title: Human, skin, pustular, spatial, rep2

city: Seoul

first: Hanjae

address: 103, Daehak-ro, Jongno-gu

institute: Seoul National University

description: Library name: Spatial_2

data_processing:
Raw sequencing reads were processed using the Cell Ranger pipeline (v7.1.0), and aligned to the GRCh38-2020-A reference genome provided by 10x Genomics.
Assembly: GRCh38 (2020-A provided by 10x Genomics)
Supplementary files format and content: High-resolution and Cytassit images in tar.gz files and processed spatial bin outputs in tar.gz files
Library strategy: Spatial Transcriptomics

source_name: Skin

extract_protocol:
The collected tissue samples were immediately processed for cell dissociation. After washing with PBS (Gibco, 10010023), adipose tissue was carefully removed. The tissue was finely minced using a scalpel and scissors, then incubated in Liberase TL solution (0.25 mg/mL; Miltenyi Biotec, 05401020001) at 37 °C for 40 minutes, with gentle vortexing or tapping every 5 minutes. Following enzymatic digestion, the sample was resuspended by pipetting 10 times using a wide-bore pipette tip. The resulting suspension was filtered through a 70 μm cell strainer and subsequently rinsed with PBS. Cells were pelleted by centrifugation at 300 ×  g for 5 minutes at 4 °C, resuspended in 1 mL of freezing medium (Cellbanker 1; Nippon Zenyaku Kogyo, BLC-1), and cryopreserved in liquid nitrogen. For the sequencing step, cryopreserved samples were thawed in a 37 °C water bath. Once only small ice crystals remained, samples were removed and 1 mL of pre-warmed culture medium (RPMI; HyClone, SH30027.01) supplemented with 10% FBS (Thermo Fisher, A3160401) was added. Cells were gently resuspended using a wide-bore pipette tip and transferred to a 15 mL Falcon tube containing 9 mL of additional warm culture medium. After centrifugation at 300 × g for 5 minutes at 20 °C, the supernatant was removed and the cell pellet was gently resuspended in 1 mL of warm culture medium. An initial cell count was performed, followed by filtration through a 40 μm cell strainer. After an additional centrifugation and resuspension step, the final cell suspension was prepared in PBS containing 0.04% BSA (Gibco, 15260037). A final cell count was recorded prior to library generation.
Spatial sequencing libraries were generated using the Visium HD Human Transcriptome Kit (10x Genomics, 1000675) according to the manufacturer’s instructions at Macrogen Inc. (Seoul, Korea). FFPE tissue blocks with DV200 values greater than 30% were selected for library preparation, and 5 μm sections were used. Libraries were sequence on a Novaseq system (Illumina).

value: Skin

tag: subject status

value: patient with PPP


title: scRNAseq_Abx_MULTI_3

status: Public on Mar 09 2026

type: SRA

city: Los Angeles

first: Dario

last: Boffelli

state: CA

address: 700 N San Vicente Blvd

department: Pediatrics

country: USA

institute: Cedars Sinai

description: Library name: multi_3

library_source: transcriptomic

data_processing:
CellRanger v 7.0.0 count is used for processing cDNA samples.
kb_kite (kallisto and bustools) with default parameters is used along with hashdrops for demultiplexing
Hashdrops was used for demultiplexing the data
Colon relevant data is subsetted for downstream data analysis, where data was SCT normalized on individual batches and then used FASTMNN for integrating the data.
Assembly: mm10
Supplementary files format and content: matrix files, barcodes.tsv, features.tsv

molecule: polyA RNA

organism: Mus musculus

source_name: Colon

extract_protocol:
The colons were opened and washed with PBS. Epithelial cells were isolated by incubating the tissue in 15 mM EDTA for 45 minutes at 37°C, followed by manual shaking. Crypts were dissociated into single cells by incubation in a dissociation buffer containing Dispase II (2 U/mL) and DNase I (30 μg/mL) for 30 minutes at 37°C. Cells were pooled by condition and sorted at a 1:1 ratio of proliferative epithelial cells (EPCAM⁺, CD44⁺, CD45⁻) and differentiated epithelial cells (EPCAM⁺, CD44⁻, CD45⁻) using fluorescence-activated cell sorting (FACS).
The library was prepared using the 10X Chromium Single Cell 3’ Library Kit according to the manufacturer’s protocol.

tag: tissue

value: Colon

tag: cell type

value: Epithelium

tag: genotype

value: wild type C57BL/6J

tag: treatment

value: Antibiotic

tag: batch


title: Human, skin, healthy control, scRNA

last: Lee

country: South Korea

description: Library name: HC

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were processed using the Cell Ranger pipeline (v7.1.0), and aligned to the GRCh38-2020-A reference genome provided by 10x Genomics.
Assembly: GRCh38 (2020-A provided by 10x Genomics)
Supplementary files format and content: The filtered_peak_bc_matrices and filtered_feature_bc_matrices files in H5 format that were generated using the default parameters of the CellRanger pipeline.

molecule: total RNA

organism: Homo sapiens

extract_protocol:
The collected tissue samples were immediately processed for cell dissociation. After washing with PBS (Gibco, 10010023), adipose tissue was carefully removed. The tissue was finely minced using a scalpel and scissors, then incubated in Liberase TL solution (0.25 mg/mL; Miltenyi Biotec, 05401020001) at 37 °C for 40 minutes, with gentle vortexing or tapping every 5 minutes. Following enzymatic digestion, the sample was resuspended by pipetting 10 times using a wide-bore pipette tip. The resulting suspension was filtered through a 70 μm cell strainer and subsequently rinsed with PBS. Cells were pelleted by centrifugation at 300 ×  g for 5 minutes at 4 °C, resuspended in 1 mL of freezing medium (Cellbanker 1; Nippon Zenyaku Kogyo, BLC-1), and cryopreserved in liquid nitrogen. For the sequencing step, cryopreserved samples were thawed in a 37 °C water bath. Once only small ice crystals remained, samples were removed and 1 mL of pre-warmed culture medium (RPMI; HyClone, SH30027.01) supplemented with 10% FBS (Thermo Fisher, A3160401) was added. Cells were gently resuspended using a wide-bore pipette tip and transferred to a 15 mL Falcon tube containing 9 mL of additional warm culture medium. After centrifugation at 300 × g for 5 minutes at 20 °C, the supernatant was removed and the cell pellet was gently resuspended in 1 mL of warm culture medium. An initial cell count was performed, followed by filtration through a 40 μm cell strainer. After an additional centrifugation and resuspension step, the final cell suspension was prepared in PBS containing 0.04% BSA (Gibco, 15260037). A final cell count was recorded prior to library generation.
ScRNA-seq libraries were generated using the Chromium Single Cell 5′ Kit v2 (10x Genomics, PN-1000265), following the manufacturer’s protocol, at the Genomic Medicine Institute Research Service Center (Seoul, Korea). Libraries were sequenced on a Novaseq system (Illumina).

tag: sample group

value: healthy control


title: scRNAseq_Abx_cDNA1

description: Library name: cDNA_1


title: scRNAseq_Abx_MULTI_2

description: Library name: multi_2


title: RNA-seq, PDS5AB-AID cells, untreated, rep1

city: San Francisco

first: Elphege

last: Nora

address: 555 Mission Bay Boulevard South

department: Cardiovascular Research Institute

institute: University of California San Francisco

description:
Library name: RSRS1
RSRS1

library_source: genomic

data_processing:
Reads were trimmed to 100 base pairs as needed using cutadapt.
Alignment of raw RNA-seq data was produced using STAR version 2.7.7a with default parameters and basic two-pass mapping in mm10. GENCODE VM23 (GRCm38.p6) was used as the reference gene set.
bigWig files were generated using bamCoverage (deepTools) separated by strand with BPM normalization.
Assembly: mm10
Supplementary files format and content: Tab delimited text file includes raw counts for each sample
Supplementary files format and content: bigWigs separated by forward and reverse strand and normalized using BPM

molecule: genomic DNA

growth_protocol: E14 mESCs are of XY karyotype and 129P2/Ola genetic background. mESCs were cultured in DMEM+Glutamax (ThermoFisher 10569044) supplemented with 15% Fetal Bovine Serum (ThermoFisher 10437028), 550µM b-mercaptoethanol (ThermoFisher 21985-023), 1X non-essential amino-acids (ThermoFisher 11140050), 104U of Leukemia inhibitory factor (Millipore ESG1107), PD0325901 (APExBIO A3013), CHIR-99021 (APExBIO A3011). Cells were maintained at a density of 0.2-1.5x105 cells/cm2 by passaging using TrypLE (ThermoFisher 12605010) every 24-48h on 0.1% gelatin-coated dishes at 37°C and 5% CO2. 0.1% gelatin was prepared in 1X PBS using Gelatin powder (Sigma Aldrich G1890). Medium was changed daily when cells were not passaged. Cells were checked for mycoplasma infection and tested negative.

extract_protocol:
Cells were washed with PBS and lysed directly with 1 mL TRIzol (Thermo Fisher 15596-018), transferred to a 1.5 mL tube, vortexed, and incubated at room temperature for 5 minutes. After incubation, mixture was supplemented with 250 µL Chloroform, vortexed again, and centrifuged at 12,000g at 4ºC for 15 minutes. Upper phase was transferred to a new tube, mixed with an equal volume of isopropanol, and spun at 12,000g at 4ºC for 15 minutes. Pellet was washed with 70% ethanol, air dried, and resuspended in 25 µL water.
Stranded RNA-seq was performed using 1000ng of DNase-treated total RNA was used as input for polyA+ capture and library preparation using the Illumina Stranded mRNA kit (Illumina 20040532)

treatment_protocol: Degradation of proteins tagged with the Auxin-Inducible Degron (44 amino-acid AID* truncation with residues 71–114) was induced by adding Indole-3-acetic acid sodium (IAA, Sigma Cat #I5148-2G) to a final concentration of 500μM. Degradation of proteins tagged with the FKBP12F36V degron was induced by adding dTAG-13 (abbreviated dTAG - Sigma Cat, SML2601) to a final concentration of 500nM (unless stipulated otherwise).

tag: cell line

value: Mouse Embryonic Stem Cells

value: PDS5A-AID, PDS5B-AID,Tir1


title: Human, skin, pustular, scRNA, rep2

description: Library name: PL_rep2

value: pustular


title: RNA-seq,Tir1-control, untreated, rep1

description:
Library name: RSRS5
RSRS5


title: Human, skin, non-pustular, scRNA, rep2

description: Library name: NPL_rep2

value: non-pustular


title: Human, skin, non-pustular, scRNA, rep1

description: Library name: NPL_rep1


title: Nrg-1#2

city: Winnipeg

first: Soheila

last: Karimi-Abdolrezaee

state: MB

address: 629-Basic Medical Sciences Building, 745 Bannatyne Avenue

department: Department of Physiology and Pathophysiology

country: Canada

institute: University of Manitoba

description:
Library name: Sample#11
Column name in Processed data file - All Samples.csv: Nrg1-12_2

data_processing:
Data were processed using Galaxy workflow
Following QC, data were trimmed using Trimmomatic package
After trimming, transcripts were mapped to mouse genome mm10
Read counts were extracted and normalized using GenCount package in Galaxy workflow
Assembly: mm10
Supplementary files format and content: csv file containing processed and normalized gene counts for all of the samples

source_name: MACS sorted for CD11b from Corpus callosum

extract_protocol:
RNA was extracted from the sorted cells by homogenization in TRI Reagent (Sigma, T9424), followed by purification using the PureLink RNA Mini Kit (Thermo Fisher Scientific, 12183018A).
RNA libraries were generated using Illumina NovaSeq PE 100 platform by Genome Qubec

tag: library preparation_method

value: polyA-enriched RNA

tag: strain

value: Microglia

value: WT

value: 10-week cuprizone diet + 2-week recovery and 30 g/kg/day Neuregulin 1 beta 1 peptide (Shenandoah Biotechnology, USA, 100-46)


title: HTS of the Cftr locus from treated B6-Tg(CFTRG542X)Cwr (CFTR G542X) mice lung 1

city: Toronto

first: Fanglin

last: Gong

state: ON

address: 144 College St

institute: University of Toronto

description: Library name: mouse-1

data_processing:
Data were processed with CRISPResso2.
Assembly: AGGAAGATGTGCCTTTCAAATTCAGATTGAGCATACTAAAAGTGACTCTCTAATTTTCTATTTTTGGTAATAGGACATCTCCAAGTTTGCAGAGAAAGACAATATAGTTCTTTGAGAAGGTGGAATCACACTGAGTGGAGGTCAACGAGCAAGAATTTCTTTAGCAAGGTGAATAACTAATTATTGGTCTAGCAAGCATTTGCTGTA
Supplementary files format and content: CRISPResso_on_7.html; CRISPResso_on_8.html; CRISPResso_on_9.html

source_name: lung

extract_protocol:
Genomic DNA was extracted by DNaeasy Extraction Kit (Qiagen, Cat# E1941).
Genomic DNA was amplified by PCR using Q5 DNA polymerase. Barcodes for Illumina sequencing were added via a second PCR step, using 1 μl of the first PCR as a template. Barcoded PCR products were pooled according to amplicon and quantified by Qubit dsDNA HS assay kit (Thermo Fisher).

value: lung


title: CutRun_HT29_TGFP_MT_rep3_H3K4me3

city: Oxford

first: Yucheng

last: Wang

state: Oxfordshire

address: Roosevelt Drive, Headington

country: United Kingdom

institute: University of Oxford

description: Library name: CutRun_HT29_TGFP_MT_rep3_H3K4me3

data_processing:
The trimmed fastq files were aligned to the human hg38 genome using the Bowtie2 aligner program (v.2.3.4.2) with parameters set as: -I 10 -X 700 –local –very-sensitive- local –no-mixed –no-discordant –no-unal. Duplicates were marked and then removed using picard program. To perform spike-in normalization, the same fastq files were aligned to the sacCer3 yeast genome using Bowtie2 with the parameters setting as: -I 10 -X 700 –local –very- sensitive-local –no-mixed –no-discordant –no-unal –no-overlap –no-dovetail. The spike-in normalization factor was calculated as the ratio between 20,000 and the total reads aligned to the yeast genome. Genome coverage of each sample was generated from the alignment files using the genomecov command in the bedtools suite (v.2.28.0) with the scale parameter setting as the spike-in normalization factor to normalize the library. Peaks were called from Human genome aligned BAM files using MACS2 with the following parameters: -q 0.01 -B –SPMR –keep-dup all.
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&Run

source_name: Colorectal cancer

extract_protocol:
1,000,000 cells per condition were immobilized on Concanavalin A-coated magnetic beads, followed by incubation with an anti-H3K4me3 antibody (Abcam, ab8580, 1:100 dilution) overnight at 4°C. After antibody binding, cells were washed with digitonin-containing wash buffer, and Protein A-MNase was added to the mixture and incubated for 1 hour at 4°C.
CUT&RUN assays were performed on CTRL and METTL3KD CRC cells using the Cell Signaling Technology (CST) CUT&RUN Assay Kit (#86652) according to the manufacturer’s protocol. Briefly, 1,000,000 cells per condition were immobilized on Concanavalin A-coated magnetic beads, followed by incubation with an anti-H3K4me3 antibody (Abcam, ab8580, 1:100 dilution) overnight at 4°C. After antibody binding, cells were washed with digitonin-containing wash buffer, and Protein A-MNase was added to the mixture and incubated for 1 hour at 4°C. To initiate chromatin cleavage, 3 µl of 100 mM CaCl₂ was added, and the reaction was allowed to proceed on ice for 30 minutes. The reaction was terminated by adding a chelation buffer containing EDTA and EGTA. The cleaved chromatin fragments were collected in the supernatant following centrifugation and purified using the QIAGEN MinElute Kit. The purified DNA was then used to prepare sequencing libraries with the NEBNext Ultra II DNA Library Prep Kit, following the manufacturer’s protocol. Libraries were sequenced using the Illumina NextSeq 2000 platform to generate paired-end reads.

value: Colorectal cancer

value: human colorectal cancer cell line

value: wild type

value: Mock treated


title: Human, skin, pustular, scRNA, rep1

description: Library name: PL_rep1

value: Skin


title: HTS of the Cftr locus from treated B6-Tg(CFTRG542X)Cwr (CFTR G542X) mice lung 3

description: Library name: mouse-3


title: Day 10 time-stamped TCL-1 mouse 97, FACS sorted Tom– B cells, time point 2

city: Lund

first: Joan

last: Yuan

address: Sölvegatan 19

country: Sweden

institute: Lund University

description: Library name: Sample_97_PB_TN_T2

data_processing:
FASTQ files were merged with PEAR v0.9.11.
Merged FASTQ files were transformed to FASTA with pRESTO package v0.7.1.
FASTA files were aligned with IMGT/High V-Quest using default settings.
Aligned files were further processed with Change-O package v1.3.0.
Processed data files were generated with "MakeDb.py" function and filtered with "ParseDb.py" function from Change-O package v1.3.0.
Assembly: IMGT reference directory (IG)
Supplementary files format and content: tab-delimited (.tsv) databases contain aligned IgHM sequence information for downstream analysis.

source_name: Peripheral blood

extract_protocol:
FACS sorted B cells were lysed in RNAzol (Sigma-Aldrich) or DNA/RNA shield (Zymo Research) and total RNA was extracted with Direct-zol RNA MiniPrep Kit (Zymo Research) according to manufacturer's instructions.
IgHM transcripts were captured via their constant region and cDNA was generated via template switch reverse transcription using SMARTScribe Reverse Transcriptase (Takara Bio). cDNA libraries were PCR amplified with Q5 High-Fidelity DNA Polymerase, purified with AMPure XP Reagent and quantified with Qubit Fluorometer (dsDNA HS Assay Kit). Up to 2.5 ng cDNA library was indexed with Nextera XT Index Kit v2 SetA (Illumina). Final cDNA library  quality was assessed with Agilent 2100 Bioanalyzer (High Sensitivity DNA Kit).

treatment_protocol: Mice were time-stamped with tamoxifen (50 mg/kg).

value: Peripheral blood

value: CD19+ Tom- B cells

value: Day 10 time-stamped


title: Nrg-1#3

description:
Library name: Sample#12
Column name in Processed data file - All Samples.csv: Nrg1-12_3

value: MACS sorted for CD11b from Corpus callosum


title: Vehicle#5

description:
Library name: Sample#9
Column name in Processed data file - All Samples.csv: Vehicle12_5

value: 10-week cuprizone diet + 2-week recovery and 0.1% bovine serum albumin (BSA) in saline


title: Nrg-1#1

description:
Library name: Sample#10
Column name in Processed data file - All Samples.csv: Nrg1-12_1


title: mouse brain, sub test16

city: Beijing

first: xiaoqun

last: wang

state: Beijing

address: 15 Datun Road, Chaoyang District

department: Institute of Biophysics

country: China

institute: Chinese Academy of Sciences

description: Library name: test16

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Assembly: mm10
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: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: detected_tissue_image.jpg: image of tisssue and spots
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial transcriptomics

source_name: mouse brain

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10um frozen sections were cut with cryostat
Spatial transcriptomics sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction

value: mouse brain


title: Day 10 time-stamped TCL-1 mouse 97, FACS sorted Tom+ B cells, time point 2

description: Library name: Sample_97_PB_TP_T2

value: CD19+ Tom+ B cells


title: mouse brain, sub test15

description: Library name: test15


title: HTS of the Cftr locus from treated B6-Tg(CFTRG542X)Cwr (CFTR G542X) mice lung 2

description: Library name: mouse-2


title: Human, skin, pustular, spatial, rep1

description: Library name: Spatial_1

value: patient with PPP


title: mouse brain, prl test14

description: Library name: test14


title: Day 10 time-stamped TCL-1 mouse 95, FACS sorted Tom– B cells, time point 2

description: Library name: Sample_95_PB_TN_T2


title: Vehicle#3

description:
Library name: Sample#7
Column name in Processed data file - All Samples.csv: Vehicle12_3

value: polyA-enriched RNA

value: Microglia


title: mouse brain, sub test18

description: Library name: test18


title: RNAseq_HCT116_METTL3KD1_MT_rep1

description:
Library name: RNAseq_HCT116_METTL3KD1_MT_rep1
RNAseq_HCT116_METTL3KD1_MT_rep1

data_processing:
FASTQ files were trimmed using the Trim_Galore program. The trimmed FASTQ files were then aligned to the human genome (hg38) using the STAR aligner program unless otherwise specified. Duplicates were marked and removed using the Picard program. A Gene Transfer Format (GTF) file containing annotations for human reference genes was downloaded from the UCSC Genome Browser as gencode.v21.annotation_GRCh38.gtf. This GTF file for gene annotation was used with the featureCounts command of the subread tools.
Assembly: hg38
Supplementary files format and content: txt, CPM

growth_protocol: HT29 and HCT116 human colorectal cancer cell lines were cultured in McCoy’s 5A medium supplemented with penicillin-streptomycin (1%), and Fetal-Bovine-serum (10%).

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit. Purified RNA was quantified by a NanoDrop 2000 spectrophotometer, and purity was considered acceptable if A260/A280 values were ≥ 1.8.
Library preparation for total RNA-sequencing was done by the Oxford Genomic Centre (OGC). Briefly, RNA samples were quantified using RiboGreen (Invitrogen) on the FLUOstar OPTIMA plate reader (BMG Labtech) and the size profile and integrity were analysed on the 2200 or 4200 TapeStation (Agilent, RNA ScreenTape). RIN estimates for all samples were between 5.5 and 10. Input material was normalised to 100 ng before library preparation. The RNA was depleted of ribosomal RNA using NEBNext rRNA Depletion Kit (NEB Human/Mouse/Rat) following manufacturer instructions. Strand-specific library preparation was completed using NEBNext Ultra II RNA kit (NEB) following the manufacturer’s instructions. Libraries were amplified (14 cycles) on a Tetrad (Bio-Rad) using unique dual indexing primers (IDT 10008053). Individual libraries were normalised using Qubit (Invitrogen), Picogreen (Thermofisher) or Quantfluor (Promega), and the size profile was analysed on the 2200 or 4200 TapeStation. Individual libraries were normalised and pooled together accordingly. The pooled library was diluted to ~10nM for storage. The 10nM library was denatured and further diluted prior to loading on the sequencer.  Paired-end sequencing was performed using a NovaSeq6000 platform (Illumina, NovaSeq 6000 S4 reagent kit, 300 cycles).

value: METTL3 knock-down


title: mouse brain, prl test13

description: Library name: test13


title: mouse brain, sub test17

description: Library name: test17


title: RNAseq_HCT116_METTL3KD1_DAC_rep1

description:
Library name: RNAseq_HCT116_METTL3KD1_DAC_rep1
RNAseq_HCT116_METTL3KD1_DAC_rep1

value: Decitabine


title: Vehicle#2

description:
Library name: Sample#6
Column name in Processed data file - All Samples.csv: Vehicle12_2

value: WT


title: Vehicle#4

description:
Library name: Sample#8
Column name in Processed data file - All Samples.csv: Vehicle12_4


title: mouse brain, prl test12

description: Library name: test12


title: Day 10 time-stamped TCL-1 mouse 95, FACS sorted Tom+ B cells, time point 2

description: Library name: Sample_95_PB_TP_T2


title: RNAseq_HCT116_METTL3KD1_DAC_rep2

description:
Library name: RNAseq_HCT116_METTL3KD1_DAC_rep2
RNAseq_HCT116_METTL3KD1_DAC_rep2

value: Colorectal cancer

value: human colorectal cancer cell line


title: Vehicle#1

description:
Library name: Sample#5
Column name in Processed data file - All Samples.csv: Vehicle12_1


title: RNAseq_HCT116_TGFP_DAC_rep1

description:
Library name: RNAseq_HCT116_TGFP_DAC_rep1
RNAseq_HCT116_TGFP_DAC_rep1

value: wild type


title: Day 10 time-stamped TCL-1 mouse 94, FACS sorted Tom– B cells, time point 2

description: Library name: Sample_94_PB_TN_T2


title: mouse brain, prl test11

description: Library name: test11


title: Day 10 time-stamped TCL-1 mouse 94, FACS sorted Tom+ B cells, time point 2

description: Library name: Sample_94_PB_TP_T2


title: Control#3

description:
Library name: Sample#3
Column name in Processed data file - All Samples.csv: Control_3


title: Control#4

description:
Library name: Sample#4
Column name in Processed data file - All Samples.csv: Control_4


title: RNAseq_HCT116_TGFP_MT_rep1

description:
Library name: RNAseq_HCT116_TGFP_MT_rep1
RNAseq_HCT116_TGFP_MT_rep1

value: Mock treated


title: Day 19 time-stamped TCL-1 mouse 91, FACS sorted Tom– B cells, time point 2

description: Library name: Sample_91_PB_TN_T2

value: Peripheral blood

value: Day 19 time-stamped


title: RNAseq_HCT116_TGFP_DAC_rep2

description:
Library name: RNAseq_HCT116_TGFP_DAC_rep2
RNAseq_HCT116_TGFP_DAC_rep2


title: Day 19 time-stamped TCL-1 mouse 91, FACS sorted Tom+ B cells, time point 2

description: Library name: Sample_91_PB_TP_T2


title: mouse brain, prl test9

description: Library name: test9


title: RNAseq_HCT116_TGFP_MT_rep2

description:
Library name: RNAseq_HCT116_TGFP_MT_rep2
RNAseq_HCT116_TGFP_MT_rep2


title: Day 19 time-stamped TCL-1 mouse 90, FACS sorted Tom– B cells, time point 2

description: Library name: Sample_90_PB_TN_T2

value: CD19+ Tom- B cells


title: Control#1

description:
Library name: Sample#1
Column name in Processed data file - All Samples.csv: Control_1

value: MACS sorted for CD11b from Corpus callosum


title: mouse brain, sub test8

description: Library name: test8


title: Day 19 time-stamped TCL-1 mouse 90, FACS sorted Tom+ B cells, time point 2

description: Library name: Sample_90_PB_TP_T2


title: Control#2

description:
Library name: Sample#2
Column name in Processed data file - All Samples.csv: Control_2


title: mouse brain, prl test10

description: Library name: test10


title: mouse brain, sub test7

description: Library name: test7


title: Axin2+EpCAM+ cells from adult small intestinal crypts of Axin2-CRE-ERT_Rosa-tdTomato mice

city: Mainz

first: Natalia

last: Soshnikova

address: Langenbeckstr. 1

department: Institute for Molecular Medicine

country: Germany

institute: University Medical Centre of the Johannes Gutenberg University

data_processing:
The resulting raw data was preprocessed according to the Illumina standard protocol and reads were mapped to GENCODE M31. Counting and demultiplexing were performed using the BD Rhapsody™ Sequence Analysis Pipeline (v2.0) yielding around 10.000 called putative cells for each sample with a mean of around 45.000 aligned reads per cell.
Pipeline output files were imported into Partek Flow software. High-quality single cells were defined based on the following criteria: 5000≤UMI per cell≤80000, 1000≤genes per cell≤9000, mitochondrial UMI<25%.
Single cell counts were normalized by Partek Flow recommended normalization order (CPM (counts_per_million), Add:1 and log2).
Assembly: mm10
Supplementary files format and content: tab separated file containing counts per gene

source_name: small intestine

extract_protocol:
The mouse small intestines were dissected in 3 equal pieces. The small intestines were cut in pieces of 4 mm2, placed into 50 ml conical tubes and washed 3 times for 20 min with 25 ml of PBS/ 5 mM EDTA on a rocking plate at room temperature. Villi were mechanically removed by gentle shaking 3 times and trituration using a 25 ml pipette. Crypts were separated from the intestine by vigorous shaking 2 times. Crypts from all three parts were collected by centrifugation at 200g for 5 min, washed twice with PBS. Crypts from three Axin2Cre-ERT2:Rosa26tdTomato mice were mixed at equal ratios. To isolate epithelial cells, single-cell suspensions were stained with APC–conjugated anti-EpCAM 1:1000 (eBioscience) antibody for 30 min at room temperature. Fluorescence-activated cell sorting was performed using BD FACS Aria III SORP cell sorter (100 μm nozzle). Living cells were gated by DAPI dye exclusion. Fifty thousand single EpCAM+ cells were sorted in PBS supplemented with 0,4% BSA.
Capturing of single cells was performed using the BD Rhapsody system (BD Biosciences). 15000 cells were loaded on a BD Rhapsody cartridge. Capture of single RNA molecules on barcoded magnetic polydT- beads and cDNA synthesis was performed as described in the manual (Single cell capture and cDNA synthesis with the BD Rhapsody single-cell analysis system; Doc ID: 210966 Rev. 1.0). BD's WTA kit was used for library preparation according to the manual. cDNA libraries were prepared following the manual (mRNA Whole Transcriptome Analysis (WTA) and sample tag library preparation protocol). Upon purifying cDNA libraries, concentration of libraries was assessed by a Qubit flex system using the DNA high sensitivity kit and average library size was determined on a bioanalyzer using a high-sensitivity DNA chip. Final sequencing library was prepared by dilution and pooling cDNA following the recommendations of the sequencing preparation sheet provided by BD. The libraries were sequenced on a Novaseq6000 (Illumina).

value: small intestine

value: mixed C57BL/6 CD1

tag: time

value: adult at P120

value: Tamoxifen at E12.75


title: RNAseq_HT29_METTL3KD1_MT_rep1

description:
Library name: RNAseq_HT29_METTL3KD1_MT_rep1
RNAseq_HT29_METTL3KD1_MT_rep1


title: P3_2021_L2: E15-RANKL-fatemap_P3, rep3

city: Fukuoka

first: Shinichiro

last: Sawa

address: 3-1-1 Maidashi, Higashiku

country: Japan

institute: Kyushu University

data_processing:
The demultiplexing, barcoded processing, gene counting were performed using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: Bone and bone marrow

extract_protocol:
Bones were isolated from limbs and minced with scissors or tweezers. The fragmented bones were incubated in DMEM containing Collagenase P, Liberase TH and DNase I at 37ºC with gentle shaking for 1h. Dissociated cells were collected every 20 min and strained with a 100 μm nylon mesh. Cells were collected by centrifuge and resuspended in FACS buffer (2% FBS/2 mM EDTA/PBS). For experiments on bone marrow cells prepared from 3-week-old mice, red blood cells were removed by 0.165 M ammonium chloride treatment. The isolated cells were stained with antibodies against CD45, Ter119 and CD31. Fixable viability dye (eBioscience) was used to stain dead cells. Cells were sorted for single cell 3' gene expression library construction.
Library construction was performed according to the manufacturer’s instructions (single cell 3’ v3.1 protocol, 10x Genomics) with slight modification. Cells up to 10,000 were directly sorted into the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM).

value: Bone and bone marrow

value: tdTomato+

value: Tnfsf11-tTA; LC1; R26-tdTom

value: Doxycycline from E15 to P3

tag: developmental stage


title: Day 10 time-stamped TCL-1 mouse 86, FACS sorted Tom– B cells, time point 2

description: Library name: Sample_86_PB_TN_T2

value: Day 10 time-stamped


title: EpCAM+ cells from adult small intestinal crypts of Axin2-CRE-ERT_Rosa-tdTomato mice


title: mouse brain, sub test6

description: Library name: test6

value: mouse brain


title: mouse brain, sub test5

description: Library name: test5


title: Day 10 time-stamped TCL-1 mouse 86, FACS sorted Tom+ B cells, time point 2

description: Library name: Sample_86_PB_TP_T2

value: CD19+ Tom+ B cells


title: RNAseq_HT29_METTL3KD1_MT_rep2

description:
Library name: RNAseq_HT29_METTL3KD1_MT_rep2
RNAseq_HT29_METTL3KD1_MT_rep2

value: Colorectal cancer

value: human colorectal cancer cell line

value: METTL3 knock-down


title: RNAseq_HT29_METTL3KD1_DAC_rep2

description:
Library name: RNAseq_HT29_METTL3KD1_DAC_rep2
RNAseq_HT29_METTL3KD1_DAC_rep2

value: Decitabine


title: P3_2021_L1: E15-RANKL-fatemap_P3, rep2


title: RNAseq_HT29_TGFP_DAC_rep2

description:
Library name: RNAseq_HT29_TGFP_DAC_rep2
RNAseq_HT29_TGFP_DAC_rep2

value: wild type


title: RNAseq_HT29_TGFP_DAC_rep1

description:
Library name: RNAseq_HT29_TGFP_DAC_rep1
RNAseq_HT29_TGFP_DAC_rep1


title: E17_2021_L2: E15-RANKL-fatemap_E17, rep3

value: Doxycycline from E15 to E17


title: Day 10 time-stamped WT control mouse 85, FACS sorted Tom+ B cells, time point 2

description: Library name: Sample_85_PB_TP_T2

value: Peripheral blood

value: WT


title: Day 10 time-stamped WT control mouse 83, FACS sorted Tom– B cells, time point 2

description: Library name: Sample_83_PB_TN_T2

value: CD19+ Tom- B cells


title: Day 10 time-stamped WT control mouse 85, FACS sorted Tom– B cells, time point 2

description: Library name: Sample_85_PB_TN_T2


title: E17_2021_L1: E15-RANKL-fatemap_E17, rep2


title: mouse brain, prl test4

description: Library name: test4


title: Day 10 time-stamped WT control mouse 83, FACS sorted Tom+ B cells, time point 2

description: Library name: Sample_83_PB_TP_T2


title: mouse brain, prl test1

description: Library name: test1


title: RNAseq_HT29_TGFP_MT_rep1

description:
Library name: RNAseq_HT29_TGFP_MT_rep1
RNAseq_HT29_TGFP_MT_rep1

value: Mock treated


title: mouse brain, prl test3

description: Library name: test3


title: RNAseq_HCT116_METTL3KD1_MT_rep2

description:
Library name: RNAseq_HCT116_METTL3KD1_MT_rep2
RNAseq_HCT116_METTL3KD1_MT_rep2


title: E15_2021_L2: E15-RANKL, rep3

value: Bone and bone marrow


title: mouse brain, prl test2

description: Library name: test2


title: Day 10 time-stamped TCL-1 mouse 97, FACS sorted Tom– B cells, time point 1

description: Library name: Sample_97_PB_TN_T1


title: RNAseq_HT29_TGFP_MT_rep2

description:
Library name: RNAseq_HT29_TGFP_MT_rep2
RNAseq_HT29_TGFP_MT_rep2


title: mouse brain, prl control14

description: Library name: con14


title: E15_2021_L1: E15-RANKL, rep2

value: tdTomato+


title: mouse brain, prl control13

description: Library name: con13


title: Day 10 time-stamped TCL-1 mouse 97, FACS sorted Tom+ B cells, time point 1

description: Library name: Sample_97_PB_TP_T1


title: PDX12, PDX, shCTR, biol rep4

city: Paris

first: Jacob

last: Torrejon Diaz

address: 26 Rue d'Ulm

country: France

institute: Curie Institute

description: Library name: Sample 7

data_processing:
RNAseq v4.0 (Nextflow rna-seq analysis pipeline, Institute Curie)
raw sequencing reads checked for quality with Fastqc and trimmed for adapter sequences
Trimmed reads aligned on the human hg38 reference genome using the STAR mapper
Generation raw count table per gene and sample
Assembly: hg38 (PDX KD AMBRA1)
Supplementary files format and content: tab-delimited text file includes raw counts for PDX KD AMBRA1 dataset

source_name: PDX12 (PDX)

growth_protocol: Tumor cells for PDXs were isolated from PDX tumor chunks with a Percoll gradient. PDX cells were cultured and infected in adherent conditions (poly-D-lysine + matrigel precoated dishes). Growth medium for PDX cells consisted of Neurobasal™ Medium (GIBCO) supplemented with 0.45% D+-Glucose (Sigma), 4 mM L-Glutamine (GIBCO), 100 U/mL penicillin/streptomycin (GIBCO), 1X Serum-free supplement B27 (GIBCO).

extract_protocol:
RNeasy Plus Mini Kit (74134, Qiagen)
Stranded mRNA prep Ligation-Illumina

treatment_protocol: Lentiviral infection with shRNAs. Cells were harvested 3 days after infection, the pellets were flash-frozen in liquid nitrogen and kept at -80°C until RNA extraction.

value: PDX12 (PDX)

value: Medulloblastoma


title: PDX12, PDX, shAMBRA1, biol rep4

description: Library name: Sample 8


title: mouse brain, sub control12

description: Library name: con12


title: RNAseq_HT29_METTL3KD1_DAC_rep1

description:
Library name: RNAseq_HT29_METTL3KD1_DAC_rep1
RNAseq_HT29_METTL3KD1_DAC_rep1


title: Tom-neg_EGFP-neg, biol rep3

data_processing:
Quality control was performed using fastp package (v.0.12.4).
Sequence reads in FASTQ format were mapped to mouse reference genome (GRCm39) from Ensembl (release 104) using HISAT2 (v.2.1.0).
Count matrix for genes was generated using featureCounts (v.2.0.1).
Assembly: mm39
Supplementary files format and content: *.txt: Tab-delimited text files include raw counts for each sample.

source_name: bone and bone marrow

extract_protocol:
Bones were isolated from limbs and minced with scissors or tweezers. The fragmented bones were incubated in DMEM containing Collagenase P, Liberase TH and DNase I at 37ºC with gentle shaking for 1h. Dissociated cells were collected every 20 min and strained with a 100 μm nylon mesh. Cells were collected by centrifuge and resuspended in FACS buffer (2% FBS/2 mM EDTA/PBS). The isolated cells were stained with antibodies against CD45, Ter119 and CD31. Fixable viability dye (eBioscience) was used to stain dead cells. Cells were sorted directly into SMART-Seq reaction buffer for library construction.
RNA libraries for RNA-seq were prepared using SMART-Seq HT Plus Kit (Takara Bio) following manufacturer's protocols.

value: bone and bone marrow

value: tdTomato-EGFP-

value: Csf1-VCre; Tnfsf11-tTA; LC1; R26-tdTomato; R26-VSV-EGFP


title: Day 10 time-stamped TCL-1 mouse 95, FACS sorted Tom– B cells, time point 1

description: Library name: Sample_95_PB_TN_T1

value: Day 10 time-stamped


title: Day 10 time-stamped TCL-1 mouse 95, FACS sorted Tom+ B cells, time point 1

description: Library name: Sample_95_PB_TP_T1

value: CD19+ Tom+ B cells


title: Day 10 time-stamped TCL-1 mouse 94, FACS sorted Tom– B cells, time point 1

description: Library name: Sample_94_PB_TN_T1


title: PDX12, PDX, shAMBRA1, biol rep3

description: Library name: Sample 6


title: Tom-neg_EGFP-pos, biol rep3

value: tdTomato-EGFP+


title: Tom-pos_EGFP-neg, biol rep3

value: tdTomato+EGFP-


title: Tom-neg_EGFP-neg, biol rep2


title: PDX12, PDX, shCTR, biol rep3

description: Library name: Sample 5


title: mouse brain, sub control11

description: Library name: con11

value: mouse brain


title: Day 10 time-stamped TCL-1 mouse 94, FACS sorted Tom+ B cells, time point 1

description: Library name: Sample_94_PB_TP_T1


title: PDX12, PDX, shAMBRA1, biol rep2

description: Library name: Sample 4


title: PDX12, PDX, shCTR, biol rep2

description: Library name: Sample 3


title: mouse brain, prl control9

description: Library name: con9


title: Tom-neg_EGFP-pos, biol rep2


title: mouse brain, sub control8

description: Library name: con8


title: PDX12, PDX, shAMBRA1, biol rep1

description: Library name: Sample 2


title: mouse brain, prl control10

description: Library name: con10


title: Day 19 time-stamped TCL-1 mouse 91, FACS sorted Tom– B cells, time point 1

description: Library name: Sample_91_PB_TN_T1

value: Day 19 time-stamped


title: Tom-pos_EGFP-neg, biol rep2


title: Day 19 time-stamped TCL-1 mouse 91, FACS sorted Tom+ B cells, time point 1

description: Library name: Sample_91_PB_TP_T1

value: Peripheral blood


title: Day 19 time-stamped TCL-1 mouse 90, FACS sorted Tom– B cells, time point 1

description: Library name: Sample_90_PB_TN_T1


title: mouse brain, sub control7

description: Library name: con7


title: PDX12, PDX, shCTR, biol rep1

description: Library name: Sample 1


title: mouse brain, sub control6

description: Library name: con6


title: Tom-pos_EGFP-pos, biol rep3

value: tdTomato+EGFP+


title: Tom-neg_EGFP-neg, biol rep1


title: Day 19 time-stamped TCL-1 mouse 90, FACS sorted Tom+ B cells, time point 1

description: Library name: Sample_90_PB_TP_T1


title: mouse brain, sub control5

description: Library name: con5


title: LX471, AT1/2-M

city: Utrecht

first: Carla

last: Pou Casellas

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
Library name: LX471 AT1/2-M
10X Genomics

data_processing:
Reads were mapped to the Human genome (CRCh38) using the CellRanger software (v.7.2.0)
Reads were demultiplexed based on genotype using the SoupOrCell algorithm (v2.5)
Assembly: GRCh38
Supplementary files format and content: The processed data files contain the barcodes (.tsv), features (.tsv), and matrix (.mtx) per sample. Additionally, donor_metadata(.tsv) files extracted from SoupOrCell are provided to distinguish tissue donor identity (assignment=="0" stands for line Lu39, assignment == "1" indicates line Lu38, and assignment == "2"refers to line Lu37).

source_name: 3 organoid donors

growth_protocol: All organoid lines were initially expanded in ALVO-EM. After 10 days, organoids were cultured in either ALVO-EM, AT2-MM, or AT1/2-M for 7 days. At day 17, the samples were harvested for scRNA-seq

extract_protocol:
After aspirating media, ~1 ml TrypLE (#12605010, Gibco) was added to one well of a 6 well plate and BME domes were disrupted mechanically by pipetting up and down. The organoid suspension was thereafter collected into a 15 ml tube and incubated at 37C for 2-4 min. Upon a suspension of mostly single cells, 10 ml of cold washing media was added, and cells were spun down at 400 g for 5 min. Live cells (DAPI-/DRAQ5+) were subsequently sorted into PBS using a BD FACSAria Fusion. Cells from the same condition but equal donors were mixed in equal parts and 25,000 cells per condition were subjected to droplet-based scRNA-seq using the 10x Genomics platform
Libraries were prepared using the 10x Genomics Chromium 3’ Gene Expression solution v3 on a GEMX machine and sequenced on a NovaSeq6000 (Illumina)

treatment_protocol: Untreated

value: Lung, EPCAM+NGFR- cells

tag: condition

tag: disease state

value: Healthy


title: Tom-neg_EGFP-pos, biol rep1


title: LX469, ALVO-EM

description:
Library name: LX469 ALVO-EM
10X Genomics

value: ALVO-EM


title: Day 10 time-stamped TCL-1 mouse 86, FACS sorted Tom– B cells, time point 1

description: Library name: Sample_86_PB_TN_T1

value: CD19+ Tom- B cells


title: mouse brain, prl control3

description: Library name: con3


title: Tom-pos_EGFP-neg, biol rep1


title: Day 10 time-stamped TCL-1 mouse 86, FACS sorted Tom+ B cells, time point 1

description: Library name: Sample_86_PB_TP_T1


title: CDDO-Me treated

first: Michela

last: Deleidi

address: 24 boulevard du Montparnasse

institute: Institut Imagine, INSERM UMR1163

data_processing:
The sequencing data was analyzed with the Cell Ranger software (version 6.0.1) provided by 10x Genomics. Demultiplexing of the sequencing reads was performed with cellranger mkfastq.gz.
For each sample, fastq.gz files generated with cellranger mkfastq.gz were subsequently processed with cellranger count. Cellranger count performs alignment, filtering, barcode counting and UMI counting. Using the filtered barcodes, it also generates feature-barcode matrices
Assembly: GRCh38-3.0.0
Supplementary files format and content: cellranger output files for raw gene-barcode matrix (barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz)

source_name: iPSC-derived neuron-astrocyte-microglia

growth_protocol: Prior to establishing the triculture, iPSC-derived cortical neurons were generated  until the final splitting at 14 DIV. After four days, iPSC-derived astrocytes from passage 3 to passage 10 after maturation were seeded onto the neurons at a ratio of 3:1 (neurons:astrocytes) and maintained in the final neuronal maturation medium. Three days later, iPSC-derived microglial precursors were added to the co-cultures at a ratio of 3:1:1 (neurons:astrocytes:microglia). The tricultures were maintained for an additional 7 days before performing the experiment.

extract_protocol:
Cells were disociated with accutase 5min at 37C and resuspended in 0,04%BSA-PBS 1x. RNA libraries were prepared using standard 10X Genomics 3' Single Cell v3.1 protocol.
Cells loaded to Chromium Chip (target cell recovery): 4,000 cells. Library Preparation Kit: Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (10x Genomics). Sequencing parameters: NovaSeq 6000, SP Flow Cell, 100 cycles. Read 1: 28 bp, i7-index: 10 bp, i5-index 10 bp, Read 2: 90 bp.

treatment_protocol: iPSC-derived tricultures were treated for 6h with 1uM of CDDO-Me or left untreated for the control experiment

value: iPSC-derived neuron-astrocyte-microglia

value: 6h, 1uM CDDO-Me treated


title: Day 10 time-stamped WT control mouse 85, FACS sorted Tom– B cells, time point 1

description: Library name: Sample_85_PB_TN_T1

value: WT


title: Tom-pos_EGFP-pos, biol rep2

value: bone and bone marrow


title: mouse brain, prl control2

description: Library name: con2


title: Tom-pos_EGFP-pos, biol rep1

value: Csf1-VCre; Tnfsf11-tTA; LC1; R26-tdTomato; R26-VSV-EGFP


title: mouse brain, prl control1

description: Library name: con1


title: Untreated control

value: Vehicle treated


title: Lesser wax moth (A. grisella) whole gut sample 3

status: Public on Mar 08 2026

city: Acton

first: Gunjan

last: Pandey

address: Clunies Ross Street

department: Environment

country: Australia

institute: Commonwealth Scientific and Industrial Research Organisation

description: Library name: LWM-gut-3

data_processing:
Quality assessment of the raw RNA-Seq reads was performed using FastQC v0.12.1 and MultiQC v1.19. Adaptor sequences and low quality bases were trimmed using TrimGalore v0.6.6 followed by a second round of quality control with FastQC and MultiQC. The cleaned reads were aligned to the corresponding wax moth genome assemblies (Achroia grisella: GCF_030625045.1) using HISAT2 v2.2.1. The resulting SAM files were sorted and converted to BAM format using SAMtools v1.18.0.
Transcript assembly and quantification were conducted using StringTie v2.2.1 in the default novel gene discovery mode allowing for identification of both known (annotated) and novel transcripts. Further, IsoformSwitchAnalyzeR v.1.17.04 R package was used to resolve the few ambiguities raised by StringTie. This dual approach allowed for comprehensive transcriptome profiling, capturing both known and novel transcripts.
Assembly: GCF_030625045.1
Supplementary files format and content: Tab-delimited text file containing raw gene counts for each sample
Supplementary files format and content: Tab-delimited text file containing normalized (TPM) gene counts for each sample

organism: Achroia grisella

source_name: Whole gut

extract_protocol:
Tissue-specific RNA was extracted using Quick-RNA Tissue/Insect Kit (Zymo; Cat. # R2030)
Libraries were constructed by Azenta Life Sciences (Suzhou, China) via an Illumina PCR-based library construction

value: Whole gut


title: Day 10 time-stamped WT control mouse 85, FACS sorted Tom+ B cells, time point 1

description: Library name: Sample_85_PB_TP_T1

value: CD19+ Tom+ B cells

value: Day 10 time-stamped


title: Lesser wax moth (A. grisella) labial glands sample 2

description: Library name: LWM-lg-2

source_name: Labial glands

value: Labial glands


title: Lesser wax moth (A. grisella) whole gut sample 2

description: Library name: LWM-gut-2


title: Lesser wax moth (A. grisella) labial glands sample 1

description: Library name: LWM-lg-1


title: Lesser wax moth (A. grisella) whole gut sample 1

description: Library name: LWM-gut-1


title: Lesser wax moth (A. grisella) fat body sample 3

description: Library name: LWM-fb-3

source_name: Fat body

value: Fat body


title: Lesser wax moth (A. grisella) labial glands sample 3

description: Library name: LWM-lg-3


title: mouse brain, prl control4

description: Library name: con4

value: mouse brain


title: Lesser wax moth (A. grisella) fat body sample 1

description: Library name: LWM-fb-1


title: Lesser wax moth (A. grisella) fat body sample 2

description: Library name: LWM-fb-2


title: Greater wax moth (G. mellonella) labial glands sample 3

description: Library name: GWM-lg-3

data_processing:
Quality assessment of the raw RNA-Seq reads was performed using FastQC v0.12.1 and MultiQC v1.19. Adaptor sequences and low quality bases were trimmed using TrimGalore v0.6.6 followed by a second round of quality control with FastQC and MultiQC. The cleaned reads were aligned to the corresponding wax moth genome assemblies (Galleria mellonella: GCF_026898425.1) using HISAT2 v2.2.1. The resulting SAM files were sorted and converted to BAM format using SAMtools v1.18.0.
Transcript assembly and quantification were conducted using StringTie v2.2.1 in the default novel gene discovery mode allowing for identification of both known (annotated) and novel transcripts. Further, IsoformSwitchAnalyzeR v.1.17.04 R package was used to resolve the few ambiguities raised by StringTie. This dual approach allowed for comprehensive transcriptome profiling, capturing both known and novel transcripts.
Assembly: GCF_026898425.1
Supplementary files format and content: Tab-delimited text file containing raw gene counts for each sample
Supplementary files format and content: Tab-delimited text file containing normalized (TPM) gene counts for each sample

organism: Galleria mellonella


title: Greater wax moth (G. mellonella) whole gut sample 3

description: Library name: GWM-gut-3


title: Greater wax moth (G. mellonella) labial glands sample 2

description: Library name: GWM-lg-2


title: Greater wax moth (G. mellonella) labial glands sample 1

description: Library name: GWM-lg-1


title: Greater wax moth (G. mellonella) fat body sample 1

description: Library name: GWM-fb-1


title: Greater wax moth (G. mellonella) fat body sample 2

description: Library name: GWM-fb-2


title: Greater wax moth (G. mellonella) fat body sample 3

description: Library name: GWM-fb-3


title: pum-RNAi, rep 2

city: San Juan

first: Jose

middle: L

last: Agosto-Rivera

state: Puerto Rico

address: 14 Ave. Universidad Ste. 1401

department: Biology

institute: University of Puerto Rico, Rio Piedras

description:
Library name: pum knockdown sample 2
Column name in all_deseq2_results.csv: pum2m; Column name in counts_allsamples.csv: pum2m

data_processing:
Raw reads were assessed for quality using FastQC v0.12.1.
Reads were trimmed for adapters and low-quality sequences using Trimmomatic v0.39.
Trimmed reads were aligned to the Drosophila melanogaster reference genome (dm6) and gene expression was quantified using STAR 2.7.11b.
Batch effects were corrected using ComBat-seq.
Differential expression analysis was performed using DESeq2.
Assembly: dm6
Supplementary files format and content: csv includes DESeq2 output and gene names (all_deseq2_results.csv)
Supplementary files format and content: csv includes raw counts for each sample (counts_allsamples.csv)

organism: Drosophila melanogaster

source_name: head

growth_protocol: Flies were reared at 18°C until transgene expression, and were collected following sleep assays and pooled in 50 mL polypropylene tubes. They were allowed to recover from transfer stress for 30 minutes in an environmentally controlled incubator at 29°C.

extract_protocol:
For each biological replicate, 10 heads were pooled in 1 mL of TRI Reagent and homogenized with RNAse-free plastic pestles. Total RNA extraction was outsourced to Novogene (Sacramento, CA, USA) and performed using standard procedures.
Stranded mRNA sequencing libraries were prepared from purified poly-A-containing mRNA. Sequencing was performed on an Illumina NovaSeq X Plus.

treatment_protocol: Flies were flash-frozen in liquid nitrogen. To separate heads from bodies, frozen flies were placed on liquid nitrogen-cooled sieves and vortexed for 20 seconds, followed by re-cooling in liquid nitrogen for 10 seconds. This cycle was repeated three times for a total of 1 minute of vortexing.

value: head

value: w1118/y1,sc*,v1,sev21; esg-Gal4, UAS-2xYFP/+; Su(H)GBE-Gal80, tub-Gal80ts/UAS-pumRNAi, where UAS-pumRNAi = P{y[+t7.7] v[+t1.8]=TRiP.HMS01564}attP2


title: Control, mCherry-RNAi, rep 3

description:
Library name: Control sample 3
Column name in all_deseq2_results.csv: mc3m; Column name in counts_allsamples.csv: mc3m

value: w1118/y1,sc*,v1;sev21; esg-Gal4, UAS-2xYFP/+; Su(H)GBE-Gal80, tub-Gal80ts/UAS-mCherryRNAi, where UAS-mCherryRNAi =P{y[+t7.7] v[+t1.8]=VALIUM20-mCherry.RNAi}attP2


title: Greater wax moth (G. mellonella) whole gut sample 1

description: Library name: GWM-gut-1


title: L-AN-5, circZNF827/hnRNPL kd / H3K27me3 / rep 3

city: Aarhus

first: Ivan

last: Zaporozhchenko

address: Universitetsbyen 83, 1874-356

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

description: Library name: ZL_3_K27me3

data_processing:
Low-quality and adapter sequences were removed from raw data using SOAPnuke (-n 0.001 -l 20 -q 0.4 --adaMR 0.25 --minReadLen 100).
Reads were aligned to the reference genome (GRCh38/hg38) using Bowtie2 v2.5.1 (--local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700).
Samples were normalized using a greenlist of genomic regions (de Mello et al., Brief Bioinform, 2024, PMID: 38279652) and peaks were called against IgG enrichments using SEACR v1.3 (-non -relaxed).
Assembly: GRCh38/hg38
Supplementary files format and content: BigWigs files contain per-sample peaks and overlapping raw read counts
Library strategy: CUT&Run

growth_protocol: L-AN-5 cells were maintained in RPMI-1640 media supplemented with 10% FBS at 37C and 5% CO2

extract_protocol:
CUT&RUN was performed using the CUT&RUN Assay Kit (Cell Signaling Technologies, #86652) according to the manufacturer's protocol. Prior to footprinting, cell aliquots were thawed, counted and diluted to ensure 150,000 cells per reaction. DNA fragments were purified from enriched chromatin samples using the DNA Purification Buffers and Spin Columns (ChIP, CUT&RUN, CUT&Tag) (Cell Signaling Technologies, #14209). Resulting ssDNA samples were stored at -80C and shipped on dry ice.
DNA libraries were prepared, quality tested and sequenced at BGI on the DNBSEQ platform generating paired-end 100 bp reads.

treatment_protocol: Cells were incubated with lentivirus dilution in RPMI media (3 MOI for each lentivirus, 6 MOI total) supplemented with 4 μg/ml polybrene for 24 hours, then media was replaced. Two days after transduction, L-AN-5 were subjected to differentiation by 10 μM retonoic acid for 4 days.

value: neuroblastoma


title: L-AN-5, circZNF827/hnRNPL kd / H3K27me3 / rep 2

description: Library name: ZL_2_K27me3


title: Greater wax moth (G. mellonella) whole gut sample 2

description: Library name: GWM-gut-2


title: Control, mCherry-RNAi, rep 1

description:
Library name: Control sample 1
Column name in all_deseq2_results.csv: mc1m; Column name in counts_allsamples.csv: mc1m


title: L-AN-5, circZNF827/hnRNPL kd / IgG / rep 3

description: Library name: ZL_3_IgG


title: L-AN-5, circZNF827/hnRNPL kd / H3K27me3 / rep 1

description: Library name: ZL_1_K27me3


title: L-AN-5, circZNF827/hnRNPL kd / IgG / rep 2

description: Library name: ZL_2_IgG


title: L-AN-5, circZNF827 kd / H3K27me3 / rep 2

description: Library name: IZ_2_K27me3


title: LX470, AT2-MM

description:
Library name: LX470 AT2-MM
10X Genomics

value: Lung, EPCAM+NGFR- cells

value: Healthy


title: L-AN-5, circZNF827/hnRNPL kd / H3K27ac / rep 3

description: Library name: ZL_3_K27ac


title: pum-RNAi, rep 1

description:
Library name: pum knockdown sample 1
Column name in all_deseq2_results.csv: pum1m; Column name in counts_allsamples.csv: pum1m


title: L-AN-5, circZNF827/hnRNPL kd / IgG / rep 1

description: Library name: ZL_1_IgG


title: pum-RNAi, rep 3

description:
Library name: pum knockdown sample 3
Column name in all_deseq2_results.csv: pum3m; Column name in counts_allsamples.csv: pum3m


title: L-AN-5, circZNF827/hnRNPL kd / H3K27ac / rep 2

description: Library name: ZL_2_K27ac


title: L-AN-5, circZNF827 kd / H3K27me3 / rep 1

description: Library name: IZ_1_K27me3


title: L-AN-5, circZNF827/hnRNPL kd / H3K4me3 / rep 3

description: Library name: ZL_3_K4me3


title: L-AN-5, circZNF827/hnRNPL kd / H3K4me3 / rep 1

description: Library name: ZL_1_K4me3


title: L-AN-5, circZNF827 kd / H3K4me3 / rep 3

description: Library name: IZ_3_K4me3


title: L-AN-5, circZNF827 kd / H3K27ac / rep 3

description: Library name: IZ_3_K27ac


title: L-AN-5, circZNF827 kd / H3K4me3 / rep 2

description: Library name: IZ_2_K4me3


title: L-AN-5, circZNF827 kd / H3K4me3 / rep 1

description: Library name: IZ_1_K4me3


title: L-AN-5, circZNF827 kd / IgG / rep 2

description: Library name: IZ_2_IgG


title: Control, mCherry-RNAi, rep 2

description:
Library name: Control sample 2
Column name in all_deseq2_results.csv: mc2m; Column name in counts_allsamples.csv: mc2m


title: L-AN-5, circZNF827 kd / H3K27me3 / rep 3

description: Library name: IZ_3_K27me3


title: L-AN-5, circZNF827/hnRNPL kd / H3K4me3 / rep 2

description: Library name: ZL_2_K4me3


title: L-AN-5, hnRNPL kd / H3K27me3 / rep 1

description: Library name: IL_1_K27me3


title: L-AN-5, circZNF827/hnRNPL kd / H3K27ac / rep 1

description: Library name: ZL_1_K27ac


title: L-AN-5, hnRNPL kd / H3K27ac / rep 2

description: Library name: IL_2_K27ac


title: L-AN-5, hnRNPL kd / H3K27ac / rep 1

description: Library name: IL_1_K27ac


title: L-AN-5, circZNF827 kd / IgG / rep 3

description: Library name: IZ_3_IgG


title: L-AN-5, circZNF827 kd / IgG / rep 1

description: Library name: IZ_1_IgG


title: L-AN-5, circZNF827 kd / H3K27ac / rep 1

description: Library name: IZ_1_K27ac


title: L-AN-5, control / H3K27me3 / rep 3

description: Library name: I_3_K27me3


title: L-AN-5, hnRNPL kd / H3K4me3 / rep 2

description: Library name: IL_2_K4me3


title: L-AN-5, control / H3K27ac / rep 3

description: Library name: I_3_K27ac


title: L-AN-5, control / H3K27me3 / rep 1

description: Library name: I_1_K27me3


title: L-AN-5, control / H3K27ac / rep 1

description: Library name: I_1_K27ac


title: L-AN-5, control / H3K27ac / rep 2

description: Library name: I_2_K27ac


title: L-AN-5, hnRNPL kd / H3K27me3 / rep 2

description: Library name: IL_2_K27me3


title: L-AN-5, control / H3K4me3 / rep 3

description: Library name: I_3_K4me3


title: L-AN-5, hnRNPL kd / IgG / rep 2

description: Library name: IL_2_IgG


title: L-AN-5, hnRNPL kd / H3K4me3 / rep 3

description: Library name: IL_3_K4me3


title: L-AN-5, control / IgG / rep 3

description: Library name: I_3_IgG


title: L-AN-5, circZNF827 kd / H3K27ac / rep 2

description: Library name: IZ_2_K27ac


title: L-AN-5, hnRNPL kd / H3K4me3 / rep 1

description: Library name: IL_1_K4me3


title: L-AN-5, hnRNPL kd / H3K27me3 / rep 3

description: Library name: IL_3_K27me3


title: L-AN-5, circZNF827 kd / rep 3

description: Library name: IZ_3

data_processing:
Low-quality and adapter sequences were removed from raw data at BGI using SOAPnuke (-n 0.001 -l 20 -q 0.4 --adaMR 0.25 --minReadLen 100).
Reads were aligned to GRCh38/hg38 using STAR v2.7.11a.
Gene-level transcript abundance was quantified using featureCounts (subread v2.0.6).
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-delimited txt file contains raw gene level counts

extract_protocol:
To obtain RNA a portion of cells was taken when preparing CUT&RUN aliquots, dissolved in TRI Reagent and stored at -20C until extraction. Extraction was performed according to manufacturers intructions. Purified RNA was dissolved in 20 uL nuclease-free water and split into aliquots stored at -80C.
Libraries were constructed at BGI using the DNBSEQ platform


title: L-AN-5, hnRNPL kd / IgG / rep 3

description: Library name: IL_3_IgG


title: L-AN-5, circZNF827 kd / rep 2

description: Library name: IZ_2


title: L-AN-5, hnRNPL kd / rep 3

description: Library name: IL_3


title: L-AN-5, hnRNPL kd / IgG / rep 1

description: Library name: IL_1_IgG


title: L-AN-5, control / H3K4me3 / rep 1

description: Library name: I_1_K4me3


title: L-AN-5, control / H3K4me3 / rep 2

description: Library name: I_2_K4me3


title: L-AN-5, hnRNPL kd / H3K27ac / rep 3

description: Library name: IL_3_K27ac


title: L-AN-5, control / IgG / rep 1

description: Library name: I_1_IgG


title: L-AN-5, circZNF827+hnRNPL kd / rep 3

description: Library name: ZL_3


title: L-AN-5, hnRNPL kd / rep 1

description: Library name: IL_1


title: L-AN-5, circZNF827+hnRNPL kd / rep 2

description: Library name: ZL_2


title: L-AN-5, control / H3K27me3 / rep 2

description: Library name: I_2_K27me3


title: L-AN-5, control / IgG / rep 2

description: Library name: I_2_IgG


title: L-AN-5, circZNF827 kd / rep 1

description: Library name: IZ_1


title: lung, aged, 3dA, rep1

first: Meimei

last: Liao

address: 7 Science Park Road ZGC Life Science Park, Beijing

institute: National Institute of Biological Sciences, Beijing.

description: Library name: Sample46

data_processing:
The clean data without adapters and low-quality reads were aligned to mouse genome (GRCm38) using Bismark software and hisat2.
Use the bismark_methylation_extractor in Bismark software to extract methylation sites and generate cov.gz files.
Assembly: GRCm38
Supplementary files format and content: The cov.gz file contains methylation sites and the level of methylation.

growth_protocol: Mice aged 6 and 15 months were provided with adequate food and water, kept at suitable temperature and humidity, under conditions of 12 hours of light and 12 hours of darkness.

extract_protocol:
DNA was extracted using a DNA Magbead Kit (TIANGEN, DP705)
The DNA was then used for library preparations and RNA-sequencing performed by Novogene Co., Ltd.

treatment_protocol:
The mix virus of AAV2/9-EF1α-DIO-hM4Di-mCherry and AAV2/9-CMV-Cre-hGH-pA was injected into the PVN of the mice. After one month of recovery, intraperitoneal injections of Clozapine N-oxide (CNO) was administered  every other day for a duration of 5 months.
Intraperitoneal injection of 50 mg/kg of 3dA or saline was administered every other day for a duration of 8 months.
Mouse liver, lung and muscle tissues were collected, followed by DNA extraction and sequencing.

value: lung

value: lung, aged, 3dA, rep1


title: L-AN-5, control / rep 2

description: Library name: I_2


title: L-AN-5, circZNF827+hnRNPL kd / rep 1

description: Library name: ZL_1


title: lung, aged, vehicle, rep1

description: Library name: Sample42

value: lung, aged, vehicle, rep1


title: lung, aged, 3dA, rep2

description: Library name: Sample47

value: lung, aged, 3dA, rep2


title: lung, aged, vehicle, rep3

description: Library name: Sample44

value: lung, aged, vehicle, rep3


title: L-AN-5, control / rep 3

description: Library name: I_3


title: L-AN-5, hnRNPL kd / rep 2

description: Library name: IL_2


title: lung, aged, 3dA, rep3

description: Library name: Sample48

value: lung, aged, 3dA, rep3


title: lung, aged, 3dA, rep4

description: Library name: Sample49

value: lung, aged, 3dA, rep4


title: lung, aged, vehicle, rep4

description: Library name: Sample45

value: lung, aged, vehicle, rep4


title: lung, aged, vehicle, rep2

description: Library name: Sample43

value: lung, aged, vehicle, rep2


title: lung, young, rep2

description: Library name: Sample39

value: lung, young, rep2


title: muscle, aged, CNO, rep3

description: Library name: Sample37

source_name: muscle

value: muscle

value: muscle, aged, CNO, rep3


title: muscle, aged, CNO, rep1

description: Library name: Sample35

value: muscle, aged, CNO, rep1


title: lung, young, rep4

description: Library name: Sample41

value: lung, young, rep4


title: muscle, aged, saline, rep4

description: Library name: Sample34

value: muscle, aged, saline, rep4


title: lung, young, rep3

description: Library name: Sample40

value: lung, young, rep3


title: muscle, aged, saline, rep2

description: Library name: Sample32

value: muscle, aged, saline, rep2


title: lung, young, rep1

description: Library name: Sample38

value: lung

value: lung, young, rep1


title: muscle, aged, CNO, rep2

description: Library name: Sample36

value: muscle, aged, CNO, rep2


title: muscle, aged, saline, rep3

description: Library name: Sample33

value: muscle, aged, saline, rep3


title: muscle, aged, saline, rep1

description: Library name: Sample31

value: muscle, aged, saline, rep1


title: L-AN-5, control / rep 1

description: Library name: I_1

value: neuroblastoma


title: muscle, aged, 3dA, rep1

description: Library name: Sample27

value: muscle, aged, 3dA, rep1


title: muscle, aged, 3dA, rep3

description: Library name: Sample29

value: muscle, aged, 3dA, rep3


title: muscle, aged, vehicle, rep3

description: Library name: Sample26

value: muscle, aged, vehicle, rep3


title: muscle, aged, 3dA, rep2

description: Library name: Sample28

value: muscle, aged, 3dA, rep2


title: muscle, young, rep4

description: Library name: Sample23

value: muscle

value: muscle, young, rep4


title: muscle, aged, vehicle, rep1

description: Library name: Sample24

value: muscle, aged, vehicle, rep1


title: RH iAP2XI-3, HA, rep2

city: Wuhan

first: Fan

last: Fuqiang

address: 1 Shizishan St

institute: Huazhong Agricultural University

description: Library name: RH iAP2XI-3 rep2

library_source: other

data_processing:
For data analysis, raw data were quality-controlled using cutadapt and mapped to the GT1 reference genome using Bowtie2. Duplicates were marked using Picard (http://broadinstitute.github.io/picard/), and peak calling was performed with MACS2. Peak overlap was analyzed using bedtools, and de novo motif searches were performed using STREME on sequences from all peaks. A cutoff of p-value < 10-9 was used to identify reliable DNA motifs.
Assembly: ToxoDB, GT1 genome, version 68
Supplementary files format and content: bw
Library strategy: CUT&Tag

molecule: other

organism: Toxoplasma

source_name: tachyzoites

extract_protocol:
CUT & Tag was performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro following the manufacturer’s protocol (Vazyme Biotech). RH iAP2Ⅺ-3-mAID-3HA strain was bound to Concanavalin A-coated beads and incubated with an anti-HA tag antibody (ab9110, Abcam). After primary and secondary antibody incubation, transposon activation and tagmentation were performed.
Targeted DNA was isolated, amplified, and purified using VAHTS DNA Clean Beads (Vazyme Biotech).

value: tachyzoites

value: RH iAP2XI-3


title: liver, aged, CNO, rep4

description: Library name: Sample19

source_name: liver

value: liver

value: liver, aged, CNO, rep4


title: muscle, young, rep1

description: Library name: Sample20

value: muscle, young, rep1


title: muscle, young, rep2

description: Library name: Sample21

value: muscle, young, rep2


title: muscle, aged, vehicle, rep2

description: Library name: Sample25

value: muscle, aged, vehicle, rep2


title: muscle, aged, 3dA, rep4

description: Library name: Sample30

value: muscle, aged, 3dA, rep4


title: RH iAP2XI-3, HA, rep1

description: Library name: RH iAP2XI-3 rep1


title: RH iAP2XI-3, HA, rep3

description: Library name: RH iAP2XI-3 rep3


title: RH Tir1, HA, rep2

description: Library name: RH Tir1 rep2

value: parental

value: RH Tir1


title: RH Tir1, HA, rep3

description: Library name: RH Tir1 rep3


title: liver, aged, CNO, rep1

description: Library name: Sample16

value: liver, aged, CNO, rep1


title: IEC139 cells treated with BMS-986158 (50 nM) for 24 h, biological replicate 3

city: Madrid

last: Mondaza-Hernandez

address: Av Reyes Católicos, 2

country: Spain

institute: Health Research Institute Fundacion Jimenez Diaz

description:
Library name: IEC139_BMS_rep3
139_24_B3

data_processing:
Raw sequencing reads were processed using Salmon (RRID:SCR_017036) and quasi-mapped to the human reference transcriptome (GRCh38) using GENCODE annotation. Transcript-level abundances were summarized to gene-level counts using the tximport package (RRID:SCR_016752) in R/Bioconductor. Differential gene expression analysis was performed using DESeq2 (RRID:SCR_015687). Variance-stabilizing transformation was applied for downstream exploratory analyses and visualization.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file containing gene-level raw counts generated using Salmon and summarized with tximport. Rows correspond to genes and columns correspond to individual RNA-seq samples.

growth_protocol: INT-SFT and IEC139 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, cat. no. 74106) according to the manufacturer's instructions.
Poly(A)-selected mRNA libraries were prepared using the TruSeq mRNA Library Preparation kit (Illumina) and sequenced on an Illumina NovaSeq X platform (150 bp paired-end) by Macrogen Inc.

treatment_protocol: Cells were treated with Mivebresib (50 nM) or BMS-986158 (50 nM) for 24 hours. Control samples were treated with vehicle (DMSO) under the same conditions.

value: Solitary fibrous tumor cells

value: primary tumor-derived


title: liver, aged, CNO, rep2

description: Library name: Sample17

value: liver, aged, CNO, rep2


title: liver, aged, CNO, rep3

description: Library name: Sample18

value: liver, aged, CNO, rep3


title: IEC139 cells treated with BMS-986158 (50 nM) for 24 h, biological replicate 1

description:
Library name: IEC139_BMS_rep1
139_24_B1


title: IEC139 cells treated with Mivebresib (50 nM) for 24 h, biological replicate 3

description:
Library name: IEC139_MIV_rep3
139_24_M3

value: Mivebresib (50 nM, 24 h)


title: liver, aged, saline, rep1

description: Library name: Sample13

value: liver, aged, saline, rep1


title: liver, aged, saline, rep3

description: Library name: Sample15

value: liver, aged, saline, rep3


title: IEC139 cells treated with BMS-986158 (50 nM) for 24 h, biological replicate 2

description:
Library name: IEC139_BMS_rep2
139_24_B2


title: liver, aged, saline, rep2

description: Library name: Sample14

value: liver, aged, saline, rep2


title: liver, aged, 3dA, rep3

description: Library name: Sample11

value: liver

value: liver, aged, 3dA, rep3


title: muscle, young, rep3

description: Library name: Sample22

value: muscle

value: muscle, young, rep3


title: IEC139 cells treated with Mivebresib (50 nM) for 24 h, biological replicate 2

description:
Library name: IEC139_MIV_rep2
139_24_M2


title: IEC139 cells treated with Mivebresib (50 nM) for 24 h, biological replicate 1

description:
Library name: IEC139_MIV_rep1
139_24_M1


title: IEC139 cells treated with vehicle control for 24 h, biological replicate 3

description:
Library name: IEC139_CTRL_rep3
139_24_C3

value: vehicle control


title: liver, aged, 3dA, rep4

description: Library name: Sample12

value: liver, aged, 3dA, rep4


title: liver, aged, 3dA, rep2

description: Library name: Sample10

value: liver, aged, 3dA, rep2


title: RH Tir1, HA, rep1

description: Library name: RH Tir1 rep1

value: tachyzoites

value: parental

value: RH Tir1


title: IEC139 cells treated with vehicle control for 24 h, biological replicate 2

description:
Library name: IEC139_CTRL_rep2
139_24_C2

value: Solitary fibrous tumor cells

value: primary tumor-derived


title: liver, aged, vehicle, rep4

description: Library name: Sample8

value: liver, aged, vehicle, rep4


title: IEC139 cells treated with vehicle control for 24 h, biological replicate 1

description:
Library name: IEC139_CTRL_rep1
139_24_C1


title: INT-SFT cells treated with BMS-986158 (50 nM) for 24 h, biological replicate 3

description:
Library name: INTSFT_BMS_rep3
INT_24_B3

source_name: INT-SFT

value: INT-SFT

value: SV40 large T antigen transformed


title: liver, aged, 3dA, rep1

description: Library name: Sample9

value: liver, aged, 3dA, rep1


title: liver, aged, vehicle, rep2

description: Library name: Sample6

value: liver, aged, vehicle, rep2


title: liver, aged, vehicle, rep3

description: Library name: Sample7

value: liver

value: liver, aged, vehicle, rep3


title: INT-SFT cells treated with BMS-986158 (50 nM) for 24 h, biological replicate 2

description:
Library name: INTSFT_BMS_rep2
INT_24_B2


title: INT-SFT cells treated with Mivebresib (50 nM) for 24 h, biological replicate 2

description:
Library name: INTSFT_MIV_rep2
INT_24_M2

value: Mivebresib (50 nM, 24 h)


title: liver, young, rep4

description: Library name: Sample4

value: liver, young, rep4


title: INT-SFT cells treated with Mivebresib (50 nM) for 24 h, biological replicate 1

description:
Library name: INTSFT_MIV_rep1
INT_24_M1


title: liver, young, rep3

description: Library name: Sample3

value: liver, young, rep3


title: INT-SFT cells treated with vehicle control for 24 h, biological replicate 3

description:
Library name: INTSFT_CTRL_rep3
INT_24_C3

value: vehicle control


title: liver, young, rep1

description: Library name: Sample1

value: liver, young, rep1


title: INT-SFT cells treated with vehicle control for 24 h, biological replicate 1

description:
Library name: INTSFT_CTRL_rep1
INT_24_C1


title: WGBS of Male F2 Offspring from F1 Progeny Sired by in vivo-Derived Spermatids.

city: Guangzhou

first: Qi

last: Li

state: Guangdong

address: No.1023,South Shatai Road, Baiyun District

department: Developmental biology

institute: Southern Medical University

description: Library name: library4

data_processing:
Sequencing reads were processed with Trim_Galore (v0.6.10) to remove adapters and low-quality reads, using ‘--clip_R1’ 9 and ‘--clip_R2’ 9 for paired-end reads. Cleaned reads were aligned to mm10 (UCSC) with Bismark (v2.5.4) in paired-end mode and ‘--non_directional’ option. Picard (v2.18.29) ‘MarkDuplicates’ removed PCR duplicates. MethylKit (v1.20.0) extracted CpG methylation sites, requiring at least 3 reads per site.
Assembly: mm10
Supplementary files format and content: txt file contains methylation information for each CpG site in each sample..

source_name: tail

extract_protocol:
Genomic DNA was isolated from mouse tissue samples using the FastPure Cell/Tissue DNA Isolation Mini Kit (Vazyme, DC102).
A total of 5ng of the isolated genomic DNA was mixed with 60 pg of unmethylated lambda DNA (ThermoFisher) and underwent bisulfite conversion. This converted DNA was subsequently purified using the Zymo EZ DNA Methylation-Gold Kit (Zymo, D4014),which employs a column-based purification strategy. Subsequent steps for library construction included random priming, library amplification, and high-throughput sequencing.

value: tail

tag: Sex

value: male


title: INT-SFT cells treated with vehicle control for 24 h, biological replicate 2

description:
Library name: INTSFT_CTRL_rep2
INT_24_C2


title: WGBS of Male F2 Offspring Originating from F1 Progeny Sired by O-Torgs-Derived Spermatids.

description: Library name: library2


title: Control subject-derived primary myotubes (MB07), DUX4.6 siRNA, Replicate 4

city: San Diego

first: Barbora

last: Malecova

address: 3020 Callan Rd

institute: Avidity Biosciences

description: Library name: H_B1_4

data_processing:
Samples were sequenced on the Illumina NovaSeq instrument and using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the NovaSeq Control Software (NCS).
RNA-seq reads were trimmed, and low-quality reads were removed using Trimgalore v0.6.3_dev with the “paired” parameter and length of 150 bps.
Trimmed fastq sequences were aligned to the human reference genome GRCh38 using STAR aligner v2.5.3a.
Raw read gene counts were obtained by using STAR aligner with options “—quantMode GeneCounts” and “--sjdbGTFfile” with gene models in GTF format obtained from human EnsEMBL release 83.
Alignment quality control and read mapping statistic were obtained from Picard tools using function “CollectMultipleMetrics”.
Raw counts were normalized to the total number of reads by calculating log2CPM (counts per million), and lowly expressed genes (average Log2CPM<-3) were eliminated before differential gene expression analysis.
Differential gene expression analysis was performed using the Limma 3.40.6 software.
Assembly: GRCh38
Supplementary files format and content: Gene expression values in the processed data file are in the unit of Log2(TPM+1)

growth_protocol: FSHD and control primary myoblasts were grown in medium containing 80% Ham’s F-10 Nutrient Mix, 20% FBS, 10ng/ml rhFGF, 1µM Dexamethasone, and Penicillin and Streptomycin.

extract_protocol:
Myotubes were collected in Trizol and stored at -80°C until processing for RNA isolation using Direct-zol-96 RNA isolation kit (Zymo Research).
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB), including enrichment of poly(A) transcripts using Oligod(T) beads.

treatment_protocol:
Myoblasts were seeded at 4000 cells/well on Matrigel-coated 96 well plates 24h prior to transfection. Next day, siRNAs (10nM) were formulated with Lipofectamine RNAiMAX (Life Technologies) and OptiMEM (Life Technologies) according to the manufacturer’s “forward transfection” instructions.
Myogenic differentiation was induced 24h post transfection with 15% KOSR-containing differentiation medium (85% DMEM/F-12, 15% KnockOutTM Serum Replacement -KOSR-, Penicillin and Streptomycin).

value: Primary myotubes

value: Normal control

value: DUX4.6 siRNA

tag: replicate


title: WGBS of Female F2 Offspring Originating from F1 Progeny Sired by O-Torgs-Derived Spermatids

description: Library name: library1

value: female


title: Control subject-derived primary myotubes (MB07), DUX4.6 siRNA, Replicate 3

description: Library name: H_B1_3


title: WGBS of Female F2 Offspring from F1 Progeny Sired by in vivo-Derived Spermatids.

description: Library name: library3


title: INT-SFT cells treated with Mivebresib (50 nM) for 24 h, biological replicate 3

description:
Library name: INTSFT_MIV_rep3
INT_24_M3

value: INT-SFT

value: Solitary fibrous tumor cells


title: Control subject-derived primary myotubes (MB07), DUX4.6 siRNA, Replicate 1

description: Library name: H_B1_1


title: Bulk-seq from testicular samples of mice treated with BU + BTT-3033 (Replicate 3)

description:
Library name: library13
Bulk-seq from testicular samples of mice treated with BU + BTT-3033.
BTT-3033_3

data_processing:
BBmap (v39.01) and Trimmomatic (v0.39) were utilized to eliminate adapter sequences and low-quality bases. Then, HISAT2 (v2.2.1) was used to align the data back to the reference genome GRCm38 (Ensembl). StringTie (v2.2.1) constructed the expression matrix.
Assembly: mm10
Supplementary files format and content: tab-separated value file includes raw counts for each Sample

source_name: testis

extract_protocol:
A total of 1 ug total RNA per sample was used as input material for the mRNA library preparation.
Most of Eukaryote 'mRNA have polyA tails, which are enriched by Oligo (dT) magnetic beads. Then, the obtained mRNA was randomly interrupted by bivalent cations, and the first strand of cDNA was synthesized in the 1st Strand Enzymes Reverse transcriptase system using the segmented mRNA as the template and the random oligonucleotide as the primer, and the second strand of cDNA was synthesized using the 2nd Strand Enzymes and dNTPs. Purified double-stranded cDNA undergoes end repair, A-tailing, and ligation with sequencing adapters. cDNA with an insert size of approximately 200-300 bp is screened. PCR amplification is performed and the PCR product is purified again, ultimately obtaining a library.And then, library quality was assessed on the Agilent 4200 TapeStation.

value: testis


title: liver, aged, vehicle, rep1

description: Library name: Sample5

value: liver, aged, vehicle, rep1


title: Control subject-derived primary myotubes (MB07), DUX4.6 siRNA, Replicate 2

description: Library name: H_B1_2


title: liver, young, rep2

description: Library name: Sample2

value: liver

value: liver, young, rep2


title: Bulk-seq from testicular samples of mice treated with BU + BTT-3033 (Replicate 2)

description:
Library name: library12
Bulk-seq from testicular samples of mice treated with BU + BTT-3033.
BTT-3033_2


title: Control subject-derived primary myotubes (MB07), Non-targeting siRNA control, Replicate 3

description: Library name: H_S_3

value: Non-targeting siRNA control


title: Bulk-seq from testicular samples of mice treated with BU + PBS (Replicate 3)

description:
Library name: library10
Bulk-seq from testicular samples of mice treated with BU + PBS.
BU_3

value: BU+PBS


title: Control subject-derived primary myotubes (MB07), Non-targeting siRNA control, Replicate 2

description: Library name: H_S_2


title: Control subject-derived primary myotubes (MB07), Non-targeting siRNA control, Replicate 1

description: Library name: H_S_1


title: FSHD patient-derived primary myotubes (MB06), DUX4.6 siRNA, Replicate 4

description: Library name: F3_B1_5

value: FSHD


title: Bulk-seq from testicular samples of mice treated with BU + PBS (Replicate 2)

description:
Library name: library9
Bulk-seq from testicular samples of mice treated with BU + PBS.
BU_2


title: FSHD patient-derived primary myotubes (MB06), DUX4.6 siRNA, Replicate 1

description: Library name: F3_B1_2


title: Bulk-seq from testicular samples of mice treated with Vehicle (Replicate 3)

description:
Library name: library7
Bulk-seq from testicular samples of mice treated with Vehicle.
Vehicle_3

value: Vehicle


title: Bulk-seq from testicular samples of mice treated with Vehicle (Replicate 2)

description:
Library name: library6
Bulk-seq from testicular samples of mice treated with Vehicle.
Vehicle_2


title: FSHD patient-derived primary myotubes (MB06), DUX4.6 siRNA, Replicate 2

description: Library name: F3_B1_3


title: DKO MEFs Transfected with C325A-MBNL1, Replicate 2

city: Atlanta

first: Adam

last: Kosti

state: GA

address: 615 Michael St

department: Cell Biology

institute: Emory University

description: Library name: DKO_C325A-MBNL1_2

data_processing:
Raw reads were trimmed with fastp (version 0.23.4) using default settings.
Trimmed reads were then aligned with STAR (version 2.7.11a) using a Gencode M33 149 bp built index with default settings.
BAM outputs from the STAR alignment were then used to perform differential splicing analysis using rMats-Turbo (version 4.2), with the following settings: --readlength 150, --variable-read-length, --allowclipping.
Assembly: mm39
Supplementary files format and content: Tab delimited files containing the rMATs Turbo junction counts/reads (JC) output for each type of splicing event (Skipped Exon, alternative 5' splice sites, alternative 3' splice sites, mutually exclusive exons and retained Introns). Comparisons were made between WT vs DKO MEFS, and DKO MEFs against WT-MBNL1 or Mutant MBNL1 transfected MEFs.

source_name: MEF

growth_protocol: DMEM, high glucose, pyruvate supplemented with 100 U/mL penicillin, 100 mg/mL streptomycin, 10mM HEPES, and 10% fetal bovine serum (FBS

extract_protocol:
RNA was extracted transfected from WT MEFs and DKO MEFs using the Quick-RNA Miniprep Kit (Zymo Research, R1054) with the on-column DNase I digestion step.
Paired-end libaries were constructed by Novogene for sequencing.

treatment_protocol: Transfections were performed using Lipofectamine 2000 (Fisher Scientific, 11-668-019) according to the manufacturer's instructions with 24- or 40-hour expression for splicing analysis.

value: MEF

value: DKO


title: Bulk-seq from testicular samples of mice treated with BU + BTT-3033 (Replicate 1)

description:
Library name: library11
Bulk-seq from testicular samples of mice treated with BU + BTT-3033.
BTT-3033_1


title: DKO MEFs Transfected with C325A-MBNL1, Replicate 3

description: Library name: DKO_C325A-MBNL1_3


title: Bulk-seq from testicular samples of mice treated with BU + PBS (Replicate 1)

description:
Library name: library8
Bulk-seq from testicular samples of mice treated with BU + PBS.
BU_1


title: FSHD patient-derived primary myotubes (MB06), Non-targeting siRNA control, Replicate 2

description: Library name: F3_S_3


title: FSHD patient-derived primary myotubes (MB06), Non-targeting siRNA control, Replicate 3

description: Library name: F3_S_4


title: FSHD patient-derived primary myotubes (MB06), Non-targeting siRNA control, Replicate 4

description: Library name: F3_S_5


title: Control subject-derived primary myotubes (MB07), Non-targeting siRNA control, Replicate 4

description: Library name: H_S_4


title: DKO MEFs Transfected with WT-MBNL1, Replicate 3

description: Library name: DKO_WT-MBNL1_3


title: DKO MEFs Transfected with WT-MBNL1, Replicate 2

description: Library name: DKO_WT-MBNL1_2


title: Bulk-seq from testicular samples of mice treated with Vehicle (Replicate 1)

description:
Library name: library5
Bulk-seq from testicular samples of mice treated with Vehicle.
Vehicle_1


title: DKO MEFs Transfected with C325A-MBNL1, Replicate 1

description: Library name: DKO_C325A-MBNL1_1


title: DKO MEFs Transfected with WT-MBNL1, Replicate 1

description: Library name: DKO_WT-MBNL1_1


title: FSHD patient-derived primary myotubes (MB06), DUX4.6 siRNA, Replicate 3

description: Library name: F3_B1_4


title: FSHD patient-derived primary myotubes (MB06), Non-targeting siRNA control, Replicate 1

description: Library name: F3_S_2


title: DKO MEFs, Replicate 2

description: Library name: DKO_MEFs_2


title: FSHD patient-derived primary myotubes (MB05), DUX4.6 siRNA, Replicate 2

description: Library name: F2_B1_2


title: DKO MEFs, Replicate 3

description: Library name: DKO_MEFs_3


title: FSHD patient-derived primary myotubes (MB05), DUX4.6 siRNA, Replicate 1

description: Library name: F2_B1_1


title: FSHD patient-derived primary myotubes (MB05), DUX4.6 siRNA, Replicate 4

description: Library name: F2_B1_4


title: FSHD patient-derived primary myotubes (MB05), DUX4.6 siRNA, Replicate 3

description: Library name: F2_B1_3


title: WT MEFs, Replicate 3

description: Library name: WT_MEFs_3

value: WT


title: FSHD patient-derived primary myotubes (MB05), Non-targeting siRNA control, Replicate 3

description: Library name: F2_S_3

value: Primary myotubes


title: FSHD patient-derived primary myotubes (MB05), Non-targeting siRNA control, Replicate 1

description: Library name: F2_S_1


title: WT MEFs, Replicate 2

description: Library name: WT_MEFs_2


title: 832/13 cells, Kyono MPRA library, plasmid input

city: Ann Arbor

first: Stephen

middle: CJ

last: Parker

state: Michigan

address: 1000 WALL ST, BREHM TOWER,RM 5474

department: Gilbert S. Omenn Department of Computational Medicine & Bioinformatics

institute: University of Michigan

description: Library name: ATS0706_plasmid

data_processing:
We processed MPRA sequencing data using a custom pipeline that quantifies barcode counts while accounting for possible sequencing errors. We extracted DNA barcodes from the first 16 bases of the R1 fastq file for the input DNA sample and clustered these at an edit distance of 0. We repeated this process for the cDNA barcode counts and used an added step to remove PCR-duplicated barcodes using the UMI information. The UMI sequence was the reverse complement of the first 6 bp in the R2 file. Finally, we used starcode to cluster and count barcodes.
Assembly: hg19
Supplementary files format and content: “library_counts.tsv” is a tab-delimited text file contained the barcode sequences, the RNA counts for the three replicates, the DNA counts for the input sample, the oligo ID, and the hg19 coordinates of each element tested in the MPRA library.

organism:
Homo sapiens
synthetic construct

source_name: plasmid

extract_protocol:
We electroporated 50 ug of plasmid into 25 million 832/13 rat insulinoma cells for each biological replicate and lysed cells with TRIzol 24 hours later. After phase separation, we used the Direct-zol RNA Miniprep Kit to isolate total RNA. We enriched for mature mRNA transcripts with fragment(dT) beads then treated 2 ug of mRNA with DNase I to remove plasmid or genomic DNA contamination. We reverse transcribed 1 ug of mRNA using SuperScript III with a custom primer containing a 6-bp unique molecular identifier (UMI) targeting transcripts derived from the MPRA plasmids (Supplemental Table 3). We treated cDNA samples with DpnI to eliminate any residual plasmid DNA.
MPRA amplicon library

value: plasmid


title: FSHD patient-derived primary myotubes (MB05), Non-targeting siRNA control, Replicate 4

description: Library name: F2_S_4


title: WT MEFs, Replicate 1

description: Library name: WT_MEFs_1


title: FSHD patient-derived primary myotubes (MB05), Non-targeting siRNA control, Replicate 2

description: Library name: F2_S_2


title: epithelial cells from vitamin A sufficient 8 week old mice

city: Dallas

first: Gabriella

last: Quinn

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description:
Library name: Vit.A+
10X Genomics

data_processing:
Data were processed using the Cell Ranger software suite for demultiplexing, barcode processing, alignment to the mm10 mouse reference genome, and initial clustering.  Seurat was used for all downstream analyses of Cell Ranger-generated filtered matrices. Cells with fewer than 10 detected features, more than 2,000 detected features, or greater than 50% nuclear transcripts were excluded for quality control, as previously described (31). Data were normalized, scaled, and integrated with a pre-annotated adult mouse small intestine reference dataset from the Mouse Cell Atlas (12). Differential gene expression analysis was performed using the limma R package, and data were visualized using Seurat v5 and the ggplot2 package.
Assembly: mm10
Supplementary files format and content: Gzipped tab separated value files and matrix files

source_name: small intestine

extract_protocol:
Small intestines were recovered from vitamin A–replete and vitamin A–deficient mice at 8 weeks of age and flushed with sterile PBS. Intestines were opened longitudinally, cut into 2-cm segments, and washed three times in PBS containing 3% FBS and 0.04% BSA, followed by decanting of the supernatant. After the final wash, EDTA was added to a final concentration of 5 mM, and tissues were incubated at 37oC for 15 minutes. Cell suspensions were passed sequentially through 100-mM and 70-mM strainers on ice, pelleted by centrifugation at 300 g for 5 minutes, and resuspended in PBS containing 3% FBS and 0.04% BSA. Samples from each dietary condition were pooled prior to library preparation.
Library preparation and sequencing were performed in the UT Southwestern Microbiome Research Laboratory. Gel bead-in-emulsion (GEM) generation was carried out using a 10X Genomics Chromium Controller with the  Chromium Next GEM Single Cell 3' kit v3.1, Chromium Next GEM Chip G, and Dual Index Kit TT Set A. cDNA and barcoded sequencing libraries were prepared according to the manufacturer’s instructions and assessed for quality and concentration using a Bioanalyzer 2100 and qPCR, respectively. Libraries passing quality control were sequenced using paired-end sequencing on a NextSeq 550 platform with a 150-cycle flow cell, generating approximately 25,000 to 30,000 reads per cell. Unique molecular identifier (UMI) counts were used to estimate the number of cells successfully captured and sequenced.

value: small intestine


title: D40_O-Torgs_rep2

description:
Library name: library6
Single-cell data of testicular organoids cultured with the optimized system on the fortieth day.

data_processing:
The raw sequencing data were processed by Fastp (Chen et al., 2018a) to trim primer sequences and low-quality bases.
Seeksoul tools (Seekgene, v1.0.0) was used to process the resulting data, demultiplex cellular barcodes and map reads to the mouse mm10 reference genome (refdata-gex-mm10-2020-A downloaded from 10X Genomics) to generate a feature-barcode matrix for downstream analyses.
Assembly: mm10
Supplementary files format and content: rds file

extract_protocol:
After harvested, tissues were washed in ice-cold PBS (Hyclone SH30256.01) and dissociated using SeekMate Tissue Dissociation Kit C (SeekGene K01501-50) from SeekGene as instructions. DNase Ⅰ (Sigma 9003-98-9) treatment was optional according to the viscosity of the homogenate. Cell count and viability was estimated using Fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent . Finally fresh cells were washed twice in the RPMI1640 (Gibco 11875119) and then resuspended at 1×106 cells per ml in RPMI1640 and 2% FBS (Gibco 10100147C).
The single-cell RNA-Seq library was prepared using the SeekOne® Digital Droplet Single Cell 3' library preparation kit (SeekGene catalog number: K00202). Briefly, an appropriate number of cells was mixed with reverse transcription reagents and then added to the sample wells of the SeekOne® Chip S3. Next, Barcoded Hydrogel Beads (BHBs) and partitioning oil were dispensed into the corresponding wells of the S3 chip, respectively. After droplet generation, reverse transcription was carried out at 42 °C for 90 min and inactivation was performed at 85 °C for 5 min. Subsequently, cDNAs were purified and used for PCR amplification. Then, the amplified cDNA products were cleaned, fragmented, subjected to end repair, and their tails were ligated to the sequencing adapters. Finally, the DNA of the 3' poly (A) portion of the genes were amplified by index PCR, which contains Cell Barcode and Unique Molecular Index. The sequencing library was cleaned up using VAHTS DNA Clean Beads (Vazyme N411-03) and analyzed using Qubit (Thermo Fisher Scientific Q33226) and Bio-Fragment Analyzer (Bioptic Qsep400). The library was sequenced on the Illumina NovaSeq 6000 with a read length of PE150.

value: optimized system


title: D40_T-Torgs_rep2

description:
Library name: library8
Single-cell data of testicular organoids cultured with the traditional system on the fortieth day.

value: traditional system


title: Embryo 6

city: Blacksburg

first: Fernando

middle: H

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

description: Library name: S6

data_processing:
The fastq files were processed using the PIPsekerTM software for Single Cell Data Analysis, with alignment to the cattle genome (Bos_taurus.ARS-UCD2.0), and fragments counted based on the Bos_taurus.ARS-UCD2.0.114 annotation
Assembly: Bos_taurus.ARS-UCD2.0

organism: Bos taurus

source_name: Day 16

growth_protocol: Embryos were produced using procedures described in Biase FH, Schettini G. Protocol for the electroporation of CRISPR-Cas for DNA and RNA targeting in Bos taurus zygotes. STAR Protoc. 2024 Mar 15;5(1):102940. doi: 10.1016/j.xpro.2024.102940. Ramos-Ibeas P, Perez-Gomez A, Gonzalez-Brusi L, Quiroga AC, Bermejo-Alvarez P. Pre-hatching exposure to N2B27 medium improves post-hatching development of bovine embryos in vitro. Theriogenology. 2023;205:73-8. 10.1016/j.theriogenology.2023.04.018. Ramos-Ibeas P, Lamas-Toranzo I, Martinez-Moro A, de Frutos C, Quiroga AC, Zurita E, et al. Embryonic disc formation following post-hatching bovine embryo development in vitro. Reproduction. 2020;160(4):579-89. 10.1530/REP-20-0243

extract_protocol: Llibraries were constructed using the PIP-seq protocl

value: Day 16


title: Embryo 8

description: Library name: S8


title: FSHD patient-derived primary myotubes (MB02), DUX4.6 siRNA, Replicate 3

description: Library name: F1_B1_3

value: DUX4.6 siRNA


title: D40_T-Torgs_rep1

description:
Library name: library7
Single-cell data of testicular organoids cultured with the traditional system on the fortieth day.

value: testis


title: Embryo 7

description: Library name: S7


title: DKO MEFs, Replicate 1

description: Library name: DKO_MEFs_1


title: epithelial cells from vitamin A deficient 8 week old mice

description:
Library name: Vit.A-
10X Genomics