark cycle, constant temperature (22 ± 2 ℃) and humidity (50% ± 10%). Standard rodent chow and sterile water were provided ad libitum.

extract_protocol:
Total RNA was extracted from mouse renal tissue using TRIzol reagent (Invitrogen) following the manufacturer’s instructions. RNA purity and concentration were determined by Nanodrop 2000 spectrophotometer. RNA integrity was verified via agarose gel electrophoresis and Agilent 2100 Bioanalyzer; only samples with RIN ≥ 7.0 were retained for library construction.
mRNA was enriched from total RNA using oligo(dT) magnetic beads, fragmented into 300–350 bp fragments. First-strand and second-strand cDNA were synthesized, followed by end repair, A-tailing and sequencing adapter ligation. Purified cDNA fragments were amplified by PCR to construct RNA-seq libraries. Qualified libraries were sequenced on Illumina NovaSeq 6000 platform with paired-end 150 bp sequencing strategy.

treatment_protocol: Mice were randomly divided into four groups: Sham group (oral PBS + intraperitoneal saline), Cisplatin model group (oral PBS + 10 mg/kg cisplatin i.p.), low-dose 7-HCG group (oral 15 mg/kg 7-HCG + 10 mg/kg cisplatin i.p.), high-dose 7-HCG group (oral 30 mg/kg 7-HCG + 10 mg/kg cisplatin i.p.). 7-HCG/PBS was intragastrically administrated once daily for 5 consecutive days. Cisplatin injection was performed on the 3rd day of pretreatment. All mice were sacrificed 72 h after cisplatin administration, and whole kidney tissues were rapidly isolated for RNA extraction.

value: kidney

value: 7-HCG 30 mg/kg treatment group


title: E2-15-7

description: Library name: Sample 15

value: 7-HCG 15 mg/kg treatment group


title: E2-30-7

description: Library name: Sample 19


title: E2-30-5

description: Library name: Sample 17


title: E2-30-1

description: Library name: Sample 16


title: E2-15-5

description: Library name: Sample 14


title: E2-15-3

description: Library name: Sample 13


title: E2-15-2

description: Library name: Sample 12


title: Olfm4_Ogt_KO_2

description: Library name: Sample5

value: Ileum

value: primarily isolated Intestinal epithelial cells

value: Ogt intestinal stem cell-specific knockout

value: total RNA


title: N206_MER_OKI_DMSO_rep1

description:
Library name: N206_MER_OKI_DMSO_rep1
N206_MER_OKI_DMSO_rep1

value: neuroblastoma cell line

value: neuroblast

value: DMSO in MER+OKI experiment


title: M-6

description: Library name: Sample 8

value: cisplatin model group


title: M-10

description: Library name: Sample 10


title: E2-15-1

description: Library name: Sample 11


title: M-3

description: Library name: Sample 7


title: M-9

description: Library name: Sample 9


title: Olfm4Ctrl_2

description: Library name: Sample2

value: LoxP


title: Postnatal day 15 bio replicate 1 (Male)

description:
Library name: p15_R1
10x Genomics

value: main olfactory epithelium

value: postnatal day 15

value: multipotent progenitors and their progeny

value: wild-type

value: Male


title: Olfm4Ctrl_1

description: Library name: Sample1


title: Con-7

description: Library name: Sample 4

value: kidney

value: control


title: Con-8

description: Library name: Sample 5


title: Con-5

description: Library name: Sample 3


title: Con-2

description: Library name: Sample 2


title: Con-1

description: Library name: Sample 1


title: Postnatal day 8 bio replicate 1 (Female)

description:
Library name: p8_R1
10x Genomics

value: postnatal day 8

value: Female


title: Postnatal day 8 bio replicate 2 (Male)

description:
Library name: p8_M
10x Genomics


title: E12_90

city: Guangzhou

first: Guizhong

last: Cui

state: Guangdong

address: 188 KaiYuan Road, Huangpu District

institute: Guangzhou Lab

description: Library name: E12_90

data_processing:
raw sequencing data were evaluated by FASTQC and were separately mapped to the mouse GRCm38 genome assemblies using HISAT2 (Pertea et al. 2016) using default settings. Mapping ratio was calculated based on the number of mapped reads and total reads for each sample.
All mapped reads were processed by Stringtie (Pertea et al. 2016) to quantify gene expression levels (measured by TPM, Transcripts Per Kilobase per Million mapped reads) using default parameters.
Submitter confirms that image files are not required for analysis of these data.
Assembly: mouse GRCm38
Supplementary files format and content: tab-separated text files include raw reads count for each samples
Library strategy: spatial transcriptomics

source_name: Optic stalk ventral proximal

extract_protocol:
Geo-seq (Chen et al. 2017). E12 and E14 mouse embryonic heads were fresh frozen embedded in OCT and cryosectioned at a thickness of 12 μm.
Geo-seq (Chen et al. 2017). Total RNA pellets were dissolved in a lysis solution (4M GuSCN), followed by reverse transcription using SuperScript II reverse transcriptase (Invitrogen), and whole transcription amplification with KAPA HiFi HotStart ReadyMix (2×; KAPA Biosystems). cDNA library was constructed using the Nextera XT Library Prep Kit (Illumina).

value: Optic stalk ventral proximal

value: Control

tag: batch

value: B


title: Nrep knockout liver biological replicate 3

city: Zunyi

first: Hongkun

last: Li

address: Campus No. 1 Road, Zunyi City, Guizhou Province, China.

institute: Zunyi Medical University

description:
Library name: NL3
NL_vs_ML.Genes.Count.xlsx

data_processing:
Raw paired-end reads from both tissue experiments were quality filtered and adapter trimmed using fastp.
Assembly: Liver: Mus musculus GRCm38, Ensembl release 94; iWAT: Mus musculus GRCm39.
Supplementary files format and content: Liver: Microsoft Excel workbook containing a complete gene-level raw read-count matrix for ML1, ML2, ML3, NL1, NL2, and NL3. Rows represent Ensembl gene identifiers, columns represent individual RNA-seq libraries, and values represent gene-level read counts generated using featureCounts.
Supplementary files format and content: iWAT: Tab-delimited matrix containing complete gene-level read counts for WT3_1, WT3_2, WT3_3, KO4_1, KO4_2, and KO4_3. Rows represent Ensembl gene identifiers, columns represent individual RNA-seq libraries, and values represent gene-level read counts.

extract_protocol:
Liver: total RNA was isolated from frozen liver tissue using TRIzol reagent. RNA degradation and contamination were assessed by agarose gel electrophoresis, and RNA purity and integrity were evaluated using a NanoPhotometer and the RNA Nano 6000 Assay Kit on an Agilent Bioanalyzer 2100. iWAT: Total RNA was extracted from inguinal white adipose tissue using QIAzol Lysis Reagent according to the manufacturer’s instructions. RNA quality was assessed using an Agilent 5300 Fragment Analyzer, and RNA concentration was measured using a NanoDrop spectrophotometer. One microgram of total RNA per sample was used for library preparation.
Liver RNA-seq libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina. Fragmented mRNA was used as the template for first-strand cDNA synthesis with random oligonucleotide primers and M-MuLV reverse transcriptase. The RNA template was subsequently degraded using RNase H, and second-strand cDNA was synthesized using DNA polymerase I and dNTPs. Purified double-stranded cDNA was subjected to end repair, dA-tailing, and sequencing-adapter ligation. cDNA fragments of approximately 250–300 bp were selected using AMPure XP beads, PCR amplified, and purified again using AMPure XP beads to generate the final libraries. Libraries were initially quantified using a Qubit 2.0 fluorometer and diluted to 1.5 ng/µL. Library fragment-size distributions were evaluated using an Agilent 2100 Bioanalyzer, and effective library concentrations were determined by quantitative PCR. Libraries with effective concentrations greater than 3 nM and acceptable fragment-size distributions were sequenced on an Illumina NovaSeq platform using a 150-bp paired-end strategy. iWAT RNA-seq libraries were prepared using the Illumina Stranded mRNA Prep Ligation Kit. Messenger RNA was enriched from 1 microgram of total RNA by poly(A) selection using oligo(dT) magnetic beads and fragmented using fragmentation buffer. Double-stranded cDNA was synthesized using random hexamer primers, followed by end repair, phosphorylation, adapter ligation, and magnetic-bead size selection of approximately 300–400-bp fragments. Libraries were amplified by PCR for 10–15 cycles and quantified using a Qubit 4.0 fluorometer. Qualified libraries were sequenced using a 150-bp paired-end strategy on Illumina NovaSeq X Plus.

value: liver

value: Nrep-/-


title: Nrep knockout liver biological replicate 1

description:
Library name: NL1
NL_vs_ML.Genes.Count.xlsx


title: WT liver biological replicate 2

description:
Library name: ML2
NL_vs_ML.Genes.Count.xlsx

value: wild type


title: WT liver biological replicate 3

description:
Library name: ML3
NL_vs_ML.Genes.Count.xlsx


title: E12_89

description: Library name: E12_89

source_name: Optic stalk ventral middle

value: Optic stalk ventral middle


title: WT liver biological replicate 1

description:
Library name: ML1
NL_vs_ML.Genes.Count.xlsx


title: Nrep knockout liver biological replicate 2

description:
Library name: NL2
NL_vs_ML.Genes.Count.xlsx


title: Postnatal day 5 bio replicate 1 (Male)

description:
Library name: p5_R1
10x Genomics

value: postnatal day 5


title: E12_88

description: Library name: E12_88

source_name: Optic stalk ventral distal

value: Optic stalk ventral distal


title: E12_87

description: Library name: E12_87

source_name: RPE ventral proximal

value: RPE ventral proximal


title: E12_86

description: Library name: E12_86

source_name: RPE ventral distal

value: RPE ventral distal


title: E12_84

description: Library name: E12_84

source_name: Optic stalk dorsal middle

value: Optic stalk dorsal middle


title: E12_82

description: Library name: E12_82

source_name: RPE dorsal proximal

value: RPE dorsal proximal


title: E12_83

description: Library name: E12_83

source_name: Optic stalk dorsal distal

value: Optic stalk dorsal distal


title: E12_62

description: Library name: E12_62


title: E12_61

description: Library name: E12_61

source_name: RPE dorsal distal

value: RPE dorsal distal


title: E12_69

description: Library name: E12_69


title: E12_68

description: Library name: E12_68


title: E12_40

description: Library name: E12_40

value: A


title: E12_63

description: Library name: E12_63


title: E12_39

description: Library name: E12_39


title: E12_36

description: Library name: E12_36


title: E12_34

description: Library name: E12_34


title: E12_31

description: Library name: E12_31


title: E12_37

description: Library name: E12_37


title: E12_33

description: Library name: E12_33


title: E12_9

description: Library name: E12_9


title: E2-30-6

description: Library name: Sample 18

value: kidney

value: 7-HCG 30 mg/kg treatment group


title: E12_5

description: Library name: E12_5

source_name: Optic stalk dorsal proximal

value: Optic stalk dorsal proximal

value: Control


title: M-2

description: Library name: Sample 6

value: cisplatin model group


title: Liver, Npc1-/-, replicate 1

city: Oak Ridge

first: Alice

last: Townsend

state: TN

address: 1 Bethel Valley Rd

institute: ORNL

description:
Library name: Sample 4
10x Genomics

data_processing:
STARSolo aligner v2.7.9a was used to generate the mouse reference genome (GRCm38) and to align the fastq file reads for each sample. The EmptyDrops methodology was used within STARSolo to filter low quality cells with minimal total UMI counts.
Assembly: mm10
Supplementary files format and content: Barcode and feature files in .tsv.gz format. Count matrix files in .mtx.gz format.

source_name: Liver

extract_protocol:
Livers were collected from 7-week old mice, 3 Npc1+/+ and 3 Npc1-/- following isoflurane euthanasia and decapitation. Liver tissue was dissected, flash frozen in liquid nitrogen, and homogenized with a glass Dounce tissue grinder 25X with pestle A and 25X with pestle B) in 2 mL of EZ PREP buffer (Sigma NUC-101). Homogenized liver tissue was incubated on ice for 5 minutes, followed by an addition of 2 mL of EZ PREP, then centrifuged at 500 g for 5 minutes at 4 °C to pellet nuclei. Resulting nuclei were washed with 4 mL EZ PREP and incubated for 5 minutes on ice then centrifuged using the same parameters. Samples were washed with 4 mL nuclear suspension buffer (0.01% BSA, RNase inhibitor [Takara 2313 A]) and centrifuged using the same parameters. 1 mL of nuclear suspension buffer was added to the pellet for resuspension, then filtered with a 35 µM cell strainer (Corning 352235) and counted. Nuclei were diluted to 800-1500 cells/µL and libraries were generated with the 10X Chromium Controller system.
Llibraries were generated with the 10X Chromium Controller system. Single-nucleus libraries were sequenced using the Illumina NovaSeq 6000.

value: Liver


title: Liver, WT, replicate 3

description:
Library name: Sample 3
10x Genomics

value: WT


title: Liver, WT, replicate 2

description:
Library name: Sample 2
10x Genomics


title: Bioreplicate 4 wildtype glutamate

city: Hamburg

first: Christina

last: Mayer

address: Falkenried 94

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description: Library name: Bio4_WT_Glut

data_processing:
Reads were aligned to the mouse reference genome GRCm38 (mm10)  with STAR v.2.5.2b
Gene counts were calculated with featureCounts v.1.5.1
DESeq2 for differential expression analysis
Assembly: Assembly: mouse reference genome GRCm38 (mm10)
Supplementary files format and content: Supplementary files format and content: Tab-delimited text file containing raw gene counts with genes in rows and samples in columns.

source_name: Cortex

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen)
RNA sequencing libraries were prepared using the TruSeq stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions. After pooling, libraries were sequenced on a NovaSeq 6000 sequencer (Illumina) generating 150 bp paired-end reads.

value: Cortex

value: primary cortical neurons

value: wildtype

value: 50 µM glutamate for 6h


title: Bioreplicate 4 Cfh KO glutamate

description: Library name: Bio4_KO_Glut

value: neuronal Cfh conditional knockout


title: Bioreplicate 3 wildtype glutamate

description: Library name: Bio3_WT_Glut


title: Bioreplicate 2 wildtype control

description: Library name: Bio2_WT_Ctrl

value: no treatment


title: Bioreplicate 2 Cfh KO glutamate

description: Library name: Bio2_KO_Glut


title: Bioreplicate 3 Cfh KO control

description: Library name: Bio3_KO_Ctrl


title: Bioreplicate 2 wildtype glutamate

description: Library name: Bio2_WT_Glut


title: Bioreplicate 2 Cfh KO control

description: Library name: Bio2_KO_Ctrl


title: Bioreplicate 1 wildtype control

description: Library name: Bio1_WT_Ctrl


title: Bioreplicate 1 Cfh KO glutamate

description: Library name: Bio1_KO_Glut


title: Single-cell RNA-seq of WT lung, Prf1-/- lung, and Prf1-/- bone samples multiplexed with hashtag oligos

city: New York

first: Morgan

last: Huse

state: NY

address: 417 E 68th St

institute: Sloan Kettering Institute

description:
Library name: LungBone_10x_Run1_RNA
Single-cell RNA sequencing was performed using 10x Genomics. Cells from WT lung, Prf1-/- lung, and Prf1-/- bone samples were multiplexed using hashtag oligonucleotides and sequenced in a single run. Demultiplexing was performed based on feature barcode counts. Processed data include gene expression matrices and a cell-level metadata table containing sample assignments. The RDS file contains a Seurat object with normalized gene expression data, clustering results, UMAP embeddings, and cell-level metadata, including sample identity determined by hashtag oligonucleotides.

data_processing:
Raw sequencing data were demultiplexed and aligned to the mouse reference genome using Cell Ranger (v6.1.2) from 10x Genomics, which was then used to generate gene expression matrices and hashtag oligonucleotide (HTO) counts for downstream analysis. Cell hashing data were demultiplexed using the Seurat (v4.3.0) HTODemux function to assign sample identity to individual cells. Low-quality cells were filtered based on mitochondrial content (>10%), unique feature counts, and total RNA counts to remove potential doublets and dead cells. Filtered data were normalized and scaled using the SCTransform function in Seurat. Principal component analysis (PCA) was performed, followed by UMAP projection for dimensionality reduction. Clustering was performed using the Louvain algorithm, and clusters were annotated based on canonical marker gene expression. Differential gene expression analysis was conducted between samples using the FindMarkers function in Seurat with the Wilcoxon rank-sum test. Genes with an adjusted p-value < 0.05 were considered statistically significant.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung; bone

extract_protocol:
Lungs and knees were digested in 1 mL of digestion buffer (2 mL Collagenase I [7.5 mg/mL], 1.49 mg DNase I, 8 mL 1% BSA in HBSS++) per mouse. For lung tissue, tumors were resected and digested in 10 mL of digestion buffer for 20 minutes at 37°C with rotation. After digestion, the material was strained, washed with 5 mL of SMEM + 2% FBS, and resuspended in 1 mL of SMEM + 2% FBS. Red blood cells were lysed with 10 mL of 1× RBC Lysis for 1 minute, neutralized with 10 mL of SMEM + 2% FBS, and strained again. Cells were Fc-blocked (1:200)  (Clone 2.4G2, cat #70-0161) for 10 minutes at 4°C, followed by staining with anti-CD45-PerCPCy5 (1:200) (Clone 30-F11, cat #103132)  and DAPI. Finally, cells were resuspended in 1 mL of PBS + 2% FBS for sorting. For knee tissue, the bones were cleaned, crushed in 1 mL of digestion buffer, and transferred to precoated Eppendorf tubes. An additional 1 mL of digestion buffer was added, and the samples were incubated at 37 °C for 30 minutes, with gentle pipetting every 10 minutes to facilitate digestion. Cells were processed following the same procedure as the lung samples. Both lung and knee tissue samples were subjected to FACS on a BD FACSAria to isolate GFP+CD45-DAPI- cancer cells.
B16F10 MTCs extracted from wild type lung, Prf1-/- lung, and Prf1-/- bone were hashed using oligonucleotide-conjugated antibodies (TotalSeq B, hashes 1, 2, and 3) to uniquely label individual samples, which were then pooled together in equal proportions to enable multiplexed scRNA-seq. The pooled cells were processed using the 10x Genomics Chromium platform to generate single-cell gel bead-in-emulsions (GEMs). Reverse transcription and cDNA amplification were performed according to the 10x Genomics 3’ v3 protocol. Separate libraries were generated for the gene expression and hashing data. Libraries were sequenced on an Illumina platform to achieve a minimum of 50,000 reads per cell for gene expression and 5,000 reads per cell for hashing.

value: lung; bone

value: B16F10 cells

value: tumor cells

value: WT; Prf1-/- (multiplexed via hashing)


title: Knockout replicate 3

description:
Library name: KO3
Bulk RNA-seq of knockout cells (biological replicate 3)

data_processing:
CutAdapt (v1.6) was used to trim adapter sequences with a minimum overlap of 10 bases. Reads shorter than half the original read length were removed.
Reads were aligned to the mouse reference genome (mm10) using STAR (v2.5.0a) in two-pass mode.
Gene-level counts were generated using HTSeq (v0.5.3) with parameters: -m intersection-strict -s reverse -t exon.
Count matrices were normalized and analyzed for differential expression using DESeq.
Assembly: mm10
Supplementary files format and content: Tab-delimited file containing normalized gene expression counts.
Supplementary files format and content: Rows correspond to genes and columns correspond to samples (NT and KO replicates).

growth_protocol: Cells were cultured under standard conditions appropriate for the experimental system.

extract_protocol:
Total RNA was extracted using standard RNA isolation methods according to manufacturer protocols.
RNA-seq libraries were prepared using standard Illumina-compatible protocols for polyA-selected RNA and sequenced using paired-end sequencing.

treatment_protocol: Knockout samples were generated using CRISPR cas9. Control samples (NT) were processed in parallel without targeting.

value: Melanoma cells

value: Spp1 Knockout

value: batch 1


title: Knockout replicate 1

description:
Library name: KO1
Bulk RNA-seq of knockout cells (biological replicate 1)


title: Knockout replicate 2

description:
Library name: KO2
Bulk RNA-seq of knockout cells (biological replicate 2)


title: Hepatocytes co-cultured with Phgdh WT cancer cells and CXCR2i rep2

first: Jason

middle: Rodencal

last: Terrell

address: 530 1st Avenue

institute: NYU Langone Health

description: Library name: Hepato_11

data_processing:
The .txt file was generated using the standard Novogene RNA-seq analysis pipeline. Raw paired-end reads were produced on an Illumina NovaSeq 6000 platform. Adapter sequences and low-quality reads were removed to obtain clean reads. Clean reads were aligned to the reference genome using HISAT2, and gene-level read counts were quantified. Gene expression levels were normalized and reported as FPKM values.
Assembly: GRCm38 (mm10)
Supplementary files format and content: excel sheet with fpkm

source_name: mouse hepatocytes

extract_protocol:
RNA was extracted using RNeasy mini kit per manufacturer's protcols and RNA quality was validated.
As per Novogene protocols

value: mouse hepatocytes

value: cocultured with WT cancer cells and CXCR2 inhibitor


title: Hepatocytes co-cultured with Phgdh KO cancer cells rep3

description: Library name: Hepato_9

value: cocultured with Phgdh KO cancer cells


title: E12_32

description: Library name: E12_32

value: RPE dorsal proximal

value: Control

value: A


title: Hepatocytes co-cultured with Phgdh KO cancer cells rep2

description: Library name: Hepato_8


title: Liver, Npc1-/-, replicate 3

description:
Library name: Sample 6
10x Genomics

value: Liver


title: Bioreplicate 4 wildtype control

description: Library name: Bio4_WT_Ctrl

value: Cortex

value: primary cortical neurons

value: wildtype


title: Bioreplicate 3 wildtype control

description: Library name: Bio3_WT_Ctrl

value: no treatment


title: Hepatocytes co-cultured with Phgdh KO cancer cells rep1

description: Library name: Hepato_7


title: Bioreplicate 1 wildtype glutamate

description: Library name: Bio1_WT_Glut

value: 50 µM glutamate for 6h


title: Hepatocytes co-cultured with Phgdh WT cancer cells rep2

description: Library name: Hepato_5

value: cocultured with WT cancer cells


title: Hashtag oligonucleotide feature barcode sequencing for multiplexed WT lung, Prf1-/- lung, and Prf1-/- bone samples

description:
Library name: LungBone_10x_Run1_HTO
Hashtag oligonucleotide (HTO) libraries were generated for multiplexed WT lung, Prf1-/- lung, and Prf1-/- bone samples using 10x Genomics feature barcoding technology. HTO counts were used for sample demultiplexing and assignment of individual cells to biological samples. Processed data include HTO count matrices and barcode annotation files.

library_source: other

molecule: other

value: lung; bone

value: B16F10 cells

value: tumor cells

value: WT; Prf1-/- (multiplexed via hashing)


title: Hepatocytes co-cultured with Phgdh WT cancer cells rep1

description: Library name: Hepato_4

value: mouse hepatocytes


title: Hepatocytes only rep3

description: Library name: Hepato_3


title: Hepatocytes only rep2

description: Library name: Hepato_2


title: Hepatocytes co-cultured with Phgdh KO cancer cells and CXCR2i rep4

description: Library name: Hepato_16

value: cocultured with KO cancer cells and CXCR2 inhibitor


title: Tbr1+/K228E, P40, Vehicle, WT, male,replicate4

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

description: Library name: TBR1_WvM_p40_4

data_processing:
Transcript abundance was estimated with Salmon(v0.11.2) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.3.6.0) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.19.11).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

source_name: prefrontal cortex

growth_protocol: Mice were maintained under standard laboratory housing conditions with ad libitum access to food. Animals were analyzed at postnatal day 40 (P40)

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq Stranded mRNA LT Sample Prep Kit  (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded mRNA Sample Preparation Guide)

treatment_protocol: Male and female mice were administered two different drugs (fluoxetine and lithium)

value: prefrontal cortex


title: Hepatocytes co-cultured with Phgdh KO cancer cells and CXCR2i rep1

description: Library name: Hepato_13


title: Hepatocytes co-cultured with Phgdh WT cancer cells and CXCR2i rep3

description: Library name: Hepato_12

value: cocultured with WT cancer cells and CXCR2 inhibitor


title: Tbr1+/K228E, P40, Vehicle, WT, female,replicate4

description: Library name: TBR1_WvF_p40_4


title: Tbr1+/K228E, P40, Vehicle, WT, male,replicate1

description: Library name: TBR1_WvM_p40_1


title: Tbr1+/K228E, P40, Vehicle, WT, female,replicate3

description: Library name: TBR1_WvF_p40_3


title: Tbr1+/K228E, P40, Vehicle, WT, female,replicate2

description: Library name: TBR1_WvF_p40_2


title: Tbr1+/K228E, P40, Vehicle, HT, male,replicate3

description: Library name: TBR1_HvM_p40_3


title: Tbr1+/K228E, P40, Vehicle, WT, female,replicate1

description: Library name: TBR1_WvF_p40_1


title: Tbr1+/K228E, P40, Vehicle, HT, male,replicate1

description: Library name: TBR1_HvM_p40_1


title: Tbr1+/K228E, P40, Vehicle, HT, female,replicate3

description: Library name: TBR1_HvF_p40_4


title: Tbr1+/K228E, P40, Vehicle, HT, female,replicate2

description: Library name: TBR1_HvF_p40_3


title: Tbr1+/K228E, P40, Vehicle, HT, female,replicate1

description: Library name: TBR1_HvF_p40_2


title: Tbr1+/K228E, P40, Lithium, HT, male,replicate4

description: Library name: TBR1_HLM_p40_4


title: Tbr1+/K228E, P40, Lithium, HT, male,replicate3

description: Library name: TBR1_HLM_p40_3


title: Tbr1+/K228E, P40, Lithium, HT, male,replicate2

description: Library name: TBR1_HLM_p40_2


title: Liver, EtOH-fed Ripk1-hepKO female mouse, S39

description: Library name: S39

source_name: liver

value: liver


title: Tbr1+/K228E, P40, Lithium, HT, male,replicate1

description: Library name: TBR1_HLM_p40_1


title: Liver, EtOH-fed Ripk1-hepKO female mouse, S37

description: Library name: S37


title: Tbr1+/K228E, P40, Lithium, HT, female,replicate3

description: Library name: TBR1_HLF_p40_3


title: Tbr1+/K228E, P40, Lithium, HT, female,replicate2

description: Library name: TBR1_HLF_p40_2


title: Tbr1+/K228E, P40, Lithium, HT, female,replicate1

description: Library name: TBR1_HLF_p40_1


title: Tbr1+/K228E, P40, Fluoxetine, HT, male,replicate4

description: Library name: TBR1_HfM_p40_4


title: Tbr1+/K228E, P40, Fluoxetine, HT, male,replicate3

description: Library name: TBR1_HfM_p40_3


title: Tbr1+/K228E, P40, Fluoxetine, HT, male,replicate1

description: Library name: TBR1_HfM_p40_1


title: Tbr1+/K228E, P40, Fluoxetine, HT, male,replicate2

description: Library name: TBR1_HfM_p40_2


title: Tbr1+/K228E, P40, Fluoxetine, HT, female,replicate3

description: Library name: TBR1_HfF_p40_3


title: Tbr1+/K228E, P40, Fluoxetine, HT, female,replicate4

description: Library name: TBR1_HfF_p40_4


title: Tbr1+/K228E, P40, Fluoxetine, HT, female,replicate2

description: Library name: TBR1_HfF_p40_2


title: Hepatocytes only rep1

description: Library name: Hepato_1


title: Tbr1+/K228E, P40, Fluoxetine, HT, female,replicate1

description: Library name: TBR1_HfF_p40_1


title: Pten, P40, Vehicle, WT, male,replicate3

description: Library name: P131_WvM_p40_3


title: Tbr1+/K228E, P40, Vehicle, WT, male,replicate3

description: Library name: TBR1_WvM_p40_3


title: Tbr1+/K228E, P40, Vehicle, WT, male,replicate2

description: Library name: TBR1_WvM_p40_2


title: Pten, P40, Vehicle, WT, male,replicate2

description: Library name: P131_WvM_p40_2


title: Pten, P40, Vehicle, WT, male,replicate1

description: Library name: P131_WvM_p40_1


title: Pten, P40, Vehicle, WT, female,replicate2

description: Library name: P131_WvF_p40_2


title: Pten, P40, Vehicle, WT, female,replicate1

description: Library name: P131_WvF_p40_1


title: Pten, P40, Vehicle, WT, female,replicate3

description: Library name: P131_WvF_p40_3


title: Pten, P40, Vehicle, HT, male,replicate4

description: Library name: P131_HvM_p40_4


title: Pten, P40, Vehicle, HT, male,replicate2

description: Library name: P131_HvM_p40_2


title: Pten, P40, Vehicle, HT, male,replicate3

description: Library name: P131_HvM_p40_3


title: Pten, P40, Vehicle, HT, male,replicate1

description: Library name: P131_HvM_p40_1


title: Pten, P40, Vehicle, HT, female,replicate4

description: Library name: P131_HvF_p40_4


title: Pten, P40, Vehicle, HT, female,replicate3

description: Library name: P131_HvF_p40_3


title: Pten, P40, Vehicle, HT, female,replicate2

description: Library name: P131_HvF_p40_2


title: Pten, P40, Vehicle, HT, female,replicate1

description: Library name: P131_HvF_p40_1


title: Pten, P40, Lithium, HT, male,replicate3

description: Library name: P131_HLM_p40_3


title: Pten, P40, Lithium, HT, male,replicate4

description: Library name: P131_HLM_p40_4


title: Tbr1+/K228E, P40, Vehicle, HT, male,replicate2

description: Library name: TBR1_HvM_p40_2


title: Pten, P40, Lithium, HT, male,replicate2

description: Library name: P131_HLM_p40_2


title: Pten, P40, Lithium, HT, male,replicate1

description: Library name: P131_HLM_p40_1


title: Pten, P40, Lithium, HT, female,replicate4

description: Library name: P131_HLF_p40_4


title: E12_81

description: Library name: E12_81

value: RPE dorsal distal

value: Control

value: B


title: Pten, P40, Lithium, HT, female,replicate3

description: Library name: P131_HLF_p40_3


title: Pten, P40, Lithium, HT, female,replicate2

description: Library name: P131_HLF_p40_2


title: Pten, P40, Lithium, HT, female,replicate1

description: Library name: P131_HLF_p40_1


title: E12_38

description: Library name: E12_38

value: Optic stalk ventral distal

value: A


title: Pten, P40, Fluoxetine, HT, male,replicate4

description: Library name: P131_HfM_p40_4


title: E12_66

description: Library name: E12_66

value: RPE ventral distal


title: Pten, P40, Fluoxetine, HT, male,replicate3

description: Library name: P131_HfM_p40_3


title: E12_6

description: Library name: E12_6


title: Pten, P40, Fluoxetine, HT, male,replicate2

description: Library name: P131_HfM_p40_2


title: Pten, P40, Fluoxetine, HT, male,replicate1

description: Library name: P131_HfM_p40_1


title: E12_7

description: Library name: E12_7

value: RPE ventral proximal


title: E12_65

description: Library name: E12_65

value: Optic stalk dorsal proximal


title: Pten, P40, Fluoxetine, HT, female,replicate3

description: Library name: P131_HfF_p40_3


title: Pten, P40, Fluoxetine, HT, female,replicate4

description: Library name: P131_HfF_p40_4


title: E12_2

description: Library name: E12_2

value: RPE dorsal proximal


title: Liver, Npc1-/-, replicate 2

description:
Library name: Sample 5
10x Genomics

value: Liver


title: Pten, P40, Fluoxetine, HT, female,replicate1

description: Library name: P131_HfF_p40_1


title: Dyrk, P40, Vehicle, WT, male,replicate3

description: Library name: Dyrk_WvM_p40_3


title: Pten, P40, Fluoxetine, HT, female,replicate2

description: Library name: P131_HfF_p40_2


title: Dyrk, P40, Vehicle, WT, male,replicate1

description: Library name: Dyrk_WvM_p40_1


title: Dyrk, P40, Vehicle, WT, female,replicate2

description: Library name: Dyrk_WvF_p40_2


title: Dyrk, P40, Vehicle, WT, female,replicate1

description: Library name: Dyrk_WvF_p40_1


title: Dyrk, P40, Vehicle, HT, male,replicate3

description: Library name: Dyrk_HvM_p40_3


title: Dyrk, P40, Vehicle, HT, male,replicate2

description: Library name: Dyrk_HvM_p40_2


title: Dyrk, P40, Vehicle, HT, male,replicate1

description: Library name: Dyrk_HvM_p40_1


title: Dyrk, P40, Vehicle, HT, female,replicate2

description: Library name: Dyrk_HvF_p40_2


title: Dyrk, P40, Vehicle, HT, female,replicate1

description: Library name: Dyrk_HvF_p40_1


title: Dyrk, P40, Vehicle, HT, female,replicate3

description: Library name: Dyrk_HvF_p40_3


title: Dyrk, P40, Lithium, HT, male,replicate2

description: Library name: Dyrk_HLM_p40_2


title: Dyrk, P40, Lithium, HT, male,replicate3

description: Library name: Dyrk_HLM_p40_3


title: Dyrk, P40, Lithium, HT, male,replicate1

description: Library name: Dyrk_HLM_p40_1


title: Dyrk, P40, Lithium, HT, female,replicate1

description: Library name: Dyrk_HLF_p40_1


title: Dyrk, P40, Fluoxetine, HT, male,replicate3

description: Library name: Dyrk_HfM_p40_3


title: Dyrk, P40, Fluoxetine, HT, male,replicate2

description: Library name: Dyrk_HfM_p40_2


title: Dyrk, P40, Lithium, HT, female,replicate2

description: Library name: Dyrk_HLF_p40_2


title: Dyrk, P40, Lithium, HT, female,replicate3

description: Library name: Dyrk_HLF_p40_3


title: Dyrk, P40, Fluoxetine, HT, male,replicate1

description: Library name: Dyrk_HfM_p40_1


title: Dyrk, P40, Fluoxetine, HT, female,replicate1

description: Library name: Dyrk_HfF_p40_1


title: Dyrk, P40, Fluoxetine, HT, female,replicate3

description: Library name: Dyrk_HfF_p40_3


title: Dyrk, P40, Fluoxetine, HT, female,replicate2

description: Library name: Dyrk_HfF_p40_2


title: ADNP, P40, Vehicle, WT, male,replicate4

description: Library name: ADNP_WvM_p40_4


title: ADNP, P40, Vehicle, WT, male,replicate2

description: Library name: ADNP_WvM_p40_2


title: ADNP, P40, Vehicle, WT, female,replicate4

description: Library name: ADNP_WvF_p40_4


title: ADNP, P40, Vehicle, WT, female,replicate2

description: Library name: ADNP_WvF_p40_2


title: ADNP, P40, Vehicle, WT, male,replicate1

description: Library name: ADNP_WvM_p40_1


title: ADNP, P40, Vehicle, WT, female,replicate1

description: Library name: ADNP_WvF_p40_1


title: ADNP, P40, Vehicle, WT, female,replicate3

description: Library name: ADNP_WvF_p40_3


title: ADNP, P40, Vehicle, WT, male,replicate3

description: Library name: ADNP_WvM_p40_3


title: ADNP, P40, Vehicle, HT, male,replicate3

description: Library name: ADNP_HvM_p40_3


title: ADNP, P40, Vehicle, HT, male,replicate2

description: Library name: ADNP_HvM_p40_2


title: ADNP, P40, Vehicle, HT, male,replicate1

description: Library name: ADNP_HvM_p40_1


title: ADNP, P40, Vehicle, HT, female,replicate4

description: Library name: ADNP_HvF_p40_4


title: ADNP, P40, Vehicle, HT, female,replicate2

description: Library name: ADNP_HvF_p40_2


title: ADNP, P40, Lithium, HT, male,replicate3

description: Library name: ADNP_HLM_p40_3


title: ADNP, P40, Vehicle, HT, female,replicate1

description: Library name: ADNP_HvF_p40_1


title: ADNP, P40, Lithium, HT, male,replicate4

description: Library name: ADNP_HLM_p40_4


title: ADNP, P40, Lithium, HT, male,replicate2

description: Library name: ADNP_HLM_p40_2


title: ADNP, P40, Lithium, HT, female,replicate3

description: Library name: ADNP_HLF_p40_4


title: ADNP, P40, Lithium, HT, female,replicate2

description: Library name: ADNP_HLF_p40_3


title: ADNP, P40, Lithium, HT, female,replicate1

description: Library name: ADNP_HLF_p40_1


title: ADNP, P40, Fluoxetine, HT, male,replicate4

description: Library name: ADNP_HfM_p40_4


title: ADNP, P40, Fluoxetine, HT, male,replicate1

description: Library name: ADNP_HfM_p40_1


title: ADNP, P40, Fluoxetine, HT, female,replicate4

description: Library name: ADNP_HfF_p40_4


title: ADNP, P40, Lithium, HT, male,replicate1

description: Library name: ADNP_HLM_p40_1


title: ADNP, P40, Fluoxetine, HT, female,replicate2

description: Library name: ADNP_HfF_p40_2


title: ADNP, P40, Fluoxetine, HT, female,replicate1

description: Library name: ADNP_HfF_p40_1


title: TBR1, Hippocampus, WT, male,replicate3

description: Library name: TBR1_HPC_WvM_3

source_name: Hippocampus

growth_protocol: Mice were maintained under standard laboratory conditions and analyzed at postnatal day 25 (P25)

value: Hippocampus

value: Wildtype

value: male


title: TBR1, Hippocampus, WT, male,replicate1

description: Library name: TBR1_HPC_WvM_1


title: TBR1, Hippocampus, WT, female,replicate3

description: Library name: TBR1_HPC_WvF_3

value: female


title: TBR1, Hippocampus, WT, female,replicate4

description: Library name: TBR1_HPC_WvF_4


title: TBR1, Hippocampus, WT, female,replicate2

description: Library name: TBR1_HPC_WvF_2


title: TBR1, Hippocampus, WT, female,replicate1

description: Library name: TBR1_HPC_WvF_1


title: TBR1, Hippocampus, HT, male,replicate4

description: Library name: TBR1_HPC_HvM_4

value: Heterozygous


title: TBR1, Hippocampus, HT, male,replicate3

description: Library name: TBR1_HPC_HvM_3


title: TBR1, Hippocampus, HT, male,replicate2

description: Library name: TBR1_HPC_HvM_2


title: TBR1, Hippocampus, HT, male,replicate1

description: Library name: TBR1_HPC_HvM_1


title: TBR1, Hippocampus, HT, female,replicate4

description: Library name: TBR1_HPC_HvF_4


title: TBR1, Hippocampus, HT, female,replicate3

description: Library name: TBR1_HPC_HvF_3


title: TBR1, Hippocampus, HT, female,replicate2

description: Library name: TBR1_HPC_HvF_2


title: Tbl, Hippocampus, WT, male,replicate3

description: Library name: Tbl_HPC_WvM_3


title: Tbl, Hippocampus, WT, male,replicate2

description: Library name: Tbl_HPC_WvM_2


title: Tbl, Hippocampus, WT, male,replicate1

description: Library name: Tbl_HPC_WvM_1


title: Tbl, Hippocampus, WT, female,replicate4

description: Library name: Tbl_HPC_WvF_4


title: TBR1, Hippocampus, HT, female,replicate1

description: Library name: TBR1_HPC_HvF_1


title: Tbl, Hippocampus, WT, female,replicate1

description: Library name: Tbl_HPC_WvF_1


title: Tbl, Hippocampus, HT, male,replicate4

description: Library name: Tbl_HPC_HvM_4


title: Tbl, Hippocampus, HT, male,replicate3

description: Library name: Tbl_HPC_HvM_3


title: Tbl, Hippocampus, HT, male,replicate2

description: Library name: Tbl_HPC_HvM_2


title: Tbl, Hippocampus, HT, male,replicate1

description: Library name: Tbl_HPC_HvM_1


title: Tbl, Hippocampus, HT, female,replicate4

description: Library name: Tbl_HPC_HvF_4


title: Tbl, Hippocampus, HT, female,replicate2

description: Library name: Tbl_HPC_HvF_2


title: Tbl, Hippocampus, HT, female,replicate1

description: Library name: Tbl_HPC_HvF_1


title: Tanc, Hippocampus, WT, male,replicate4

description: Library name: Tanc_HPC_WvM_4


title: Tanc, Hippocampus, WT, male,replicate3

description: Library name: Tanc_HPC_WvM_3


title: Tanc, Hippocampus, WT, male,replicate2

description: Library name: Tanc_HPC_WvM_2


title: Tanc, Hippocampus, WT, female,replicate3

description: Library name: Tanc_HPC_WvF_3


title: Tanc, Hippocampus, WT, female,replicate4

description: Library name: Tanc_HPC_WvF_4


title: Tanc, Hippocampus, WT, female,replicate2

description: Library name: Tanc_HPC_WvF_2


title: Tanc, Hippocampus, WT, female,replicate1

description: Library name: Tanc_HPC_WvF_1


title: Tanc, Hippocampus, HT, male,replicate4

description: Library name: Tanc_HPC_HvM_4


title: Tanc, Hippocampus, HT, male,replicate3

description: Library name: Tanc_HPC_HvM_3


title: ADNP, P40, Fluoxetine, HT, male,replicate2

description: Library name: ADNP_HfM_p40_2

value: prefrontal cortex


title: Tanc, Hippocampus, HT, male,replicate1

description: Library name: Tanc_HPC_HvM_1


title: Tanc, Hippocampus, HT, female,replicate4

description: Library name: Tanc_HPC_HvF_4


title: Tanc, Hippocampus, HT, female,replicate2

description: Library name: Tanc_HPC_HvF_2


title: Tanc, Hippocampus, HT, female,replicate1

description: Library name: Tanc_HPC_HvF_1


title: T12, Hippocampus, WT, male,replicate3

description: Library name: T12_HPC_WvM_3


title: T12, Hippocampus, WT, male,replicate2

description: Library name: T12_HPC_WvM_2


title: T12, Hippocampus, WT, male,replicate1

description: Library name: T12_HPC_WvM_1


title: T12, Hippocampus, WT, female,replicate4

description: Library name: T12_HPC_WvF_4


title: Tbl, Hippocampus, WT, female,replicate3

description: Library name: Tbl_HPC_WvF_3


title: Tbl, Hippocampus, WT, female,replicate2

description: Library name: Tbl_HPC_WvF_2


title: T12, Hippocampus, WT, female,replicate3

description: Library name: T12_HPC_WvF_3


title: T12, Hippocampus, WT, female,replicate1

description: Library name: T12_HPC_WvF_1


title: T12, Hippocampus, WT, female,replicate2

description: Library name: T12_HPC_WvF_2


title: T12, Hippocampus, HT, male,replicate4

description: Library name: T12_HPC_HvM_4


title: T12, Hippocampus, HT, male,replicate1

description: Library name: T12_HPC_HvM_1


title: T12, Hippocampus, HT, female,replicate3

description: Library name: T12_HPC_HvF_4


title: T12, Hippocampus, HT, female,replicate1

description: Library name: T12_HPC_HvF_2


title: T12, Hippocampus, HT, female,replicate2

description: Library name: T12_HPC_HvF_3


title: SdC, Hippocampus, WT, male,replicate3

description: Library name: SdC_HPC_WvM_3


title: SdC, Hippocampus, WT, male,replicate1

description: Library name: SdC_HPC_WvM_1


title: Tanc, Hippocampus, HT, female,replicate3

description: Library name: Tanc_HPC_HvF_3


title: T12, Hippocampus, WT, male,replicate4

description: Library name: T12_HPC_WvM_4


title: SdC, Hippocampus, WT, female,replicate3

description: Library name: SdC_HPC_WvF_3


title: SdC, Hippocampus, HT, male,replicate4

description: Library name: SdC_HPC_HvM_4


title: SdC, Hippocampus, HT, male,replicate3

description: Library name: SdC_HPC_HvM_3


title: SdC, Hippocampus, HT, male,replicate2

description: Library name: SdC_HPC_HvM_2


title: SdC, Hippocampus, HT, female,replicate4

description: Library name: SdC_HPC_HvF_4


title: SdC, Hippocampus, HT, female,replicate3

description: Library name: SdC_HPC_HvF_3


title: SdC, Hippocampus, HT, female,replicate2

description: Library name: SdC_HPC_HvF_2


title: SdC, Hippocampus, HT, female,replicate1

description: Library name: SdC_HPC_HvF_1


title: T12, Hippocampus, HT, male,replicate3

description: Library name: T12_HPC_HvM_3


title: T12, Hippocampus, HT, male,replicate2

description: Library name: T12_HPC_HvM_2


title: SdC, Hippocampus, WT, male,replicate2

description: Library name: SdC_HPC_WvM_2


title: SdC, Hippocampus, WT, male,replicate4

description: Library name: SdC_HPC_WvM_4


title: Scn, Hippocampus, WT, male,replicate4

description: Library name: Scn_HPC_WvM_4


title: Scn, Hippocampus, WT, male,replicate1

description: Library name: Scn_HPC_WvM_1


title: Scn, Hippocampus, WT, male,replicate3

description: Library name: Scn_HPC_WvM_3


title: SdC, Hippocampus, WT, female,replicate2

description: Library name: SdC_HPC_WvF_2


title: Scn, Hippocampus, WT, male,replicate2

description: Library name: Scn_HPC_WvM_2


title: Scn, Hippocampus, WT, female,replicate3

description: Library name: Scn_HPC_WvF_3


title: SdC, Hippocampus, WT, female,replicate1

description: Library name: SdC_HPC_WvF_1


title: Scn, Hippocampus, WT, female,replicate1

description: Library name: Scn_HPC_WvF_1


title: Scn, Hippocampus, HT, male,replicate4

description: Library name: Scn_HPC_HvM_4


title: Scn, Hippocampus, HT, male,replicate3

description: Library name: Scn_HPC_HvM_3


title: Scn, Hippocampus, WT, female,replicate4

description: Library name: Scn_HPC_WvF_4


title: Scn, Hippocampus, WT, female,replicate2

description: Library name: Scn_HPC_WvF_2


title: Scn, Hippocampus, HT, male,replicate2

description: Library name: Scn_HPC_HvM_2


title: Scn, Hippocampus, HT, male,replicate1

description: Library name: Scn_HPC_HvM_1


title: Scn, Hippocampus, HT, female,replicate4

description: Library name: Scn_HPC_HvF_4


title: Scn, Hippocampus, HT, female,replicate3

description: Library name: Scn_HPC_HvF_3


title: Scn, Hippocampus, HT, female,replicate1

description: Library name: Scn_HPC_HvF_1


title: Scn, Hippocampus, HT, female,replicate2

description: Library name: Scn_HPC_HvF_2


title: SdC, Hippocampus, HT, male,replicate1

description: Library name: SdC_HPC_HvM_1


title: P131, Hippocampus, WT, male,replicate4

description: Library name: P131_HPC_WvM_4


title: P131, Hippocampus, WT, male,replicate3

description: Library name: P131_HPC_WvM_3


title: P131, Hippocampus, WT, male,replicate2

description: Library name: P131_HPC_WvM_2


title: P131, Hippocampus, WT, male,replicate1

description: Library name: P131_HPC_WvM_1


title: P131, Hippocampus, WT, female,replicate4

description: Library name: P131_HPC_WvF_4


title: P131, Hippocampus, WT, female,replicate3

description: Library name: P131_HPC_WvF_3


title: P131, Hippocampus, WT, female,replicate1

description: Library name: P131_HPC_WvF_1


title: P131, Hippocampus, WT, female,replicate2

description: Library name: P131_HPC_WvF_2


title: P131, Hippocampus, HT, male,replicate4

description: Library name: P131_HPC_HvM_4


title: P131, Hippocampus, HT, male,replicate3

description: Library name: P131_HPC_HvM_3


title: P131, Hippocampus, HT, male,replicate2

description: Library name: P131_HPC_HvM_2


title: P131, Hippocampus, HT, female,replicate4

description: Library name: P131_HPC_HvF_4


title: P131, Hippocampus, HT, male,replicate1

description: Library name: P131_HPC_HvM_1


title: P131, Hippocampus, HT, female,replicate2

description: Library name: P131_HPC_HvF_2


title: P131, Hippocampus, HT, female,replicate3

description: Library name: P131_HPC_HvF_3


title: Na, Hippocampus, WT, male,replicate4

description: Library name: Na_HPC_WvM_4


title: P131, Hippocampus, HT, female,replicate1

description: Library name: P131_HPC_HvF_1


title: Na, Hippocampus, WT, male,replicate3

description: Library name: Na_HPC_WvM_3


title: Na, Hippocampus, WT, male,replicate2

description: Library name: Na_HPC_WvM_2


title: Na, Hippocampus, WT, male,replicate1

description: Library name: Na_HPC_WvM_1


title: Na, Hippocampus, WT, female,replicate4

description: Library name: Na_HPC_WvF_4


title: Na, Hippocampus, WT, female,replicate3

description: Library name: Na_HPC_WvF_3


title: Na, Hippocampus, WT, female,replicate1

description: Library name: Na_HPC_WvF_1


title: Na, Hippocampus, WT, female,replicate2

description: Library name: Na_HPC_WvF_2


title: Na, Hippocampus, HT, male,replicate4

description: Library name: Na_HPC_HvM_4


title: Na, Hippocampus, HT, male,replicate3

description: Library name: Na_HPC_HvM_3


title: Dyrk, P40, Vehicle, WT, female,replicate3

description: Library name: Dyrk_WvF_p40_3


title: Na, Hippocampus, HT, male,replicate1

description: Library name: Na_HPC_HvM_1


title: Na, Hippocampus, HT, male,replicate2

description: Library name: Na_HPC_HvM_2


title: Na, Hippocampus, HT, female,replicate3

description: Library name: Na_HPC_HvF_3


title: Na, Hippocampus, HT, female,replicate4

description: Library name: Na_HPC_HvF_4


title: Na, Hippocampus, HT, female,replicate2

description: Library name: Na_HPC_HvF_2


title: Na, Hippocampus, HT, female,replicate1

description: Library name: Na_HPC_HvF_1


title: Mt1, Hippocampus, WT, male,replicate4

description: Library name: Mt1_HPC_WvM_4


title: Mt1, Hippocampus, WT, male,replicate3

description: Library name: Mt1_HPC_WvM_3


title: Mt1, Hippocampus, WT, male,replicate2

description: Library name: Mt1_HPC_WvM_2


title: Mt1, Hippocampus, WT, male,replicate1

description: Library name: Mt1_HPC_WvM_1


title: Mt1, Hippocampus, WT, female,replicate4

description: Library name: Mt1_HPC_WvF_4


title: Mt1, Hippocampus, WT, female,replicate3

description: Library name: Mt1_HPC_WvF_3


title: Mt1, Hippocampus, HT, male,replicate4

description: Library name: Mt1_HPC_HvM_4


title: Mt1, Hippocampus, WT, female,replicate1

description: Library name: Mt1_HPC_WvF_1


title: Mt1, Hippocampus, WT, female,replicate2

description: Library name: Mt1_HPC_WvF_2


title: Mt1, Hippocampus, HT, male,replicate3

description: Library name: Mt1_HPC_HvM_3


title: Mt1, Hippocampus, HT, male,replicate2

description: Library name: Mt1_HPC_HvM_2


title: Mt1, Hippocampus, HT, male,replicate1

description: Library name: Mt1_HPC_HvM_1


title: Mt1, Hippocampus, HT, female,replicate2

description: Library name: Mt1_HPC_HvF_2


title: Mt1, Hippocampus, HT, female,replicate3

description: Library name: Mt1_HPC_HvF_3


title: Mt1, Hippocampus, HT, female,replicate4

description: Library name: Mt1_HPC_HvF_4


title: L68P, Hippocampus, WT, male,replicate4

description: Library name: L68P_HPC_WvM_4


title: L68P, Hippocampus, WT, male,replicate3

description: Library name: L68P_HPC_WvM_3


title: Mt1, Hippocampus, HT, female,replicate1

description: Library name: Mt1_HPC_HvF_1


title: L68P, Hippocampus, WT, male,replicate2

description: Library name: L68P_HPC_WvM_2


title: L68P, Hippocampus, WT, male,replicate1

description: Library name: L68P_HPC_WvM_1


title: L68P, Hippocampus, WT, female,replicate4

description: Library name: L68P_HPC_WvF_4


title: TBR1, Hippocampus, WT, male,replicate2

description: Library name: TBR1_HPC_WvM_2


title: L68P, Hippocampus, HT, male,replicate4

description: Library name: L68P_HPC_HvM_4


title: L68P, Hippocampus, WT, female,replicate2

description: Library name: L68P_HPC_WvF_2


title: L68P, Hippocampus, WT, female,replicate3

description: Library name: L68P_HPC_WvF_3


title: L68P, Hippocampus, WT, female,replicate1

description: Library name: L68P_HPC_WvF_1


title: L68P, Hippocampus, HT, male,replicate2

description: Library name: L68P_HPC_HvM_2


title: L68P, Hippocampus, HT, male,replicate1

description: Library name: L68P_HPC_HvM_1


title: L68P, Hippocampus, HT, female,replicate4

description: Library name: L68P_HPC_HvF_4


title: L68P, Hippocampus, HT, female,replicate3

description: Library name: L68P_HPC_HvF_3


title: L68P, Hippocampus, HT, female,replicate2

description: Library name: L68P_HPC_HvF_2


title: K5B, Hippocampus, WT, male,replicate4

description: Library name: K5B_HPC_WvM_4


title: L68P, Hippocampus, HT, female,replicate1

description: Library name: L68P_HPC_HvF_1


title: K5B, Hippocampus, WT, male,replicate3

description: Library name: K5B_HPC_WvM_3


title: L68P, Hippocampus, HT, male,replicate3

description: Library name: L68P_HPC_HvM_3


title: K5B, Hippocampus, WT, male,replicate1

description: Library name: K5B_HPC_WvM_1


title: K5B, Hippocampus, WT, male,replicate2

description: Library name: K5B_HPC_WvM_2


title: K5B, Hippocampus, WT, female,replicate4

description: Library name: K5B_HPC_WvF_4


title: K5B, Hippocampus, WT, female,replicate3

description: Library name: K5B_HPC_WvF_3


title: K5B, Hippocampus, WT, female,replicate2

description: Library name: K5B_HPC_WvF_2


title: K5B, Hippocampus, WT, female,replicate1

description: Library name: K5B_HPC_WvF_1


title: K5B, Hippocampus, HT, male,replicate4

description: Library name: K5B_HPC_HvM_4


title: K5B, Hippocampus, HT, male,replicate2

description: Library name: K5B_HPC_HvM_2


title: K5B, Hippocampus, HT, male,replicate1

description: Library name: K5B_HPC_HvM_1


title: K5B, Hippocampus, HT, male,replicate3

description: Library name: K5B_HPC_HvM_3


title: K5B, Hippocampus, HT, female,replicate3

description: Library name: K5B_HPC_HvF_3


title: K5B, Hippocampus, HT, female,replicate2

description: Library name: K5B_HPC_HvF_2


title: K5B, Hippocampus, HT, female,replicate1

description: Library name: K5B_HPC_HvF_1


title: K5B, Hippocampus, HT, female,replicate4

description: Library name: K5B_HPC_HvF_4


title: G2b, Hippocampus, WT, male,replicate4

description: Library name: G2b_HPC_WvM_4


title: G2b, Hippocampus, WT, male,replicate3

description: Library name: G2b_HPC_WvM_3


title: G2b, Hippocampus, WT, male,replicate1

description: Library name: G2b_HPC_WvM_1


title: G2b, Hippocampus, WT, male,replicate2

description: Library name: G2b_HPC_WvM_2


title: G2b, Hippocampus, WT, female,replicate4

description: Library name: G2b_HPC_WvF_4


title: G2b, Hippocampus, WT, female,replicate3

description: Library name: G2b_HPC_WvF_3


title: G2b, Hippocampus, WT, female,replicate2

description: Library name: G2b_HPC_WvF_2


title: G2b, Hippocampus, WT, female,replicate1

description: Library name: G2b_HPC_WvF_1


title: G2b, Hippocampus, HT, male,replicate3

description: Library name: G2b_HPC_HvM_3


title: G2b, Hippocampus, HT, male,replicate4

description: Library name: G2b_HPC_HvM_4


title: G2b, Hippocampus, HT, male,replicate2

description: Library name: G2b_HPC_HvM_2


title: G2b, Hippocampus, HT, male,replicate1

description: Library name: G2b_HPC_HvM_1


title: G2b, Hippocampus, HT, female,replicate3

description: Library name: G2b_HPC_HvF_3


title: G2b, Hippocampus, HT, female,replicate2

description: Library name: G2b_HPC_HvF_2


title: Dyrk, Hippocampus, WT, male,replicate4

description: Library name: Dyrk_HPC_WvM_4


title: G2b, Hippocampus, HT, female,replicate1

description: Library name: G2b_HPC_HvF_1


title: Dyrk, Hippocampus, WT, male,replicate3

description: Library name: Dyrk_HPC_WvM_3


title: Dyrk, Hippocampus, WT, male,replicate1

description: Library name: Dyrk_HPC_WvM_1


title: Dyrk, Hippocampus, WT, male,replicate2

description: Library name: Dyrk_HPC_WvM_2


title: Dyrk, Hippocampus, WT, female,replicate4

description: Library name: Dyrk_HPC_WvF_4


title: Dyrk, Hippocampus, WT, female,replicate1

description: Library name: Dyrk_HPC_WvF_1


title: Dyrk, Hippocampus, HT, male,replicate3

description: Library name: Dyrk_HPC_HvM_3


title: Dyrk, Hippocampus, HT, male,replicate4

description: Library name: Dyrk_HPC_HvM_4