title: Dissected 14 somite limbbud tissue_rnaseq_rep2

city: Austin

first: Vighnesh

last: Ghatpande

state: Texas

address: 2500 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

description: Library name: 20230907_ALt17_NEB

data_processing:
The ribosome profiling libraries were processed using the Riboflow pipeline v.0.0.1 using deduplication with unique molecular identifiers - UMItools (Ozadam et al., 2020).
Assembly: GRCm38
Supplementary files format and content: .ribo file containing the matched Riboseq and RNAseq read counts.

source_name: embryonic limb tissue

growth_protocol: Embryos of the mentioned somite stages were obtained from Swiss Webster mice.

extract_protocol:
10- and 14-somite embryos were bisected transversely between 7- and 10-somites in dPBS. These core regions were transferred to a base Ribo-ITP buffer containing 20 mM Bis-Tris, 5 mM MgCl2, 5 mM CaCl2, 100 mM NaCl, 1 mM DTT, 0.25% BSA and the somatic LPM and overlying ectoderm was removed from the left side of the embryo using dissecting knives and flash frozen.
Frozen limb bud tissue samples were thawed on ice and Triton-X 100 and Cycloheximide were added to a final concentration of 0.1% and 0.1 mg/mL respectively. The lysate was separated into two tubes, 5μL for Ribo-ITP and 3μL for SmartSeq3 (Hagemann-Jensen et al., 2020). For Ribo-ITP, 1μL 1:300 diluted RNaseI (Ambion) was added and digestion was performed at 37°C for 30mins. Digestion was halted by adding 1μL of 0.7% SDS following which Ribo-ITP was performed as described in (Ozadam et al., 2023). The final indexing PCR was performed for 15 cycles. SmartSeq3 was performed as described in (Ref) with the following modifications, the preamplification PCR was performed for 13 cycles and indexing PCR was performed for 16 cycles. Both the ribosome profiling and RNASeq libraries were cleaned with AmPureXP beads with additional PAGE purification for Ribo-ITP libraries. The libraries were sequenced by Illumina Novaseq 6000.

value: embryonic limb tissue

value: 14 somite stage

value: Swiss Webster mice


title: Dissected 14 somite limbbud tissue_rnaseq_rep1

status: Public on Feb 25 2026

type: SRA

country: USA

description: Library name: 20230907_ALt16_NEB

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: developmental stage

tag: genotype


title: HoLEP29 [HoLEP_29_A_S90]

city: San Francisco

first: Jon

last: Akutagawa

address: 513 Parnassus Ave

institute: UCSF

description:
Library name: HoLEP_29_A_S90
SeqWell

library_source: transcriptomic single cell

data_processing:
The sequenced data were preprocessed and aligned using the dropseq_workflow on Terra (app.terra.bio). A digital gene expression matrix was generated for each sample, parsed, and analyzed following a customized pipeline
Sequencing results were received as paired FASTQ files. Each pair of FASTQ files was aligned against GRCh38 reference genome using a WDL-based Dropseq workflow (https://cumulus.readthedocs.io/en/latest/drop_seq.html) on Terra. All default parameters were used in the alignment except the parameter –dropseq_tools_force_cells set as 2,000 to ensure maximum cell capture. The alignment results include aligned and corrected bam files, gene expression matrices in .txt.gz format, and txt files of alignment reports such as the list of barcodes, the number of reads, and alignment summaries.
Assembly: hg38
Supplementary files format and content: differential gene expression matrix files

molecule: total RNA

organism: Homo sapiens

source_name: Prostate

extract_protocol:
Patients were positioned in the lithotomy position. The 2 lateral lobes and median lobe of the prostate were enucleated using a Holmium laser. Each lobe was dissected away from the surgical capsule in a distal to proximal approach and released from the bladder neck. Prostate tissue was minced and evacuated by a Piranha morcellator (Richard Wolf). Morcellation was performed according to manufacturer’s recommendations up to 1,500 rpm with dual inflow saline irrigation. Morcellated tissue was collected in a canister and placed on ice prior to dissociation and preparation for single cell RNA-sequencing. Morcellated tissue was immediately delivered to the laboratory and further minced to ~1-5mm3 pieces with surgical scissors in a petri dish with 10 mL RP-10 (RPMI + 10% FBS) on ice for up to 5 mins and washed with cold RP-10 (RPMI + 10% FBS). Each sample was centrifuged at 1200 rpm x5 mins at 4°C and resuspended in 10 mL warmed digestive media (HBSS + 1% HEPES) with 1,000 U/mL collagenase type IV (Worthington, Cat: LS004188), and rotated for 30 min at 37 °C. Samples were triturated by pipetting 10 times at the end of the incubation. Each sample was filtered through a 70-µm filter (Falcon, Cat: 352350), washed with RP-10, centrifuged at 1200 rpm x5 mins at 4°C, washed again with RP-10, and resuspended in RP-10.
Sequencing was largely based on the Seq-Well S^3 protocol. One to two arrays were used per sample. Each array was loaded as previously described with approximately 110,000 barcoded mRNA capture beads (ChemGenes, Cat: MACOSKO-2011-10(V+)) and with 15,000–20,000 cells. Arrays were sealed with functionalized polycarbonate membranes (Sterlitech, Cat: PCT00162X22100) and were incubated at 37 °C for 40 min. After sealing, each array was incubated in lysis buffer (5 M guanidine thiocyanate, 1 mM EDTA, 0.5% sarkosyl, 1% BME). After detachment and removal of the top slides, arrays were rotated at 50 rpm for 20 min. Each array was washed with hybridization buffer (2 M NaCl, 4% PEG8000) and was then rocked in a hybridization buffer for 40 min. Beads from different arrays were collected separately. Each array was washed ten times with wash buffer (2 M NaCl, 3 mM MgCl2, 20 mM Tris-HCl pH 8.0, 4% PEG8000) and scraped ten times with a glass slide to collect beads into a conical tube. For each array, beads were washed with Maxima RT buffer (ThermoFisher, Cat: EP0753) and resuspended in reverse transcription mastermix with Maxima RT buffer, PEG8000, Template Switch Oligo, dNTPs (NEB, Cat: N0447L), RNase inhibitor (Life Technologies, Cat: AM2696) and Maxima H Minus Reverse Transcriptase (ThermoFisher, Cat: EP0753) in water. Samples were rotated end-to-end, first at room temperature for 30 min and then at 52 °C overnight. Beads were washed once with TE-TW, once with TE-SDS, twice with TE-TW, and once with 10 mM Tris-HCl pH 8.0.
They were treated with exonuclease I (NEB), rotating for 50 min at 37 °C. Beads were washed once with TE-SDS and twice with TE-TW. They were resuspended in 0.1 M NaOH and rotated for 5 min at room temperature. They were subsequently washed with TE-TW and TE. They were taken through second strand synthesis with Maxima RT buffer, PEG8000, dNTPs, dN-SMRT oligo, and Klenow Exo- (NEB, Cat: M0212L) in water. After rotating at 37 °C for 1 h, beads were washed twice with TE-TW, once with TE and once with water. KAPA HiFi Hotstart Readymix PCR Kit (Kapa Biosystems, Cat: KK2602) and SMART PCR Primer were used in whole transcriptome amplification (WTA). For each array, beads were distributed among 24 PCR reactions. Following WTA, three pools of eight reactions were made and were then purified using SPRI beads (Beckman Coulter), first at 0.6× and then at a 1× volumetric ratio. For each sample, one pool was run on an HSD5000 tape (Agilent, Cat: 5067–5592). The concentration of DNA for each of the three pools was measured via the Qubit dsDNA HS Assay kit (ThermoFisher, Cat: Q33230). Libraries were prepared for each pool, using 1000 pg of DNA and the Nextera XT DNA Library Preparation Kit. They were dual-indexed with N700 and N500 oligonucleotides.

value: Prostate

tag: age

tag: prostate size_(cc)

tag: ethnicity

value: Korean

tag: 5ari treatment

value: Yes


title: RNA3, clr4Δ, heat-treatment 2.5min, rep3

city: Bunkyo, Tokyo

first: Soichi

last: Inagaki

department: Department of Biological Sciences

country: Japan

institute: Graduate School of Science, The University of Tokyo

data_processing:
ChIP-seq reads were trimmed using Trimmomatic ver 0.33 with SE, CROP:50, ILLUMINACLIP:TruSeq3-SE.fa:2:10:10, SLIDINGWINDOW:5:20, MINLEN:30 parameters. Trimmed reads were mapped on the S.pombe ASM294v2 genome using Bowtie ver 0.12.9. The read count for each transcription unit was calculated using the coverage function of BEDTools ver 2.17.0. The bigwig files were created using deeptools software.
RNA-seq reads were trimmed using Trimmomatic ver 0.33 with SE, CROP:50, ILLUMINACLIP:TruSeq3-SE.fa:2:10:10, SLIDINGWINDOW:5:20, MINLEN:30 parameters. Trimmed reads were mapped on the S.pombe ASM294v2 genome using STAR aligner with -- outFilterType, BySJout; -- alignSJoverhangMin, 8; -- alignSJDBoverhangMin, 1; -- quantMode GeneCounts parameters. When we analyzed the expression of DNA sequence inculding repeat regions such as heterochromatin genes, we calculated the readcounts from bedgraph file, which was produced using the coverage function of BEDTools ver 2.17.0. Those readcount files were named as “mRNA_XXX_for_HGs.txt".
PRO-seq reads were mapped on S.pombe ASM294v2 genome using Bowtie ver 0.12.9. The read count for each transcription unit was calculated using the coverage function of BEDTools ver 2.17.0. The bigwig files were created from bedgraph files using bedGraphToBigWig program.
Assembly: ASM294v2
Supplementary files format and content: bigwig file for ChIP-seq and PRO-seq
Supplementary files format and content: tab-delimited text file for RNA-seq

organism: Schizosaccharomyces pombe

source_name: S.pombe cells

growth_protocol: Cells were grown in YES medium until mid-log phase at 30 ºC.

extract_protocol:
Total RNA for mRNA-seq was extracted by the hot-phenol method, as previously described (Iyer,V. and Struhl,K. 1996). Cell permeabilization and extraction of biotinylated RNA for PRO-seq was performed as previously described (Mahat et al., 2016). Chromatin for ChIP-seq, extracted from cell lysate of 1% formaldehyde fixed-cells, was sonicated using a Picoruptor (Diagenode).
ChIP-seq libraries were constructed using the ThruPLEX DNA-seq Kit (Clontech). mRNA-seq libraries were constructed using the KAPA mRNA HyperPrep Kit (Kapa Biosystems). cDNA libraries for PRO-seq were converted from the RNA, to which 3' and 5' adaptors were ligated, by revearse transcription.

treatment_protocol: The non-treated samples (0 min) were harvested immediately, and the heet-treated samples were moved from a 30 ºC water bath to 37.5 ºC and incuvated during the designated term (2.5, 5 and 25 min) with shaking.

tag: cell type

value: S.pombe cells

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ clr4{delta}::NatMX6

tag: treatment

value: 2.5 min atter heat-treatment


title: Lung, control diet, filtered air, 1

city: Columbus

first: Michael

middle: J

last: Yaeger

state: OH

address: 473 W 12th Ave

institute: The Ohio State University

description: Library name: 5913

data_processing:
Partek Flow
Sequence reads were trimmed for adaptor sequence/low-quality sequence Partek Flow
Trimmed sequence reads were mapped to mm39 using STAR in Partek Flow
Read count extraction and normalization were performed using HT-seq on Partek Flow
Assembly: mm39
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample

source_name: Lung

extract_protocol:
RNA was extrated using the Qiagen RNeasy Mini Kit (Fisher Scientific)
RNA libraries for RNA-seq were prepared by Genewiz.

value: Lung


title: HoLEP28 [HoLEP_28B_S89]

description:
Library name: HoLEP_28B_S89
SeqWell

value: White

value: No


title: Saline1

city: Jinan

first: Donghai

last: Wang

state: Shandong

address: Wenhuaxi Road

country: China

institute: Qilu Hospital of Shandong University

description:
Library name: Sample1
Saline1

data_processing:
CLC Genomics Workbench v11.0.1
Sequence reads were trimmed for adaptor sequencellow-quality sequence using CLC genomic benchwork (parmeter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarty faction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwvork
Assembly: mm10
Supplementary files format and content: tab-delimited text fles include RPKM values for each Sample

source_name: Brain

growth_protocol: Male wild-type C57 mice; housed in SPF conditions (12 h light/dark, 22 ± 2 °C, 50 ± 10% humidity); food and water ad libitum.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).1.3ug of total RNA was yused for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER MRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: Photochemically induced stroke models were established via intravenous injection at a dose of 100 mg/kg. A 250 mW 532 nm laser with a 1.5 mm diameter was focused on the left cerebral hemisphere and irradiated for 5 minutes. At 2 hours post-photothrombosis, 100 μL of saline or PLEA nanoparticles was administered via tail vein injection.The mice were then perfused with pre-chilled phosphate-buffered saline (PBS). Brains were promptly harvested and snap-frozen in liquid nitrogen for subsequent storage.

value: Brain

value: WT

value: Saline

tag: batch

value: Day 3


title: PRO2, clr4Δ, heat-treatment 0min, rep1

library_source: other

data_processing:
library strategy: PRO-seq
ChIP-seq reads were trimmed using Trimmomatic ver 0.33 with SE, CROP:50, ILLUMINACLIP:TruSeq3-SE.fa:2:10:10, SLIDINGWINDOW:5:20, MINLEN:30 parameters. Trimmed reads were mapped on the S.pombe ASM294v2 genome using Bowtie ver 0.12.9. The read count for each transcription unit was calculated using the coverage function of BEDTools ver 2.17.0. The bigwig files were created using deeptools software.
RNA-seq reads were trimmed using Trimmomatic ver 0.33 with SE, CROP:50, ILLUMINACLIP:TruSeq3-SE.fa:2:10:10, SLIDINGWINDOW:5:20, MINLEN:30 parameters. Trimmed reads were mapped on the S.pombe ASM294v2 genome using STAR aligner with -- outFilterType, BySJout; -- alignSJoverhangMin, 8; -- alignSJDBoverhangMin, 1; -- quantMode GeneCounts parameters. When we analyzed the expression of DNA sequence inculding repeat regions such as heterochromatin genes, we calculated the readcounts from bedgraph file, which was produced using the coverage function of BEDTools ver 2.17.0. Those readcount files were named as “mRNA_XXX_for_HGs.txt".
PRO-seq reads were mapped on S.pombe ASM294v2 genome using Bowtie ver 0.12.9. The read count for each transcription unit was calculated using the coverage function of BEDTools ver 2.17.0. The bigwig files were created from bedgraph files using bedGraphToBigWig program.
Assembly: ASM294v2
Supplementary files format and content: bigwig file for ChIP-seq and PRO-seq
Supplementary files format and content: tab-delimited text file for RNA-seq

molecule: other

value: 0 min (non treated)


title: HoLEP26 [HoLEP_26B_S87]

description:
Library name: HoLEP_26B_S87
SeqWell


title: Lung, control diet, filtered air, 2

description: Library name: 5914


title: HoLEP28 [HoLEP_28A_S88]

description:
Library name: HoLEP_28A_S88
SeqWell


title: RNA3, clr4Δ, heat-treatment 5min, rep3

value: 5 min atter heat-treatment


title: Adjacent normal tissue, patient 248, MeRIP-Seq

city: Wenzhou

first: wenjing

last: zhao

address: Central North Road

institute: wenzhou medical university

description: Library name: 248N.m5c

data_processing:
Raw reads were quality controlled with Q30 threshold and adapters were trimmed using cutadapt (v1.9.3).
MeRIP-Seq reads were aligned using STAR (v2.5.1b), m5C peaks called using MACS2 (v2.2.7.1).
Differential expression analysis performed using edgeR (v3.16.5), GO and KEGG enrichment analysis conducted for differentially expressed genes.
Assembly: GRCh37/hg19
Supplementary files format and content: BED files contain m5C peak locations; TXT files contain raw gene counts; XLSX files contain differential expression results and clinical metadata.
Library strategy: MeRIP-Seq

source_name: MeRIP-Seq of adjacent normal tissue

extract_protocol:
Total RNA was extracted from gastric cancer tissues and adjacent normal tissues using TRIzol reagent (Invitrogen) following the manufacturer's protocol. RNA quality was assessed by Agilent 2100 Bioanalyzer with RIN >7.0 for all samples.
RNA was fragmented and immunoprecipitated with anti-m5C antibody, then library construction was performed using KAPA HyperPrep Kit.

value: stomach


title: Dissected 10 somite limbbud tissue_rnaseq_rep2

description: Library name: 20231215_ALt14_NEB

value: embryonic limb tissue

value: 10 somite stage

value: Swiss Webster mice


title: Adjacent normal tissue, patient 255, MeRIP-Seq

description: Library name: 255N.m5c


title: HoLEP26 [HoLEP_26A_S86]

description:
Library name: HoLEP_26A_S86
SeqWell

value: Prostate


title: RNA3, clr4Δ, heat-treatment 0min, rep3

value: S.pombe cells


title: Dissected 10 somite limbbud tissue_rnaseq_rep1

description: Library name: 20230907_ALt13_NEB


title: RNA3, clr4Δ, heat-treatment 5min, rep2

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ clr4{delta}::NatMX6


title: Gastric cancer tissue, patient 260, MeRIP-Seq

description: Library name: 260C.m5c

source_name: MeRIP-Seq of cancer tissue


title: rVSV-D7-GEX

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description: Library name: rVSV-D7-GEX

data_processing:
The mRNA data was mapped to the mm10 genome using the STARsolo framework (STAR version 2.7.10a) (Dobin et al. 2013).
Gene quantification made use of a custom GFT file based on the ensembl gene annotation (version 102). The cell barcode whitelist used for STAR is the file 737K-august-2016.txt provided by 10x. Other non-standard command line options for STAR included "--outFilterType BySJout --outFilterMultimapNmax 10 --outSAMmultNmax 1 --outSAMtype BAMSortedByCoordinate --outSAMunmapped Within --soloType CB_UMI_Simple --soloStrand Reverse --outFilterScoreMin 30 --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIlen 10 --soloUMIfiltering MultiGeneUMI_CR --soloUMIdedup 1MM_CR --soloCellFilter None --soloMultiMappers EM --soloBarcodeReadLength 0 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloFeatures Gene --outSAMattributes NH HI AS nM CR CY UR UY GX GN CB UB".
The cDNA fastq files for cell surface hashtag data (ADT+HTO) were first trimmed with the tool fastp (version 0.20.1) (Chen et al. 2018) and command line options "-b 15 -f 10 -t 0 -A -Q -G -L". After cDNA trimming cell surface hastag data was mapped and quantified with STARsolo, by using the same cell barcode whitelist as for GEX data. The genome index was build from the hashtag sequences as well as the GTF file used for quantification. Additional command line options included "--outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --soloType CB_UMI_Simple --soloStrand Forward --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIlen 10 --soloUMIfiltering MultiGeneUMI_CR --soloUMIdedup 1MM_CR --soloCellFilter None --soloBarcodeReadLength 0 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloFeatures Gene".
Assembly: Mouse mm10
Supplementary files format and content: Three files per sample which are the raw output of STARsolo: 1. gene counts (<sample_id>_matrix.mtx), 2. tab separated text file with gene/cell surface hashtag IDs (<sample_id>_features.tsv), 3. tab separated text file with cell barcodes (<sample_id>_barcodes.tsv)

source_name: Spleen

extract_protocol:
Murine spleens were isolated and mechanically disrupted using a metal mesh and a syringe plunger, and cells were counted with a Immunospot S6 device (C.T.L.). CD8 T cells were enriched by magnetic-activated cell sorting using the CD8+ T cells Isolation Kit, mouse (STEMCELL), but the antibody mix in the kit was replaced by a mix containing the following biotin-conjugated antibodies from BioLegend: anti-B220 (RA3-6B2), anti-CD19 (6D5), Ly-76 (TER-119), anti-CD4 (H129.19) and anti-CD138 (281-2). Cell suspensions were stained with antibodies against CD45R/B220 (RA3-6B2), CD8 (53-6.7) and DAPI purchased from BioLegend, PE-conjugated H2-Kb tetramers loaded with the SARS-CoV-2 spike epitope VNFNFNGL (produced by the University of Lausanne Tetramer core facility).  Cells were stained with oligo-conjugated antibodies (ADT) for surface markers using TotalSeq-C0250 anti-KLRG1 (138433, BioLegend), TotalSeq-C0563 anti-CX3CR1 (149043, BioLegend), TotalSeq-C0198 anti-CD127 (104455, BioLegend) and TotalSeq-C0112 anti-CD62L (135047, BioLegend) . Each condition included 3 biological replicates which were labelled with hashtag oligos (HTOs): TotalSeq-C0301 (155861, BioLegend), TotalSeq-C0302 (155863, BioLegend) or TotalSeq-C0303 (155865, BioLegend) before being pooled Tetramer-binding CD8 T cells were FACS-sorted (FACS Aria II, BD) and the recovered cells were immediately processed for cell capture and library preparation
Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) with Feature Barcode technology for Cell Surface Protein & Immune Receptor Mapping (CG000330 Rev D)

value: Spleen

value: CD8 T cells

value: rVSV

tag: timepoint

tag: library type

value: GEX


title: HoLEP23 [HoLEP_23A_S84]

description:
Library name: HoLEP_23A_S84
SeqWell

value: Chinese

value: No


title: Gastric cancer tissue, patient 248, MeRIP-Seq

description: Library name: 248C.m5c


title: MV4-11-XR

city: Taipei

first: Yu-Hsuan

last: Fu

address: No.1, Chang-Te St

department: Department of Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

data_processing:
Sequencing was performed on Illumina NextSeq 500 platform.
Paired-end sequencing alignment toward hg19 and reads mapping to known genes were performed by Bowtie2.
Gene expression level was calculated by RSEM with Maximum likelihood abundance estimates using the Expectation Maximization (EM) algorithm for its statistical model.
Differentially expressed genes (DEGs) identification between groups were conducted with EBSeq, with a threshold of fold change ≥ 2 or ≤ 0.5 and p-value of ≤ 0.05.
Assembly: hg19 (GRCh37)
Supplementary files format and content: *csv: comma-separated values of row counts for each known gene (HGNC symbol) in columns and sample in rows.

growth_protocol: Indiacted cells were cultured in RPMI1640 medium suppled with 10% FBS and 1% antibiotic in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNAs were isolated with NucleoSpin® RNA kit (Macherey-Nagel); The final library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.
Strand-specific RNA library were built by TruSeq stranded protocols from Illumina

treatment_protocol: The cabozantinib-resistant cells (Molm13-XR and MV4-11-XR) were derived by culturing the parental cells in low-concentration cabozantinib and escalating the dose once the cells were recovered.

tag: cell line

value: The cabozantinib-resistant cells (MV4-11-XR) were derived by culturing the parental cells in low-concentration cabozantinib and escalating the dose once the cells were recovered.


title: RNA3, clr4Δ, heat-treatment 2.5min, rep2

value: 2.5 min atter heat-treatment


title: RNA3, clr4Δ, heat-treatment 0min, rep2

value: 0 min (non treated)


title: HoLEP21 [HoLEP_21B_S83]

description:
Library name: HoLEP_21B_S83
SeqWell

value: White


title: RNA3, clr4Δ, heat-treatment 5min, rep1

value: 5 min atter heat-treatment


title: Gastric cancer tissue, patient 255, MeRIP-Seq

description: Library name: 255C.m5c

value: stomach


title: Dissected 14 somite limbbud tissue_riboseq_rep2

description: Library name: 20230907_ALt17_ITP

data_processing:
The ribosome profiling libraries were processed using the Riboflow pipeline v.0.0.1 using deduplication with unique molecular identifiers - UMItools (Ozadam et al., 2020).
Assembly: GRCm38
Supplementary files format and content: .ribo file containing the matched Riboseq and RNAseq read counts.
Library strategy: Ribo-Seq

molecule: cytoplasmic RNA

value: embryonic limb tissue

value: 14 somite stage


title: Dissected 14 somite limbbud tissue_riboseq_rep1

description: Library name: 20230907_ALt16_ITP

value: Swiss Webster mice


title: Dissected 10 somite limbbud tissue_riboseq_rep1

description: Library name: 20230907_ALt13_ITP

value: 10 somite stage


title: Dissected 10 somite limbbud tissue_riboseq_rep2

description: Library name: 20231213_ALt14_ITP


title: CCG379

city: Houston

first: Qi

state: TX

address: 7007 Bertner Ave

institute: UT MD Anderson Cancer Center

description: Library name: Sample_25-CCG379

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
RNA-seq reads were aligned to GRCh38 genome using tophat v2.0.13
Assembly: GRCh38
Supplementary files format and content: RNA-seq/miRNAseq reads TPM

source_name: osteosarcoma cell

extract_protocol:
RNeasy Mini Kit (50)
RNA libraries for RNA-seq were prepared at the Advanced Technology Genomics Core at MD Anderson Cancer Center.

value: osteosarcoma cell


title: HoLEP21 [HoLEP_21A_S82]

description:
Library name: HoLEP_21A_S82
SeqWell

value: Prostate


title: RNA3, clr4Δ, heat-treatment 2.5min, rep1

value: S.pombe cells

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ clr4{delta}::NatMX6


title: CCG368

description: Library name: Sample_23-CCG368


title: RNA-Seq of MNK3:sample5

city: Los Angeles

first: Zhiheng

last: He

state: CA

address: 1450 Biggy Street NRT 5514 NRT 5514

department: Immunology and Immune Therapeutics

institute: University of Southern California

description:
Library name: MNK3_sgDab2ip_Rep2
MNK3 Scramble or sgDab2ip subjected to Il-1β activation

data_processing:
Library preparation and sequencing were performed as DNBSEQ eukaryotic strand-specific mRNA libraries; six libraries in total were sequenced on the DNBSEQ platform with paired-end 150-bp reads (PE150) and Phred+33 quality encoding.
Reads were quality-checked and trimmed, aligned to the mouse genome (mm10) with STAR
Reads were counted with featureCounts.
Differential expression was computed using DESeq2; genes with FDR-adjusted P < 0.05 and |log₂ (fold change) | ≥ 1 were called significant.
Assembly: mm10
Supplementary files format and content: The tabularly arranged text file contains the  normalized processed count data for each sample.

growth_protocol: MNK3 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), antibiotics,IL-7, and IL-15 with  5% CO2 at 37C

extract_protocol:
MNK3 cells were cultured in the DMEM medium supplemented with 10% FBS antibiotics,IL-7, and IL-15 overnight, after which they were treatment with x10ng/ml IL-1β for 30 minutes.
RNA was harvested using Rneasy mini plus kit (Qiagen). 0.8ug of total RNA was used for the construction of sequencing libraries.

treatment_protocol: MNK3 cells was activated by treatment with 10ng/ml IL-1β for 30 minutes.

value: ILC3 cell line


title: CCG396

description: Library name: Sample_26-CCG396


title: HoLEP20 [HoLEP_20B_S81]

description:
Library name: HoLEP_20B_S81
SeqWell

value: Yes


title: RNA3, pcr1Δ, heat-treatment 5min, rep3

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ pcr1{delta}::KanMX6


title: RNA3, clr4Δ, heat-treatment 0min, rep1


title: CCG366

description: Library name: Sample_22-CCG366


title: CCG377

description: Library name: Sample_24-CCG377


title: RNA-Seq of MNK3:sample4

description:
Library name: MNK3_sgDab2ip_Rep1
MNK3 Scramble or sgDab2ip subjected to Il-1β activation


title: HoLEP23 [HoLEP_23B_S85]

description:
Library name: HoLEP_23B_S85
SeqWell

value: Chinese

value: No


title: CCG365

description: Library name: Sample_21-CCG365


title: RNA3, pcr1Δ, heat-treatment 0min, rep3

value: 0 min (non treated)


title: RNA-Seq of MNK3:sample3

description:
Library name: MNK3_Scramble_Rep3
MNK3 Scramble or sgDab2ip subjected to Il-1β activation

value: Scramble


title: RNA-Seq of MNK3:sample6

description:
Library name: MNK3_sgDab2ip_Rep3
MNK3 Scramble or sgDab2ip subjected to Il-1β activation


title: WT and Fgf10 knockout mouse limb bud tissue

description:
Library name: 20240629_scRNA_seq
Parse Biosciences

data_processing:
The scRNA-seq datasets were analyzed and visualized using the Parse Biosciences Pipeline TrailmakerTM web tool (Pipeline v1.2.1, analysis completed on 09.16.2024). The raw FASTQ files were processed using TrailmakerTM pipeline module to demultiplex the combinatorial barcodes and obtain cell-by-gene count matrices.
Assembly: GRCm39, v112
Supplementary files format and content: .Rds files with per cell read count matrix.

source_name: embryonic limb bud tissue

growth_protocol: Embryos were obtained from Fgf10tm1.1Sms allele (Abler et al., 2009) maintained on a mixed background (~75% Swiss Webster).

extract_protocol:
Two 15 somite-stage Fgf10+/+ and two 16 somite-stage Fgf10-/- embryos (E8.75) were dissected in cold 1X DPBS . The heart and tissues anterior to somite 7 and posterior to somite 13 were dissected away. The resulting core of embryonic tissue included the forelimb field as well as other embryonic tissues present at this axial level. Single embryos were trypsinized and then filtered through a cell strainer, transferred into a 1% BSA coated tube and centrifuged for 10 minutes at 500g at 4°C. Cells were fixed as described using (Tran et al., 2022) and ~58-73k cells per embryo were stored in -80℃.
scRNASeq libraries were prepared using the Parse Evercode WT Mini v2 kit according to the manufacturers protocol. The libraries were sequenced on an Illumina NovaSeq X Plus.

value: embryonic limb bud tissue

tag: somite stage

value: 15 and 16 somite

value: WT and Fgf10 knockout


title: CCG355

description: Library name: Sample_20-CCG355


title: HoLEP20 [HoLEP_20A_S80]

description:
Library name: HoLEP_20A_S80
SeqWell

value: White


title: RNA3, pcr1Δ, heat-treatment 5min, rep2

value: 5 min atter heat-treatment


title: HoLEP18 [HoLEP_18A_18B_S78]

description:
Library name: HoLEP_18A_18B_S78
SeqWell


title: HoLEP17 [HoLEP_17A_S97]

description:
Library name: HoLEP_17A_S97
SeqWell


title: RNA3, pcr1Δ, heat-treatment 0min, rep2


title: HoLEP17 [HoLEP_17B_S76]

description:
Library name: HoLEP_17B_S76
SeqWell


title: RNA3, pcr1Δ, heat-treatment 5min, rep1


title: RNA-Seq of MNK3:sample2

description:
Library name: MNK3_Scramble_Rep2
MNK3 Scramble or sgDab2ip subjected to Il-1β activation


title: HoLEP14 [RU_HoLEP14_B_S11]

description:
Library name: RU_HoLEP14_B_S11
SeqWell


title: HoLEP16 [HoLEP_16B_S75]

description:
Library name: HoLEP_16B_S75
SeqWell


title: Untreated and IL-7 treated CD8 T cells Gene expression

city: Atlanta

first: Donald

last: McGuire

state: GA

address: 1462 Clifton Road room 412

institute: Emory University School of Medicine

description:
Library name: Library 1 GEX
10x Gene expression library.  Read 1 is barcode, read 2 is mRNA sequence.

data_processing:
Fastq files form were alligned and counts obtained with Cellranger 8.0.1.  Intron counts were not included.  Data were normialized with Seurat 5 R package
Cite seq id's were used to sepereate untreated, day 8 Nt-i7 treated, d14 Nt-i7 treated cells in R using the Seurat R 5 package.
Assembly: mm10
Supplementary files format and content: H5 file with gene expression and CITE-seq counts outputed from Cell ranger 8.0.1: filtered_feature_bc_matrix.h5
Supplementary files format and content: CSV file with cell anotations from clustering and treatment ID derived from alaysis with Seurat 5 R package.  Row.names are cell barcodes:cell_id.csv

molecule: protein

extract_protocol:
8 days or 14 days after the treatment, splenocytes were isolated from the mice and resuspended in ice cold FACS buffer (Ca2+/Mg2+ PBS supplemented with 4% FBS and 2mM EDTA). Splenocytes were stained with antibodies and LCMV-GP33 Tetramer in FACS buffer on ice for 30min. Cells were washed and resuspended in FACS buffer, LCMV-GP33 Tet+ CD8 T cells were sorted using FACSAria II(BD) Library was contructed using manufactures protcol for single cell 5' v2 10x genomics
Library prepared occording 10x genomics instructions using 5' library and CITE-seq with TotalSeq-C Cell hash antibodies.

treatment_protocol: C57Bl/6J mice were intravenously infected with 2x10^6 LCMV clone-13 with transient CD4 depletion. >45 days post infection, mice were treated with a single dose of injection buffer or 200ug NT-I7, a hybrid Fc-fused recombinant human IL-7 (hIL-7-hyFc, efineptakin alfa, NeoimmuneTech).

value: Spleen

value: CD 8 T cells

value: mRNA


title: RNA-Seq of MNK3:sample1

description:
Library name: MNK3_Scramble_Rep1
MNK3 Scramble or sgDab2ip subjected to Il-1β activation


title: CCG354

description: Library name: Sample_19-CCG354

value: osteosarcoma cell


title: HoLEP16 [HoLEP_16A_S99]

description:
Library name: HoLEP_16A_S99
SeqWell

value: Prostate


title: Untreated and IL-7 treated CD8 T cells CITE

description:
Library name: Library 1 CITE
10x CITE-seq library of Totalseq-C hash antibodies.  Read 1 is bardcode, Read 2 is antibody barcode sequence

data_processing:
Fastq files form were alligned and counts obtained with Cellranger 8.0.1.  Intron counts were not included.  Data were normialized with Seurat 5 R package
Cite seq id's were used to sepereate untreated, day 8 Nt-i7 treated, d14 Nt-i7 treated cells in R using the Seurat R 5 package.
Assembly: mm10
Supplementary files format and content: H5 file with gene expression and CITE-seq counts outputed from Cell ranger 8.0.1: filtered_feature_bc_matrix.h5
Supplementary files format and content: CSV file with cell anotations from clustering and treatment ID derived from alaysis with Seurat 5 R package.  Row.names are cell barcodes:cell_id.csv
Library strategy: CITE-seq

value: HTO

tag: hto

value: TotalSeq-C0301 anti-mouse hashtag antibody 1 (untreated),  TotalSeq-C0302 anti-mouse hashtag antibody 2 (Nt-i7 treated day 8),  TotalSeq-C0303 anti-mouse hashtag antibody 3 (Nt-i7 treated day 14),


title: CCG343

description: Library name: Sample_18-CCG343


title: RNA3, pcr1Δ, heat-treatment 0min, rep1

value: S.pombe cells

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ pcr1{delta}::KanMX6


title: CCG340

description: Library name: Sample_16-CCG340


title: RNA3, atf1Δ, heat-treatment 5min, rep3

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ atf1{delta}::KanMX6


title: RNA3, atf1Δ, heat-treatment 0min, rep3

value: 0 min (non treated)


title: CCG337

description: Library name: Sample_15-CCG337


title: LPM KO, MafB3, Rep2

city: Liège

first: Thomas

last: Marichal

address: Avenue de l'Hopital 11

department: GIGA Institute

country: Belgium

institute: University of Liege

description: Library name: LPM_KO_MafB3_R2-NGS25-K147

library_source: genomic

data_processing:
Raw reads were processed using the nf-core/cutandrun pipeline for adapter trimming, alignment to the mouse reference genome (GRCm38/mm10), and quality control. For MafB CUT&RUN, peaks were called using SEACR (Sparse Enrichment Analysis for CUT&RUN) in stringent mode.
Normalized tag counts were calculated with the annotatePeaks.pl function from HOMER. MafB binding sites were defined as peaks with higher normalized tag counts in wild-type compared with Mafb-deficient cells. MafB binding sites were assigned to target genes based on proximity to transcription start sites (±2 kb) using HOMER. CUT&RUN signal tracks were visualized with the Integrative Genomics Viewer (IGV).
Assembly: GRCm38
Supplementary files format and content: bedGraph
Library strategy: CUT&Run

molecule: genomic DNA

source_name: Peritoneum

extract_protocol:
Bone marrow derived macrophages BMMos were isolated from BM using Monocyte Isolation Kit (BM) (Miltenyi Biotec, 130100629) and were seeded in tissue culture-treated plates and cultured for 4 days in RPMI supplemented with 10% FBS, 1 mM Sodium Pyruvate (Thermo Fisher Scientific, 11360070), 1X Minimum Essential Medium Non-Essential Amino Acids (MEM NEAA; Thermo Fisher Scientific, 11140050), 50 µM β-mercaptoethanol (Thermo Fisher Scientific, 31350010) and 40 ng/ml Csf-1 (Peprotech, 31502) to differentiate them into BMDMs.  Large peritoneal macrophages Lyz2CreMafbfl/fl mice and Mafbfl/fl littermate controls were terminally anesthetized and peritoneal lavage was obtained by injecting 10 ml PBS (Thermo Fisher Scientific, 14190094) containing 10 mM EDTA into the peritoneal cavity and collecting the washout. LPMs were FACS sorted from the peritoneal lavage as CD45+Lin−Ly6C−CD11b+CD115+F4/80+MHC-II− live cells.  Human monocyte-derived macrophages Buffy coats from healthy volunteers were obtained through the Belgian Red Cross. Peripheral blood mononuclear cells were isolated by density gradient centrifugation on Lymphoprep (1.077 g/ml; StemCell Technologies). Classical monocytes were negatively selected using the Classical Monocyte Isolation Kit (Miltenyi Biotec, 130117337) according to the manufacturer’s instructions. Monocytes were seeded in Petri dishes (10 × 106 cells/dish) in RPMI supplemented with 10% FBS, 1× MEM NEAA (Thermo Fisher Scientific, 11140050), 50 µM β-mercaptoethanol, and 50 ng/ml recombinant human CSF-1 (Immunotools, 11343115). Fresh differentiation medium was added on day 3. On day 7, monocyte-derived macrophages (MDMs) were detached using cold PBS containing 0.25 mM EDTA.
CUT&RUN was performed using the CUTANA ChIC/CUT&RUN Kit (EpiCypher, 141048) according to the manufacturer’s instructions, with minor modifications. BMDMs or LPMs from Mafbfl/fl or Lyz2CreMafbfl/fl mice, as well as human MDMs from healthy donors, were washed with ice-cold PBS and fixed with 0.1% formaldehyde in PBS for 2 min at room temperature. Fixation was quenched with 0.125 M glycine (Merck, 104691000). For each CUT&RUN sample, 0.5 × 106 fixed cells were incubated with 0.5 µg antibody. The following antibodies were used: IgG (EpiCypher, 13-0042) MafB1 (Sigma, HPA005653) MafB2 (Cell Signaling Technology, 41019) MafB3 (Proteintech, 20189-1-AP)
CUT&RUN libraries were prepared using the CUTANA CUT&RUN Library Prep Kit  (EpiCypher, 141001) following the manufacturer’s instructions and sequenced on a NovaSeq 6000 (Illumina) with an S4 flow cell at a depth of 10 million reads per sample.

value: Peritoneum

value: Large Peritoneal Macrophage

value: Lyz2Cre Mafbfl/fl (Mafb KO)

tag: cut&run antibody

value: MafB3 (Proteintech, 20189-1-AP)


title: CCG342

description: Library name: Sample_17-CCG342


title: HoLEP10 [RU_HoLEP10_B_S7]

description:
Library name: RU_HoLEP10_B_S7
SeqWell

value: White

value: No


title: HoLEP10 [RU_HoLEP10_A_S6]

description:
Library name: RU_HoLEP10_A_S6
SeqWell


title: LPM KO, MafB3, Rep1

description: Library name: LPM_KO_MafB3_R1-NGS25-K146


title: RNA3, atf1Δ, heat-treatment 5min, rep2

value: 5 min atter heat-treatment


title: CCG322

description: Library name: Sample_14-CCG322


title: LPM KO, MafB2, Rep2

description: Library name: LPM_KO_MafB2_R2-NGS25-K145

value: MafB2 (Cell Signaling Technology, 41019)


title: RNA3, atf1Δ, heat-treatment 0min, rep2


title: HoLEP11 [RU_HoLEP11_AB_S8]

description:
Library name: RU_HoLEP11_AB_S8
SeqWell


title: CCG308

description: Library name: Sample_13-CCG308


title: HoLEP9 [RU_HoLEP9_A_S4]

description:
Library name: RU_HoLEP9_A_S4
SeqWell

value: African American


title: CCG301

description: Library name: Sample_12-CCG301

value: osteosarcoma cell


title: LPM KO, MafB2, Rep1

description: Library name: LPM_KO_MafB2_R1-NGS25-K144


title: HoLEP9 [RU_HoLEP9_B_S5]

description:
Library name: RU_HoLEP9_B_S5
SeqWell

value: Prostate


title: LPM KO, MafB1, Rep2

description: Library name: LPM_KO_MafB1_R2-NGS25-K143

value: MafB1 (Sigma, HPA005653)


title: CCG300

description: Library name: Sample_11-CCG300


title: HoLEP4 [PA_HoLEP4_B_S14]

description:
Library name: PA_HoLEP4_B_S14
SeqWell


title: LPM KO, MafB1, Rep1

description: Library name: LPM_KO_MafB1_R1-NGS25-K142


title: CCG242

description: Library name: Sample_10-CCG242


title: HoLEP4 [PA_HoLEP4_A_S13]

description:
Library name: PA_HoLEP4_A_S13
SeqWell


title: RNA3, atf1Δ, heat-treatment 5min, rep1


title: ChIP3, clr3Δ, H3K9me2, heat-treatment 0min, rep2

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ clr3{delta}::KanMX6


title: ChIP3, clr3Δ, H3K9me2, heat-treatment 5min, rep2

value: S.pombe cells


title: LPM WT, MafB3, Rep2

description: Library name: LPM_WT_MafB3_R2-NGS25-K139

value: Mafbfl/fl (Mafb WT)


title: RNA3, atf1Δ, heat-treatment 0min, rep1

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ atf1{delta}::KanMX6


title: PHLDA1-NT3_good

city: Suqian

first: Liangru

last: Shen

address: Qingyang road

institute: Kangshen Hospital

description: Library name: sample 6

data_processing:
Provided FASTQ files were aligned using STAR; reads were counted using featureCounts with -p -t exon -O -g gene_id -s 0. Sequencing quality was assessed using FASTQC. DEGs were analysed with the “DESeq2” R package and genes with adjusted p-value<0.05 and log2|fold change|≥ 1 were considered significant.
Assembly: GRCh38
Supplementary files format and content: excel file includes counts and FPKM for each sample

source_name: kidney

extract_protocol:
Cell RNA was isolated using the RNeasy Mini Kit  according to the manufacturer’s instructions
rRNA was depleted within 200 ng of total RNA, and sequencing libraries were generated using the NEBNext Ultra II Directional RNA library kit according to the manufacturer’s protocol

value: kidney

value: Epithelial cells


title: ChIP3, clr3Δ, H3K9me2, heat-treatment 5min, rep1


title: OPM2, 100 nM ricolinostat 20 h, replicate 2

city: Yokohama

first: Yuki

last: Yamaguchi

state: Kanagawa

address: 4259, Nagatsutacho, Midori-ku

department: School of Life Science and Technology

institute: Institute of Science Tokyo

description:
Library name: Sample20
Ricolinostat_20h_2

data_processing:
Base-calling and demultiplexing were carried out by Eurofins Genomics using the Illumina standard pipeline.
Paired-end sequencing reads from the FASTQ files were aligned to the reference genome using HISAT2.
The resulting alignment files were processed using Samtools.
Read counts per gene were generated with FeatureCounts.
Assembly: GRCh38.
Supplementary files format and content: Tab-delimited text file including raw counts for each sample.

source_name: Bone marrow

growth_protocol: OPM2 cells were maintained in RPMI 1640 with 10% FBS and antibiotics in humidified atmosphere at 37 °C with 5% CO₂.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol.
RNA library preparation and mRNA sequencing were outsourced to Eurofins Genomics (Japan). Briefly, poly(A)+ RNA was purified, fragmented, and reverse-transcribed using random primers to generate first-strand cDNA. Strand-specific libraries were constructed through second-strand synthesis, adaptor ligation, and amplification. Paired-end 100 bp sequencing was performed on a HiSeq 4000 platform (Illumina, San Diego, USA).

treatment_protocol: OPM2 cells were seeded at an appropriate density and treated with 10 nM panobinostat, 10 nM romidepsin, or 100 nM ricolinostat for 2, 5, or 20 h.

value: Bone marrow

value: Multiple myeloma cell

value: 10 nM ricolinostat for 20 h

value: Unknown


title: ChIP3, clr3Δ, H3K9me2, heat-treatment 0min, rep1

value: 0 min (non treated)


title: LPM WT, MafB3, Rep1

description: Library name: LPM_WT_MafB3_R1-NGS25-K138

value: Peritoneum

value: Large Peritoneal Macrophage

value: MafB3 (Proteintech, 20189-1-AP)


title: LPM WT, MafB2, Rep2

description: Library name: LPM_WT_MafB2_R2-NGS25-K137

value: MafB2 (Cell Signaling Technology, 41019)


title: OPM2, 100 nM ricolinostat 5 h, replicate 2

description:
Library name: Sample18
Ricolinostat_5h_2

value: 10 nM ricolinostat for 5 h


title: ChIP3, clr3Δ, H3, heat-treatment 5min, rep2

value: 5 min atter heat-treatment


title: OPM2, 100 nM ricolinostat 5 h, replicate 1

description:
Library name: Sample17
Ricolinostat_5h_1


title: ChIP3, clr3Δ, H3, heat-treatment 0min, rep2

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ clr3{delta}::KanMX6


title: ChIP3, clr3Δ, H3, heat-treatment 5min, rep1

value: S.pombe cells


title: PHLDA1-KO1_good

description: Library name: sample 1


title: OPM2, 100 nM ricolinostat 20 h, replicate 1

description:
Library name: Sample19
Ricolinostat_20h_1


title: LPM WT, MafB2, Rep1

description: Library name: LPM_WT_MafB2_R1-NGS25-K136

value: Mafbfl/fl (Mafb WT)


title: PHLDA1-NT1_good

description: Library name: sample 4


title: PHLDA1-NT2_good

description: Library name: sample 5


title: OPM2, 100 nM ricolinostat 2 h, replicate 2

description:
Library name: Sample16
Ricolinostat_2h_2

value: 10 nM ricolinostat for 2 h


title: OPM2, 100 nM ricolinostat 2 h, replicate 1

description:
Library name: Sample15
Ricolinostat_2h_1


title: PHLDA1-KO3_good

description: Library name: sample 3

value: kidney


title: PHLDA1-KO2_good

description: Library name: sample 2

value: Epithelial cells


title: OPM2, 10 nM romidepsin 20 h, replicate 2

description:
Library name: Sample14
Romidepsin_20h_2

value: Bone marrow

value: 10 nM romidepsin for 20 h


title: BMDM KO, MafB3, Rep2

description: Library name: BMDM_KO_MafB3_R2-NGS25-J849

source_name: Bone Marrow

value: Bone Marrow

value: Macrophage

value: Lyz2Cre Mafbfl/fl (Mafb KO)


title: SONOEX_rep3

city: Berlin

first: IBRAHIM

middle: AVSAR

last: ILIK

state: Berlin

address: Ihnestraße 63-73

country: Germany

institute: Max-Planck-Institut für molekulare Genetik

description: Library name: SONOEX_rep3

data_processing:
Base calling, demultiplexing and FASTQ conversion
Read alignment to the human genome (GRCh38 assembly) using STAR 2.7.9a
Read alignments (.bam files) converted to bigWigs using bamCoverage 3.5.1
Assembly: hg38
Supplementary files format and content: RPKM normalized RNA-seq coverage in bigWig format

organism: Pimephales promelas

source_name: EPC

extract_protocol:
Total RNA was extracted from cells with Quick-RNA MicroPrep kit (Zymo) after fractionation. Polyadenylated RNA was then isolated using Dynabeads™ mRNA Purification Kit. Purification was done twice to increase purity.
Strand-specific libraries were generated using KAPA Stranded RNA-seq Library Preparation Kit (Roche)

value: EPC

value: wt

value: Human SON overexpression


title: ChIP3, pcr1Δ, H3K9me2, heat-treatment 5min, rep2

data_processing:
ChIP-seq reads were trimmed using Trimmomatic ver 0.33 with SE, CROP:50, ILLUMINACLIP:TruSeq3-SE.fa:2:10:10, SLIDINGWINDOW:5:20, MINLEN:30 parameters. Trimmed reads were mapped on the S.pombe ASM294v2 genome using Bowtie ver 0.12.9. The read count for each transcription unit was calculated using the coverage function of BEDTools ver 2.17.0. The bigwig files were created using deeptools software.
RNA-seq reads were trimmed using Trimmomatic ver 0.33 with SE, CROP:50, ILLUMINACLIP:TruSeq3-SE.fa:2:10:10, SLIDINGWINDOW:5:20, MINLEN:30 parameters. Trimmed reads were mapped on the S.pombe ASM294v2 genome using STAR aligner with -- outFilterType, BySJout; -- alignSJoverhangMin, 8; -- alignSJDBoverhangMin, 1; -- quantMode GeneCounts parameters. When we analyzed the expression of DNA sequence inculding repeat regions such as heterochromatin genes, we calculated the readcounts from bedgraph file, which was produced using the coverage function of BEDTools ver 2.17.0. Those readcount files were named as “mRNA_XXX_for_HGs.txt".
PRO-seq reads were mapped on S.pombe ASM294v2 genome using Bowtie ver 0.12.9. The read count for each transcription unit was calculated using the coverage function of BEDTools ver 2.17.0. The bigwig files were created from bedgraph files using bedGraphToBigWig program.
Assembly: ASM294v2
Supplementary files format and content: bigwig file for ChIP-seq and PRO-seq
Supplementary files format and content: tab-delimited text file for RNA-seq

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ pcr1{delta}::KanMX6


title: LPM IgG

description: Library name: LPM_IgG_R1-NGS25-K132

value: Peritoneum

value: Large Peritoneal Macrophage

value: IgG (EpiCypher, 13-0042)


title: SONOEX_rep2

description: Library name: SONOEX_rep2


title: LPM WT, MafB1, Rep2

description: Library name: LPM_WT_MafB1_R2-NGS25-K135

value: MafB1 (Sigma, HPA005653)


title: OPM2, 10 nM romidepsin 20 h, replicate 1

description:
Library name: Sample13
Romidepsin_20h_1

value: Multiple myeloma cell

value: Unknown


title: ChIP3, clr3Δ, H3, heat-treatment 0min, rep1

value: S.pombe cells

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ clr3{delta}::KanMX6

value: 0 min (non treated)


title: ChIP3, pcr1Δ, H3K9me2, heat-treatment 0min, rep2


title: BMDM KO, MafB3, Rep1

description: Library name: BMDM_KO_MafB3_R1-NGS25-J848

value: MafB3 (Proteintech, 20189-1-AP)


title: LPM WT, MafB1, Rep1

description: Library name: LPM_WT_MafB1_R1-NGS25-K134

value: Mafbfl/fl (Mafb WT)


title: control_rep2

description: Library name: control_rep2

value: control


title: BMDM KO, MafB2, Rep2

description: Library name: BMDM_KO_MafB2_R2-NGS25-J847

value: Bone Marrow

value: Macrophage

value: Lyz2Cre Mafbfl/fl (Mafb KO)

value: MafB2 (Cell Signaling Technology, 41019)


title: OPM2, 10 nM romidepsin 2 h, replicate 1

description:
Library name: Sample9
Romidepsin_2h_1

value: Bone marrow

value: 10 nM romidepsin for 2 h


title: ChIP3, pcr1Δ, H3K9me2, heat-treatment 0min, rep1

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ pcr1{delta}::KanMX6


title: OPM2, 10 nM romidepsin 5 h, replicate 2

description:
Library name: Sample12
Romidepsin_5h_2

value: 10 nM romidepsin for 5 h


title: OPM2, 10 nM romidepsin 2 h, replicate 2

description:
Library name: Sample10
Romidepsin_2h_2


title: ChIP3, pcr1Δ, H3, heat-treatment 5min, rep2

value: 5 min atter heat-treatment


title: OPM2, 10 nM romidepsin 5 h, replicate 1

description:
Library name: Sample11
Romidepsin_5h_1

value: Multiple myeloma cell


title: OPM2, 10 nM panobinostat 20 h, replicate 2

description:
Library name: Sample8
Panobinostat_20h_2

value: 10 nM panobinostat for 20 h

value: Unknown


title: ChIP3, pcr1Δ, H3, heat-treatment 0min, rep1

value: S.pombe cells


title: KMT5A knockout embryos, Day3, biol rep 2

city: Lexington

first: Kaan Ihsan

last: Eskut

state: Kentucky

address: 195 Huguelet Dr.

department: Biology

institute: University of Kentucky

description:
Library name: D3_KMT5a_2
column name in raw counts:D3_KMT5a_2

data_processing:
RNA-seq reads from this study were aligned to the reference genome using HISAT2 v2.2.1
Gene expression was quantified from these alignments using StringTie v2.2.3
Differential expression was assessed using the DEseq2 R package v1.42.1
Assembly: UKy_Petmar_22M1.pri1.0
Supplementary files format and content: comma separated file with raw counts from stringtie v2.2.3

organism: Petromyzon marinus

source_name: Embryos

growth_protocol: Eggs and sperm were collected from mature adults by stripping gametes into crystallization dishes and containing 10% Holtfreter’s solution and incubated for 10 min to permit fertilization. After visually confirming activation, embryos were rinsed in distilled water to remove excess sperm and maintained in 10% Holtfreter’s solution at 18 °C throughout development.

extract_protocol:
Total RNA was extracted from two pools of approximately 100 snap frozen embryos for each condition, following the standard Trizol extraction protocol with the addition of 10 mM dithiothreitol(DTT) to the lysis reaction.
Library preparation and sequencing were conducted by Novogene using their "Plant and Animal Eukaryotic mRNA" pipeline.

treatment_protocol: Cas9 ribonucleotide complexes were generated by adding 5 μL 3μM gRNA for each guide sequence, 0.5 μL of 10μg/μL Cas9 protein and 1 μL of Dextran Fluorescein. Embryos were injected with ~2-3 nL of this solution and screened for fluorescence at 24 hours post fertilization.

value: Embryos

value: KMT5A knockout


title: OPM2, 10 nM panobinostat 5 h, replicate 2

description:
Library name: Sample6
Panobinostat_5h_2

value: 10 nM panobinostat for 5 h


title: BMDM WT, MafB2, Rep2

description: Library name: BMDM_WT_MafB2_R2-NGS25-J839

value: Mafbfl/fl (Mafb WT)


title: control_rep3

description: Library name: control_rep3

value: EPC

value: wt

value: control


title: SONOEX_rep1

description: Library name: SONOEX_rep1

value: Human SON overexpression


title: KMT5A knockout embryos, Day3, biol rep 1

description:
Library name: D3_KMT5a_1
column name in raw counts:D3_KMT5a_1


title: KMT1 knockout embryos, Day3, biol rep 1

description:
Library name: D3_KMT1_1
column name in raw counts:D3_KMT1_1

value: KMT1 knockout


title: BMDM KO, MafB2, Rep1

description: Library name: BMDM_KO_MafB2_R1-NGS25-J846

value: Bone Marrow

value: Macrophage

value: Lyz2Cre Mafbfl/fl (Mafb KO)

value: MafB2 (Cell Signaling Technology, 41019)


title: BMDM WT, MafB3, Rep1

description: Library name: BMDM_WT_MafB3_R1-NGS25-J840

value: MafB3 (Proteintech, 20189-1-AP)


title: ChIP3, atf1Δ, H3K9me2, heat-treatment 5min, rep2

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ atf1{delta}::KanMX6

value: 5 min atter heat-treatment


title: OPM2, 10 nM panobinostat 20 h, replicate 1

description:
Library name: Sample7
Panobinostat_20h_1

value: Bone marrow

value: Multiple myeloma cell

value: 10 nM panobinostat for 20 h

value: Unknown


title: BMDM WT, MafB3, Rep2

description: Library name: BMDM_WT_MafB3_R2-NGS25-J841

value: Mafbfl/fl (Mafb WT)


title: BMDM KO, MafB1, Rep1

description: Library name: BMDM_KO_MafB1_R1-NGS25-J844

value: MafB1 (Sigma, HPA005653)


title: ChIP3, pcr1Δ, H3, heat-treatment 5min, rep1

value: S.pombe cells

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ pcr1{delta}::KanMX6


title: KMT1 knockout embryos, Day3, biol rep 2

description:
Library name: D3_KMT1_2
column name in raw counts:D3_KMT1_2

value: Embryos


title: BMDM KO, MafB1, Rep2

description: Library name: BMDM_KO_MafB1_R2-NGS25-J845


title: ChIP3, pcr1Δ, H3K9me2, heat-treatment 5min, rep1


title: control_rep1

description: Library name: control_rep1

value: EPC

value: wt

value: control


title: ChIP3, pcr1Δ, H3, heat-treatment 0min, rep2

value: 0 min (non treated)


title: ChIP3, atf1Δ, H3K9me2, heat-treatment 0min, rep2


title: ChIP3, atf1Δ, H3K9me2, heat-treatment 5min, rep1


title: ChIP3, atf1Δ, H3K9me2, heat-treatment 0min, rep1


title: BMDM WT, MafB2, Rep1

description: Library name: BMDM_WT_MafB2_R1-NGS25-J838

value: Bone Marrow

value: Macrophage

value: MafB2 (Cell Signaling Technology, 41019)


title: BMDM WT, MafB1, Rep2

description: Library name: BMDM_WT_MafB1_R2-NGS25-J837


title: OPM2, 10 nM panobinostat 5 h, replicate 1

description:
Library name: Sample5
Panobinostat_5h_1

value: 10 nM panobinostat for 5 h


title: WT embryos, Day3, biol rep 1

description:
Library name: D3_WT_1
column name in raw counts:D3_WT_1

value: Wildtype


title: OPM2, 10 nM panobinostat 2 h, replicate 1

description:
Library name: Sample3
Panobinostat_2h_1

value: Bone marrow

value: Multiple myeloma cell

value: 10 nM panobinostat for 2 h


title: WT embryos, Day3, biol rep 2

description:
Library name: D3_WT_2
column name in raw counts:D3_WT_2


title: BMDM, IgG

description: Library name: BMDM_IgG-NGS25-J834

value: Mafbfl/fl (Mafb WT)

value: IgG (EpiCypher, 13-0042)


title: OPM2, DMSO, replicate 2

description:
Library name: Sample2
DMSO_2

value: DMSO

value: Unknown


title: BMDM WT, MafB1, Rep1

description: Library name: BMDM_WT_MafB1_R1-NGS25-J836

value: MafB1 (Sigma, HPA005653)


title: OPM2, 10 nM panobinostat 2 h, replicate 2

description:
Library name: Sample4
Panobinostat_2h_2


title: ChIP3, atf1Δ, H3, heat-treatment 0min, rep2

value: S.pombe cells

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ atf1{delta}::KanMX6


title: KMT5A knockout embryos, Day2, biol rep 1

description:
Library name: D2_KMT5a_1
column name in raw counts:D2_KMT5a_1

value: Embryos

value: KMT5A knockout


title: iWAT, PM2.5, 3

city: Hangzhou

first: Renjie

last: Hu

address: 548 Binwen Rd

institute: Zhejiang chinese medical university

description:
Library name: Sample 6
GEXSCOP

data_processing:
Celescope was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 24bp GEXSCOPE barcode and the 12bp UMI (bases 25-36). Read 2 contains the cDNA information.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: iWAT

extract_protocol:
Focal areas of solid and GG components were identified by tissue appearance and compute tomography (CT) at the same time. Different components were macrodissected and stored at 4 ℃ GEXSCOPETM Tissue Preservation Solution. Then, we washed samples for 3 times with Hanks Balanced Salt Solution (HBSS) and minced them into 1–2 mm-thick pieces, 2 ml GEXSCOPETM Tissue Dissociation Solution (Singleron Biotechnologies) was added to each sample and allowed for digestion at 37 ℃ for 15 minutes to dissociate the tissue into single cells. Then, we filtrate the samples using 40-μm sterile strainers, followed by centrifuging at 1,000 rpm for 5 minutes. After the centrifugation, the precipitation was resuspended in 1 ml phosphate-buffered saline (PBS; HyClone, Marlborough, United States). Subsequently, 2 ml GEXSCOPETM Red Blood Cell Lysis Buﬀer (Singleron Biotechnologies) was added into the cell suspension and incubated at 25°C for 10 minutes to remove red blood cells. After that, the mixture was centrifuged at 500 × g for 5 minutes, followed by re-suspending the precipitation with PBS.
We used GEXSCOPETM Single Cell RNA Library Kit Tissue (Singleron Biotechnologies) to barcode single cells, capture mRNA from isolated single cells, and generate cDNA libraries for scRNA-seq. Then, individual libraries were diluted to 4 ng/μl, and pooled for sequencing on a Illumina NovaSeq 6000 with 150 bp paired-end reads.

value: iWAT

value: Maternal PM2.5 exposure


title: KMT1 knockout embryos, Day2, biol rep 1

description:
Library name: D2_KMT1_1
column name in raw counts:D2_KMT1_1

value: KMT1 knockout


title: OPM2, DMSO, replicate 1

description:
Library name: Sample1
DMSO_1


title: HCFs, NAV3 siRNA, 48 hrs, rep2

city: Rochester

first: Duan

last: Liu

email: liud25@gmail.com, liu.duan@mayo.edu

state: MN

address: 200 1st ST SW

department: MPET

institute: Mayo Clinic

description: Library name: HCF_siNAV3_2

data_processing:
RNA sequencing quality was determined with FastQC.
Sequencing reads were aligned to human genome using STAR.
Raw counts were generated with featureCounts.
Differential expression analysis was conducted with the EdgeR package using R
Assembly: hg38
Supplementary files format and content: tab-delimited text files  which is a matrix table with raw gene counts for every gene and every sample.

source_name: Primary HCF

growth_protocol: Cryopreserved adult human cardiac fibroblasts (HCFs) were purchased from Cell Applications, Inc. (Cat#:306V-05a, San Diego, CA). Cell culture and subculture were performed following the manufacturer’s Instructions for HCF Culture.

extract_protocol:
Total RNA was extracted with TRIzol® Reagent (ThermoFisher) and the miRNAeasy kit (QIAGEN) per the manufacturer’s instructions.
RNA-seq libraries were generated using the Illumina TruSeq RNA Library Prep Kit v2 (Illumina, San Diego, CA) following the manufacturer’s protocol.

value: Primary HCF

value: cardiac fibroblast


title: WT embryos, Day2, biol rep 2

description:
Library name: D2_WT_2
column name in raw counts: D2_WT_2

value: Wildtype


title: iWAT, PM2.5, 2

description:
Library name: Sample 5
GEXSCOP


title: KMT5A knockout embryos, Day2, biol rep 2

description:
Library name: D2_KMT5a_2
column name in raw counts:D2_KMT5a_2


title: iWAT, PM2.5, 1

description:
Library name: Sample 4
GEXSCOP


title: KMT1 knockout embryos, Day2, biol rep 2

description:
Library name: D2_KMT1_2
column name in raw counts:D2_KMT1_2


title: HCFs, NAV3 siRNA, 48 hrs, rep1

description: Library name: HCF_siNAV3_1


title: ChIP3, atf1Δ, H3, heat-treatment 0min, rep1

extract_protocol:
Total RNA for mRNA-seq was extracted by the hot-phenol method, as previously described (Iyer,V. and Struhl,K. 1996). Cell permeabilization and extraction of biotinylated RNA for PRO-seq was performed as previously described (Mahat et al., 2016). Chromatin for ChIP-seq, extracted from cell lysate of 1% formaldehyde fixed-cells, was sonicated using a Picoruptor (Diagenode).
ChIP-seq libraries were constructed using the ThruPLEX DNA-seq Kit (Clontech). mRNA-seq libraries were constructed using the KAPA mRNA HyperPrep Kit (Kapa Biosystems). cDNA libraries for PRO-seq were converted from the RNA, to which 3' and 5' adaptors were ligated, by revearse transcription.

value: 0 min (non treated)


title: ChIP3, atf1Δ, H3, heat-treatment 5min, rep1

value: 5 min atter heat-treatment


title: iWAT, FA, 3

description:
Library name: Sample 3
GEXSCOP

value: Maternal FA exposure


title: ChIP3, atf1Δ, H3, heat-treatment 5min, rep2


title: WT embryos, Day2, biol rep 1

description:
Library name: D2_WT_1
column name in raw counts: D2_WT_1


title: iWAT, FA, 2

description:
Library name: Sample 2
GEXSCOP


title: Oligomer-treated muscle, 2 weeks, biological replicate 4

city: West Lafayette

first: Rachel

middle: A

last: Morrison

state: IN

address: 206 S Martin Jischke Dr

department: Weldon School of Biomedical Engineering

institute: Purdue University

description:
Library name: VML18L_2wk_replicate4_B1
Fresh frozen spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed with Space Ranger v3.1.2 (10X Genomics).
The sequence data were aligned to the rat reference genome mRatBN7.
The filtered feature-spot matrices generated by Space Ranger were used for further analysis.
Assembly: mRatBN7
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scale_factors_json.json: scale factors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: spatial_enrichment.csv: list of gene-signature enrichment scores per spatial barcode
Library strategy: Spatial Transcriptomics

organism: Rattus norvegicus

source_name: muscle

extract_protocol:
Samples were harvested at 2 and 8 weeks post-treatment, bisected at the defect midline, and embedded in OCT for cryosectioning.  Samples were flash frozen in liquid nitrogen and stored at -80°C.
Spatial transcriptomics was performed on the 10X Visium platform following the manufacturer’s protocol (CG000239, Visium Spatial Gene Expression for Fresh Frozen). The final libraries were sequenced on an Illumina NovaSeq X PLUS sequencer.

treatment_protocol: Full-thickness defects encompassing ~30% of tibialis anterior (TA) muscle volume were created in Lewis rats, and defects were treated with Oligomer Scaffolds.

value: muscle

tag: strain

value: Lewis

value: volumetric muscle loss treated with Oligomer scaffolds

tag: time point

value: 2 weeks


title: Untreated H1299 cells-Rep2

type: RNA

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

institute: Taiwan National Health Research Institute

description: Untreated OC3 cells

hyb_protocol: Samples were hybridized with Human Clariom S Array (Affymetrix) and scanned at the NHRI Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: The data were analyzed using Affymetrix Transcriptome Analysis Console (TAC) Software (version 4.0.2) default analysis settings and RMA (Robust Multi-Array) summarization and normalization options.

label: Biotin

source_name: Untreated NSCLC H1299 cells

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Plus cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: A549 and H1299 cells, with or without ultrasound treatment, were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin, and maintained at 37°C in a humidified incubator with 5% CO₂. All cells were grown under identical conditions before and after ultrasound treatment and subcultured at 70–80% confluency to ensure optimal growth and viability.

extract_protocol: Total RNA was isolated from cultured cells with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: RNA was extracted from cells 48 hours after ultrasound treatment, with untreated cells serving as controls.

tag: gender

value: male

value: Caucasian

tag: tissue

value: metastatic lymph node lesion

tag: tumor type

value: Large cell lung carcinoma

tag: tumor stage


title: iWAT, FA, 1

description:
Library name: Sample 1
GEXSCOP

value: iWAT


title: ChIP3, iss10Δ, H3K9me2, heat-treatment 0min, rep2

city: Bunkyo, Tokyo

first: Soichi

last: Inagaki

institute: Graduate School of Science, The University of Tokyo

source_name: S.pombe cells

value: S.pombe cells

tag: genotype

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ iss10{delta}::KanMX6


title: mESC, H3K27me3, Re-introduction 2

city: Mexico City

first: Víctor

middle: Julián

last: Valdés

state: Mexico City

address: Circuito Exterior s/n, Ciudad Universitaria

department: Departamento de Biología Celular y Desarrollo

country: Mexico

institute: Instituto de Fisiología Celular (IFC), Universidad Nacional Autónoma de México (UNAM)

description: Library name: Re-introduction_K27_Biol_2

data_processing:
The peaks obtained from the processing of our auxin induced experiment were merged into non-redundant union sets for each of the immunoprecipitation antibodies with Bedtools v2.30.0
To create visualization files and plots such as BigWig and heatmaps, we calculate scaling factors for all sam-ples for each immunoprecipitation condition with deepTools 3.5.0.
Peak calling was performed per replicate using MACS2 v2.2.7.1
Assembly: mm10
Supplementary files format and content: bigWig, broad peak

source_name: Mouse embryonic stem cells, mESC

growth_protocol: J1 mouse embryonic stem cells (mESC) were cultured under standard conditions on 0.1% gelatin-coated plates and in ES medium: DMEM High Glucose supplemented with 15% FBS (Biowest L0101-500), 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM MEM non-essential amino acids (NEAA), 1% nucleoside mix, 50 U/mL Penicillin/Streptomycin (P/S), Leukemia inhibitory factor (LIF, made in house) and 2i inhibitors: 1 μM PD0325901 and 3 μM CHIR99021. Cells were passed every other day using 0.05% Trypsin/EDTA. All cells were grown at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
Cells were dissociated with 0.05% trypsin, fixed with 1% formaldehyde solution for 10 min at room temperature (RT), and quenched with fresh 125 mM glycine for 5 min RT. After PBS washed, nuclei were isolated using sequential lysis buffers: B1 (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100, 1x protease inhibi-tors; 10 min at 4°C), B2 (10 mM Tris-HCL, pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, and 1x pro-tease inhibitors; 10 min at 4°C), and B3 (10 mM Tris-HCL, pH 8, at 4 C, 100 mM NaCl,1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-Lauroylsarcosine sodium salt, and 1x protease inhibitors). Chromatin was fragmented to an average size of 250-500 bp using a Diagenode Bioruptor and triton X-100 was added to a final concentration of 1%. ChIP was performed using 1 ug of antibody per 2 million of cells incubated and rotated overnight at 4 ºC. Antibodies: rabbit anti-GFP (Abcam, ab290), rabbit anti-H3K27me3 (Cell signaling, 9733). Dynabeads (10 µL pero µg Ab) were pre-washed in PBS + 0.5% BSA and rotated for 2 hours at 4 ºC before adding to the IPs.  Then washes X5 with ChIP RIPA buffer 4°C (50mM HEPES-KOH, pH 7.5 at 4 °C, 500 mM LiCl, 1 mM EDTA, 1% NP-40, and 0.7% Na-deoxycholate) and one wash with TE + 50 mM NaCl. DNA was eluted in freshly prepared elution buffer (50 mM Tris, pH 8, 10 mM EDTA, 1% SDS) at 65 °C for 20 min and then de-crosslinked overnight at 65 °C. Samples were treated with RNase A and proteinase K and DNA was purified by phenol:chloroform:isoamyl alcohol (P:C:IA).
Libraries were pre-pared using NEBNext Ultra II DNA Library Prep Kit (NEB), quantified by Qubit dsDNA HS Assay, quality-checked with Aligent Bioanalyzer HS DNA chip. Libraries were sequenced as 150 pb paired-end reads on the Illumina HiSeq platform.

treatment_protocol: Auxin (indole-3-acetic acid, IAA; Sigma, catalog no. I5148) was dissolved in water to a 200 mM stock solution and stored at -20 ºC. For AID-mediated degradation, auxin was titrated and used at a final concentration of 50 μM in culture media. Auxin treatment last 96 hours. Washout reintroduction treatment last 4.5 h.

value: Mouse embryonic stem cells, mESC

value: Re-introduction


title: mESC, H3K27me3, Re-introduction 1

description: Library name: Re-introduction_K27_Biol_1


title: ChIP3, iss10Δ, H3K9me2, heat-treatment 0min, rep1


title: Untreated H1299 cells-Rep1

description: Untreated OC3 cells

tag: ethnicity


title: H1299 cells 48 hours after LIUS (T2) treatment-Rep2

description: OC3 cells 48 hours after LIUS (T1) treatment

source_name: LIUS (T2) treated NSCLC H1299 cells


title: ChIP3, iss10Δ, H3, heat-treatment 5min, rep1

tag: cell type


title: H1299 cells 48 hours after LIUS (T2) treatment-Rep1


title: mESC, Suz12-mAID-mClover, Re-introduction 2

description: Library name: Re-introduction_GFP_Biol_2

tag: treatment


title: Untreated A549 cells-Rep2

description: Untreated OC3 cells

source_name: Untreated NSCLC A549 cells

value: lung alveolar basal epithelium

value: lung adenocarcinoma

value: early stage


title: Oligomer-treated muscle, 8 weeks, biological replicate 2

description:
Library name: VML55L_8wk_replicate2_B1
Fresh frozen spatial transcriptome sequencing

value: 8 weeks

tag: batch


title: Oligomer-treated muscle, 2 weeks, biological replicate 1

description:
Library name: VML66L_2wk_replicate1_C1
Fresh frozen spatial transcriptome sequencing

value: muscle


title: mESC, Suz12-mAID-mClover, Re-introduction 1

description: Library name: Re-introduction_GFP_Biol_1


title: ChIP3, iss10Δ, H3, heat-treatment 5min, rep2

value: 5 min atter heat-treatment


title: A549 cells 48 hours after LIUS (T2) treatment-Rep2

source_name: LIUS (T2) treated NSCLC A549 cells


title: mESC, H3K27me3, Control 2

description: Library name: Mock_K27_Biol_2

value: Control


title: ChIP3, iss10Δ, H3K9me2, heat-treatment 5min, rep1


title: Untreated A549 cells-Rep1

description: Untreated OC3 cells


title: Oligomer-treated muscle, 2 weeks, biological replicate 3

description:
Library name: VML17L_2wk_replicate3_A1
Fresh frozen spatial transcriptome sequencing

value: Lewis

value: volumetric muscle loss treated with Oligomer scaffolds

value: 2 weeks


title: ChIP3, iss10Δ, H3, heat-treatment 0min, rep1

value: 0 min (non treated)


title: Oligomer-treated muscle, 2 weeks, biological replicate 2

description:
Library name: VML65L_2wk_replicate2_D1
Fresh frozen spatial transcriptome sequencing


title: UVB_Transgenic P1.hMR 5

city: Paris

first: Linxin

last: Zhu

state: Paris

address: 15 Rue de l'École de Médecine, Centre de Cordeliers

department: Centre de la recherche des corderliers

country: France

institute: INSERM

description: Library name: U_TG_396532

data_processing:
Quality of raw data was evaluated with FastQC.
Poor quality sequences has been trimmed or removed with Trimmomatic software to retain only good quality paired reads with following parameters : cutoff: '20' leading: '10' minlen: '50' slidingwindow: '4' trailing: '10'
Illumina DRAGEN bio-IT Plateform (v3.8.4) was used to align reads on reference genome rd6 using standard options.
Quantification was performed with genecode vM25 annotation gtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools
Assembly: rn7
Supplementary files format and content: tab-delimited text file includes TPM counts for each  sample

source_name: Meibomian gland

extract_protocol:
Total RNA was isolated from tissues using the RNeasy Mini Kit inluding DNase I treatment (Qiagen). 1µg of total RNA was used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 10-12 weeks old female Wild-Type (WT) and P1.hMR rats were subjected to 5-days UVB irrdiation on eyelids, together with age- and sex- matched rats without UVB-induced model. Rats were euthanized and the meibomian glands were dissected for RNA-sequencing.

value: Meibomian gland

value: Transgenic P1.hMR

value: UVB treatment on eyelids


title: ChIP3, iss10Δ, H3, heat-treatment 0min, rep2

value: S.pombe cells

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ iss10{delta}::KanMX6


title: Oligomer-treated muscle, 8 weeks, biological replicate 1

description:
Library name: VML56L_8wk_replicate1_A1
Fresh frozen spatial transcriptome sequencing


title: ChIP3, iss10Δ, H3K9me2, heat-treatment 5min, rep2


title: A549 cells 48 hours after LIUS (T2) treatment-Rep1

value: male

value: Caucasian


title: mESC, Re-introduction 3

description: Library name: mesc_Re-introduction_3

data_processing:
Adapter sequences and low-quiality reads were trimmed with Trim Galore v0.6.10 with default parameters
Files were verified with FastQC v0.12.1
Trimmed reads were aligned to the mm10 mouse reference genome using Bowtie2 v2.5.3 then BAM files were obtained using samtools 1.20, then sorted and indexed with samtools sort and samtools index with default parameters.
With sorted BAM files as input we estimated raw sequencing reads abundance over the Ensembl gene annota-tion (mm10) mouse genome using FeatureCounts v2.0.6
Assembly: mm10
Supplementary files format and content: txt files with FeatureCounts

extract_protocol:
Total RNA was purified in triplicates from mESCs with TRIzol (Life Technologies), and RNA integrity (RIN) was corroborated using an Aligent Bioanalyzer. We follow the manufacturer's TruSeq RNA Sample Prep v2 (Illumina, USA) instructions for transcriptome sequencing. The mRNA was purified utilizing poly-T oligo-attached magnetic beads. After purification, the mRNA was fragmented and converted into first-strand cDNA utilizing reverse transcriptase and random primers. The second strand, cDNA, is then synthesized using DNA Polymerase. Actinomycin D was added to prevent DNA-dependent synthesis and improve strand specificity. The cDNA fragments undergo a single 'A' base addition and subsequent adapter ligation.
After purification and PCR enrichment, the final cDNA library is suitable for subsequent cluster generation and DNA sequencing. We sequenced the libraries using a NextSeq 500 platform (Illumina) in 75 bp paired end reads format.

value: Mouse embryonic stem cells, mESC

value: Re-introduction


title: UVB_Transgenic P1.hMR 4

description: Library name: U_TG_381797


title: ChIP3, red1Δ, H3K9me2, heat-treatment 0min, rep2

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ red1{delta}::KanMX6


title: mESC, H3K27me3, Control 1

description: Library name: Mock_K27_Biol_1


title: ChIP3, red1Δ, H3K9me2, heat-treatment 5min, rep2


title: UVB_Transgenic P1.hMR 3

description: Library name: U_TG_380381


title: mESC, Re-introduction 2

description: Library name: mesc_Re-introduction_2


title: mESC, Re-introduction 1

description: Library name: mesc_Re-introduction_1


title: mESC, Suz12-mAID-mClover, Control 1

description: Library name: Mock_GFP_Biol_1


title: mESC, Suz12-mAID-mClover, Control 2

description: Library name: Mock_GFP_Biol_2


title: ChIP3, red1Δ, H3K9me2, heat-treatment 0min, rep1


title: ChIP3, red1Δ, H3, heat-treatment 5min, rep2


title: mESC, Mock 2

description: Library name: mesc_mock_2

value: Mock


title: UVB_Transgenic P1.hMR 2

description: Library name: U_TG_372932


title: mESC, Mock 3

description: Library name: mesc_mock_3


title: UVB_Transgenic P1.hMR 1

description: Library name: U_TG_91817


title: mESC, H3K27me3, Auxin 1

description: Library name: Auxin_K27_Biol_1

value: Auxin


title: UVB_Wild-type 3

description: Library name: U_WT_904250

value: Wild-type


title: ChIP3, red1Δ, H3, heat-treatment 5min, rep1

value: 5 min atter heat-treatment


title: mESC, Mock 1

description: Library name: mesc_mock_1


title: UVB_Wild-type 2

description: Library name: U_WT_713642


title: mESC, Suz12-mAID-mClover, Auxin 2

description: Library name: Auxin_GFP_Biol_2


title: mESC, H3K27me3, Auxin 2

description: Library name: Auxin_K27_Biol_2


title: UVB_Wild-type 1

description: Library name: U_WT_395857


title: mESC, Suz12-mAID-mClover, Auxin 1

description: Library name: Auxin_GFP_Biol_1


title: ChIP3, red1Δ, H3, heat-treatment 0min, rep2


title: mESC, Auxin 2

description: Library name: mesc_aux_2


title: ChIP3, red1Δ, H3, heat-treatment 0min, rep1


title: mESC, Auxin 3

description: Library name: mesc_aux_3


title: mESC, Auxin 1

description: Library name: mesc_aux_1


title: ChIP3, red1Δ, H3K9me2, heat-treatment 5min, rep1


title: C57_MUS_ZQD_RH2

city: Jinan, Shandong Province

first: Yiyang

last: Jiang

address: Shandong University of Traditional Chinese Medicine, Qianfoshan Campus

institute: Shandong university of traditional Chinese medic

description: Library name: Sample 6

data_processing:
Raw data in Fastq format were first processed by a perl script to remove splice sequences, filter out low-quality (low-quality, bases with base quality values less than or equal to 25 accounted for more than 60% of the total reads) and N (N denotes that the base information could not be determined) ratio of more than 5% of the reads, and obtain clean reads that could be used for subsequent analyses.
Clean reads were compared to the reference genome using HISAT2 software (http://daehwankimlab.github.io/hisat2/) to obtain mapped reads for subsequent analysis.
FeatureCounts (http://subread.sourceforge.net/) is used to calculate the number of reads compared to each gene, and the FPKM value for each gene is calculated based on the length of the gene.
Differential expression analysis of genes between groups was performed using DESeq2 (http://bioconductor.org/packages/release/bioc/html/DESeq2.html) with default screening thresholds for differentially expressed genes: | log2FC | > 1 and Padj < 0.05.
Assembly: Hisat2
Supplementary files format and content: txt file include raw counts for each sample
Supplementary files format and content: txt file include FPKM values for each sample

source_name: Lewis lung carcinoma

extract_protocol:
The total RNA was extracted and purified from tumor tissues using TRIzol reagent. Nanodrop ND-2000 (Thermo Scientific, USA) was used to detect the A260/A280 absorbance ratio of the RNA samples, and Agilent Bioanalyzer 4150 (Agilent Technologies, CA, USA) was used to determine the RIN value of RNA. Only RNAs that passed the quality control were used for library construction.
According to the ABclonal mRNA-seq Lib Prep Kit (ABclonal, China) instructions, PE libraries were prepared. The mRNA was purified from 1 μg of total RNA using oligo(dT) magnetic beads, followed by mRNA fragmentation in ABclonal First Strand Synthesis Reaction Buffer. Subsequently, the first strand of cDNA was synthesised using random primers and reverse transcriptase (RNase H) using the mRNA fragments as templates, and then the second strand of cDNA was synthesised using DNA polymerase I, RNAseH, buffer and dNTPs. The synthesised double stranded cDNA fragments were ligated to the junction sequence and used for PCR amplification. PCR products were purified and library quality was assessed using an Agilent Bioanalyzer 4150. Finally, sequencing was performed using Illumina Novaseq 6000 / MGISEQ-T7 sequencing platform.

treatment_protocol: At 6 weeks old, the C57BL/6J mice received a subcutaneous injection of 100 µL of phosphate-buffered saline containing 5 × 105 LLC cells into their right axilla. After 3 days, the experimental mice were randomly assigned to four groups (n = 8 per group): model and ZQD-H (42.67 g/kg). All mice were euthanized on the 22nd day after modeling. Tumor tissues were analyzed.

value: Subcutanous tumor

value: Tumor cell

value: WT

value: Ze-qi decoction treatment


title: Contro_Transgenic P1.hMR 4

description: Library name: C_TG_914001

value: Meibomian gland

value: Transgenic P1.hMR

value: no treatment


title: Tumor_853

city: Quebec city

first: Francois

last: Potus

address: 2725 Ch Ste-Foy

country: Canada

institute: IUCPQ-Laval university

description:
Library name: Tumor_853
Sample name in processed data file:Tumor_853

data_processing:
Sequencing generated 150 bp paired-end reads, targeting 50 million clusters per sample (100 million reads total)
FASTQ files were aligned to the mRatBN7.2 rat reference genome with Ensembl gene annotations (build 98) using STAR (v2.6.1a)
Gene quantification was performed using RSEM (v1.3.1), and quality control analysis was carried out with multiQC
Downstream analysis was conducted in R 4.0, with separate analysis for each tissue type. Initial filtering of genes was performed using the filterByExpr() function from the edgeR package. Differential expression analysis was then conducted using the DESeq2 protocol
Gene ontology and pathway enrichment analyses were performed using the KEGG, Gene Ontology Biological Process, Gene Ontology Cellular Component, and Gene Ontology Molecular Function databases via ShinyGO
Assembly: build 98
Supplementary files format and content: Processed file is a csv of raw counts

source_name: Breast tumor

extract_protocol:
Direct-zol RNA Miniprep Kit (#R2051, Zymo Research, USA)
Total RNA was extracted from DMBA-induced mammary tumor samples of Bmpr2+/Δ71 and WT female rats (n = 3 per condition) using the Direct-zol RNA Miniprep Kit (#R2051, Zymo Research, USA). RNA libraries were prepared using the Illumina Stranded mRNA Library Preparation Kit and sequenced on an Illumina NovaSeq platform

treatment_protocol: DMBA-Induced Tumor Development - Seven-week-old (180 g) WT and Bmpr2+/Δ71 female Sprague-Dawley rats were randomized into four groups: Group A: 27 WT rats received DMBA (D3254-1G, Lot# SLCC3858, Sigma) to induce mammary tumors via oral administration (20 mg/mL in soybean oil at a dose of 1 mL per 183 g of body weight). Group B: 13 WT rats received vehicle only (1 mL of soybean oil per 183 g of body weight). Group C: 27 Bmpr2+/Δ71 rats received DMBA under the same conditions as Group A. Group D: 13 Bmpr2+/Δ71 rats received vehicle only. DMBA-treated animals were monitored weekly until the appearance of the first tumor, which occurred after an average of 6 weeks. Subsequently, tumor progression (volume and number) was monitored daily. The study endpoint was reached when the tumor size reached 10 cm³, as per ethical committee recommendations

value: Breast tumor

value: mammary tumor


title: C57_MUS_ZQD_RH1

description: Library name: Sample 5


title: ChIP3, rdp1Δ, H3K9me2, heat-treatment 5min, rep2

value: S.pombe cells

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ rdp1{delta}::KanMX6


title: Tumor_828

description:
Library name: Tumor_828
Sample name in processed data file:Tumor_828


title: Contro_Transgenic P1.hMR 5

description: Library name: C_TG_914783


title: C57_MUS_ZQD_RH3

description: Library name: Sample 7


title: Contro_Transgenic P1.hMR 2

description: Library name: C_TG_396092


title: ChIP3, rdp1Δ, H3K9me2, heat-treatment 0min, rep1

value: 0 min (non treated)


title: C57_MUS_CTRL_RM4

description: Library name: Sample 4


title: Tumor_827

description:
Library name: Tumor_827
Sample name in processed data file:Tumor_827


title: Control_Wild-type 4

description: Library name: C_WT_396953


title: Contro_Transgenic P1.hMR 3

description: Library name: C_TG_904261


title: Tumor_817

description:
Library name: Tumor_817
Sample name in processed data file:Tumor_817


title: C57_MUS_CTRL_RM2

description: Library name: Sample 2


title: C57_MUS_CTRL_RM1

description: Library name: Sample 1


title: ChIP3, rdp1Δ, H3K9me2, heat-treatment 5min, rep1


title: Contro_Transgenic P1.hMR 1

description: Library name: C_TG_382924


title: Tumor_622

description:
Library name: Tumor_622
Sample name in processed data file:Tumor_622


title: ChIP3, rdp1Δ, H3, heat-treatment 5min, rep1


title: Tumor_826

description:
Library name: Tumor_826
Sample name in processed data file:Tumor_826


title: ChIP3, rdp1Δ, H3K9me2, heat-treatment 0min, rep2


title: ChIP3, rdp1Δ, H3, heat-treatment 0min, rep2


title: Control_Wild-type 2

description: Library name: C_WT_235951


title: ChIP3, rdp1Δ, H3, heat-treatment 0min, rep1


title: Control_Wild-type 3

description: Library name: C_WT_396025


title: Retina, 24w, Rs1KO

city: Bucheon

first: Hun Soo

last: Chang

address: 170, Jomaru-ro

country: South Korea

institute: Soonchunhyang University

description:
Library name: Sample4
10x genomics

data_processing:
The demultiplexing, barcode procfessing, gene counting and aggregation were conducted using CellRanger v8.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/8.0)
Assembly: GRCm39-2024-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Retina

extract_protocol:
Each pooled retina was incubated in 1 mL of digestion solution containing 20 U/mL papain (Worthington Biochemical Corporation, Lakewood, NJ) and 0.005% DNase I (Sigma-Aldrich, St. Louis, MO) at 8 °C for 40 minutes, followed by an additional 10-minute incubation at 28 °C. After enzymatic digestion, the solution was carefully removed without disturbing the tissue. To inactivate enzymatic activity, 700 μL of pre-warmed inactivation solution was added. The tissue was then gently dissociated by pipetting 10 times. Subsequently, 700 μL of washing solution was added, and the mixture was centrifuged at 200 × g for 5 minutes at 4 °C. The supernatant was discarded, and the pellet was resuspended in 3 mL of DPBS containing 0.04% BSA (Gibco, Waltham, MA). The resulting cell suspension was filtered through a 40 μm cell strainer (Corning, Corning, NY) and immediately examined under a brightfield EVOS microscope (Thermo Fisher Scientific, Waltham, MA) to assess cell morphology and viability.
The samples were processed for library preparation using Chromium GEM-X Single Cell 3p RNA library v4 (10× Genomics, Pleasanton, CA). After cell dissociation and viability assessment, the cells were mixed with master mix and loaded onto a chromium GEM-X chip with Single Cell 3′ v4 Gel Beads and Partitioning Oil. RNA transcripts from single cells were uniquely barcoded and reverse transcribed within droplets. The cDNA molecules were pooled and processed for library construction. The libraries were then quantified using quantitative PCR and qualified using Agilent Technologies 4200 TapeStation (Santa Clara, CA). Finally, the libraries were sequenced using the HiSeq platform (Illumina, San Diego, CA).

treatment_protocol: Retinoschisin (Rs1) Exon2 knock out

value: Retina

value: Rs1 Exon2 deletion


title: Retina, 8w, Rs1KO

description:
Library name: Sample3
10x genomics


title: C57_MUS_CTRL_RM3

description: Library name: Sample 3


title: H-2D 4

city: Changsha

first: Chaoyong

last: He

address: Tianma road

institute: Hunan university

description:
Library name: Sample 8
High 4

data_processing:
Reads mapping and gene expression quantification: cDNA library samples were sequenced as described above. After removing the reads with adapters, any reads containing ‘n’ (> 10%) and low-quality reads (sQ ≤ 5), the remaining clean reads were checked by FastQC (v.0.11.5). Clean reads were aligned to the Rattus norvegicus Rnor 6.0.98 using STAR (v.2.5.3a) and the raw counts matrix were obtained by featureCounts. The expression level of genes was calculated using CPM (count per millon) as a metric, and filtered using the sum of relative abundance to eliminate the effects of sequencing depths.
PCA analysis, DEG obtain and clustering: Normalized gene expression values used to calculate the correlation coefficient among biological replicates for PCA and hierarchical clustering. The PCA was calculated with the prcomp function in R with default settings. Hierarchical clustering was performed using the pheatmap package with default settings using Pearson’s correlation. The DEGs in pairwise comparisons were identified by the R package edgeR, which performs data normalization using the trimmed mean of M-values (TMM) method. Genes with at least a two-fold change in expression and P value < 0.05 were considered to be expressed differentially. A k-means approach was used (R package pheatmap) to cluster all the DEGs identified through pairwise comparisons.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

source_name: brain tissue from SD rats at 1 day

growth_protocol: NSCs were isolated from cerebral cortices of 1–day-old neonatal Sprague-Dawley rats.

extract_protocol:
NSCs were expanded as neutrospheres at 37°C, 5% CO2 for 3-4 days in proliferation culture medium, which contained DMEM/F12 supplemented with 1% glutamine (Gibco), 1% sodium pyruvate (Gibco), 1% NEAA (Gibco), 2% B27 (Gibco), 0.02 ng/mL EGF, 0.02 ng/mL bFGF, 1.83 ng/mL heparin and 1% streptomycin penicillin (Gibco). The proliferation medium was replaced every 2 days. Thereafter, the NSCs neutrospheres were gathered through centrifugation (300×g, 5min), and digested with 0.25% trypsin-EDTA (Gibco) at 37℃ for 18 min. After terminating digestion mixture using 10% FBS, the cells were collected by countrification and filtered through 70 μm and 40 μm mech of cell strainer successively to obtain the NSCs of single-cell suspension. 0.2% (W/V) of Col solution mixed with equal volume of NSCs single-cell suspension to obtain final 0.75, 1.5, 3 million/mL of cell packing density system.
RNA-seq library preparation. Total RNA was isolated from each sample using the RNAmini kit (Qiagen, Germany). RNA quality was examined by gel electrophoresis and with Qubit (Thermo, Waltham, MA, USA). Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA), through reverse transcription using S1000TM Touch Thermal Cycler (Bio Rad) at 53°C (45 min) - 85°C (5 min) - 4°C cycle. The generated cDNA was amplified, and quality estimated using Agilent 4200 (performed by CapitalBio Technology, Beijing). The sequences of libraries were finally obtained using the Illumina Novaseq6000 sequencer with pair-end 150 bp (PE150).

treatment_protocol: tissue pieces of dissociation, the mixed cortical cells were first passed through a 100 μm mesh of nylon cell strainer, then plated into tissue culture flasks.

value: brain tissue

value: Neural Stem Cells

value: wild type

value: High crowding


title: H-2D 3

description:
Library name: Sample 7
High 3


title: ChIP3, dcr1Δ, H3K9me2, heat-treatment 5min, rep2

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ dcr1{delta}::KanMX6

value: 5 min atter heat-treatment


title: ChIP3, dcr1Δ, H3K9me2, heat-treatment 0min, rep2


title: Cortical neurons derived from BIONi010-C iPSCs with homozygous CHMP2B G26403C mutation, biological replicate 3

city: Worcester

first: Evan

middle: Phillip

last: Hass

state: MA

address: 264 Plantation Street, LRB 560D

department: MCCB

institute: UMass Chan Medical School

description: Library name: Subject2_CHMP2B_homo_mut_rep3

data_processing:
Adpater sequences were removed from reads using trimmomatic with the following parameters: ILLUMINACLIP:NexteraPE-PE.fa:2:25:7:1:true TRAILING:3 SLIDINGWINDOW:4:10 TRAILING:3 MINLEN:10
Trimmed reads were aligned to hg38 using bowtie2 using -N 1 -X 1000.
PCR duplicate reads were removed using Picard SortSam followed by MarkDuplicates with REMOVE_DUPLICATES=TRUE.
Samtools was used to remove reads with a MAPQ score less than 10, mitochondrial reads were removed using the grep command, and fragments longer than 100 bp in length were removed using awk.
The HOMER suite was used to make tag directories and bedGraph files, which were in turn converted to bigWig files using bedGraphToBigWig.
Assembly: hg38
Supplementary files format and content: All processed data files are in bigWig format and show ATAC-seq coverage.

growth_protocol: iPSCs were cultured on Matrigel-coated wells (Corning, 354230) and passaged using Accutase (EMD Millipore, SCR005) at approximately 60% confluency. The following day, the culture medium was replaced with neuroepithelial progenitor (NEP) medium, and differentiation was induced through sequential stages, including NEP induction, neural progenitor expansion, and neuronal maturation. Differentiated neurons were plated on chambered coverslips (ibidi, 80826 or 80426) pre-coated with poly-L-lysine (0.1 mg/mL, overnight at 37 °C) and laminin (10 µg/mL, for at least 2 h at 37 °C), on poly-D-lysine/laminin-coated glass coverslips (Corning, 354087), or on Matrigel-coated plates, and maintained for 1–3 months before use.

extract_protocol:
ATAC-seq DNA was isolated as described previously (Grandi et al. 2022, Nature Protocols) with the following modifications. 1x105 cells were used to generate each library. Tagmentase (Diagenode) and home-made 2x TD Buffer (20 mM Tris-HCl pH 7.5, 10 mM MgCl2, 20% dimethylformamide) were used in place of the previously described TDE1 enzyme and 2x TD Buffer from Illumina. After tagmentation, DNA was isolated using the Qiagen MinElute PCR Purification Kit.
Libraries were generated from isolated DNA essentially as described previously (Grandi et al. 2022, Nature Protocols). Libraries were amplified with 10 cycles of PCR, and fragments between 150 and 500 bp were gel purified using the Qiagen Gel Extraction Kit.

value: iPSC-derived cortical neurons

value: CHMP2B G26403C homozygous


title: Retina, 8w, wild-type

description:
Library name: Sample1
10x genomics

value: Wild-type


title: Control_Wild-type 1

description: Library name: C_WT_91431

value: Meibomian gland

value: no treatment


title: Cortical neurons derived from BIONi010-C iPSCs with homozygous CHMP2B G26403C mutation, biological replicate 2

description: Library name: Subject2_CHMP2B_homo_mut_rep2


title: ChIP3, rdp1Δ, H3, heat-treatment 5min, rep2


title: ChIP3, dcr1Δ, H3K9me2, heat-treatment 0min, rep1


title: H-2D 2

description:
Library name: Sample 6
High 2


title: liver, RYGB HFD, 5

city: Mineola

first: Louis

last: Ragolia

state: New York

address: 101 Mineola Blvd, Suite 4-004

department: Foundations of Medicine

institute: NYU Grossman Long Island School of Medicine

description:
Library name: Sample20
Sample name in raw counts rHFD5

data_processing:
Raw sequencing reads were processed using Trimmomatic v0.36 with default parameters to remove adapters, poly-N regions, and low-quality reads. Quality of trimmed reads was assessed using FastQC. Cleaned reads were aligned to the Mus musculus reference genome (mm10) using HISAT2 v2.1.0 with default settings. Gene-level counts were generated using FeatureCounts v1.5.0-p3 from the Subread package.
Assembly: mm10
Supplementary files format and content: csv file contains raw count data for each sample

source_name: liver

extract_protocol:
Total RNA extraction was performed using Trizol reagent (Ambion, Life Technologies, Carlsbad, CA), followed by purification and concentration using RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany; #74204). RNA purity was assessed by 260/280 and 260/230 ratios and samples were sent for sequencing.
mRNA was enriched from total RNA using poly-T oligo-attached magnetic beads, then fragmented using divalent cations at elevated temperature. First-strand cDNA synthesis was performed using random hexamer primers and reverse transcriptase, followed by second-strand synthesis using DNA Polymerase I and RNase H with dUTP incorporation to maintain strand specificity. After end repair, A-tailing, and adapter ligation, cDNA fragments were size-selected and amplified. Library quality and concentration were assessed using an Agilent Bioanalyzer, Qubit Fluorometer, and qPCR.

value: liver


title: liver, RYGB HFD, 4

description:
Library name: Sample19
Sample name in raw counts rHFD4


title: L-2D 4

description:
Library name: Sample 4
Low 4

value: Low crowding


title: Cortical neurons derived from BIONi010-C iPSCs with heterozygous CHMP2B G26403C mutation, biological replicate 2

description: Library name: Subject2_CHMP2B_het_mut_rep2

value: CHMP2B G26403C heterozygous


title: Retina, 24w, wild-type

description:
Library name: Sample2
10x genomics


title: Cortical neurons derived from BIONi010-C iPSCs with heterozygous CHMP2B G26403C mutation, biological replicate 3

description: Library name: Subject2_CHMP2B_het_mut_rep3


title: L-2D 3

description:
Library name: Sample 3
Low 3


title: L-2D 1

description:
Library name: Sample 1
Low 1


title: Cortical neurons derived from BIONi010-C iPSCs with homozygous CHMP2B G26403C mutation, biological replicate 1

description: Library name: Subject2_CHMP2B_homo_mut_rep1


title: liver, RYGB HFD, 2

description:
Library name: Sample17
Sample name in raw counts rHFD2


title: Cortical neurons derived from BIONi010-C iPSCs with heterozygous CHMP2B G26403C mutation, biological replicate 1

description: Library name: Subject2_CHMP2B_het_mut_rep1


title: liver, RYGB HFD, 1

description:
Library name: Sample16
Sample name in raw counts rHFD1


title: L-2D 2

description:
Library name: Sample 2
Low 2


title: Cortical neurons derived from BIONi010-C iPSCs, biological replicate 3

description: Library name: Subject2_CHMP2B_WT_rep3

value: CHMP2B wild type


title: ChIP3, dcr1Δ, H3, heat-treatment 0min, rep1

value: S.pombe cells

value: 0 min (non treated)


title: ChIP3, dcr1Δ, H3K9me2, heat-treatment 5min, rep1