title: 7_TREx 20 hour uninduced Bisulfite treated R1

city: Leeds

first: Timothy

last: Mottram

address: Faculty of Biological Sciences

institute: University of Leeds

description:
Merged_del_count.csv
Sample_3-7_table.txt

data_processing:
library strategy: RNA Bisulfite-Seq
BS and NBS reads were subjected to adaptor trimming (Illumina paired-end sequencing adapters) using Cutadapt v1.2.1 (24) with parameter -O = 3, and low-quality reads removal using Sickle v1.2 (25) with parameters (minimum window quality score > 20 and read length > 15 bp). Quality filtered and adapter trimmed reads were aligned to the NC_009333.1 (NCBI) assembly of the Human herpesvirus 8 strain GK18 genome using BWA-Meth (26) with default parameters. RNA modifications (Pseudouridine) were identified on the alignment files using RBSSeqTools (27) with the following parameters (Bisulfite reads (BS) : ≥ 5 deletions, ≥ 0.02 fraction deletion and ≥ 10 coverage). We merged adjacent positions to form deletion groups, which were pruned to remove positions with less than half the maximum observed fraction deletion in the group.
Supplementary files format and content: .txt table file scontaining counts and statistics for identified deletion groups within NBS/BS sample comparisons
Supplementary files format and content: merged_del_count.csv, nucleotide and position counts combined from all samples with corresponding locations

source_name: TREx BCBL1-Rta

extract_protocol:
Total RNA was isolated using TRIzol Reagent (Invitrogen) and samples were depleted of rRNA using the NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) according to the manufacturer’s instructions. Samples were then split, half of which were bisulfite treated using an EZ RNA Methylation Kit (Zymo Research)
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to generate paired-end libraries according to manufacturers instructions.

treatment_protocol: TREx BCBL1-Rta cells were seeded at 5x105 cells per ml in T25 flasks. Cells were reactivated with 2ug/ml doxycycline hyclate and harvested at 8 hours and 20 hours post reactivation.

value: TREx BCBL1-Rta

value: B cell

value: Bisulfite treated


title: LCCC1212_553

status: Public on Nov 05 2025

type: SRA

city: Chapel Hill

first: William

last: Kim

state: NC

address: 450 West Dr

department: Lineberger Comprehensive Cancer Center

country: USA

institute: UNC Chapel Hill

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v6.1.1
Assembly: hg38
Supplementary files format and content: H5 format files of cell ranger output for each scRNAseq samples

molecule: total RNA

organism: Homo sapiens

source_name: bladder tumor

extract_protocol:
Single cell suspensions of tumors were generated using the Miltenyi Biotec Tumor Dissociation Kit and the gentleMACS Dissociator. Red blood cells were lysed using Miltenyi Biotec Red Blood Cell Lysis Solution and dead cells were removed using the Miltenyi Biotec Dead Cell Removal Kit. Single cell suspensions were subsequently loaded onto the 10X Genomics Chromium Controller to generate single-cell gel beads in emulsions (GEMs)
scRNAseq libraries were prepared using Chromium Single Cell 3' Reagent Kits (v3.1 Chemistry) according to the manufacter's instructions

tag: tissue

value: bladder tumor


title: 8_TREx 20 hour induced Bisulfite treated R1

middle: James

country: United Kingdom

description:
Merged_del_count.csv
Sample_4-8_table.txt

library_source: transcriptomic

tag: cell line

tag: cell type

tag: treatment

value: Doxycyline Induced - Bisulfite treated


title: Marchantia polymorpha, 5mM glutamine treatment for 48h, Rep 2

city: Singapore

first: Grace

middle: Zi Hao

last: Tan

address: 1 Research Link National University of Singapore, 03-48

country: Singapore

institute: Temasek Life Sciences Laboratory

data_processing:
The raw sequence reads was mapped using STAR (v.2.7) with the reference genome
The raw readcounts were normalised using DeSeq2 package from R
The differentially expressed genes were used for downstream analysis
Assembly: M.Polymorpha v5.1, Athaliana TAIR
Supplementary files format and content: comma-separated values file includes raw read counts for each sample
Supplementary files format and content: comma-separated values file includes log-transformed read counts for each sample

organism: Marchantia polymorpha

source_name: Gemmalings

growth_protocol: Arabidopsis seedlings were germinated on full-strength solid MS media (pH5.8, 1% sucrose) for eight days at 22°C, under 24h light. Marchantia polymorpha gemmalings were raised in liquid half-strength B5 media (pH5.5, no sucrose) for ten days at 80rpm, at 22°C, under 24h light.

extract_protocol:
RNA was extracted using the QIAGEN Plant RNeasy kit
Directional mRNA library preparation (poly A enrichment)

treatment_protocol: Arabidopsis seedlings were transferred to liquid MS media (pH 5.7, 1% sucrose) containing the chemical of interest and grown for 48h at 80rpm, at 22°C, under 24h light. Marchantia gemmalings were washed, then transferred to liquid half-strength B5 media (pH5.5, no sucrose) containing the chemical of interest and grown for 48h at 80rpm, at 22°C, under 24h light

value: Gemmalings

tag: genotype

value: 5mM glutamine treatment for 48h


title: Low glucose conditions Sample 1

city: Dortmund

first: Jeffrey

middle: Lesslie

last: Schloßhauer

address: Otto-Hahn-Straße 11

department: Chemical Genomics Centre

country: Germany

institute: Max Planck Institute of Molecular Physiology

description: low replicates were joined (processed file)

data_processing:
The zarp pipeline was followed to process fastq files; Adapters were trimmed through Cutadapt
The reads were mapped to the human genome (hg38, Genome Reference Consortium GRCh38) using STAR
Assembly: hg38, Genome Reference Consortium GRCh38
Supplementary files format and content: Tab Separated Values file includes joined peaks of for each condition and an annotation

source_name: Molm13 cells

extract_protocol:
Total RNA was isolated from 3-5 × 106 cultured Molm13 cells using TRIzol reagent (Thermo Fisher Scientific)
For library preparation, we removed rRNA using the FastSelect-rRNA HMR Kit (QIAseq) following strand-specific cDNA library preparation with the Stranded Total RNA Lib Kit (QIAseq)

value: Molm13 cells

value: AML

value: Low glucose conditions


title: Non-cachectic tumor mouse, Heart, Mouse #86

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

institute: Helmholtz Zentrum München

description: Library name: NC_H86_1

data_processing:
This analysis was performed at Novogene (Cambridge, UK). Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to count the read numbers mapped to each gene. FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was then calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm39
Supplementary files format and content: csv files include gene counts values for each sample

organism: Mus musculus

source_name: Heart

growth_protocol: 10 week-old male Balb/c mice from Charles River. All mice were maintained under specific pathogen-free conditions on a 12h light–dark cycle at 22 °C with ad libitum access to regular rodent chow diet (Kliba Nafag #3437, Promivi Kliba AG, Kaiseraugst, Switzerland) and water.

extract_protocol:
Pieces of mouse frozen tissues were homogenized in TRIzol (Life Technologies #15596018). RNA was then isolated by adding chloroform. After centrifugation at 12,000 x g for 20min, the upper phase containing RNA was collected and a volume of 0.6 absolute ethanol was added (e.g., 240 µL ethanol for 400µL of collected upper phase). RNA samples were then loaded onto an Econospin column (Econospin # 1920-250), washed three times with RPE buffer (Qiagen #1018013), dried and eluted by adding RNA/DNAse-free water. RNA samples were then sent to Novogene (Cambridge, UK) for RNA-seq.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount. Further detailed methods can be found in the original paper of the study.

treatment_protocol: Animals were divided into 4 groups: mice injected with PBS, healthy controls, no tumor (PBS); mice injected with NC26 cancer cells, non-cachectic tumor controls (NC); mice injected with C26 cancer cells and killed before onset of weight loss, pre-cachectic tumor mice (Pre); mice injected with C26 cancer cells and killed once they reached a body weight loss of 5-10 %, cachectic tumor mice (Cax).

value: Heart

value: Balb/c mice, Wild type

value: NC26 tumors, non-cachectic


title: Non-cachectic tumor mouse, Heart, Mouse #87

description: Library name: NC_H87_1


title: Low glucose conditions Sample 2


title: Galactose conditions Sample 2

description: Replicates for each conditions were merged and annotated (processed file)

data_processing:
The zarp pipeline was followed to process fastq files; Adapters were trimmed through Cutadapt
The reads were mapped to the human genome (hg38, Genome Reference Consortium GRCh38) using STAR
Assembly: hg38, Genome Reference Consortium GRCh38
Supplementary files format and content: Tab Separated Values file includes merged processed data of for each condition and an annotation

value: Galactose conditions


title: Galactose conditions Sample 2

description: Gal replicates were joined (processed file)


title: Marchantia polymorpha, untreated control, Rep 3


title: 6_TREx 8 hour induced Bisulfite treated R1

description:
Merged_del_count.csv
Sample_2-6_table.txt


title: Non-cachectic tumor mouse, Inguinal adipose tissue, Mouse #83

description: Library name: NC_I83_1

source_name: Inguinal adipose tissue

value: Inguinal adipose tissue


title: 3_TREx 20 hour uninduced Non-bisulfite treated R1

value: Non-bisulfite treated


title: 5_TREx 8 hour uninduced Bisulfite treated R1

description:
Merged_del_count.csv
Sample_1-5_table.txt


title: 4_TREx 20 hour induced Non-bisulfite treated R1

value: Doxycyline Induced


title: Creinhardtii strain CC-4533 basal transcriptome rep 4

city: Berkeley

first: Sean

middle: D.

last: Gallaher

state: California

address: 176 Stanley Hall, room 408

department: California Institute for Quantitative Biosciences

institute: UC Berkeley

description: Library name: Cr059_I_4533_basal_2_B4

data_processing:
mapping to the C. reinhardtii reference assembly with STAR with --alignIntronMax 3000 --outSAMtype BAM SortedByCoordinate --outMultimapperOrder Random --outSAMmultNmax 1 --limitBAMsortRAM 2000000000 --outSAMunmapped Within
reads assigned to genes with featureCounts() function in R using annot.ext=annotations, isGTFAnnotationFile="SAF", useMetaFeatures=TRUE, allowMultiOverlap=TRUE, fracOverlap=0.5, minOverlap=30, largestOverlap=TRUE, countMultiMappingReads=TRUE, fraction=TRUE, minMQS=0, primaryOnly=TRUE, ignoreDup=FALSE, strandSpecific=2, genome=genome, isLongRead=FALSE, isPairedEnd=FALSE, countReadPairs=TRUE, checkFragLength=TRUE, minFragLength=50, maxFragLength=3000, countChimericFragments=FALSE, autosort=TRUE
reads per transcript normalized with DESeq2 using dds <- DESeqDataSetFromMatrix(), dds <- DESeq(dds)
transcript lengths added with mcols(dds)$basepairs <- transcriptLengths
transcript abundances calculated as Fragments Per Kb per Million mapped reads (FPKMs) with DESeq2 using fpkm(dds, robust = TRUE)
Assembly: Chlamydomonas reinhardtii reference assembly v6 from phytozome.net
Supplementary files format and content: normalized transcript abundance estimates as Fragments per KB per Million mapped reads (FPKMs)

molecule: polyA RNA

organism: Chlamydomonas reinhardtii

source_name: strain

growth_protocol: Growth to mid-logorithmic phase (~2 x 10^6 cells/mL) in Tris-Acetate-Phosphate (TAP) media supplemented with Kropat's trace nutrients, on a shaking platform (180 rpm), under continuous light at 50-70 µmol m^-2 s^-1.

extract_protocol:
Extraction by QIAgen TriZol reagent, followed by QIAgen RNeasy kit  wiht DNase treatment.
Standard Illumina library preparation kit.

treatment_protocol: All cultures grown under identical conditions to mid-log phase without any specific "treatment". The only difference between samples is which WT strain was examined.

value: strain

tag: mating type

value: mt-

value: mid-log, photohetertrophic growth


title: Marchantia polymorpha, untreated control, Rep 1


title: Marchantia polymorpha, 5mM glutamine treatment for 48h, Rep 1


title: Non-cachectic tumor mouse, Heart, Mouse #88

description: Library name: NC_H88_1


title: 2_TREx 8 hour induced Non-bisulfite treated R1

value: TREx BCBL1-Rta

value: B cell

value: Doxycyline Induced - Non-bisulfite treated


title: Non-cachectic tumor mouse, Heart, Mouse #83

description: Library name: NC_H83_1


title: 1_TREx 8 hour uninduced Non-bisulfite treated R1


title: Creinhardtii strain CC-4533 basal transcriptome rep 2

description: Library name: Cr059_I_4533_basal_2_B2


title: GLIS3A 24hr timepoint replicate 1

city: Cambridge

first: Alok

last: Jaiswal

state: MASSACHUSETTS

address: 415 Main Street

institute: The Broad Institute of MIT and Harvard

data_processing:
Demultiplex and basecall to fastq with bcl2fastq
FASTQ reads were aligned to the Grch38 human transcriptome. Processed using FastQC, Trim Galore! and SortMeRNA to remove low-quality reads, adapters and ribosomal RNA
Alignment with STAR
Counting of transcripts with Salmon
Differential expression with DESeq2
Assembly: GRCh38
Supplementary files format and content: salmon.merged.gene_counts.tsv: raw gene counts of genes quantified by Salmon
Supplementary files format and content: salmon.merged.gene_tpm.tsv: TPM values of genes quantified by Salmon

source_name: Skin

growth_protocol: Fibroblasts plated in DMEM supplemented with 10% FBS.

extract_protocol:
RNA extraction with Trizol reagent
RNA libraries for RNA-seq were prepared using Nextera XT DNA library Preparation Kit (Illumina) following the manufacturer's protocols.
Libraries were sequenced on the Illumina NextSeq 500 upto 100 cycles per manufacturer’s instructions.

treatment_protocol: Fibroblasts were stimulated with 10ng/ml recombinant human TGFb+IL1b.

value: Skin

value: ATCC, CRL-4001, IL-11mNG reporter, Cas9+, KO for GLIS3

value: Fibroblast

value: GLIS3 activation

tag: condition

value: GLIS3 A


title: Non-cachectic tumor mouse, Inguinal adipose tissue, Mouse #86

description: Library name: NC_I86_1

value: Balb/c mice, Wild type


title: Marchantia polymorpha, untreated control, Rep 2

value: Gemmalings


title: Non-cachectic tumor mouse, Inguinal adipose tissue, Mouse #88

description: Library name: NC_I88_1

value: NC26 tumors, non-cachectic


title: Creinhardtii strain CC-4533 basal transcriptome rep 1

description: Library name: Cr059_I_4533_basal_2_B1


title: Non-cachectic tumor mouse, Liver, Mouse #83

description: Library name: NC_L83_1

source_name: Liver

value: Liver


title: Creinhardtii strain CC-125 basal transcriptome rep 4

description: Library name: Cr059_F_0125_basal_2_B4

value: mt+


title: GLIS3A 12hr timepoint replicate 3


title: rcMSC 2

city: Hiroshima

first: Kiyoharu

last: Shimizu

state: Hiroshima

address: 1-2-3, Kasumi, Minami-ku

department: Neurosurgery

country: Japan

institute: Graduate School of Biomedical and Health Sciences Hiroshima University

data_processing:
FPKM values were calculated from mapped reads by normalizing to total counts and transcript.
DEGs were detected using the DESeq2 package (version 1.20.0).
The list of differentially expressed genes detected by DESeq2 (basemean > 5 and fold-change < 0.25, or basemean > 5 and fold-change > 4) were used for GO enrichment analysis by clusterProfiler package.
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: cranial bone marrow

extract_protocol:
Total RNA was extracted with NucleoSpinm® RNA (MACHEREY-NAGEL GmbH & Co. KG, Duren, Germany) in accordance with the manufacture’s protocol.
RNA-seq libraries were sequenced using paired end reads (150nt of read1 and read2) on a DNBSEQ-G400RS instrument (MGI Tech). Obtained raw reads were trimmed and quality-filtered using the Trim Galore! (version 0.6.7), Trimmotaic (version 0.39) software. Trimmed reads were then mapped to the Rat mRatBN7.2 genome using STAR (version 2.7.9a). Reads in annotated genes were counted using featureCounts (version 2.0.1).

value: cranial bone marrow

value: mesenchymal stem cells

value: WT


title: Galactose conditions Sample 1

value: Molm13 cells

value: AML

value: Galactose conditions


title: GLIS3A 12hr timepoint replicate 2


title: GLIS3A 24hr timepoint replicate 3


title: Non-cachectic tumor mouse, Liver, Mouse #86

description: Library name: NC_L86_1


title: Creinhardtii strain CC-125 basal transcriptome rep 3

description: Library name: Cr059_F_0125_basal_2_B3

value: strain

value: mid-log, photohetertrophic growth


title: Creinhardtii strain CC-4533 basal transcriptome rep 3

description: Library name: Cr059_I_4533_basal_2_B3

value: mt-


title: GLIS3A 6hr timepoint replicate 3

value: Skin

value: ATCC, CRL-4001, IL-11mNG reporter, Cas9+, KO for GLIS3

value: Fibroblast


title: Creinhardtii strain CC-125 basal transcriptome rep 2

description: Library name: Cr059_F_0125_basal_2_B2


title: GLIS3A 12hr timepoint replicate 1

value: GLIS3 activation

value: GLIS3 A


title: Non-cachectic tumor mouse, Liver, Mouse #87

description: Library name: NC_L87_1

value: Balb/c mice, Wild type

value: NC26 tumors, non-cachectic


title: GLIS3A 6hr timepoint replicate 2


title: GLIS3A 24hr timepoint replicate 2


title: rbMSC 2

source_name: ferms and tibias bone marrow

value: ferms and tibias bone marrow


title: rcMSC 3

value: cranial bone marrow


title: rbMSC 3

value: mesenchymal stem cells


title: Healthy control mouse (PBS-injected), Epididymal adipose tissue, Mouse #59

description: Library name: PBS_E59_1

source_name: Epididymal adipose tissue

value: Epididymal adipose tissue

value: No tumor, PBS-injected


title: rbMSC 1

value: WT


title: GLIS3A 6hr timepoint replicate 1


title: Non-cachectic tumor mouse, Liver, Mouse #88

description: Library name: NC_L88_1

value: Liver


title: Non-cachectic tumor mouse, Inguinal adipose tissue, Mouse #87

description: Library name: NC_I87_1

value: Inguinal adipose tissue


title: Creinhardtii strain CC-125 basal transcriptome rep 1

description: Library name: Cr059_F_0125_basal_2_B1

value: strain

value: mt+

value: mid-log, photohetertrophic growth


title: Creinhardtii strain CC-4532 basal transcriptome rep 4

description: Library name: Cr059_E_4532_basal_1_B4

value: mt-


title: GLIS3A 0hr timepoint replicate 3

value: Skin

value: ATCC, CRL-4001, IL-11mNG reporter, Cas9+, KO for GLIS3

value: Fibroblast


title: rcMSC 1


title: Yeast cultures MetC

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

description:
Library name: sample39
Shon_10C

data_processing:
FASTQ files were analyzed using Partek Flow build version 10.0.21.0411. Reads were trimmed to remove low-quality bases from the 3’ end (Phred score<20). The RNA-seq reads were mapped to the S. cerevisiae reference genome (GCF_000146045.2) obtained from the NCBI Genome Assembly database. Alignment was performed using STAR (v2.7.8a). Reads were quantified using Partek E/M
Assembly: GCF_000146045.2
Supplementary files format and content: Levkovich_RNA-seq_Norm.xls

organism: Saccharomyces cerevisiae

source_name: Yeast cultures

extract_protocol:
RNA was extracted using the MasterPure Yeast RNA purification kit, followed by DNase I treatment for 30 min.
cDNA libraries were generated from 300 ng of total RNA using the NEBNext Ultra II Directional RNA Library Prep Kit, with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7760)

value: Yeast cultures

value: Met

tag: batch

value: C


title: Yeast cultures MetD

description:
Library name: sample40
Shon_10D

value: D


title: Healthy control mouse (PBS-injected), Epididymal adipose tissue, Mouse #65

description: Library name: PBS_E65_1

value: Balb/c mice, Wild type


title: Healthy control mouse (PBS-injected), Epididymal adipose tissue, Mouse #68

description: Library name: PBS_E68_1

value: Epididymal adipose tissue


title: Creinhardtii strain CC-4532 basal transcriptome rep 2

description: Library name: Cr059_E_4532_basal_1_B2


title: Yeast cultures MetB

description:
Library name: sample38
Shon_10B

value: B


title: GLIS3A 0hr timepoint replicate 1

value: GLIS3 activation

value: GLIS3 A


title: Yeast cultures MetA

description:
Library name: sample37
Shon_10A

value: A


title: CtrlA 24hr timepoint replicate 3

value: WT

value: Control for WT


title: Healthy control mouse (PBS-injected), GC muscle, Mouse #59

description: Library name: PBS_GC59_1

source_name: GC muscle

value: GC muscle

value: No tumor, PBS-injected


title: GLIS3A 0hr timepoint replicate 2

value: Skin


title: Healthy control mouse (PBS-injected), GC muscle, Mouse #65

description: Library name: PBS_GC65_1


title: Creinhardtii strain CC-1691 basal transcriptome rep 2

description: Library name: Cr059_D_1691_basal_1_B2

value: strain

value: mt-

value: mid-log, photohetertrophic growth


title: Healthy control mouse (PBS-injected), Epididymal adipose tissue, Mouse #74

description: Library name: PBS_E74_1


title: Creinhardtii strain CC-1691 basal transcriptome rep 3

description: Library name: Cr059_D_1691_basal_1_B3


title: Creinhardtii strain CC-4532 basal transcriptome rep 1

description: Library name: Cr059_E_4532_basal_1_B1


title: CtrlA 24hr timepoint replicate 2

value: ATCC, CRL-4001, IL-11mNG reporter, Cas9+, KO for GLIS3

value: Fibroblast


title: Yeast cultures ValD

description:
Library name: sample36
Shon_9D

value: Yeast cultures

value: Val

value: D


title: Yeast cultures ValB

description:
Library name: sample34
Shon_9B

value: B


title: Healthy control mouse (PBS-injected), GC muscle, Mouse #68

description: Library name: PBS_GC68_1

value: Balb/c mice, Wild type


title: Yeast cultures ValC

description:
Library name: sample35
Shon_9C

value: C


title: CtrlA 24hr timepoint replicate 1


title: Creinhardtii strain CC-1691 basal transcriptome rep 4

description: Library name: Cr059_D_1691_basal_1_B4


title: Creinhardtii strain CC-1690 basal transcriptome rep 3

description: Library name: Cr059_C_1690_basal_1_B3

value: mt+


title: Healthy control mouse (PBS-injected), GC muscle, Mouse #74

description: Library name: PBS_GC74_1


title: Creinhardtii strain CC-1690 basal transcriptome rep 4

description: Library name: Cr059_C_1690_basal_1_B4


title: CtrlA 12hr timepoint replicate 2

value: WT


title: CtrlA 12hr timepoint replicate 3

value: Control for WT


title: Healthy control mouse (PBS-injected), Heart, Mouse #59

description: Library name: PBS_H59_1

value: Heart


title: Yeast cultures ValA

description:
Library name: sample33
Shon_9A

value: A


title: Yeast cultures TrpC

description:
Library name: sample31
Shon_8C

value: Trp


title: Healthy control mouse (PBS-injected), Heart, Mouse #68

description: Library name: PBS_H68_1

value: No tumor, PBS-injected


title: CtrlA 6hr timepoint replicate 3

value: Skin


title: Creinhardtii strain CC-4532 basal transcriptome rep 3

description: Library name: Cr059_E_4532_basal_1_B3

value: strain

value: mt-

value: mid-log, photohetertrophic growth


title: Yeast cultures TrpD

description:
Library name: sample32
Shon_8D

value: Yeast cultures


title: Yeast cultures TrpB

description:
Library name: sample30
Shon_8B


title: CtrlA 12hr timepoint replicate 1

value: ATCC, CRL-4001, IL-11mNG reporter, Cas9+, KO for GLIS3

value: Fibroblast


title: Healthy control mouse (PBS-injected), Heart, Mouse #74

description: Library name: PBS_H74_1


title: Creinhardtii strain CC-1690 basal transcriptome rep 2

description: Library name: Cr059_C_1690_basal_1_B2


title: CtrlA 6hr timepoint replicate 2


title: Creinhardtii strain CC-1690 basal transcriptome rep 1

description: Library name: Cr059_C_1690_basal_1_B1


title: Yeast cultures TrpA

description:
Library name: sample29
Shon_8A


title: Creinhardtii strain CC-1691 basal transcriptome rep 1

description: Library name: Cr059_D_1691_basal_1_B1


title: Creinhardtii strain CC-1009 basal transcriptome rep 4

description: Library name: Cr059_B_1009_basal_1_B4


title: Healthy control mouse (PBS-injected), Inguinal adipose tissue, Mouse #59

description: Library name: PBS_I59_1

value: Inguinal adipose tissue


title: CtrlA 6hr timepoint replicate 1


title: CtrlA 0hr timepoint replicate 3


title: Yeast cultures GlyC

description:
Library name: sample27
Shon_7C

value: Gly


title: Healthy control mouse (PBS-injected), Inguinal adipose tissue, Mouse #65

description: Library name: PBS_I65_1

value: Balb/c mice, Wild type


title: Creinhardtii strain CC-1009 basal transcriptome rep 3

description: Library name: Cr059_B_1009_basal_1_B3


title: Yeast cultures GlyD

description:
Library name: sample28
Shon_7D

value: D


title: Creinhardtii strain CC-1009 basal transcriptome rep 2

description: Library name: Cr059_B_1009_basal_1_B2


title: Healthy control mouse (PBS-injected), Heart, Mouse #65

description: Library name: PBS_H65_1


title: Healthy control mouse (PBS-injected), Inguinal adipose tissue, Mouse #68

description: Library name: PBS_I68_1


title: Creinhardtii strain CC-1009 basal transcriptome rep 1

description: Library name: Cr059_B_1009_basal_1_B1


title: Yeast cultures GlyB

description:
Library name: sample26
Shon_7B

value: B


title: CtrlA 0hr timepoint replicate 2

value: WT

value: Control for WT


title: CtrlA 0hr timepoint replicate 1


title: Healthy control mouse (PBS-injected), Inguinal adipose tissue, Mouse #74

description: Library name: PBS_I74_1


title: Yeast cultures GlyA

description:
Library name: sample25
Shon_7A

value: A


title: Creinhardtii strain CC-124 basal transcriptome rep 4

description: Library name: Cr059_A_0124_basal_1_B4


title: GLIS3KO 24hr timepoint replicate 3

value: GLIS3 knock out

value: GLIS3 KO


title: Yeast cultures CysD

description:
Library name: sample24
Shon_6D

value: Cys


title: Healthy control mouse (PBS-injected), Liver, Mouse #59

description: Library name: PBS_L59_1

value: Liver

value: No tumor, PBS-injected


title: Creinhardtii strain CC-124 basal transcriptome rep 3

description: Library name: Cr059_A_0124_basal_1_B3

value: strain

value: mt-

value: mid-log, photohetertrophic growth


title: Healthy control mouse (PBS-injected), Liver, Mouse #65

description: Library name: PBS_L65_1


title: GLIS3KO 24hr timepoint replicate 2

value: Skin

value: ATCC, CRL-4001, IL-11mNG reporter, Cas9+, KO for GLIS3

value: Fibroblast


title: Yeast cultures CysC

description:
Library name: sample23
Shon_6C

value: Yeast cultures

value: C


title: Creinhardtii strain CC-124 basal transcriptome rep 2

description: Library name: Cr059_A_0124_basal_1_B2


title: Healthy control mouse (PBS-injected), Liver, Mouse #68

description: Library name: PBS_L68_1

value: Balb/c mice, Wild type


title: GLIS3KO 24hr timepoint replicate 1


title: Healthy control mouse (PBS-injected), Liver, Mouse #74

description: Library name: PBS_L74_1


title: Creinhardtii strain CC-124 basal transcriptome rep 1

description: Library name: Cr059_A_0124_basal_1_B1


title: GLIS3KO 12hr timepoint replicate 3


title: Yeast cultures CysB

description:
Library name: sample22
Shon_6B

value: B


title: GLIS3KO 12hr timepoint replicate 2


title: Yeast cultures IleD

description:
Library name: sample20
Shon_5D

value: Ile

value: D


title: Pre-cachectic tumor mouse, Epididymal adipose tissue, Mouse #60

description: Library name: Pre_E60_1

value: Epididymal adipose tissue

value: C26 tumors, pre-cachectic


title: GLIS3KO 12hr timepoint replicate 1

value: GLIS3 knock out

value: GLIS3 KO


title: Pre-cachectic tumor mouse, Epididymal adipose tissue, Mouse #69

description: Library name: Pre_E69_1


title: GLIS3KO 6hr timepoint replicate 3


title: Yeast cultures IleB

description:
Library name: sample18
Shon_5B


title: GLIS3KO 6hr timepoint replicate 2


title: Yeast cultures IleC

description:
Library name: sample19
Shon_5C


title: Pre-cachectic tumor mouse, Epididymal adipose tissue, Mouse #73

description: Library name: Pre_E73_1


title: Yeast cultures IleA

description:
Library name: sample17
Shon_5A

value: A


title: Pre-cachectic tumor mouse, GC muscle, Mouse #60

description: Library name: Pre_GC60_1

value: GC muscle


title: Pre-cachectic tumor mouse, Epididymal adipose tissue, Mouse #76

description: Library name: Pre_E76_1


title: GLIS3KO 6hr timepoint replicate 1


title: Yeast cultures ThrD

description:
Library name: sample16
Shon_4D

value: Thr


title: Pre-cachectic tumor mouse, GC muscle, Mouse #69

description: Library name: Pre_GC69_1


title: Yeast cultures ThrC

description:
Library name: sample15
Shon_4C


title: Pre-cachectic tumor mouse, GC muscle, Mouse #73

description: Library name: Pre_GC73_1


title: Yeast cultures CysA

description:
Library name: sample21
Shon_6A

value: Cys


title: GLIS3KO 0hr timepoint replicate 3

value: Skin


title: Yeast cultures ThrB

description:
Library name: sample14
Shon_4B


title: GLIS3KO 0hr timepoint replicate 2

value: ATCC, CRL-4001, IL-11mNG reporter, Cas9+, KO for GLIS3


title: ATF6 269_ATF6.tg.12M

type: genomic

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

hyb_protocol: Hybridisation and washing of slides was carried out according to Agilent's protocol for array CGH.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing:
Foreground and background intensities were imported into R followed by normalisation and correction for spatial artefacts using the MANOR Bioconductor package. Normalised log2-ratios were corrected for GC waving patterns using the CGHwave package (Mark van de Wiel) prior circular binary segmentation and copy number calling using functions of the Bioconductor CGHcall package.
mm9 genomeliftover mm10

molecule: genomic DNA

source_name: mouse liver tissue

label_protocol: 125 ng of DNA were labelled with Cy3 and Cy5, respectively using the CYTAG kit (Enzo).

growth_protocol: Mice were grown until the timepoint of analysis. Tissue was taken out and subjected to dissociation prior to genomic DNA extraction.

extract_protocol: Genomic DNA was extracted from cell line pellets using the Qiagen Allprep kit.

value: ATF6 transgenic

tag: time point [months]

source_name: pooled normals reference DNA

tag: tag

value: Reference DNA


title: ATF6 270_ATF6.tg.12M


title: ATF6 273_ATF6.tg.12M


title: Yeast cultures ThrA

description:
Library name: sample13
Shon_4A

value: Yeast cultures


title: Pre-cachectic tumor mouse, GC muscle, Mouse #76

description: Library name: Pre_GC76_1

value: Balb/c mice, Wild type


title: ATF6 268_ATF6.tg.12M


title: ATF6 263_ATF6.tg.12M


title: Pre-cachectic tumor mouse, Heart, Mouse #60

description: Library name: Pre_H60_1

value: Heart


title: ATF6 265_ATF6.tg.12M


title: CtrlKO 24hr timepoint replicate 3

value: Fibroblast

value: WT

value: Control for KO


title: ATF6 010_ATF6.tg.3M


title: Yeast cultures PheD

description:
Library name: sample12
Shon_3D

value: Phe

value: D


title: Pre-cachectic tumor mouse, Heart, Mouse #69

description: Library name: Pre_H69_1

value: C26 tumors, pre-cachectic


title: CtrlKO 24hr timepoint replicate 2


title: ATF6 011_ATF6.tg.3M


title: Yeast cultures PheB

description:
Library name: sample10
Shon_3B

value: B


title: Yeast cultures PheC

description:
Library name: sample11
Shon_3C

value: C


title: Pre-cachectic tumor mouse, Heart, Mouse #73

description: Library name: Pre_H73_1


title: CtrlKO 24hr timepoint replicate 1


title: Yeast cultures PheA

description:
Library name: sample9
Shon_3A

value: A


title: CtrlKO 12hr timepoint replicate 3


title: Pre-cachectic tumor mouse, Inguinal adipose tissue, Mouse #60

description: Library name: Pre_I60_1

value: Inguinal adipose tissue


title: CtrlKO 12hr timepoint replicate 2

value: Skin


title: Yeast cultures AlaD

description:
Library name: sample8
Shon_2D

value: Ala


title: ATF6 005_ATF6.tg.3M

value: ATF6 transgenic


title: GLIS3KO 0hr timepoint replicate 1

value: ATCC, CRL-4001, IL-11mNG reporter, Cas9+, KO for GLIS3

value: GLIS3 knock out

value: GLIS3 KO


title: Pre-cachectic tumor mouse, Inguinal adipose tissue, Mouse #69

description: Library name: Pre_I69_1

value: Balb/c mice, Wild type


title: CtrlKO 12hr timepoint replicate 1

value: Fibroblast


title: ATF6 004_ATF6.tg.3M

value: Reference DNA


title: Pre-cachectic tumor mouse, Inguinal adipose tissue, Mouse #73

description: Library name: Pre_I73_1


title: CtrlKO 6hr timepoint replicate 3

value: WT

value: Control for KO


title: Yeast cultures AlaB

description:
Library name: sample6
Shon_2B

value: Yeast cultures


title: Yeast cultures AlaC

description:
Library name: sample7
Shon_2C


title: Yeast cultures AlaA

description:
Library name: sample5
Shon_2A


title: CtrlKO 6hr timepoint replicate 2


title: Yeast cultures CtrlD

description:
Library name: sample4
Shon_1D

value: Ctrl

value: D


title: ChronicDSS-3

description:
Library name: 081624_ChronicDSS_3
10x genomics

data_processing:
Demultiplex and basecall to fastq with cellranger mkfastq pipeline made available by CellRanger v7.1.0 software (10x Genomics)
FASTQ reads were aligned to the mm10 human transcriptome, to extract cell barcodes and UMI barcodes using the cellranger count function. A digital gene expression (DGE) matrix for each sample was processed further
Cells that satisfied any one of the following criteria were removed: 1) Cells with < 200 detected genes; 2) Cells having outlier number of unique molecular identifiers (UMIs) >10000; 3) percentage of mitochondrial gene expression > 10%
Assembly: mm10
Supplementary files format and content: mm_pdgfra.h5ad: contains gene expression raw UMI and normalized expression values. Can be read using scanpy

source_name: Large intestine

extract_protocol:
20,000 live single cells resuspended in PBS with 0.4% BSA were submitted for 10X Genomics single cell sequencing Chromium Next GEM Chip G (v3.1).
Libraries were sequenced across 1.2 lanes of an Illumina NovaSeqX flow cell (10B reads, up to 300 cycles).

value: Large intestine

value: chronic DSS

tag: replicate


title: Pre-cachectic tumor mouse, Inguinal adipose tissue, Mouse #76

description: Library name: Pre_I76_1

value: Inguinal adipose tissue

value: C26 tumors, pre-cachectic


title: Pre-cachectic tumor mouse, Liver, Mouse #60

description: Library name: Pre_L60_1

value: Liver


title: CtrlKO 6hr timepoint replicate 1

value: Skin


title: ATF6 266_WT.12M

value: wildtype


title: Pre-cachectic tumor mouse, Liver, Mouse #69

description: Library name: Pre_L69_1


title: Yeast cultures CtrlC

description:
Library name: sample3
Shon_1C

value: C


title: ChronicDSS-1

description:
Library name: 081624_ChronicDSS_1
10x genomics


title: Pre-cachectic tumor mouse, Heart, Mouse #76

description: Library name: Pre_H76_1

value: Heart


title: Pre-cachectic tumor mouse, Liver, Mouse #73

description: Library name: Pre_L73_1

value: Balb/c mice, Wild type


title: AcuteDSS-3

description:
Library name: 081624_AcuteDSS_3
10x genomics

value: Fibroblast

value: acute DSS


title: CtrlKO 0hr timepoint replicate 3

value: ATCC, CRL-4001, IL-11mNG reporter, Cas9+, KO for GLIS3

value: WT


title: CtrlKO 0hr timepoint replicate 2

value: Control for KO


title: Yeast cultures CtrlB

description:
Library name: sample2
Shon_1B

value: Yeast cultures

value: Ctrl

value: B


title: Pre-cachectic tumor mouse, Liver, Mouse #76

description: Library name: Pre_L76_1


title: ATF6 261_WT.12M

value: Reference DNA


title: ATF6 002_WT.3M


title: ATF6 267_WT.12M


title: ATF6 001_WT.3M


title: AcuteDSS-2

description:
Library name: 081624_AcuteDSS_2
10x genomics

value: Large intestine


title: Yeast cultures CtrlA

description:
Library name: sample1
Shon_1A

value: A


title: AcuteDSS-1

description:
Library name: 081624_AcuteDSS_1
10x genomics


title: WT_ZT12_Cort_rep3

status: Public on Nov 04 2025

first: fabiana

last: quagliarini

address: Ingolstaedter Landstr 1

institute: helmholtz munich

description:
Library name: Sample 90
24L016778

data_processing:
Sequence quality was checked using FastQC and MultiQC
Adapter reads were trimmed using Trimmomatics
Reads were aligned using Salmon to mm10
Salmon quant.sf files were imported in R using tximport to generate read counts
Raw read counts were transformed by variance  stabilizing transformation (VST) method.
Assembly: mm10
Supplementary files format and content: tab-separate files containing raw read counts from Salmon
Supplementary files format and content: tab-separate files containing VST counts from DESeq2

source_name: Mouse liver

growth_protocol: C57BL/6J mice were fed with chow diet

extract_protocol:
RNA was extracted using the QIAZOL reagent. 1 μg of RNA was used for library preparation.
Libraries were prepped from 1µg total RNA with the Illumina TruSeq RNA library prep kit v2 chemistry in an automated system (Agilent Bravo liquid handling) platform).

treatment_protocol: Mice were either night-restricted fed (NRF), or NRF + reduced calorie intake across the weeks with end point of 40% less calories

value: Mouse liver

tag: strain

value: Corticosterone supllementation


title: ATF6 009_ATF6.tg.3M

value: ATF6 transgenic


title: WT_ZT12_Cort_rep2

description:
Library name: Sample 89
24L016777


title: WT_ZT12_Cort_rep1

description:
Library name: Sample 88
24L016775


title: WT_ZT12_NR_rep2

description:
Library name: Sample 86
24L016770

value: Night Restricted Feeding (NR)


title: P23 3 (Treatment 2)

city: Ciudad Real

first: Rita

last: Vaz-Rodrigues

address: Ronda de Toledo 12

department: SaBio

country: Spain

institute: Instituto de Investigación en Recursos Cinegéticos (IREC) - University of Castilla-La Mancha (UCLM)

description: Library name: Sample 9

data_processing:
Raw reads on FASTQ format were processed using in-house Perl scripts to generate clean reads by removing adapter sequences, poly-N reads, and low-quality reads.
The final BAM files were quantified with the featureCounts function available in Bioconductor R package Rsubread using BIME_Iper_1.3 annotations.
Raw count units were normalized using the FPKM method.
Assembly: Mapping was performed using the I. persulcatus genome (assembly BIME_Iper_1.3) serving as reference and Bowtie 2 (v2.5.3) as the alignment tool.
Supplementary files format and content: MS Excel spreadsheet contains raw counts for each sample.

organism: Ixodes ricinus

source_name: Midgut

extract_protocol:
Total mRNA was isolated from samples employing 500µl of TRI Reagent (Sigma-Aldrich, Taufkirchen, Germany), following manufacturer’s instructions.
Sequencing libraries were generated using the Novogene NGS RNA Library Prep Set (PT042; Novogene, Beijing, China), following manufacturer’s instructions.

value: Midgut


title: WT_ZT12_NR_rep1

description:
Library name: Sample 85
24L016769


title: P23 1 (Treatment 2)

description: Library name: Sample 7


title: MET 3 (Treatment 1)

description: Library name: Sample 6


title: P23 2 (Treatment 2)

description: Library name: Sample 8


title: GFP 2 (Control)

description: Library name: Sample 2


title: GFP 1 (Control)

description: Library name: Sample 1


title: MET 1 (Treatment 1)

description: Library name: Sample 4


title: GFP 3 (Control)

description: Library name: Sample 3


title: CtrlKO 0hr timepoint replicate 1

value: Skin


title: No Touch DNA from sample 38 aged 24 months

type: other

city: Oklahoma City

first: Jonathan

middle: D

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes and Human Disease

institute: Oklahoma Medical Research Foundation

description: Genomic DNA bypassed the conversion process and was started from the "Create the BCD Plate" step from Illumina protocol, the rest of the processing was following the manufacturer protocol.

hyb_protocol: DNA was amplified, fragmented and hybridized to the Infinium Mouse Methylation BeadChip using the standard protocol. Since conversion was a variable in the study, conversion conditions for each sample are available in their associated metadata.

scan_protocol: Arrays were imaged using the Illumina iScan with recommended Illumina settings

data_processing:
methylprep package v 1.7.1
Average Beta

label: Cy5 and Cy3

molecule: other

source_name: hippocampus

label_protocol: standard protocol

extract_protocol: genomic DNA was isolated using the ALlPrep DNA/RNA Mini Kit (Qiagen) according to standard manufacturer protocol.

value: hippocampus


title: No Touch DNA from sample 39 aged 24 months


title: No Touch DNA from sample 9 aged 8 months


title: No Touch DNA from sample 10 aged 8 months


title: No Touch DNA from sample 36 aged 24 months


title: No Touch DNA from sample 35 aged 24 months


title: No Touch DNA from sample 37 aged 24 months


title: Unconverted DNA from sample 38 aged 24 months

description: Genomic DNA was subject to the same PCR conditions of the Zymo protocol but without addition of the conversion reagent. After the bisulfite-free "conversion" step, the standard Illumina microarray protocol was followed.


title: Unconverted DNA from sample 39 aged 24 months


title: Zebrafish Liver PacBio

city: Lausanne

first: James

middle: A

last: Holzwarth

state: Vaud

address: EPFL Innovation Park, G

department: NIFSAS

country: Switzerland

institute: Nestlé

data_processing:
Illumina fastx_toolbox quality control and filtering
Illumina HiSat2 mapping
PacBio lima demultiplex and remove barcodes
PacBio isoseq3 refine remove polyA and concatamers
PacBio isoseq3 cluster to cluster reads
PacBio minimap2 for mapping
stringtie to assemble into transcripts
gffcompare annotate transcripts
bedtools getfasta extract cDNA sequences
SixFrame convert to protein sequences
gtf files (generated by stringtie).  These have normalized count FPKM and TPM. The files also have information about exon coverage. Some of the transcripts identified by stringtie do not correspond to any annotated transcripts, and I have been left in the files.
Assembly: GRCz9
Supplementary files format and content: fasta files containing translated protein sequences of transcripts
Supplementary files format and content: gtf files containing normalized count FPKM and TPM
Library strategy: Iso-Seq

organism: Danio rerio

source_name: liver

growth_protocol: Adult and larval zebrafish of the AB line were raised at 27.5 °C, on a 14/10 hours light/dark cycle, under standard husbandry conditions. Fertilized wild type eggs were collected via natural spawning and reared in egg water at 28.5 °C incubation up to 4 days post fertilization (dpf). Adult zebrafish euthanasia and organs sampling were carried out according to the Swiss and EU ethical guidelines based on article 22, paragraph 3 of the ordonnance on animal by-products (permit VD-H13).

extract_protocol:
Tissues were put in a Lysing Matrix D tube placed on ice. Then 600 µL of lysis buffer were added. The tubes were firmly closed and agitated for 2×60 s at speed 6 m/s on a FastPrep-24 homogenizer. Total RNA was then extracted using the Agencourt RNAdvance Tissue Kit following the provider’s recommendations. Total RNA was quantified using the Quant-iT™ RiboGreen™ RNA Assay Kit on a Spectramax M2. Total RNA quality was assessed using Fragment Analyzer-96 with DNF-471-0500 Standard Sensitivity RNA Analysis Kit.
RNA-Seq:  An amount of 500 ng of total RNA was used for each sample. A bead-based mRNA capture followed by a fragmentation, first and second strand synthesis, an end repair, and a 3`adenylation and indexed linker ligation were performed. The adapter ligated cDNA library fragments were then enriched by pPolymerase chain reaction (PCR) using 15 cycles of amplification (Illumina TruSeq Stranded mRNA protocol). Samples were then bead purified, pooled equimolar
Iso-Seq:  An amount of 300 ng of total RNA was used to prepare the Iso-Seq libraries for PacBio following exactly the Iso-Seq Express Template Preparation for Sequel and Sequel II Systems version 02 (October 2019). Libraries sizes were assessed using a FemtoPulse with FP-1002-0275 gDNA 165kb Analysis Kit. Libraries quantifications were performed using a Qubit fluorometer with Q32854 Qubit dsDNA HS Assay Kit (500×).

treatment_protocol: Muscle, brain and liver tissues were dissected, sampled and snap-frozen from male zebrafishes. In addition, 4 dpf whole larvae or tails dissected from larvae were pooled and snap-frozen

value: liver


title: Unconverted DNA from sample 37 aged 24 months


title: Zebrafish Brain PacBio

source_name: brain

value: brain


title: WT_ZT12_NR_rep3

description:
Library name: Sample 87
24L016771

value: WT


title: Unconverted DNA from sample 36 aged 24 months


title: Unconverted DNA from sample 35 aged 24 months


title: Unconverted DNA from sample 34 aged 24 months


title: Zebrafish Larvae PacBio

source_name: Entire larvae

value: Entire larvae


title: Zebrafish Larvae tail PacBio

source_name: Larvae tail

value: Larvae tail


title: MET 2 (Treatment 1)

description: Library name: Sample 5


title: H. sapiens granuloma single-cell RNAseq, replicate 2, stimulated

city: Bethesda

first: Philip

last: Murphy

state: MD

address: 10 CENTER DR RM 11N111

institute: National Institutes of Health

description: Library name: Human2.stim

data_processing:
Fastq files were pre-processed and filtered using ScaleBio Seq Suite: RNA, a cloud-based pipeline on the basepair cloud using nextflow version 23.10.0 and Mmul_10 for rhesus macaque or GRCh38 for human as the reference genome.
The Seurat standard preprocessing and clustering workflow was performed for dimensionality reduction and clustering. Briefly, raw counts were normalized, and the top 2,000 highly variable genes were selected using Seurat’s FindVariableFeatures with vst.
RunPCA was performed on the variable genes and an SNNgraph was created with FindNeighbors with 20 principal components as determined by an Elbowplot. Clusters were generated with Findclusters and RunUMAP was used to produce the visualization.
Filtered barcode, features, and matrix files were used to create rds objects then merged with unique identifiers. Data were analyzed and statistical testing was performed using Seurat V5.0.0 for both macaque and human samples.
Assembly: GRCh38/Mmul_10
Supplementary files format and content: Hda5 format, containing counts and barcodes/UMIs

source_name: Granuloma

growth_protocol: Healthy male Indian-origin rhesus macaques aged ~3 years from the National Institute of Allergy and Infectious Diseases breeding colony on Morgan Island, South Carolina were used in this experiment.

extract_protocol:
Granuloma samples were processed with the ScaleBio Low Input Fixation protocol for single cell RNA sequencing with the ScaleBio Sample Fixation Kit (Scale Biosciences #2020001) with additional fixation time required for BSL3 procedures.
Fixed frozen samples were thawed on ice, counted, resuspended in Wash Buffer at 2000 cells per μL and processed with the ScaleBio Single cell RNA sequencing Kit v1.1 (Cat #950884) and laboratory protocol RevA NOV2023 from ScaleBiosciences. Approximately 10,000 cells were added per well to the RT-barcode plate on ice.

treatment_protocol: These animals were treated with isotype control rhesus macaque IgG (Nonhuman Primate Reagent Resource RRID:AB_2716330) at 10mg/kg on weeks 0, 2, 4, 6, 8, 9, 10, 11, and 12 via intravenous infusion and intratracheal instillation. Rhesus macaques were anesthetized with ketamine and dexmedetomidine and 2 ml of physiological saline containing ~25 CFU of Mtb H37Rv was bronchoscopically instilled into the lower right lobe of the lungs. Stimulated samples also received MHC-I and MHC-II MTB300 Mtb peptide megapools which were added at 1μg/mL and 2μg/mL, respectively.

value: Granuloma


title: Unconverted DNA from sample 32 aged 18 months


title: Unconverted DNA from sample 31 aged 18 months


title: H. sapiens granuloma single-cell RNAseq, replicate 2

department: National Institute of Allergy and Infectious Diseases

description: Library name: Human2


title: H. sapiens granuloma single-cell RNAseq, replicate 1, stimulated

description: Library name: Human.stim


title: Unconverted DNA from sample 30 aged 18 months


title: H. sapiens granuloma single-cell RNAseq, replicate 1

description: Library name: Human


title: Unconverted DNA from sample 29 aged 18 months


title: Unconverted DNA from sample 27 aged 18 months


title: scSeq_CAR17_Seq2

city: München

first: Jessica

last: Pauli

state: Bayern

address: Biedersteiner Str. 29

department: Molecular Vascular Medicine

institute: TUM Universitätsklinikum (Klinikum rechts der Isar)

description: Library name: CAR17_Seq2

data_processing:
The demultiplexing, alignment and gene counting were made using the Cell Ranger software v7.0.0, using GRCh 38 and Gencode annotation v33
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: carotid artery

extract_protocol:
Human carotid arteries were harvested during carotid endarterectomy or open repair in our Department of Vascular and Endovascular Surgery. The tissue was transported in PBS on ice to our laboratory. The two distinct pieces of each tissues were minced and digested using the Multi Tissue Dissociation Kit 2 (Miltenyi Biotech, 130-110-203), GentleMACS Dissociator (Miltenyi Biotech, 130-093-235), GentleMACS C tubes (Miltenyi Biotech, 130-096-334) and the 37C_Mulit_G program, all according to the manufacturer´s instructions. The cell suspension was strained (70 µm, 40 µm) and Dead Cell Removal (Miltenyi Biotech, 130-090-101) using MS Columns (Miltenyi Biotech, 130-042-201) was performed. Cells were resuspended in PBS + 0,04% BSA.
Cells were loaded into a 10x Genomics microfluidics Chip G and encapsulated with barcoded oligo-dT-containing gel beads using the 10x Genomics Chromium Controller. Gel Beads-in-emulsion (GEM) cleanup, cDNA Amplification and 3´Gene Expression Dual Index Library Construction was performed according to the manufacturer´s instructions (CG000315 Rev C). Libraries from individual samples were multiplexed into partial lanes on an Illumina NovaSeqXPlus instrument

value: carotid artery

value: primary cells

value: all cells from tissue


title: scSeq_CAR16_Seq2

description: Library name: CAR16_Seq2


title: Unconverted DNA from sample 26 aged 18 months


title: scSeq_CAR16_Seq1

description: Library name: CAR16_Seq1


title: Zebrafish Muscle PacBio

source_name: muscle

value: muscle


title: Unconverted DNA from sample 28 aged 18 months


title: Unconverted DNA from sample 25 aged 14 months


title: Unconverted DNA from sample 23 aged 14 months


title: scSeq_CAR15_Seq1

description: Library name: CAR15_Seq1


title: Unconverted DNA from sample 21 aged 14 months


title: Unconverted DNA from sample 20 aged 14 months


title: scSeq_CAR13_Seq2

description: Library name: CAR13_Seq2


title: Unconverted DNA from sample 24 aged 14 months


title: scSeq_CAR14_Seq2

description: Library name: CAR14_Seq2


title: scSeq_CAR13_Seq1

description: Library name: CAR13_Seq1


title: scSeq_CAR12_Seq2

description: Library name: CAR12_Seq2


title: Unconverted DNA from sample 19 aged 14 months


title: scSeq_CAR14_Seq1

description: Library name: CAR14_Seq1


title: scSeq_CAR17_Seq1

description: Library name: CAR17_Seq1


title: scSeq_CAR11_Seq1

description: Library name: CAR11_Seq1


title: Unconverted DNA from sample 16 aged 11 months


title: Unconverted DNA from sample 15 aged 11 months


title: scSeq_CAR11_Seq2

description: Library name: CAR11_Seq2


title: HGSO6_wt_pt2

first: Mirjana

last: Kessler

address: Pettenkoferstrasse 8a

department: Department of Obstetrics and Gynecology

institute: Ludwig Maximilian University Munich

description: Library name: sample6

data_processing:
Raw data (raw reads) of fastq format were first processed through perl scripts. In this step, clean reads were obtained by removing reads containing adapter, reads containing ploy-N, and low-quality reads from raw data. At the same time, Q20, Q30, and GC content of the clean data were calculated. (Service Novogene Ltd)
Assembly: Alignment of FASTQ files was performed using the R package Rsubread with a genomic index built from the GRCh38 primary assembly genome sequence (Gencode release 45). Annotation and feature counting were also performed using the Rsubread package, utilizing the corresponding GTF annotation file from the same source.
Supplementary files format and content: A matrix count file (.txt) was generated for each sample, including raw counts and corresponding annotations.

source_name: ovarian cancer

growth_protocol: Patient-derived organoids, generated from solid tumor deposits of high-grade serous ovarian cancer were grown in BME Type2 matrix, in  DMEM-F12 medium supplemented with, HEPES, Glutamax, antibiotics, and a cocktail of growth factors stabilizing maintenance of stemness potential in vitro including (B27, NAC, NIC, N2, Y-27632, A83-01, EGF, BMP2)

extract_protocol:
RNA was isolated with an RNA easy kit ( Qiagen) and quantified by Quibit. Sample quality and integrity were checked by QC testing with RIN values (9-10).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for the non-directional library. It was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. ( Service Novogene Ltd)

treatment_protocol: Organoids were singularized by trypsinization, mechanical dissociation, and straining through a 200 µm filter, and 50,000 cells/well, were seeded in 24-well plate format. At day 7 post seeding,  the freshly formed organoids were treated for 48h with carboplatin at five concentrations (dilution in organoid medium to 6.25 μM, 12.5 μM, 25 μM, 50 μM, and 100 μM), alongside a control followed by 72-hour recovery phase in a carboplatin-free organoid medium. Next, passaging was performed to a 48-well format and ptGPC lines were recovered for the highest exposure of platinum where long-term expansion subsequently could still be achieved.  For HGSO8  post 12,5 µM and in the case of HGSO6 post 6,25µM. For HGSO6, one sample was also harvested after the second round of ODR testing (pt2 in the name of the sample).In comparison, mRNA samples were also isolated from control organoids that did not undergo drug treatment.

value: ovarian cancer

value: patient-derived organoids

value: epithelial

value: wt

value: carboplatin (2x)


title: HGSO6_wt_pt1.2

description: Library name: sample5

value: carboplatin


title: Unconverted DNA from sample 14 aged 11 months

value: hippocampus


title: scSeq_CAR15_Seq2

description: Library name: CAR15_Seq2


title: HGSO6_wt_pt1

description: Library name: sample4


title: HGSO6_wt

description: Library name: sample3

value: control


title: Unconverted DNA from sample 13 aged 11 months


title: HGSO8_wt_pt1

description: Library name: sample2


title: Unconverted DNA from sample 33 aged 18 months


title: Unconverted DNA from sample 11 aged 11 months


title: HGSO8_wt

description: Library name: sample1


title: Unconverted DNA from sample 12 aged 11 months


title: Unconverted DNA from sample 22 aged 14 months


title: Unconverted DNA from sample 9 aged 8 months


title: Unconverted DNA from sample 10 aged 8 months


title: Unconverted DNA from sample 7 aged 5 months


title: T-47D cells, 1 uM palbociclib, 24 hr, rep 3

first: Archishma

last: Kavalipati

state: North Carolina

address: 120 Mason Farm Rd

department: Pharmacology

description:
Library name: PALBO_S3_GCCAAT_S6
Sample names match column names in FPKM file. Samples are not provided in DESeq2 output. In MATS columns, each IncLevel column entry contains information on 3 samples each. IncLevel1 samples correspond to PALBO_S1_TGACCA_S4, PALBO_S2_ACAGTG_S5, and PALBO_S3_GCCAAT_S6 respectively. IncLevel2 columns correspond to DMSO_S1_ATCACG_S1, DMSO_S2_CGATGT_S2, and DMSO_S3_TTAGGC_S3 respectively.

data_processing:
Sequence reads were trimmed using fastp 0.23.2 with option --detect-adapter_for_pe and --length_required 100. Transcript quantification was performed from trimmed reads with salmon 1.10.2. These quantifications were used for differential expression analysis with DESeq2 1.44.0. Alignments were generated using STAR v2.7.10b and indexed using samtools 1.16. Splicing analysis was done using rMATS-turbo 4.3.0. Genome build GRCh38 was used for all analysis and obtained from GENCODE v47.
Assembly: GRCh38 (GENCODE 47 release)
Supplementary files format and content: 20250318.DESeq2.PALBOvDMSO.FPKM.tsv contains FPKM output for each sample generated from DESeq2.
Supplementary files format and content: 20241206.conditionPALBOvsDMSO.DESeq.tsv contains differential expression output generated from DESeq2.
Supplementary files format and content: SE.MATS.JCEC.txt contains skipped exon events output by rMATS.
Supplementary files format and content: RI.MATS.JCEC.txt contains retained intron events output by rMATS.
Supplementary files format and content: A3SS.MATS.JCEC.txt contains alternative 3' splice site events output by rMATS.
Supplementary files format and content: A5SS.MATS.JCEC.txt contains alternative 5' splice site events output by rMATS.
Supplementary files format and content: MXE.MATS.JCEC.txt contains mutually exclusive exon events output by rMATS.

source_name: Breast

growth_protocol: T-47D cells were obtained from ATCC and grown in DMEM complete medium (Gibco, Cat# 11-965-092) supplemented with 10% fetal bovine serum (EMD Millipore, Cat# F2442). Samples for protein analysis by immunoblot were lysed in NETN buffer [20 mM Tris-HCl (pH 8.0), 100 mM NaCl, 0.5 mM EDTA and 0.5 % (v/v) Nonidet P-40 (NP-40)] supplemented with 2 µg/ml pepstatin, 2 µg/ml apoprotinin, 10 µg/ml leupeptin, 1 mM AEBSF [4-(2 Aminoethyl) benzenesulfonyl fluoride] and 1 mM Na3VO4.

extract_protocol:
RNAs were extracted from cells with RNeasy Kit (Qiagen, 74104).
RNA libraries were then generated with KAPA mRNA HyperPrep Kit (Roche, KK8580). Libraries were sequenced on a NextSeq500 Illumina platform.

value: Breast

value: epithelial cell

value: 1 uM palbociclib


title: Unconverted DNA from sample 8 aged 8 months


title: T-47D cells, 1 uM palbociclib, 24 hr, rep 2

description:
Library name: PALBO_S2_ACAGTG_S5
Sample names match column names in FPKM file. Samples are not provided in DESeq2 output. In MATS columns, each IncLevel column entry contains information on 3 samples each. IncLevel1 samples correspond to PALBO_S1_TGACCA_S4, PALBO_S2_ACAGTG_S5, and PALBO_S3_GCCAAT_S6 respectively. IncLevel2 columns correspond to DMSO_S1_ATCACG_S1, DMSO_S2_CGATGT_S2, and DMSO_S3_TTAGGC_S3 respectively.

value: WT


title: scSeq_CAR12_Seq1

description: Library name: CAR12_Seq1


title: Unconverted DNA from sample 18 aged 14 months


title: Unconverted DNA from sample 17 aged 11 months


title: Unconverted DNA from sample 6 aged 5 months


title: Unconverted DNA from sample 5 aged 5 months


title: Unconverted DNA from sample 4 aged 5 months


title: T-47D cells, DMSO (control), 24 hr, rep 2

description:
Library name: DMSO_S2_CGATGT_S2
Sample names match column names in FPKM file. Samples are not provided in DESeq2 output. In MATS columns, each IncLevel column entry contains information on 3 samples each. IncLevel1 samples correspond to PALBO_S1_TGACCA_S4, PALBO_S2_ACAGTG_S5, and PALBO_S3_GCCAAT_S6 respectively. IncLevel2 columns correspond to DMSO_S1_ATCACG_S1, DMSO_S2_CGATGT_S2, and DMSO_S3_TTAGGC_S3 respectively.

value: DMSO


title: T-47D cells, DMSO (control), 24 hr, rep 1

description:
Library name: DMSO_S1_ATCACG_S1
Sample names match column names in FPKM file. Samples are not provided in DESeq2 output. In MATS columns, each IncLevel column entry contains information on 3 samples each. IncLevel1 samples correspond to PALBO_S1_TGACCA_S4, PALBO_S2_ACAGTG_S5, and PALBO_S3_GCCAAT_S6 respectively. IncLevel2 columns correspond to DMSO_S1_ATCACG_S1, DMSO_S2_CGATGT_S2, and DMSO_S3_TTAGGC_S3 respectively.


title: Unconverted DNA from sample 3 aged 4 months


title: CFAP20-KO and WT cells labeled for 15min with EdU plate 8

city: Utrecht

first: Jeroen

last: van den Berg

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

library_source: genomic

data_processing:
scEdU-seq Libraries were sequenced 2x100 bp on Illumina NextSeq2000
See van den Berg et al.,(scEdU-seq, 2024)
Assembly: GRCh38 (Gencode)
Supplementary files format and content: deduplicated single cell count tables (tsv.gz)
Library strategy: scEdU-seq

source_name: RPE-1 hTERT

growth_protocol: RPE-1 hTERT WT and CFAP20-KO were cultured in DMEM/F12 supplemtend with 10% serum and 1X PenStrep. Cells were labeled for 15 minutes with 10uM EdU. After which, cells were fixed in 70 % Ethanol for 24. Subsequnenlty, cells were sorted in a 384-well plate and processed with the scEdU-seq protocol

extract_protocol:
van den Berg et al.,(scEdU-seq, 2024)
van den Berg et al.,(scEdU-seq, 2024)

treatment_protocol: there was no treatment outside of a singgle pulse EdU labeling

value: RPE-1 hTERT

value: retinal pigment epithelial


title: Unconverted DNA from sample 2 aged 4 months


title: CFAP20-KO and WT cells labeled for 15min with EdU plate 6


title: No Touch DNA from sample 34 aged 24 months


title: CFAP20-KO and WT cells labeled for 15min with EdU plate 5


title: CFAP20-KO and WT cells labeled for 15min with EdU plate 4


title: No Touch DNA from sample 31 aged 18 months


title: No Touch DNA from sample 30 aged 18 months


title: No Touch DNA from sample 23 aged 14 months


title: CFAP20-KO and WT cells labeled for 15min with EdU plate 3


title: CFAP20-KO and WT cells labeled for 15min with EdU plate 2


title: T-47D cells, DMSO (control), 24 hr, rep 3

institute: UNC Chapel Hill

description:
Library name: DMSO_S3_TTAGGC_S3
Sample names match column names in FPKM file. Samples are not provided in DESeq2 output. In MATS columns, each IncLevel column entry contains information on 3 samples each. IncLevel1 samples correspond to PALBO_S1_TGACCA_S4, PALBO_S2_ACAGTG_S5, and PALBO_S3_GCCAAT_S6 respectively. IncLevel2 columns correspond to DMSO_S1_ATCACG_S1, DMSO_S2_CGATGT_S2, and DMSO_S3_TTAGGC_S3 respectively.


title: No Touch DNA from sample 5 aged 5 months


title: No Touch DNA from sample 4 aged 5 months


title: T-47D cells, 1 uM palbociclib, 24 hr, rep 1

description:
Library name: PALBO_S1_TGACCA_S4
Sample names match column names in FPKM file. Samples are not provided in DESeq2 output. In MATS columns, each IncLevel column entry contains information on 3 samples each. IncLevel1 samples correspond to PALBO_S1_TGACCA_S4, PALBO_S2_ACAGTG_S5, and PALBO_S3_GCCAAT_S6 respectively. IncLevel2 columns correspond to DMSO_S1_ATCACG_S1, DMSO_S2_CGATGT_S2, and DMSO_S3_TTAGGC_S3 respectively.


title: No Touch DNA from sample 2 aged 4 months


title: CFAP20-KO and WT cells labeled for 15min with EdU plate 1


title: Converted DNA from sample 39 aged 24 months

description: Bisulfite conversion was performed using the Zymo EZ DNA Methylation Kit following standard manufacturer protocol


title: CFAP20-KO and WT cells labeled for 15min with EdU plate 7


title: Converted DNA from sample 38 aged 24 months


title: Unconverted DNA from sample 1 aged 4 months


title: No Touch DNA from sample 1 aged 4 months


title: Converted DNA from sample 37 aged 24 months


title: Converted DNA from sample 36 aged 24 months


title: Converted DNA from sample 35 aged 24 months


title: Converted DNA from sample 34 aged 24 months


title: Converted DNA from sample 32 aged 18 months


title: Converted DNA from sample 31 aged 18 months


title: Converted DNA from sample 33 aged 18 months


title: Converted DNA from sample 29 aged 18 months


title: Converted DNA from sample 28 aged 18 months


title: Converted DNA from sample 26 aged 18 months


title: Converted DNA from sample 25 aged 14 months


title: Converted DNA from sample 27 aged 18 months


title: VINC_LOAEL_PND83_732

type: RNA

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
treatment: VINC
dose: LOAEL
sample number: 732

hyb_protocol: Agilent : 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Arrays file were read and quantile normalized using the Bioconductor package limma. No background subtraction was performed. PND21 samples were normalized separately.

source_name: Testis

label_protocol: Agilent - Low RNA input QuickAmp starting from 200 ng total RNA

extract_protocol: Total RNAs were isolated from frozen testicular powder using TRIzol reagent (Invitrogen, Cergy Pontoise, France) coupled with column purification of RNA (High pure miRNA isolation kit, Roche Diagnostics, Meylan, France) and DNase treatment.

treatment_protocol: Antiandrogenic substances were administered in aqueous preparations. Pregnant females (20/group) were treated by gavage from gestation day (GD) 6 until postnatal (PND) day 21. After weaning, the offspring received the same test-substance as their mothers by oral gavage. Twenty males were selected to be raised until the weaning (Subset 1, PND21), the day of sexual maturation (Subset 2, puberty at PND30-40) or early adulthood (Subset 3, PND83±2). At each subset, testes were used for transcriptome and miRNome analyses. Three antiandrogenic substances were tested: Flutamide (FLUT), Prochloraz (PROC), Vinclozolin (VINC), at 3 doses. Flutamide: ADI = 0.0025mg/kg/d, NOAEL = 0.25mg/kg/d, LOAEL = 2.5mg/kg/d. Prochloraz: ADI=0.01 mg/kg/d, NOAEL=5 mg/kg/d, LOAEL=30 mg/kg/d. Vinclozolin: ADI=0.005 mg/kg/d, NOAEL=4 mg/kg/d, LOAEL=20 mg/kg/d

tag: background strain

value: Wistar

tag: age

value: postnatal day (PND) 83


title: VINC_NOAEL_PND83_723

description:
treatment: VINC
dose: NOAEL
sample number: 723


title: Converted DNA from sample 24 aged 14 months


title: VINC_ADI_PND83_712

description:
treatment: VINC
dose: ADI
sample number: 712


title: VINC_LOAEL_PND83_734

description:
treatment: VINC
dose: LOAEL
sample number: 734


title: VINC_ADI_PND83_716

description:
treatment: VINC
dose: ADI
sample number: 716


title: VINC_LOAEL_PND83_731

description:
treatment: VINC
dose: LOAEL
sample number: 731


title: VINC_NOAEL_PND83_724

description:
treatment: VINC
dose: NOAEL
sample number: 724


title: VINC_NOAEL_PND83_722

description:
treatment: VINC
dose: NOAEL
sample number: 722


title: PROC_LOAEL_PND83_793

description:
treatment: PROC
dose: LOAEL
sample number: 793


title: VINC_ADI_PND83_717

description:
treatment: VINC
dose: ADI
sample number: 717


title: Converted DNA from sample 23 aged 14 months


title: PROC_LOAEL_PND83_794

description:
treatment: PROC
dose: LOAEL
sample number: 794


title: PROC_LOAEL_PND83_792

description:
treatment: PROC
dose: LOAEL
sample number: 792


title: VINC_NOAEL_PND83_721

description:
treatment: VINC
dose: NOAEL
sample number: 721


title: Converted DNA from sample 30 aged 18 months


title: Converted DNA from sample 21 aged 14 months


title: VINC_LOAEL_PND83_733

description:
treatment: VINC
dose: LOAEL
sample number: 733


title: Converted DNA from sample 22 aged 14 months


title: PROC_NOAEL_PND83_784

description:
treatment: PROC
dose: NOAEL
sample number: 784


title: PROC_NOAEL_PND83_781

description:
treatment: PROC
dose: NOAEL
sample number: 781


title: Converted DNA from sample 20 aged 14 months

description: Bisulfite conversion was performed using the Zymo EZ DNA Methylation Kit following standard manufacturer protocol


title: PROC_LOAEL_PND83_791

description:
treatment: PROC
dose: LOAEL
sample number: 791


title: PROC_NOAEL_PND83_783

description:
treatment: PROC
dose: NOAEL
sample number: 783


title: Converted DNA from sample 19 aged 14 months


title: PROC_ADI_PND83_774

description:
treatment: PROC
dose: ADI
sample number: 774


title: Converted DNA from sample 18 aged 14 months


title: Converted DNA from sample 16 aged 11 months


title: Converted DNA from sample 17 aged 11 months


title: VINC_ADI_PND83_714

description:
treatment: VINC
dose: ADI
sample number: 714


title: Converted DNA from sample 15 aged 11 months


title: PROC_NOAEL_PND83_782

description:
treatment: PROC
dose: NOAEL
sample number: 782


title: PROC_ADI_PND83_772

description:
treatment: PROC
dose: ADI
sample number: 772


title: Converted DNA from sample 12 aged 11 months


title: Converted DNA from sample 10 aged 8 months


title: Converted DNA from sample 9 aged 8 months


title: Converted DNA from sample 13 aged 11 months


title: Converted DNA from sample 8 aged 8 months


title: PROC_ADI_PND83_771

description:
treatment: PROC
dose: ADI
sample number: 771


title: Converted DNA from sample 14 aged 11 months


title: FLUT_LOAEL_PND83_764

description:
treatment: FLUT
dose: LOAEL
sample number: 764


title: Converted DNA from sample 7 aged 5 months


title: FLUT_LOAEL_PND83_763

description:
treatment: FLUT
dose: LOAEL
sample number: 763


title: Converted DNA from sample 6 aged 5 months


title: Converted DNA from sample 3 aged 4 months


title: FLUT_NOAEL_PND83_753

description:
treatment: FLUT
dose: NOAEL
sample number: 753


title: FLUT_NOAEL_PND83_751

description:
treatment: FLUT
dose: NOAEL
sample number: 751


title: FLUT_NOAEL_PND83_754

description:
treatment: FLUT
dose: NOAEL
sample number: 754


title: Converted DNA from sample 11 aged 11 months


title: FLUT_LOAEL_PND83_761

description:
treatment: FLUT
dose: LOAEL
sample number: 761


title: FLUT_LOAEL_PND83_762

description:
treatment: FLUT
dose: LOAEL
sample number: 762


title: FLUT_ADI_PND83_741

description:
treatment: FLUT
dose: ADI
sample number: 741


title: Converted DNA from sample 2 aged 4 months


title: Converted DNA from sample 4 aged 5 months


title: FLUT_ADI_PND83_742

description:
treatment: FLUT
dose: ADI
sample number: 742


title: FLUT_NOAEL_PND83_752

description:
treatment: FLUT
dose: NOAEL
sample number: 752


title: CTRL_PND83_704

description:
treatment: CTRL
dose: --
sample number: 704


title: Converted DNA from sample 1 aged 4 months

description: Bisulfite conversion was performed using the Zymo EZ DNA Methylation Kit following standard manufacturer protocol


title: Converted DNA from sample 5 aged 5 months


title: T-47D cells, 1 uM Palbociclib, 24 hr, biological replicate 3

description:
Library name: PALBO_3_S6
Column: /work/users/j/c/jcmtnez/T47D_ATAC/bams/Palbo_3_S6.dedup.bam

data_processing:
Cleaning: We first assessed the quality of paired-end ATAC-seq reads using FastQC (v0.12.1-0). To reduce alignment noise from non-nuclear sources, we employed a serial pre-alignment strategy. We initially aligned reads to a ribosomal DNA (rtDNA) index using Bowtie2 (v2.5.4-6) with the parameters --local --very-sensitive-local. Reads that did not align to rtDNA were subsequently aligned to the mitochondrial genome (chrM) using the same parameters. The remaining unaligned reads, representing the clean nuclear fraction, proceeded to genomic alignment.
Alignment: We aligned the clean paired-end reads to the GRCh38 human reference genome assembly using Bowtie2 with parameters --local --very-sensitive-local -X 2000. We piped these alignments to Samtools (v1.22.1-0) to filter for properly paired reads with a mapping quality score (MAPQ) of at least 30, while excluding supplementary alignments, unmapped reads, and secondary alignments (flag 1804). We then position-sorted the filtered alignments and identified and removed PCR duplicates using Picard (v3.4.0-0) MarkDuplicates with the REMOVE_DUPLICATES=true option. We indexed the final deduplicated BAM files with Samtools. Throughout the pipeline, we collected quality control metrics, including alignment statistics with Samtools flagstat and stats, and fragment insert size distributions with Picard CollectInsertSizeMetrics.
For downstream analysis, we adjusted alignment start sites to center reads on the Tn5 transposase cutting site. We performed this step using the alignmentSieve command from deepTools (v3.5.6-0) with the --ATACshift option. We then sorted the resulting Tn5-shifted BAM files by position and indexed them with Samtools.
Peak calling and Analysis: We performed peak calling using two methods within the MACS3 (v3.0.3-0)103 framework. First, we called peaks on the Tn5-shifted BAM files using the macs3 callpeak command with a sq-value cutoff of 0.05. We specified the --nomodel option along with --shift -75 and --extsize 150 to define the nucleosome-free region model based on the known Tn5 insertion offset. In parallel, we ran the macs3 hmmratac command on the original (unshifted) deduplicated BAM files to utilize its Hidden Markov Model for identifying accessible chromatin regions. For both methods, we filtered the resulting peak sets to exclude regions listed in the ENCODE hg38 blacklist (v2). Resulting IDR BED files were merged using bedtools v2.31104 and converted to SAF format. Counts were calculated using the featureCounts option from subread v2.0.6105,106 to count chromatin accessibility peaks. Differential chromatin accessibility was calculated using DESeq2 and filtered according to vignette specifications.
Assembly: GRCh38 (GENCODE V47)
Supplementary files format and content: featureCounts matrix

growth_protocol: We adapted the ATAC-seq protocol from the original methods described by Buenrostro et al. and Corces et al. We cultured T-47D cells from three distinct biological replicates in separate 60 mm dishes and allowed them to reach 60-70% confluency. Media: DMEM with 10% FBS, Penicillin, and Streptomycin.

extract_protocol:
We washed the cells three times with ice-cold PBS, then incubated them with 0.25% Trypsin-EDTA for 5 minutes. We quenched the trypsin with complete media (twice the volume) and centrifuged the cells at 500 × g for 5 minutes. Cells were washed twice more with ice-cold PBS, resuspended in ATAC resuspension buffer (RSP; 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2), and counted. We aliquoted 50,000 cells per biological replicate, centrifuged them, and resuspended the pellets in lysis buffer (RSP supplemented with 0.1% Tween-20, 0.1% NP-40, and 0.01% Digitonin) for a 5-minute incubation. We added 1 mL of wash buffer (RSP with 0.1% Tween-20), centrifuged the cells again, and resuspended them in tagmentation buffer (Diagenode 2× buffer [C01019043] diluted to 1×, supplemented with 0.01% Digitonin, 0.1% Tween-20, and 2.5 µL Diagenode Tn5 enzyme [C01070010]). We incubated the reaction for 30 minutes at 37°C. We purified the DNA using the Zymo DNA Clean & Concentrator kit, following the manufacturer's instructions, and eluted in 10 µL.
For library amplification, we used the NEBNext® High-Fidelity 2X PCR Master Mix (M0541) and Diagenode UDI Tagmentation Library Set (C01011034) following this thermal cycling protocol: 72°C for 5 minutes, 98°C for 30 seconds, 10 cycles of: 98°C for 10 seconds, 63°C for 30 seconds, and one last cycle of 72°C for 1 minute. We size-selected libraries within a range of 200-700 bp using SPRISelect (B23317) beads, pooled the libraries, and sequenced them using a NextSeq 1000 platform.

treatment_protocol: We replaced the culture media (DMEM with 10% FBS, Penicillin, and Streptomycin) entirely with media containing either 0.1% DMSO (control) or 1 µM palbociclib and incubated for 24 hours prior to the ATAC assay.


title: T-47D cells, 1 uM Palbociclib, 24 hr, biological replicate 1

description:
Library name: PALBO_1_S4
Column: /work/users/j/c/jcmtnez/T47D_ATAC/bams/Palbo_1_S4.dedup.bam


title: T-47D cells, DMSO, 24 hr, biological replicate 3

description:
Library name: DMSO_3_S3
Column: /work/users/j/c/jcmtnez/T47D_ATAC/bams/DMSO_3_S3.dedup.bam


title: CTRL_PND83_701

description:
treatment: CTRL
dose: --
sample number: 701


title: FLUT_ADI_PND83_744

description:
treatment: FLUT
dose: ADI
sample number: 744


title: VINC_LOAEL_PND30-40_532

description:
treatment: VINC
dose: LOAEL
sample number: 532

value: postnatal day (PND) 30-40


title: T-47D cells, 1 uM Palbociclib, 24 hr, biological replicate 2

description:
Library name: PALBO_2_S5
Column: /work/users/j/c/jcmtnez/T47D_ATAC/bams/Palbo_2_S5.dedup.bam


title: WO_Young-42

city: Shenzhen

first: Zhihua

last: Wang

address: No. 12, Langshan Road, Xili Street, Nanshan District, Shenzhen

department: Shenzhen Key Laboratory of Cardiovascular Disease

country: China

institute: Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen

data_processing:
BGI used BGISEQ 500 platform for RNA-Seq
The raw data include low quality, contamination of joints, and high levels of unknown base n reads, which need to be removed before analysis to ensure the reliability of the results
The clean reads were align to the reference genome sequnence using HISAT
The clean reads were align to the reference genome sequnence using Bowtie2
Assembly: NCBI, Mus_musculus , GCF_000001635.27_GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: heart tissue

growth_protocol: All mice were housed in a stable environment with a 12 h light/12 h dark cycle (room temperature, 24 ± 3°C; room humidity, 55 ± 5%) and fed a normal diet.

extract_protocol:
RNA from mouse heart was extracted using Trizol reagent according to the manufacturer's instructions.
RNA libraries were prepared for sequencing according to manufacturer's instructions of Beijing Genomics Institution (BGI)

treatment_protocol: Young mice and systemic Armh4 knockout mice were raised to 25 months and 8 weeks of age, respectively, and were divided into WT_Aged group, KO_Aged group, WT_Young group and KO_Young group, with at least 6 mice in each group. The mice were anesthetized with inhaled anesthetics and euthanized by cervical dislocation. The hearts were immediately dissected and stored at -80°C.

value: heart tissue

value: Young


title: T-47D cells, DMSO, 24 hr, biological replicate 2

city: Chapel Hill

description:
Library name: DMSO_2_S2
Column: /work/users/j/c/jcmtnez/T47D_ATAC/bams/DMSO_2_S2.dedup.bam

value: epithelial


title: T-47D cells, DMSO, 24 hr, biological replicate 1

description:
Library name: DMSO_1_S1
Column: /work/users/j/c/jcmtnez/T47D_ATAC/bams/DMSO_1_S1.dedup.bam


title: FLUT_ADI_PND83_743

description:
treatment: FLUT
dose: ADI
sample number: 743


title: CTRL_PND83_702

description:
treatment: CTRL
dose: --
sample number: 702


title: VINC_LOAEL_PND30-40_533

description:
treatment: VINC
dose: LOAEL
sample number: 533


title: WO_Young-39


title: VINC_LOAEL_PND30-40_531

description:
treatment: VINC
dose: LOAEL
sample number: 531


title: VINC_LOAEL_PND30-40_534

description:
treatment: VINC
dose: LOAEL
sample number: 534


title: WO_Young-29


title: WO_Young-34


title: PROC_ADI_PND83_773

description:
treatment: PROC
dose: ADI
sample number: 773


title: WT_Aged-1

value: Aged


title: VINC_NOAEL_PND30-40_523

description:
treatment: VINC
dose: NOAEL
sample number: 523


title: VINC_NOAEL_PND30-40_522

description:
treatment: VINC
dose: NOAEL
sample number: 522


title: WT_Aged-5


title: VINC_NOAEL_PND30-40_524

description:
treatment: VINC
dose: NOAEL
sample number: 524


title: VINC_ADI_PND30-40_512

description:
treatment: VINC
dose: ADI
sample number: 512


title: VINC_ADI_PND30-40_511

description:
treatment: VINC
dose: ADI
sample number: 511


title: VINC_ADI_PND30-40_513

description:
treatment: VINC
dose: ADI
sample number: 513


title: VINC_NOAEL_PND30-40_521

description:
treatment: VINC
dose: NOAEL
sample number: 521


title: PROC_LOAEL_PND30-40_594

description:
treatment: PROC
dose: LOAEL
sample number: 594


title: VINC_ADI_PND30-40_514

description:
treatment: VINC
dose: ADI
sample number: 514


title: PROC_LOAEL_PND30-40_593

description:
treatment: PROC
dose: LOAEL
sample number: 593


title: WT_Aged-4


title: WT_Aged-12


title: KO_Young-38


title: KO_Young-53


title: KO_Young-31


title: KO_Aged-122


title: CR, GR_WT, rep2, ATAC

description:
Library name: CR_WT_3108_ATAC
22L010125

library_source: genomic single cell

data_processing:
The sequences were aligned to the mm10 genome using the CellRanger ARC 2.0.2 software from 10X Genomics with the –include introns flag.
Assembly: mm10
Supplementary files format and content: Filtered feature barcode matrix (hdf5), ATAC Per fragment information file (tsv.gz), ATAC Per fragment information index (tsv.gz index), and comma-separated file

source_name: mouse liver

growth_protocol: Mice fed only during the night,  caloric restricted, and night-restricted-fed mice. All mice were fed using regular chow diet

extract_protocol:
Frozen liver was minced, and later homogenized by Dounce homogenizer. Nuclei were centrifuged in 4°C,washed, filtered, and permeabilized. Then nuclei quality was assessed under microscope, continued with single cell Multiome according to the 10x Genomics protocol.
The single-nuclei libraries were constructed by following the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression user guide.

value: mouse liver

value: Wild-type

value: Caloric Restriction (CR)


title: KO_Aged-114


title: CR, GR_WT, rep1, ATAC

description:
Library name: CR_WT_24_ATAC
22L010109


title: CR, GR_WT, rep1, GEX

description:
Library name: CR_WT_24_mRNA
22L010139

molecule: nuclear RNA


title: KO_Young-27


title: KO_Aged-125


title: KO_Aged-115


title: PROC_LOAEL_PND30-40_592

description:
treatment: PROC
dose: LOAEL
sample number: 592


title: PROC_LOAEL_PND30-40_591

description:
treatment: PROC
dose: LOAEL
sample number: 591


title: CR, GR_WT, rep2, GEX

description:
Library name: CR_WT_3108_mRNA
22L010143


title: CR, GR_KO, rep2, GEX

description:
Library name: CR_KO_7_mRNA
22L010140

value: Glucocorticoid receptor, hepatocyte-specific knock-out (GR-LKO)


title: PROC_ADI_PND30-40_574

description:
treatment: PROC
dose: ADI
sample number: 574


title: PROC_NOAEL_PND30-40_583

description:
treatment: PROC
dose: NOAEL
sample number: 583


title: CTRL_PND83_703

description:
treatment: CTRL
dose: --
sample number: 703


title: FLUT_LOAEL_PND30-40_563

description:
treatment: FLUT
dose: LOAEL
sample number: 563


title: FLUT_LOAEL_PND30-40_564

description:
treatment: FLUT
dose: LOAEL
sample number: 564


title: PROC_ADI_PND30-40_572

description:
treatment: PROC
dose: ADI
sample number: 572


title: PROC_NOAEL_PND30-40_582

description:
treatment: PROC
dose: NOAEL
sample number: 582


title: CR, GR_KO, rep2, ATAC

description:
Library name: CR_KO_7_ATAC
22L010113


title: PROC_NOAEL_PND30-40_584

description:
treatment: PROC
dose: NOAEL
sample number: 584


title: PROC_ADI_PND30-40_571

description:
treatment: PROC
dose: ADI
sample number: 571


title: PROC_NOAEL_PND30-40_581

description:
treatment: PROC
dose: NOAEL
sample number: 581


title: FLUT_LOAEL_PND30-40_561

description:
treatment: FLUT
dose: LOAEL
sample number: 561


title: PROC_ADI_PND30-40_573

description:
treatment: PROC
dose: ADI
sample number: 573


title: NR, GR_WT, rep1, ATAC

description:
Library name: NR_WT_3274_ATAC
22L010101

value: Night restricted feeding (NRF)


title: FLUT_LOAEL_PND30-40_562

description:
treatment: FLUT
dose: LOAEL
sample number: 562


title: FLUT_NOAEL_PND30-40_554

description:
treatment: FLUT
dose: NOAEL
sample number: 554


title: CR, GR_KO, rep1, ATAC

description:
Library name: CR_KO_3107_ATAC
22L010129


title: FLUT_NOAEL_PND30-40_552

description:
treatment: FLUT
dose: NOAEL
sample number: 552


title: FLUT_ADI_PND30-40_543

description:
treatment: FLUT
dose: ADI
sample number: 543


title: FLUT_NOAEL_PND30-40_553

description:
treatment: FLUT
dose: NOAEL
sample number: 553


title: NR, GR_KO, rep2, ATAC

description:
Library name: NR_KO_3271_ATAC
22L010133


title: NR, GR_KO, rep2, GEX

description:
Library name: NR_KO_3271_mRNA
22L010145


title: NR, GR_KO, rep1, ATAC

description:
Library name: NR_KO_3264_ATAC
22L010121


title: NR, GR_WT, rep2, ATAC

description:
Library name: NR_WT_3326_ATAC
22L010117


title: CR, GR_KO, rep1, GEX

description:
Library name: CR_KO_3107_mRNA
22L010144


title: NR, GR_WT, rep2, GEX

description:
Library name: NR_WT_3326_mRNA
22L010141


title: anterior segment, EGFP mRNA + CART 8, rep5

city: Stanford

middle: K

state: CA

address: 1291 Welch Rd

institute: Stanford University

description: Library name: CART-5

data_processing:
FASTQ files were mapped to the mm10 genome using Bowtie2 (version 2.3.4.1), filtered for a MAPQ score >10 using SAMtools (version 1.16.1), and subjected to PCR duplicate removal using Picard MarkDuplicates to generate BAM files. Gene expression counts were obtained from BAM files using HTSeq (version 2.0.1) and differentially expressed genes identified using DESeq2 (version 1.26.0).
Assembly: mm10
Supplementary files format and content: raw counts text files

source_name: eye

extract_protocol:
RNA-seq of sorted cells: eyes from Ai9 mice were cut circumferentially 1 mm posterior to the limbus to isolate the cornea, iris, and part of the ciliary body. Isolated tissues were digested with 625 units/mL of collagenase type I (Sigma-Alrich) in PBS for 45 minutes at 37°C followed by 0.25% Trypsin-EDTA (Gibco) for 10 minutes at 37°C to isolate single-cell suspensions, then washed with PBS and stained with 0.1 μg/mL of DAPI to exclude dead cells. tdTomato-positive cells were sorted from eyes that received Cre mRNA with CART 8. Two eyes were pooled for each sample and a minimum of 500 cells sorted. Anterior segment control cells were collected from eyes without treatment. One eye was used for each sample and 1,000 cells sorted. Total RNA from sorted cells was collected using a Quick-RNA Microprep Kit (Zymo). RNA-seq of whole anterior segments: eyes from C57BL/6J mice were cut circumferentially 1 mm posterior to the limbus to isolate the cornea, iris, and part of the ciliary body. Isolated tissues were homogenized using a handheld pellet pestle (Kimble Chase) in 300 μL of RNA Lysis Buffer (Zymo) and centrifuged at 16,000 x g for 5 minutes. Total RNA was collected from the supernatant using a Quick-RNA Microprep Kit (Zymo).
Ultra-low input RNA-seq library construction and sequencing was performed by Azenta Life Sciences (South Plainfield, NJ, USA) with a target depth of 20 million reads per sample.

value: eye

value: anterior segment

value: EGFP mRNA + CART 8


title: anterior segment, EGFP mRNA + CART 8, rep4

description: Library name: CART-4


title: FLUT_ADI_PND30-40_541

description:
treatment: FLUT
dose: ADI
sample number: 541


title: NR, GR_WT, rep1, GEX

description:
Library name: NR_WT_3274_mRNA
22L010137


title: anterior segment, EGFP mRNA + CART 8, rep3

description: Library name: CART-3


title: CTRL_PND30-40_503

description:
treatment: CTRL
dose: --
sample number: 503


title: anterior segment, EGFP mRNA + CART 8, rep6

description: Library name: CART-6


title: FLUT_ADI_PND30-40_544

description:
treatment: FLUT
dose: ADI
sample number: 544


title: NR, GR_KO, rep1, GEX

description:
Library name: NR_KO_3264_mRNA
22L010142


title: anterior segment, EGFP mRNA only, rep4

description: Library name: GFPonly-4

value: EGFP mRNA


title: CTRL_PND30-40_502

description:
treatment: CTRL
dose: --
sample number: 502


title: anterior segment, EGFP mRNA + CART 8, rep2

description: Library name: CART-2


title: anterior segment, EGFP mRNA + CART 8, rep1

description: Library name: CART-1


title: VINC_LOAEL_PND21_334

description:
treatment: VINC
dose: LOAEL
sample number: 334

value: postnatal day (PND) 21


title: tdTomato-positive anterior segment cells, rep3

description: Library name: Tdtomato-RNA-3

value: Cre mRNA + CART 8


title: anterior segment, EGFP mRNA only, rep3

description: Library name: GFPonly-3


title: VINC_LOAEL_PND21_331

description:
treatment: VINC
dose: LOAEL
sample number: 331

value: Wistar


title: FLUT_NOAEL_PND30-40_551

description:
treatment: FLUT
dose: NOAEL
sample number: 551

value: postnatal day (PND) 30-40


title: CTRL_PND30-40_501

description:
treatment: CTRL
dose: --
sample number: 501


title: FLUT_ADI_PND30-40_542

description:
treatment: FLUT
dose: ADI
sample number: 542


title: VINC_NOAEL_PND21_324

description:
treatment: VINC
dose: NOAEL
sample number: 324


title: VINC_NOAEL_PND21_323

description:
treatment: VINC
dose: NOAEL
sample number: 323


title: VINC_ADI_PND21_314

description:
treatment: VINC
dose: ADI
sample number: 314


title: VINC_LOAEL_PND21_333

description:
treatment: VINC
dose: LOAEL
sample number: 333


title: VINC_NOAEL_PND21_321

description:
treatment: VINC
dose: NOAEL
sample number: 321


title: anterior segment, EGFP mRNA only, rep1

description: Library name: GFPonly-1


title: VINC_NOAEL_PND21_322

description:
treatment: VINC
dose: NOAEL
sample number: 322


title: VINC_LOAEL_PND21_332

description:
treatment: VINC
dose: LOAEL
sample number: 332


title: untreated anterior segment cells, rep3

description: Library name: mouseAC-RNA-3

value: untreated anterior segment cells


title: tdTomato-positive anterior segment cells, rep2

description: Library name: Tdtomato-RNA-2


title: CTRL_PND30-40_504

description:
treatment: CTRL
dose: --
sample number: 504


title: untreated anterior segment cells, rep2

description: Library name: mouseAC-RNA-2


title: tdTomato-positive anterior segment cells, rep1

description: Library name: Tdtomato-RNA-1


title: anterior segment, EGFP mRNA only, rep2

description: Library name: GFPonly-2


title: untreated anterior segment cells, rep1

description: Library name: mouseAC-RNA-1


title: Downscaling 1k ES cells H2AZ

city: Copenhagen

first: Erkut

last: Ilaslan

address: Blegdamsvej 3

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description: Library name: 1k-AZ-oc

data_processing:
Additional runs concatenated to first FastQ file. For samples with a 3rd run, these runs processed seperately.
FastQ files trimmed using Trim Galore.
Trimmed FastQ files mapped to mm10 using bowtie1 with -m 1 parameter.
BAM files sorted using SAMtools and converted to BED format using BEDtools.
BED files from 3rd run merged to the BED files contaning 1st and 2nd runs before downstream analysis in EaSeq (http://easeq.net). Gzip compressed WIG files generated using EaSeq. Scores represent fragments per kilobasepairs per million reads
Assembly: mm10
Supplementary files format and content: wig files containing mapped reads.

source_name: E14 ES cells

growth_protocol: Postnatal day 7 (P7), P10, and P12 CD-1 females were used for collection of growing oocyte (GO) sample pools. C57BL/6NRj females aged 4 weeks were used for collecting NSN, SN and MII oocytes. To induce superovulation for collection of these three stages, the mice received an intraperitoneal injection with 5 international units (IU) of pregnant mare serum gonadotropin (PMSG; Prospec, HOR-272) at 2pm. For NSN and SN stages, the oocytes were collected ~45 hours after the PMSG injection. For collection of MII stage oocytes, an intraperitoneal injection with 5 IU of human chorionic gonadotropin (hCG; Sigma, C1063) was given 45-48 hours following PMSG injection. Subsequently, MII oocytes were collected 66-67 hours after the PMSG injection. Mouse E14 ES cells were obtained from a stock at passage P2 equal to those used for the mouse ENCODE project and cultured following the corresponding instructions (https://www.encodeproject.org/biosamples/ENCBS171HGC/). Prior to collection, cells were passaged once on gelatinized, feeder-free plates.

extract_protocol:
The samples were transferred to 1.5 ml tubes. SDS/RNase-free elution buffer (20 mM Tris–HCl/pH-7.5), 50 mM NaCl, 5 mM EDTA/pH-8.0) was added to 415 µl final volume, and the aqueous phase was sequentially extracted using equal volumes of phenol:chloroform:isoamylalcohol (Invitrogen, 15593-031) and chloroform:isoamylalcohol (Sigma-Aldrich, C0549). The 400 µl of the last aqueous phase were precipitated with 1 ml ice-cold ethanol, 11 µl linear acrylamide (Thermo Fisher Scientific, AM9520) and 44 µl 1 M sodium acetate (Invitrogen, AM9740) at least overnight at -80°C. For reconstitution, the pellets were centrifuged (swing-out, 16,000 x g, 4°C), and recovered using 15 µl of Qiagen EB (10 mM Tris, Qiagen, 19086) overnight at 4°C.
Sequencing libraries were prepared using the Qiaseq ultralow input kit (Qiagen, 180492 + 180310) with modifications to minimize material loses. These included prolonged incubations during the AMPure XP bead extractions (>15 min bead/sample incubation, >15 min DNA elution) (Beckman coulter, A63881), and an increased volume of beads (1.2 volume equivalents) during the second bead extraction. Double-stranded DNA concentration was determined using the Qubit HS DNA kit (ThermoFisher Scientific, Q32851), while DNA fragment size analyses were performed with TapeStation D1000 HS (Agilent, 5067-5585). Libraries were then and pooled in equimolar amounts. Sequential AMPure XP extractions (1.2 volume equivalents) were employed to drastically reduce adapter dimers from the pool prior to sequencing.

treatment_protocol: Oocytes were cross-linked in a solution of 50 µl M2 media, 50 µl PBS (Life Technologies, 14190-094), and a final concentration of 1% w/v formaldehyde (Sigma-Aldrich, F8775). After 8 min at room temperature, 14.3 µl 1 M Glycine (Merck, 67419) was added to inactivate the fixative. After 5 min at room temperature, ice cold PBS was used to wash the oocytes three times in a 0.6 ml tube (MaxymumRecovery, Axygen), resulting in a final volume of 10 µl. The fixative was added either in droplets under the microscope, or directly in the 0.6 ml tube followed by the washes and centrifugations at 700 x g for 10 min at 4°C with careful supernatant removal. Correspondingly, liquids were mixed by droplet pipetting or by gentle tube vortexing during cross-linking and glycine inactivation. Samples were snap-frozen in liquid nitrogen before storage at -80°C. Pelleted ES cells (around 20 million) were resuspended in 20 ml of a 1 % w/v formaldehyde (Sigma-Aldrich, F8775) solution in PBS with 20 mM of sodium butyrate (Sigma-Aldrich, 19-137), cross-linked at room temperature for 8 min, and inactivated using 2.4 ml of an aqueous 1.25 M glycine (Sigma, G8790) solution. Then, the pellet was washed twice with ice cold PBS supplemented with 20 mM of sodium butyrate (650 x g, 10 min, 4°C), cells were counted, diluted, and aliquoted into 0.6 ml tubes (MaxymumRecovery, Axygen) at different cell numbers. Finally, the cells were centrifuged, the supernatant removed, leaving 10 µl, and snap-frozen in liquid nitrogen before storage at -80°C.

value: E14 ES cells


title: Downscaling ES cells Input

description: Library name: INP-AZ


title: Downscaling 10k ES cells H2AZ

description: Library name: 10k-AZ-std


title: placental labyrinth of GD 17.5 C57BL/6J mice

city: Tokyo

first: Pharmaceutics

last: Keio

address: 1-5-30 Shibakoen, Minato-ku

department: Pharmacy

institute: Keio University

description:
Library name: Sample 1
Column name in Raw_counts.csv: mouse_LZ

data_processing:
Before adaptor trimming, a published RNA-seq dataset from size-filtered, syncytiotrophoblast-enriched fractions of human placental villous tissue (accession number GSE182381) was utilized. The original human placental samples were obtained from uncomplicated, full-term, singleton pregnancies delivered by the cesarean section.
RNA-seq reads were firstly cleaned by processing FASTQ format data with Trimmomatic (ver 0.3.9) software.
Salmon (ver 1.9.0) was then employed to map the clean reads to the reference genome assembly (human: GRCh38.p14, mouse: GRCm39, rat: GRCr8) and the read counts for RefSeq genes with the accession number prefixes NM_ were extracted.
RefSeq IDs were converted to gene symbols using the bitr function from the clusterProfiler (ver. 4.14.6) package and organism-specific annotation packages (human: org.Hs.eg.db (ver. 3.20.0), mouse: org.Mm.eg.db (ver. 3.20.0), rat: org.Rn.eg.db (ver. 3.20.0)).
The count values for each sample were summarized as “Raw_counts.csv”. If the corresponding gene was not present for a species, the count value was set to NA. However, in the downstream analysis, it was treated as 0 instead of NA for convenience.
Assembly: GRCm39, GRCr8, GRCh38.p14
Supplementary files format and content: The CSV file includes raw counts by gene symbols for each sample.

source_name: placental labyrinth

extract_protocol:
Total RNA was extracted from the placental labyrinth of gestational day (GD) 17.5 C57BL/6J mice and GD20.5 SD rats using ISOGEN II (Nippon Gene, Tokyo, Japan). Equal amounts of RNA from three to four different litters were then pooled as one biological sample
The RNA-seq library preparation and sequencing of the samples were performed by Rhelixa (Tokyo, Japan). Used kits there were "NEBNext® Poly(A) mRNA Magnetic Isolation Module (for PolyA selection)" and "NEBNext® Ultra™ ll Directional RNA Library Prep Kit".

value: placental labyrinth

tag: developmental stage

value: gestational day (GD) 17.5


title: PROC_LOAEL_PND21_394

description:
treatment: PROC
dose: LOAEL
sample number: 394