title: 165_5_G_C

city: Dallas

first: Marek

last: Napierala

state: TX

address: Marek Napierala

institute: University of Texas Southwestern Medical Center

data_processing:
Data Quality Control: filtering reads containing adapter or with low quality
Statistics Analysis of Data Production and Quality
Mapping Reads to Reference Genome
Gene Expression Quantification
Assembly: hg38
Supplementary files format and content: Microsoft excel spreadsheet includes gene count of the sample

source_name: skin

extract_protocol:
RNA was isolated from MEF using the RNeasy Plus Mini Kit (Qiagen, #74134). Genomic DNA contamination was removed with the TURBO DNA-free™ Kit (Invitrogen, #AM1907).
Sequencing libraries were generated at Novogene Co., Ltd using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

value: skin

value: primary fibroblasts


title: TrIP KO P14 CD8+ T cells, TCR stimulated, Treated with the PI3Kδ inhibitor, replicate 1

status: Public on Jul 10 2025

type: SRA

city: Pittsburgh

first: Lawrence

middle: P.

last: Kane

state: PA

address: 5051 Centre Ave.

department: Immunology

country: USA

institute: University of Pittsburgh

description: Library name: A3_KO_Stim_Plus_WITH_inhibitor_S22

library_source: transcriptomic

data_processing:
FASTq reads were quality checkedand  mapped with GRCm38 ref genome usingCLC genomics workbench V25 default setting
Map reads were quantified  using CLC genomics workbench
Raw count data was downloaded from CLC genomics and uploaded to Partekflow
Assembly: GRCm39
Supplementary files format and content: Excel file with individual sample read counts and normalization

molecule: polyA RNA

organism: Mus musculus

source_name: Spleen

extract_protocol:
Illumina Stranded mRNA (PolyA+)
lumina DNA Prep kit (Illumina: 20060059)

treatment_protocol: Splenocytes from P14 TCR Tg mice were stimulated with gp33 peptide (100ng/ml) for 24hrs and then CD8 T cells were sorted out and subject to sequencing

tag: tissue

value: Spleen

tag: cell type

value: CD8 T cells

tag: genotype

value: TrIP KO P14tg

tag: treatment

value: Il-2, IL-12, gp33 peptide stim, PI3Kδi


title: Control5, Input

city: Tel-Aviv

first: Boaz

last: Barak

address: Chaim Levanon street, 55

country: Israel

institute: Tel-Aviv University

description: Library name: Control5, Input

library_source: genomic

data_processing:
Uniquely mapped ChIP-Seq reads were mapped to the GRCm39 genome using Bowtie2.
Differential peak calling was performed using Macs2 (version 2.2.9.1) with the command line 'callpeak -t IP.bam -c Input.bam -g mm -f BAMPE -q 0.1 --nolambda --keep-dup all –B’, where immunoprecipitate (IP) over input scores were calculated.
Additional manual filtration was performed to exclude peaks with; q-value > 0.05, fragment size larger then 600bp and peaks that were mapped to mitochondrial DNA.
The Bedtools package (using the intersect and cluster tools) was employed to identify Tfii-i consensus peaks, defined as those present in at least three out of five samples in the Control group. Peaks were classified as "lost" if no overlap was observed between the KO group and the Tfii-i consensus peaks.
Assembly: mm39
Supplementary files format and content: bed files (IP files only)

molecule: genomic DNA

source_name: OL-enriched primary cell culture

growth_protocol: DMEM/F12 supplemented with L-glutamine, penicillin-streptomycin and SM1 supplement (STEMCELL technologies, catalog no. 05711). To increase OPC differentiation into OLs, T3 (Sigma-Aldrich, catalog no. T5516) was added to the medium at a final concentration of 340 ng/mL.

extract_protocol:
Differentiated OLs from 4-5 P1 mice were pooled by genotype. At DIV7 cells were washed gently with PBS to remove cellular debris then harvested and pooled using Trypsin A (Sigma-Aldrich, catalog no. T4049). Trypsin activity was neutralized by adding DMEM/F12 supplemented with L-glutamine and 20% FBS. Cells were then centrifuged at 500 rpm for 5 minutes. The pellets were then crosslinked in 1% PFA for 10 minutes at room temperature. To avoid over-fixation, 100 µl of glycine (Cell Signaling, catalog no. 7005S) was added after 10 minutes. The lysates were then centrifuged at 5000 rpm for 5 minutes, and the supernatant was carefully removed. Three washing steps with PBS and centrifugation with the same parameters were then performed. Fresh sonication buffer containing 1% SDS, 50 mM Tris-HCl, pH 8.8, 20 mM EDTA, and a protease inhibitor in DEPC was then added to each sample. DNA shearing was performed by 9 rounds of sonication (Covaris) of 10 pulses each to obtain 200-800 bp DNA fragments.
Library preparation and paired-end sequencing using Illumina NovaSeq S1 (100 cycles) was performed at the Crown Genomics institute, Weizmann Institute of Science, Israel.

value: OL-enriched primary cell culture

value: Control

tag: batch


title: KO, rOSM treated, rep2

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: Library name: ATII_KO_rOSM_DC#13

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

molecule: total RNA

source_name: Lung

extract_protocol:
Total RNA was isolated from whole lung using Qiagen RNeasy kit.
Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3′) and converted to cDNA via reverse transcription. First strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 12 cycles using barcoded primers such that each sample carries a specific combination of eight base Illumina P5 and P7 barcodes and pooled together prior to sequencing. Smart-seq paired-end sequencing is performed on an Illumina NextSeq500 (two full NextSeq runs per batch of 96 samples, for 10M raw reads/sample on average) using 2 x 38bp reads with no further trimming.

value: Lung

value: 7x daily treatments with rOSM, intratracheal


title: H3K27ac ChIP-seq on 1014 NOTCH2-Inactivated TRIM28-dTAG-HA  knock-in cells with DMSO Rep2

first: Yixiang

last: Li

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: Library name: 1014_N2_Inactivated_-dTAG_H3K27ac_Rep2

data_processing:
Sequenced read were aligned to the UCSC hg38 or mm10 reference genome assembly using BWA(v0.7.15) and peaking calling performed using MACS3.
Assembly: mm10 and hg38
Supplementary files format and content: bw files except for input samples

source_name: 1014 TRIM28-dTAG-HA knock-in

growth_protocol: Murine SCLC cells were cultured with RPMI-1640 with 10% FBS, P/S, and HITES (10 nM hydrocortisone (Sigma Aldrich # H0135), Insulin-Transferrin-Selenium (Gemini #400-145), and 10 nM beta-estradiol (Sigma Aldrich# E2257), 100 U/mL of penicillin (P), and 100 μg/mL of streptomycin (S)] and culture with 5% CO2 at 37C.  NCI-H1048 cells were cultured with DMEM F12 with 5% FBS, P/S, and HITES (10 nM hydrocortisone (Sigma Aldrich # H0135), Insulin-Transferrin-Selenium (Gemini #400-145), and 10 nM beta-estradiol (Sigma Aldrich# E2257), 100 U/mL of penicillin (P), and 100 μg/mL of streptomycin (S)] and culture with 5% CO2 at 37C.

extract_protocol:
Cells were  collected, and centrifuged. The supernatant was removed and the cells were washed once in PBS. For the TRIM28-HA ChIP experiments, cells were cross-linked by incubation with 2 mM disuccinimidyl glutarate (DSG) with rocking for 30 minutes at room temperature prior to fixation step. Then, for all ChIP experiments, cells were fixed in 1% paraformaldehyde diluted in PBS for 10 minutes at room temperature. Excess formaldehyde was quenched by dropwise addition of freshly made Glycine at a final concentration 1.25 M followed by rocking the cells for an additional 5 minutes at room temperature. The paraformaldehyde/glycine was then removed by spinning at 400 x g for 5 minutes at 4°C and the cells were washed twice with ice cold PBS.     The cells were then resuspended in 1 mL of lysis buffer (50 mM Hepes-NaOH pH 8, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% TX-100 supplemented with a protease inhibitors and phosphatase inhibitors) and incubated by rotating for 10 minutes at 4°C. Intact nuclei were then collected by centrifugation at 1900 x g for 5 minutes at 4°C. The supernatant was then gently aspirated and the pellet was resuspended in 1 mL of wash buffer (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, supplemented with a protease inhibitor cocktail and phosphatase inhibitors) and incubated by rotating for 10 minutes at 4°C. The nuclei were again collected by centrifugation at 1900 x g for 5 minutes at 4°C. The supernatant was then gently aspirated and the tube was rinsed with 500 μL of shearing buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris-HCl pH 8.0 supplemented with protease inhibitors and phosphatase inhibitors). The nuclei were again collected by centrifugation at 1900 x g for 5 minutes at 4°C, the supernatant was carefully removed, and the pellet was gently resuspended in 1mL shearing buffer and transferred to a 1 mL AFA fiber tube (Covaris #520130). The chromatin was then sonicated using a Covaris E220 sonicator at 100 peak incident power, 10% duty cycles, 200 cycles per burst, water level 15 (left indicator)/10 (right indicator) for 900 seconds. The samples were then transferred to 1.5 mL Eppendorf tubes and centrifuged in an Eppendorf microcentrifuge at 15,900 x g for 5 minutes at 4°C. 900 μL of the supernatants were transferred to a new Eppendorf tube, to which 1% Triton X-100 and 150 mM NaCl were added. 20μl of Dynabeads Protein G (ThermoFisher #10004D), prewashed with Shearing Buffer, was then added and samples were rotated for 1 hour at 4°C to pre-clear the sonicated chromatin. The Dynabeads were then removed using a magnetic stand and the supernatants were transferred to new tubes. 5% of the total lysate was removed to make genomic DNA to be used for the ChIP-sequencing input DNA. The TRIM28-HA ChIPs were performed separately also using 5% input and 95% for ChIP. 10 μg of the rabbit anti-HA (CST #3724) primary antibodies were added. For the H3K9me3 and H3K27ac ChIPs, the remaining lysate (95% of total) were equally distributed into two Eppendorf tubes to perform the H3K9me3 and H3K27ac ChIPs. 5 μg of the rabbit anti-H3k9me3 (EPR16601) (Abcam, # ab176916) or 5 μg of the rabbit anti-H3K27ac (Diagenode# C15410196) primary antibodies were added. All samples were incubated overnight while rotating at 4°C. The following morning, 50 μL of Dynabeads, prewashed with Shearing buffer, were added and the samples were incubated for another 2 hours while rotating at 4°C. A magnetic stand was used to isolate the Dynabeads. The supernatant was removed and the Dynabeads were washed once in 1 mL of low salt immune complex wash buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 0.1% SDS, 1% TX-100, 2 mM EDTA) and incubated for 5 minutes while rotating at 4°C. The beads were again isolated using a magnetic stand. Following removal of the supernatant the Dynabeads were washed once in 1 mL of high salt immune complex wash buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 0.1% SDS, 1% TX-100, 2 mM EDTA) and incubated for 5 minutes while rotating at 4°C. The beads were again pelleted with a magnetic stand. Following removal of the supernatant, the Dynabeads were washed once in 1 mL of Lithium Chloride immune complex wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% SDS, 1% NP-40, 1 mM EDTA) and incubated for 5 minutes while rotating at 4°C. The beads were then washed twice in TE pH8 at room temperature and the beads were then resuspended in 100μL TE pH8. RNase A (Qiagen #19101) was then added to a final concentration of 0.2 mg/mL and the samples were incubated for 30 minutes at 37°C. To reverse the formaldehyde crosslinking and remove protein, Proteinase K was then added to a final concentration of 0.8 mg/mL and the samples were incubated for 30 minutes at 42°C and then an additional 6 hours at 65°C. 300 μL QG buffer and 100 μL of isopropanol was then added to each sample and a magnetic stand was used to pellet the Dynabeads. The supernatant was then collected and DNA was isolated using QIAquick gel extraction kit (Qiagen #28706) according to the manufacturer’s instructions.
ChIPseq libraries were prepared using IDT XGen DNAseq library prep reagents on a Beckman Coulter Biomek i7 liquid handling platform from approximately 1ng of DNA according to manufacturer’s protocol and 14 cycles of PCR amplification. Finished sequencing libraries were quantified by Qubit fluorometer and Agilent TapeStation 2200.  Library pooling and indexing was evaluated with shallow sequencing on an Illumina MiSeq. Subsequently, libraries were sequenced on an Illumina NovaSeq X Plus targeting 40 million 150bp read pairs.

treatment_protocol: For the ChIP-seq of H3K9me3 and H3K27ac, murine 1014 TRIM28-dTAG-HA knock-in NOTCH2-isogenic cells (NOTCH2-WT or NOTCH2-inactivated) treated with 100 nM dTAG-V1 for 72 hours to degrade TRIM28 or with DMSO as a control.

tag: cell line

value: 1014 TRIM28-dTAG-HA knock-in

value: SCLC cell line

tag: chip antibody

value: H3K27ac Diagenode C15410196


title: PH078, Sedentary

city: Tarrytown

first: Michael

last: Stec

state: NY

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals

description: Fresh Frozen Saptial Transcriptomic Sequencing

data_processing:
Raw sequencing data were processed using the 10X Genomics Space Ranger (V2) to generate FASTQ files
Sequences were aligned to GRCh38 genome to gene expression count using Space Ranger's default setting
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial  barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

organism: Homo sapiens

source_name: Skeletal Muscle

extract_protocol:
Muscle biopsies were cryosectioned at 10µm thickness onto SuperFrost Plus charged slides and stored at -80°C until staining and processing via the Visium CytAssist pipeline.
The 10x Genomics Visium CytAssist Spatial Gene Expression for FFPE platform was used for spatial transcriptomics experiments. Tissue sections mounted on standard glass slides were hybridized to the 10x Genomics human transcriptome probe set for CytAssist (v2) according to the manufacturer’s protocol (10x Genomics). The CytAssist machine was used to transfer hybridized probes from the tissue sections to Visium 6.5mm slides.

value: Skeletal Muscle

value: Sedentary

tag: developmental stage

value: young


title: Control4, ChIP

description: Library name: Control4, ChIP

value: Tfii-I antibody (Cell Signaling, #4562)


title: Control5, ChIP

description: Library name: Control5, ChIP


title: H3K27ac ChIP-seq on 1014 NOTCH2-WT TRIM28-dTAG-HA knock-in  cells with dTAGV1 Rep2

description: Library name: 1014_N2_WT_+dTAG_H3K27ac_Rep2


title: HEPG2-TM1

city: Hefei

first: Yue

last: Zhu

address: The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China

country: China

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
The 150 bp paired-end reads were mapped to the reference genome by using bowtie2 (v2.11.1).
Significant peak regions of each samples were identified using MACS2 (v2.1.2) with parameters "-q 0.05 --nomodel --shift -100 --extsize 200".
Assembly: hg38
Supplementary files format and content: Differential genes and motif in text file

source_name: liver

extract_protocol:
Lysates were clarified from the sonicated nuclei, and DNA was extracted
The chromatin DNA was isolated from cells for library construction using EpiTM ATAC-seq kit(Epibiotek, cat. no EPI20180202)

value: liver

value: Human HCC cells

value: TM


title: Control4, Input

description: Library name: Control4, Input


title: HEPG2-CEM2

institute: The First Affiliated Hospital of Anhui Medical University


title: Control6, Input

description: Library name: Control6, Input


title: H3K27ac ChIP-seq on 1014 NOTCH2-WT TRIM28-dTAG-HA knock-in  cells with dTAGV1 Rep1

description: Library name: 1014_N2_WT_+dTAG_H3K27ac_Rep1


title: KO, rOSM treated, rep1

description: Library name: ATII_KO_rOSM_DC#12


title: Control3, Input

description: Library name: Control3, Input


title: H3K27ac ChIP-seq on 1014 NOTCH2-WT TRIM28-dTAG-HA knock-in  cells with DMSO Rep2

description: Library name: 1014_N2_WT_-dTAG_H3K27ac_Rep2


title: HEPG2-CELL2

value: DMSO


title: WT, rOSM treated, rep3

description: Library name: ATII_WT_rOSM_DC#07


title: Control3, ChIP

description: Library name: Control3, ChIP


title: HEPG2-CELL1


title: H3K27ac ChIP-seq on 1014 NOTCH2-WT TRIM28-dTAG-HA knock-in  cells with DMSO Rep1

description: Library name: 1014_N2_WT_-dTAG_H3K27ac_Rep1


title: WT, rOSM treated, rep2

description: Library name: ATII_WT_rOSM_DC#06


title: KO, PBS treated, rep3

description: Library name: ATII_KO_PBS_DC#10

value: 7x daily treatments with PBS, intratracheal


title: WT, rOSM treated, rep1

description: Library name: ATII_WT_rOSM_DC#05


title: HA ChIP-seq on 1014 NOTCH2-Inactivated TRIM28-dTAG-HA knock-in cells Rep2

description: Library name: 1014_N2_Inactivated_TRIM28_HA_Rep2

value: HA Cell Signaling Technology 3724


title: CD8 thymocytes, donor-derived

city: Kyoto

first: Yann

last: Pretemer

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Center for iPS Cell Research and Application, Kyoto University

data_processing:
All data processing steps were performed using Repertoire Genesis analysis software v20180912. Sequences of TCRb genes TRBV and TRBJ were assigned based on the international ImMunoGeneTics information system (IMGT) database.
Assembly: IMGT
Supplementary files format and content: Excel (xlsx) file includes raw counts for each sample

source_name: thymocyte

extract_protocol:
iTEC/thymocyte organoids were homogenized with pestles and cells were washed in buffer consisting of 1% FBS in PBS. Cells were stained with antibodies diluted 1:10 in the same buffer on ice for 20 min, and, after one more wash, they were analyzed with the BD FACSAria II. The CD45+CD3+TCRab+CD4+ and CD45+CD3+TCRab+CD8a+CD8b+ populations were sorted and resuspended in ISOGEN-LS. RNA was extracted with the RNeasy Lipid Tissue Mini Kit (Qiagen). For donor-derived controls, thymocytes were isolated from homogenized 2-3 mm thymus pieces, whose supernatant cells were incubated in RBC Lysis Buffer (BioLegend) for 10 min on ice and frozen before being subjected to the same staining, sorting, and RNA extraction protocols as the iTEC-supported thymocytes.
RNA was reverse transcribed with Superscript III reverse transcriptase (Thermo Fisher), after which TCRb genes were amplified with adaptor-ligation PCR. Index sequences were added using the Nextera XT Index Kit v2 Set A or Set D (Illumina).

value: thymocyte

tag: culture

tag: population

tag: Sex

value: male


title: HA ChIP-seq on 1014 NOTCH2-Inactivated TRIM28-dTAG-HA knock-in cells Rep1

description: Library name: 1014_N2_Inactivated_TRIM28_HA_Rep1


title: CD4 thymocytes, donor-derived


title: Control1, Input

description: Library name: Control1, Input

value: OL-enriched primary cell culture

value: Control


title: HA ChIP-seq on 1014 NOTCH2-WT TRIM28-dTAG-HA knock-in cells Rep1

description: Library name: 1014_N2_WT_TRIM28_HA_Rep1

value: 1014 TRIM28-dTAG-HA knock-in


title: KO, PBS treated, rep2

description: Library name: ATII_KO_PBS_DC#09

value: Lung


title: Sample18

type: genomic

city: Detroit

first: Adi

last: Tarca

state: MI

address: 3990 John R. St, 4 Brush South

institute: Wayne State University

hyb_protocol: For each sample, 250 ng of DNA was bisulfite converted using Zymo’s EZ DNA Methylation kit, following the manufacturer’s incubation parameters specific for Illumina methylation arrays. The cleaned-up samples were then sent to the UM Advanced Genomics Core for hybridization to the Infinium MethylationEPIC BeadChip array, as well as for washing and scanning, according to the manufacturer’s instructions (Illumina EPIC Datasheet).

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting.

data_processing: Raw red and green IDAT files were imported into R using the minfi package from Bioconductor. Normalization was performed using the beta-mixture quantile normalization (BMIQ) method, implemented via the ChAMP package from Bioconductor.

label: Cy5 and Cy3

source_name: PTL

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from tissues using the Quick-DNA™ MagBead Plus Kit (Zymo Research, Irvine, CA) automated on the epMotion® 5075 liquid handler (Eppendorf, Enfield, CT) for high throughput sample isolation. Briefly, solid tissues were digested with Proteinase K in DNA Elution Buffer and Biofluid & Solid Tissue Buffer. The samples were centrifuged at ≥10,000 x g with a microcentrifuge for one minute to pellet the debris. The supernatants were transferred to new tubes. The samples were then mixed with Quick-DNA™ MagBinding Buffer and MagBinding Beads. After binding DNA in samples, the beads were pre-washed with Pre-wash buffer and washed with g-DNA Wash Buffer three times. Finally, the gDNA was eluted with DNA Elution Buffer. Purified DNA was quantified using a Qubit 3.0 fluorometer with a Qubit dsDNA BR assay kit (Life Technologies, Carlsbad, CA), according to the manufacturer’s protocol. Purified DNA was then stored at −20°C for the next application.

value: Placenta

tag: gestational age (weeks)

tag: group

value: PTL

tag: birth weight percentile


title: HA ChIP-seq on 1014 NOTCH2-WT TRIM28-dTAG-HA knock-in cells Rep2

description: Library name: 1014_N2_WT_TRIM28_HA_Rep2

value: SCLC cell line


title: Control1, ChIP

description: Library name: Control1, ChIP


title: RNA-seq NPC 48h recovery after TSA washout rep3

city: Montpellier

first: Marco

last: Di Stefano

address: 141 rue de la Cardonille

country: France

institute: Institut de Génétique Humaine - CNRS

description: Library name: RNAseq_NPC_REC48_expt5_rep3

data_processing:
Data were mapped and counted using the align andg featureCounts functions of the subread package.
Assembly: mm10
Supplementary files format and content: Processed files represent raw counts for each condition and replicate.

growth_protocol: ESC were grown in FBS+LIF media with standard conditions.

extract_protocol:
For mESCs, RNA was extracted usint Rnaeasy mini Qiagen kit with RLT buffer supplemented with 2-mercaptoethanol and on-column DNaseI digestion. For gastruloids, Qiagen columns and buffer were swapped for Zymo RNA Clean & Concentrator reagents.
Total RNA-seq libraries were done by rRNA depletion and constructed by BGI Tech Solutions; polyA RNA-seq libraries were donw by polyA capture by BGI Tech Solutions.

treatment_protocol: 1) ESCs, NPCs - DMSO: 0.01% DMSO for 4 hours; TSA: 100 ng/ml TSA for 4 hours; REC: 4 hours TSA (100 ng/ml) followed by 16-20-24-48-72-96 hours of recovery; reTSA: 4 hours TSA (100 ng/ml) re-treatment; following 24 hours of recovery; reREC: 24 hours of recovery following the second round of TSA treatment. OHT: 800 nM OHT (72h for DMSO, TSA; 96h for REC and reTSA; 120h for reREC); Romi: 0.03 nM romidepsin. 2) Gastruloids - 48h Ctrl: 0.002% DMSO from 44h to 48h; 48h TSA: 20 ng/ul TSA from 44h to 48h; 120h Ctrl: 0.002% DMSO from 44h to 48h followed by washes and 72h recovery; 120h TSA: 20 ng/ul TSA from 44h to 48h followed by washes and 72h recovery

value: NPC

value: Wild type

value: TSA followed by 48 hours of recovery


title: Ad_Shox2_3

city: Guangzhou

first: Xiaoyu

last: Liu

address: 253 Industrial Avenue

institute: Zhujiang Hospital, Southern Medical University

data_processing:
The sequencing data was filtered with SOAPnuke by removing reads containing sequencing adapter
Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%
Removing reads whose unknown base ratio is more than 5%，afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2(v2.0.4)
Bowtie2(v2.2.5) was applied to align the clean reads to the reference coding gene set
The expression level of gene was calculated by RSEM (v1.2.12).
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: xls file includes FPKM, TPM values and read counts for each sample

source_name: vascular smooth muscle cells

growth_protocol: Human vascular smooth muscle cells were cultured in growth medium (GM).

extract_protocol:
Total RNA of human vascular smooth muscle cells were extracted using TRIzol regents and RNA quality was determined using Agilent 2100 Bioanalyser.
mRNA molecules were purified from total RNA using oligo (dT)-attached magnetic beads. Then, mRNA molecules were fragmented into small pieces using fragmentation reagent after reaction a certain period in proper temperature. First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The synthesis cDNA was subjected to end-repair and then was 3'-adenylated. Adapters were ligated to the ends of these 3'-adenylated cDNA fragments. PCR was used to amplify the cDNA fragments with adapters from previous step. PCR products were purified with Ampure XP Beads (AGENCOURT), and dissolved in EB solution. Library was validated on the Agilent Technologies 2100 Bioanalysers.

treatment_protocol: Human vascular smooth muscle cells were cultured in calcifying medium (CM) and transfected with Ad/GFP (CM+Ad/GFP)，or cultured in CM and tranfected with Ad/Shox2 (CM+Ad/Shox2).

value: vascular smooth muscle cells

value: calcifying medium with Ad/Shox2


title: KO, PBS treated, rep1

description: Library name: ATII_KO_PBS_DC#08


title: RNA-seq NPC 48h recovery after TSA washout rep2

description: Library name: RNAseq_NPC_REC48_expt5_rep2


title: RNA-seq NPC 48h recovery after TSA washout rep1

description: Library name: RNAseq_NPC_REC48_expt5_rep1


title: RNA-seq NPC 24h recovery after TSA washout rep3

description: Library name: RNAseq_NPC_REC24_expt5_rep3

value: TSA followed by 24 hours of recovery


title: CD4 thymocytes, iTEC-supported

value: 3D organoid culture


title: Ad_Shox2_2


title: WT, PBS treated, rep3

description: Library name: ATII_WT_PBS_DC#03

value: 7x daily treatments with PBS, intratracheal


title: Sample16

source_name: PPROM

value: PPROM


title: WT, PBS treated, rep2

description: Library name: ATII_WT_PBS_DC#02


title: RNA-seq NPC 24h recovery after TSA washout rep1

description: Library name: RNAseq_NPC_REC24_expt5_rep1


title: WT, PBS treated, rep1

description: Library name: ATII_WT_PBS_DC#01


title: Ad_Shox2_1


title: Sample15


title: CD8 thymocytes, iTEC-supported

value: thymocyte

value: male


title: Sample14


title: CM3

value: calcifying medium with Ad/GFP


title: Sample13

source_name: TERMPE

value: TERMPE


title: WT2_TCR

city: New Haven

first: Chuanpeng

last: Dong

state: CT

address: 850 West Campus Dr

department: Genetics

institute: Yale University School of Medicine

description:
Library name: WT2_TCR
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 with --expect-cells=5000 --nosecondary commands.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scTCR-seq

source_name: tumor

extract_protocol:
For mouse tumor infiltrating lymphocytes (TILs), tumors were harvested at day 10 post tumor inoculation, digested to single cells, and were stained with PE-CD11b, APC-CD45, and PE/Cy7- CD3 for 30 min, followed by viability dye eFluo™ 506 for 5 min, and subjected to FACSFuson sorter for isolating the viable mouse TILs. A total of 10,000 TILs (CD11b-CD45+CD3+viability dye-) were isolated from each sample for the subsequent library prep and single-cell sequencing.
scRNA-seq library prep was  following the protocol from 10x Genomics Chromium Next GEM Single Cell 5’ Reagent Kits V2.

value: tumor

value: TILs

value: WT


title: Sample12

source_name: TERMSGA

value: Placenta

value: TERMSGA


title: RNA-seq NPC TSA-treated rep3

description: Library name: RNAseq_NPC_TSA_expt5_rep3

value: NPC

value: Wild type

value: 100 ng/ml TSA


title: CM2

value: vascular smooth muscle cells


title: WT1_TCR

description:
Library name: WT1_TCR
10x Genomics


title: CM1


title: GM3

value: growth medium


title: WT4_TCR

description:
Library name: WT4_TCR
10x Genomics


title: RNA-seq NPC 24h recovery after TSA washout rep2

description: Library name: RNAseq_NPC_REC24_expt5_rep2

value: TSA followed by 24 hours of recovery


title: Sample11

value: PTL


title: RNA-seq NPC TSA-treated rep2

description: Library name: RNAseq_NPC_TSA_expt5_rep2


title: Sample17


title: RNA-seq NPC TSA-treated rep1

description: Library name: RNAseq_NPC_TSA_expt5_rep1


title: Mut3_TCR

description:
Library name: Mut3_TCR
10x Genomics

value: Mut


title: Sample10

value: PPROM


title: Mut2_TCR

description:
Library name: Mut2_TCR
10x Genomics


title: RNA-seq NPC DMSO control rep2

description: Library name: RNAseq_NPC_DMSO_expt5_rep2


title: GM1


title: Sample9


title: RNA-seq NPC DMSO control rep1

description: Library name: RNAseq_NPC_DMSO_expt5_rep1


title: MPPH2_Litter3_Silent1_IUE268_1_1

city: Sioux Falls

first: Louis-Jan

last: Pilaz

state: SD

address: 2301 E 60th Street North

department: Pediatrics and Rare Disease

institute: Sanford Research

description:
Library name: Sample 7
Litter 3 Silent Control Brain 1

data_processing:
trimming with Cutadapt
mappping with RNA star
read counts measured with featureCounts
Differential gene expression analysis with DESeq2
Assembly: mm10
Supplementary files format and content: Excel file containing the results of the DESeq2 analysis

source_name: E15.5 embyonic cortex

extract_protocol:
RNeasy kit (Qiagen)
PolyA enrichment

value: E15.5 embyonic cortex

value: Wildtype

value: Breasi-CRISPR Silent Control

value: Litter 3


title: RNA-seq PCGF2 depleted for 120h rep3

description: Library name: RNAseq_PCGF2_OHT120_expt4_rep3

value: mESC

value: PCGF4-/- PCGF2fl/fl

value: 120h 800nM OHT


title: Sample8

value: Placenta


title: MPPH2_Litter3_MPPH1_IUE268_2_1

description:
Library name: Sample 6
Litter 3 MPPH Brain 1

value: Breasi-CRISPR Ccnd2 Thr280Ala


title: WT4

description:
Library name: WT4
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 with --expect-cells=5000 --nosecondary commands.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

value: tumor

value: TILs

value: WT


title: Mut4_TCR

description:
Library name: Mut4_TCR
10x Genomics


title: Sample7

value: TERMSGA


title: RNA-seq PCGF2 depleted for 120h rep1

description: Library name: RNAseq_PCGF2_OHT120_expt4_rep1


title: WT1

description:
Library name: WT1
10x Genomics


title: WT2

description:
Library name: WT2
10x Genomics


title: MPPH2_Litter2_Silent1_IUE267_1_1

description:
Library name: Sample 5
Litter 2 Silent Control Brain 1

value: Litter 2


title: Sample6

source_name: PRETERMSGA

value: PRETERMSGA


title: RNA-seq PCGF2 depleted for 96h rep3

description: Library name: RNAseq_PCGF2_OHT96_expt4_rep3

value: 96h 800nM OHT


title: GM2

value: vascular smooth muscle cells

value: growth medium


title: MPPH2_Litter2_MPPH1_IUE267_2_1

description:
Library name: Sample 4
Litter 2 MPPH Brain 1

value: E15.5 embyonic cortex

value: Wildtype


title: Sample4

source_name: PRETERMPE

value: PRETERMPE


title: Sample5

value: PPROM


title: MPPH2_Litter1_Silent2_IUE266_1_2

description:
Library name: Sample 3
Litter 1 Silent Control Brain 2

value: Breasi-CRISPR Silent Control

value: Litter 1


title: RNA-seq PCGF2 depleted for 96h rep2

description: Library name: RNAseq_PCGF2_OHT96_expt4_rep2

value: mESC

value: PCGF4-/- PCGF2fl/fl


title: RNA-seq PCGF2 depleted for 96h rep1

description: Library name: RNAseq_PCGF2_OHT96_expt4_rep1


title: RNA-seq NPC DMSO control rep3

description: Library name: RNAseq_NPC_DMSO_expt5_rep3

value: NPC

value: Wild type


title: Mut3

description:
Library name: Mut3
10x Genomics

value: tumor

value: TILs

value: Mut


title: MPPH2_Litter1_Silent1_IUE266_1_1

description:
Library name: Sample 2
Litter 1 Silent Control Brain 1


title: Mut1_TCR

description:
Library name: Mut1_TCR
10x Genomics


title: MPPH2_Litter1_MPPH1_IUE266_2_1

description:
Library name: Sample 1
Litter 1 MPPH Brain 1

value: Breasi-CRISPR Ccnd2 Thr280Ala


title: Mut2

description:
Library name: Mut2
10x Genomics


title: Sample3

value: Placenta


title: RNA-seq PCGF2 depleted 24h recovery after second TSA treatment rep3

description: Library name: RNAseq_PCGF2_OHT_reREC_expt4_rep3

value: 120h 800nM OHT; 24h recovery from a second round of TSA treatment


title: Sample2

value: PRETERMSGA


title: RNA-seq PCGF2 depleted for 120h rep2

description: Library name: RNAseq_PCGF2_OHT120_expt4_rep2

value: 120h 800nM OHT


title: spermatogonia, CAST/EiJ, RNA-seq, rep2

city: Badalona

first: Tanya

last: Vavouri

state: BARCELONA

address: Ctra de Can Ruti, Cami de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukemia Research Institute

description:
Library name: sample46
piRNAcluster_normCounts_Inbred_RNAseq.tsv

data_processing:
Reads were mapped using HISAT2. For inbred strains, RNA-seq data was mapped to the indicated inbred strain genome. For samples from the outbred strain ICR, RNA-seq data was mapped to the reference mouse genome GRCm38/mm10.
Assembly: BL6 (GRCm38/mm10), C3H (C3H_HeJ_v1), 129S1 (129S1_SvImJ_v1), NOD (NOD_ShiLtJ_v1), CAST (CAST_EiJ_v1)
Supplementary files format and content: TSV file. DESeq2-normalized counts of reads mapping to piRNA clusters from Li et al. (2013)

source_name: testis

extract_protocol:
RNA was isolated using TRIzol® Reagent (Invitrogen) according to manufacturer's instructions.
RNA was sequenced using TruSeq Stranded Total RNA with Ribo-Zero H/M/R_Gold libraries. For spermatogonia samples, polyA molecules were selected.

value: testis

value: spermatogonia

value: CAST/EiJ


title: Sample1

source_name: CONTROLS

value: CONTROLS


title: RNA-seq PCGF2 depleted 24h recovery after second TSA treatment rep2

description: Library name: RNAseq_PCGF2_OHT_reREC_expt4_rep2


title: nB_KO_3

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using STAR and the GENCODE v27 reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor.
Assembly: mm10
Supplementary files format and content: tab delimited text file of RPKM normalized read counts for each gene

source_name: Spleen

extract_protocol:
Spleen from (un) infected mice were homogenized, red blood cells lysed with ACK Lysis buffer (150mM NH4Cl, 10mM KHCO3 and 0.5M EDTA (pH 7.3)). Splenocytes from LPS infected mice at 72hrs were stained for cell sorting. 1,000 Activated B cells and Plasma cells were sorted into RLT (Qiagen) + 1%BME, snap frozen and stored at -80°C till processing. Naive B cells were enriched from uninfected mice using CD43 (Ly-48) MicroBeads kit (Miltenyi Biotec) according to manufacturers protocol and 1,000 cells resuspended in RLT (Qiagen) + 1%BME, snap frozen and stored at -80°C till processing.
Total RNA was purified from 1,000 enriched Naïve B cells or sorted Activated B cells or Plasma cells using the Quick-RNA MicroPrep Kit (Zymo Research). cDNA was synthesized using the SMART-seq v4 cDNA synthesis kit (Takara). 200pg cDNA, the NexteraXT kit with the NexteraXT indexing primers (Illumina) was used to generate final libraries.

treatment_protocol: Mice were innoculated with 50µg/100µl Lipopolysaccharide through tail vein injection for 72 hrs or kept uninfected.

value: Spleen

tag: strain

value: naive B cells

value: G9afl/fl Cd19Cre/+

value: Uninfected

tag: sorting markers

value: CD43- enriched naive B cells


title: spermatogonia, CAST/EiJ, RNA-seq, rep1

description:
Library name: sample44
piRNAcluster_normCounts_Inbred_RNAseq.tsv


title: Mut4

description:
Library name: Mut4
10x Genomics

value: tumor


title: nB_KO_2


title: spermatogonia, C57BL/6J, RNA-seq, rep2

description:
Library name: sample42
piRNAcluster_normCounts_Inbred_RNAseq.tsv


title: RNA-seq PCGF2 depleted re-treated with TSA after recovery rep3

description: Library name: RNAseq_PCGF2_OHT_reTSA_expt4_rep3

value: mESC

value: PCGF4-/- PCGF2fl/fl

value: 96h 800nM OHT; 100 ng/ml TSA re-treatment following 24h recovery from TSA treatment


title: nB_KO_1


title: RNA-seq PCGF2 depleted 24h recovery after second TSA treatment rep1

description: Library name: RNAseq_PCGF2_OHT_reREC_expt4_rep1


title: SJMMNORM059933_C1 (undifferentiated reticulocytes)

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description:
Library name: SJMMNORM059933_C1
SJMM_ret_cell_count_matrix.txt

data_processing:
RNA-seq
BWA align
HTSEQ count
Assembly: mm9
Supplementary files format and content: matrix of raw counts

source_name: bone marrow

growth_protocol: ex vivo cell sorted

extract_protocol:
RNAeasy
total stranded

treatment_protocol: genetic transformation and time differential

value: bone marrow

value: reticulocytes

value: ex vivo sorted reticulocytes from HoxA7-TPO (K3)-adoptively transferred day6 mice


title: spermatogonia, C57BL/6J, RNA-seq, rep1

description:
Library name: sample41
piRNAcluster_normCounts_Inbred_RNAseq.tsv


title: SJMMNORM059931_C1 (undifferentiated reticulocytes)

description:
Library name: SJMMNORM059931_C1
SJMM_ret_cell_count_matrix.txt


title: RNA-seq PCGF2 depleted re-treated with TSA after recovery rep1

description: Library name: RNAseq_PCGF2_OHT_reTSA_expt4_rep1


title: nB_Cre_Ctrl_3


title: nB_Cre_Ctrl_2


title: SJMMNORM059929_C1 (undifferentiated reticulocytes)

description:
Library name: SJMMNORM059929_C1
SJMM_ret_cell_count_matrix.txt


title: testis, NOD/ShiLtJ, RNA-seq, rep2

description:
Library name: sample55
piRNAcluster_normCounts_Inbred_RNAseq.tsv

value: NOD/ShiLtJ


title: testis, C57BL/6J, RNA-seq, rep2

description:
Library name: sample57
piRNAcluster_normCounts_Inbred_RNAseq.tsv

value: testis


title: SJMMNORM059930_C1 (undifferentiated reticulocytes)

description:
Library name: SJMMNORM059930_C1
SJMM_ret_cell_count_matrix.txt


title: Mut1

description:
Library name: Mut1
10x Genomics

value: TILs

value: Mut


title: testis, C57BL/6J, RNA-seq, rep1

description:
Library name: sample56
piRNAcluster_normCounts_Inbred_RNAseq.tsv


title: Patient_34_Embryonal_Carcinoma_2

city: Baltimore

first: Taibo

state: MD

address: 1830 E Monument Street, Suite 2-300

institute: Johns Hopkins School of Medicine

description: Library name: S21_28102_2g

data_processing:
We performed raw read QC using FastQC, followed by adapter trimming using Trim Galore (version0.6.3) We filtered reads from likely contamination, and the adaptor was trimmed from the 3’ end. Because microrna length is defined as being between 17-22bp, we discarded all the reads with a length < 15bp. Flash version 1.2.11 was used to merge the read1 and read 2 and fastx_toolkit version 0.0.14 was used to convert the merged fastq file to fasta format.
We performed sequence alignment against miRBase mature miRNA using blast version 2.2.30 and performed alignment against a snRNA, snoRNA, tRNA, MTncrna database using blast version 2.2.30. For each sample, we calculated the number of reads that aligned to any of the microRNA. Only the hits with 100% identity and matching the whole length of microRNA were used for downstream analysis.
To summarize read count for each miRNA species, we applied featureCounts from the Subread package (release 2.0.6). We filtered miRNA which have low reads across all samples, requiring each species to have at least 5 reads in at least 2 samples, resulting in a total of 2,606 miRNA included in the downstream analysis.
Assembly: hg38
Supplementary files format and content: raw txt count files for each sample

source_name: Aortocaval lymph nodes

extract_protocol:
miRNA from each sample was isolated using the miRNAeasy FFPE kit (Qiagen, Germantown, MD) according to manufacturer protocols.
500 nanograms of total RNA was used as input for the llumina TruSeq Small RNA Sample Kit according to the manufacturer’s instructions.  This approach uses a naturally occurring miRNA specific structure with a 5’-phosphate and a 3’-hydroxyl to ligate adapter sequences exclusively to miRNA species. After adapter ligation, reverse transcription, PCR amplification and polyacrylamide gel electrophoresis were performed to generate a library. Library quality and quantity were assessed with the Agilent Bioanalyzer using the High Sensitivity Chip according to manufacturer’s instructions.

value: RPLND

value: Aortocaval lymph nodes

tag: tissue type

value: testicular cancer

value: WT


title: RNA-seq PCGF2 depleted 24h recovery after TSA washout rep3

description: Library name: RNAseq_PCGF2_OHT_REC_expt4_rep3

value: 96h 800nM OHT; TSA followed by 24 hours of recovery


title: testis, C3HeB/FeJ, RNA-seq, rep3

description:
Library name: sample53
piRNAcluster_normCounts_Inbred_RNAseq.tsv

tag: tissue


title: RNA-seq PCGF2 depleted TSA-treated rep3

description: Library name: RNAseq_PCGF2_OHT_TSA_expt4_rep3

tag: cell type

value: 72h 800nM OHT; 100 ng/ml TSA


title: RNA-seq PCGF2 depleted 24h recovery after TSA washout rep2

description: Library name: RNAseq_PCGF2_OHT_REC_expt4_rep2

tag: genotype


title: PC_KO_4

value: Spleen

value: Plasma cells

value: G9afl/fl Cd19Cre/+

tag: treatment

value: 72h post Lipopolysaccharide infection

value: Zombie yellow -, F4/80-, Cd11b-, Thy1.2-, B220/Cd45Rmid/lowCD138+ sorted PC


title: PC_KO_1


title: RNA-seq PCGF2 depleted TSA-treated rep2

description: Library name: RNAseq_PCGF2_OHT_TSA_expt4_rep2

value: mESC

value: PCGF4-/- PCGF2fl/fl


title: testis, C3HeB/FeJ, RNA-seq, rep2

description:
Library name: sample52
piRNAcluster_normCounts_Inbred_RNAseq.tsv

tag: batch


title: testis, NOD/ShiLtJ, RNA-seq, rep1

description:
Library name: sample54
piRNAcluster_normCounts_Inbred_RNAseq.tsv

value: NOD/ShiLtJ


title: PC_Cre_Ctrl_4


title: RNA-seq PCGF2 depleted 24h recovery after TSA washout rep1

description: Library name: RNAseq_PCGF2_OHT_REC_expt4_rep1

tag: cell line


title: Patient_34_Embryonal_Carcinoma_1

description: Library name: S21_19272_1k

source_name: TESTICLE

value: orchiectomy

value: TESTICLE


title: Patient_33_Seminoma_1

description: Library name: S21_18003_2c


title: Patient_34_Mixed_NSGCT_or_GCNIS

description: Library name: S21_19272_1f


title: PC_KO_3


title: PC_Cre_Ctrl_3


title: SJMMNORM059932_C1 (undifferentiated reticulocytes)

description:
Library name: SJMMNORM059932_C1
SJMM_ret_cell_count_matrix.txt

value: bone marrow

value: reticulocytes

value: ex vivo sorted reticulocytes from HoxA7-TPO (K3)-adoptively transferred day6 mice


title: RNA-seq PCGF2 depleted TSA-treated rep1

description: Library name: RNAseq_PCGF2_OHT_TSA_expt4_rep1


title: RNA-seq PCGF2 depleted re-treated with TSA after recovery rep2

description: Library name: RNAseq_PCGF2_OHT_reTSA_expt4_rep2

value: 96h 800nM OHT; 100 ng/ml TSA re-treatment following 24h recovery from TSA treatment


title: testis, C3HeB/FeJ, RNA-seq, rep1

description:
Library name: sample51
piRNAcluster_normCounts_Inbred_RNAseq.tsv

value: testis


title: nB_Cre_Ctrl_1

value: naive B cells

value: Uninfected

value: CD43- enriched naive B cells


title: testis, 129S1/SvImJ, RNA-seq, rep3

description:
Library name: sample50
piRNAcluster_normCounts_Inbred_RNAseq.tsv


title: testis, 129S1/SvImJ, RNA-seq, rep2

description:
Library name: sample49
piRNAcluster_normCounts_Inbred_RNAseq.tsv


title: Patient_32_Seminoma

description: Library name: S21_05159_2g

source_name: Retroperitoneal Mass

value: RPLND

value: Retroperitoneal Mass

value: testicular cancer

value: WT


title: RNA-seq PCGF2 depleted DMSO control rep3

description: Library name: RNAseq_PCGF2_OHT_DMSO_expt4_rep3

value: mESC


title: PC_Cre_Ctrl_1

value: Spleen

value: Plasma cells

value: 72h post Lipopolysaccharide infection

value: Zombie yellow -, F4/80-, Cd11b-, Thy1.2-, B220/Cd45Rmid/lowCD138+ sorted PC


title: RNA-seq PCGF2 depleted DMSO control rep2

description: Library name: RNAseq_PCGF2_OHT_DMSO_expt4_rep2

value: PCGF4-/- PCGF2fl/fl


title: ActB_KO_4

value: Activated B cells

value: G9afl/fl Cd19Cre/+

value: Zombie yellow -, F4/80-, Cd11b-, Thy1.2-, B220+GL7+ sorted ActB


title: testis, 129S1/SvImJ, RNA-seq, rep1

description:
Library name: sample48
piRNAcluster_normCounts_Inbred_RNAseq.tsv

value: testis


title: Patient_33_Seminoma_2

description: Library name: S21_18003_2j

value: orchiectomy

value: TESTICLE


title: RNA-seq PCGF2 depleted DMSO control rep1

description: Library name: RNAseq_PCGF2_OHT_DMSO_expt4_rep1


title: Patient_30_Teratoma

description: Library name: S20_12434_1b


title: ActB_KO_1


title: Tsc2-deficient MEFs exposed to oleic acid (30 mM, 1% FBS) replicate 2

city: L'Hospitalet del llobregat

first: Miquel Angel

last: Pujana

state: Barcelona

address: Gran via 199, Hospital Duran i Reynals

department: ProCURE

institute: Catalan Institute of Oncology IDIBELL

description:
Library name: MEFs OA 2
0106_2025

data_processing:
Illumina Casava 2.20 software used for basecalling.
The RNA sequencing reads were trimmed for adaptors, masked for low-complexity or low-quality sequence, and subsequently mapped to the mouse genome using STAR (2.7.10a)
The SAM/BAM files were further processed using the SAMtools (v1.18) and read count quantitations were obtained using BEDTools multicov (v2.31.0).
Gene expression was quantified by as transcripts per million (TPM).
Assembly: mm10
Supplementary files format and content: TPM data matrix of gene expression.

source_name: MEFs

growth_protocol: DMEM + 1 % FBS, 70 % confluence

extract_protocol:
Total RNA from tumor tissue lines was extracted using the RNeasy kit (Qiagen) and RNA quality was assessed by Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina TruSeq protocols

treatment_protocol: DMEM + 1 % FBS +/-  oleic acid (30 mM) for 72 hours

value: MEFs

value: Oleic acid


title: Patient_29_Seminoma_2

description: Library name: S20_01396_1l


title: RNA-seq PCGF2 untreated 24h recovery after second TSA treatment rep3

description: Library name: RNAseq_PCGF2_UT_reREC_expt4_rep3

value: 24h recovery from a second round of TSA treatment


title: Tsc2-deficient MEFs exposed to oleic acid (30 mM, 1% FBS) replicate 1

description:
Library name: MEFs OA 1
0105_2025


title: RNA-seq PCGF2 untreated 24h recovery after second TSA treatment rep2

description: Library name: RNAseq_PCGF2_UT_reREC_expt4_rep2


title: Patient_29_Seminoma_1

description: Library name: S20_01396_1k

value: testicular cancer


title: Patient_28_Teratoma

description: Library name: S19_72293_6k

source_name: ABDOMINAL MASS

value: RPLND

value: ABDOMINAL MASS

value: WT


title: ActB_Cre_Ctrl_3

value: Spleen


title: ActB_Cre_Ctrl_4

value: 72h post Lipopolysaccharide infection


title: RNA-seq PCGF2 untreated re-treated with TSA after recovery rep3

description: Library name: RNAseq_PCGF2_UT_reTSA_expt4_rep3

value: mESC

value: 100 ng/ml TSA re-treatment following 24h recovery from TSA treatment


title: Tsc2-deficient MEFs basal (1% FBS) replicate 1

description:
Library name: MEFs CNTRL 1
0103_2025

value: Basal


title: Tsc2-deficient MEFs basal (1% FBS) replicate 2

description:
Library name: MEFs CNTRL 2
0104_2025


title: 1014 sgNotch2sg2_plus_dTAG_Rep2

description: Library name: N2sg2_pdtg_2

data_processing:
Original data file from Illumina is transformed into sequenced reads (raw data, FASTQ formate files) by CASAVA base recognition.
Sequencing reads were mapped to the mm10 genome by STAR.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: 1014 TRIM28-dTAG-HA knock-in

growth_protocol: Murine SCLC cells were cultured with RPMI-1640 with 10% FBS, P/S, and HITES (10 nM hydrocortisone (Sigma Aldrich # H0135), Insulin-Transferrin-Selenium (Gemini #400-145), and 10 nM beta-estradiol (Sigma Aldrich# E2257), 100 U/mL of penicillin (P), and 100 μg/mL of streptomycin (S)] and culture with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using Quick-RNA™ Miniprep kit (Cat # R1055, Zymo Research, CA, USA) including a DNase digestion step according to the manufacturer’s instructions and RNA sequencing was performed.
The libraries for RNA-seq are prepared using NEBNext Ultra II non-stranded kit.  Paired end 150bp sequencing was performed on Novaseq6000 sequencer using S4 flow cell.

treatment_protocol: 1014 NOTCH2 isogenic TRIM28-dTAG-HA knock-in cells are treated with 100 nM dTAG-V1 for 72 hours to degrade TRIM28 or with DMSO as a control.

value: 1014 TRIM28-dTAG-HA knock-in

value: SCLC cell line

value: 100nM dTAG V1 for 3 days


title: ActB_Cre_Ctrl_1

value: Activated B cells

value: Zombie yellow -, F4/80-, Cd11b-, Thy1.2-, B220+GL7+ sorted ActB


title: RNA-seq PCGF2 untreated re-treated with TSA after recovery rep2

description: Library name: RNAseq_PCGF2_UT_reTSA_expt4_rep2

value: PCGF4-/- PCGF2fl/fl


title: Patient_27_Seminoma

description: Library name: S19_41943_1b

value: Partial orchiectomy

value: TESTICLE


title: Patient_31_Seminoma

description: Library name: S20_13637_1a

value: Completion Orchiectomy

value: testicular cancer


title: 1014 sgNotch2sg2_plus_dTAG_Rep1

description: Library name: N2sg2_pdtg_1


title: Patient_26_Seminoma

description: Library name: S19_40900_2g

value: orchiectomy


title: RNA-seq PCGF2 untreated re-treated with TSA after recovery rep1

description: Library name: RNAseq_PCGF2_UT_reTSA_expt4_rep1


title: 1014 sgNotch2sg2_minus_dTAG_Rep2

description: Library name: N2sg2_mdtg_2

value: DMSO


title: ActB_KO_3

value: Spleen

value: G9afl/fl Cd19Cre/+


title: nB_KO_2

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using Bowtie
bigWig files were normalized to reads per million and generated using GenomicRanges and bedGraphToBigWig function from the UCSC genome browser
Assembly: mm10
Supplementary files format and content: reads per million normalized bigWig files

extract_protocol:
Spleen of (un-) infected mice were homogenized, red blood cells lysed with ACK Lysis buffer(150mM NH4Cl, 10mM KHCO3 and 0.5M EDTA (pH 7.3)). Splenocytes from LPS infected mice at 72hrs were stained for cell sorting. 5,000 Activated B cells and Plasma cells were sorted into B-cell media (RPMI supplemented with 10% FBS, 1x MEM-Non Essential Amino Acids, 1mM Sodium Pyruvate, 10mM HEPES, 1x Penicillin-Streptomycin and β-Mercaptoethanol). Naive B cells were enriched from uninfected mice using CD43 (Ly-48) MicroBeads kit (Miltenyi Biotec) according to manufacturers protocol and 5,000 cells resuspended in B-cell media.
5,000 enriched Naïve B cells or sorted Activated B cells or Plasma cells were centrifuged for 10 minutes at 500xg at 4°C, resuspended in tagmentation reaction mix (2X TD buffer, 1µl Tagmentation enzyme, molecular grade H2O (Illumina Inc.)) and tagmentation reaction incubated for 60 minutes at 37°C. the tagmentation reaction was stopped by addition of 23µl of Tagmentatin Clean-up buffer (326mM Na Cl, 109 mM EDTA, 0.63% SDS) and 2µl 10mg/ml Proteinase-K and incubation for 30 minutes at 40°C. DNA was isolated following a 0.3x negative-SPRI-size selection followed by a 1.2x positive selection. DNA was amplified into a sequencing library with KAPA HiFi Polymerase and the dual indexing primers (Nextera Indexing Kit, Illumina, Inc). Following PCR amplification, a 1.0x SPRI bead enrichment was performed.

value: naive B cells

value: Uninfected

tag: sorting/enrichment markers

value: Enriched CD43- B-cells


title: nB_KO_3


title: Patient_25_Seminoma

description: Library name: S19_39311_1f

value: WT


title: RNA-seq PCGF2 untreated 24h recovery after TSA washout rep3

description: Library name: RNAseq_PCGF2_UT_REC_expt4_rep3

value: mESC

value: TSA followed by 24 hours of recovery


title: Patient_24_NonGCT

description: Library name: S19_31004_1a

value: unknown

value: Chemo


title: RNA-seq PCGF2 untreated 24h recovery after TSA washout rep2

description: Library name: RNAseq_PCGF2_UT_REC_expt4_rep2

value: PCGF4-/- PCGF2fl/fl


title: Patient_23_Embryonal_Carcinoma

description: Library name: S19_30788_1f


title: RNA-seq PCGF2 untreated 24h recovery after second TSA treatment rep1

description: Library name: RNAseq_PCGF2_UT_reREC_expt4_rep1

value: 24h recovery from a second round of TSA treatment


title: 1014 sgNotch2sg2_minus_dTAG_Rep1

description: Library name: N2sg2_mdtg_1

value: 1014 TRIM28-dTAG-HA knock-in

value: SCLC cell line


title: nB_Cre_Ctrl_3


title: nB_KO_1


title: 1014 sgNotch2sg1_plus_dTAG_Rep2

description: Library name: N2sg1_pdtg_2

value: 100nM dTAG V1 for 3 days


title: RNA-seq PCGF2 untreated 24h recovery after TSA washout rep1

description: Library name: RNAseq_PCGF2_UT_REC_expt4_rep1


title: RNA-seq PCGF2 untreated TSA-treated rep3

description: Library name: RNAseq_PCGF2_UT_TSA_expt4_rep3

value: 100 ng/ml TSA


title: Patient_21_Teratoma

description: Library name: S19_29204_4d

source_name: PARAAORTIC MASS

value: RPLND

value: PARAAORTIC MASS

value: testicular cancer


title: Patient_22_Seminoma

description: Library name: S19_29419_1f

value: orchiectomy

value: TESTICLE


title: nB_Cre_Ctrl_1

value: Spleen

value: naive B cells

value: Uninfected

value: Enriched CD43- B-cells


title: nB_Cre_Ctrl_2


title: 1014 sgNotch2sg1_minus_dTAG_Rep2

description: Library name: N2sg1_mdtg_2

value: DMSO


title: RNA-seq PCGF2 untreated TSA-treated rep2

description: Library name: RNAseq_PCGF2_UT_TSA_expt4_rep2

value: mESC


title: Patient_20_Teratoma

description: Library name: S19_20788_1a

value: WT


title: 1014 sgNotch2sg1_minus_dTAG_Rep1

description: Library name: N2sg1_mdtg_1


title: PC_KO_4

value: Plasma cells

value: G9afl/fl Cd19Cre/+

value: 72h post Lipopolysaccharide infection

value: Zombie yellow -, F4/80-, Cd11b-, Thy1.2-, B220/Cd45Rmid/lowCD138+ sorted PC


title: RNA-seq PCGF2 untreated TSA-treated rep1

description: Library name: RNAseq_PCGF2_UT_TSA_expt4_rep1

value: PCGF4-/- PCGF2fl/fl

value: 100 ng/ml TSA


title: 1014 sgControl_plus_dTAG_Rep2

description: Library name: sgctrl_pdtg_2

value: 1014 TRIM28-dTAG-HA knock-in

value: SCLC cell line

value: 100nM dTAG V1 for 3 days


title: RNA-seq PCGF2 untreated DMSO control rep3

description: Library name: RNAseq_PCGF2_UT_DMSO_expt4_rep3


title: PC_KO_3


title: 1014 sgControl_plus_dTAG_Rep1

description: Library name: sgctrl_pdtg_1


title: PC_KO_1


title: Patient_18_Embryonal_Carcinoma

description: Library name: S19_19749_3c

source_name: intra aortic caval mass

value: RPLND

value: intra aortic caval mass

value: testicular cancer


title: RNA-seq PCGF2 untreated DMSO control rep2

description: Library name: RNAseq_PCGF2_UT_DMSO_expt4_rep2


title: Patient_17_Seminoma

description: Library name: S19_18396_8a

source_name: Paraaortic Mass

value: Paraaortic Mass


title: RNA-seq PCGF2 untreated DMSO control rep1

description: Library name: RNAseq_PCGF2_UT_DMSO_expt4_rep1


title: 1014 sgControl_minus_dTAG_Rep2

description: Library name: sgctrl_mdtg_2


title: Patient_16_Teratoma

description: Library name: S19_12737_1c

source_name: PARACAVAL LYMPH NODES

value: PARACAVAL LYMPH NODES


title: 1014 sgNotch2sg1_plus_dTAG_Rep1

description: Library name: N2sg1_pdtg_1


title: PC_Cre_Ctrl_1

value: Spleen


title: Patient_15_Embryonal_Carcinoma

description: Library name: S19_10747_1g

value: orchiectomy

value: TESTICLE


title: PC_Cre_Ctrl_4

value: Plasma cells


title: RNA-seq mESC romidepsin-treated rep3

description: Library name: RNAseq_ROMI_expt1_rep3

value: mESC wt

value: Wild type

value: 0.03 nM romidepsin


title: RNA-seq mESC romidepsin-treated rep2

description: Library name: RNAseq_ROMI_expt1_rep2


title: RNA-seq mESC romidepsin-treated rep1

description: Library name: RNAseq_ROMI_expt1_rep1


title: Patient_15_Seminoma

description: Library name: S19_10747_1f

value: WT


title: Suspension_K60_Trim28sg2_Rep1

description: Library name: S60_T2_1

source_name: Suspension K60

value: Suspension K60


title: Patient_19_Embryonal_Carcinoma

description: Library name: S19_20501_1c

source_name: inter-aortocaval mass

value: inter-aortocaval mass


title: Patient_14_Seminoma

description: Library name: S19_10173_3c


title: ActB_KO_3

value: Activated B cells

value: G9afl/fl Cd19Cre/+

value: 72h post Lipopolysaccharide infection

value: Zombie yellow -, F4/80-, Cd11b-, Thy1.2-, B220+GL7+ sorted ActB


title: ActB_KO_4


title: RNA-seq mESC 48h recovery then 48h recovery after second TSA treatment rep3

description: Library name: RNAseq_REC48_reREC48_expt3_rep3

value: 48h recovery from TSA treatment followed by 48h recovery from a second TSA treatment


title: Suspension_K69_Trim28sg1_Rep2

description: Library name: S60_T1_2

value: SCLC cell line


title: Patient_13_Teratoma

description: Library name: S18_79899_3k

source_name: INTER-AORTOCAVAL MASSES AND LYMPH NODES

value: RPLND

value: INTER-AORTOCAVAL MASSES AND LYMPH NODES

value: testicular cancer

value: Chemo


title: ActB_Cre_Ctrl_4

value: Spleen


title: Suspension_K60_Trim28sg1_Rep1

description: Library name: S60_T1_1


title: Patient_12_Mixed_NSGCT_or_GCNIS

description: Library name: S18_6861_1k

value: orchiectomy

value: TESTICLE


title: ActB_KO_1


title: RNA-seq mESC 48h recovery then 48h recovery after second TSA treatment rep2

description: Library name: RNAseq_REC48_reREC48_expt3_rep2

value: mESC wt

value: Wild type


title: Suspension_K60_NT_Rep2

description: Library name: S60_N_2

value: Suspension K60


title: RNA-seq mESC 48h recovery then 48h recovery after second TSA treatment rep1

description: Library name: RNAseq_REC48_reREC48_expt3_rep1


title: PC_Cre_Ctrl_3

value: Plasma cells

value: Zombie yellow -, F4/80-, Cd11b-, Thy1.2-, B220/Cd45Rmid/lowCD138+ sorted PC


title: Patient_12_Seminoma

description: Library name: S18_6861_1i

value: WT


title: 1014 sgControl_minus_dTAG_Rep1

description: Library name: sgctrl_mdtg_1

value: 1014 TRIM28-dTAG-HA knock-in

value: DMSO


title: Suspension_K60_NT_Rep1

description: Library name: S60_N_1


title: Suspension_K60_Trim28sg2_Rep2

description: Library name: S60_T2_2


title: RNA-seq mESC 48h recovery then 24h recovery after second TSA treatment rep3

description: Library name: RNAseq_REC48_reREC24_expt3_rep3

value: 48h recovery from TSA treatment followed by 24h recovery from a second TSA treatment


title: Suspension_K93_Trim28sg2_Rep2

description: Library name: S93_T2_2

source_name: Suspension K93

value: Suspension K93

value: SCLC cell line


title: Patient_12_Embryonal_Carcinoma

description: Library name: S18_6861_1g


title: ActB_Cre_Ctrl_3

value: Activated B cells

value: 72h post Lipopolysaccharide infection

value: Zombie yellow -, F4/80-, Cd11b-, Thy1.2-, B220+GL7+ sorted ActB


title: Patient_11_Embryonal_Carcinoma

description: Library name: S18_38123_1a

value: testicular cancer


title: RNA-seq mESC 48h recovery then 24h recovery after second TSA treatment rep1

description: Library name: RNAseq_REC48_reREC24_expt3_rep1


title: Patient_10_Seminoma_1

description: Library name: S18_32334_1e

value: orchiectomy


title: RNA-seq mESC re-treated with TSA after 48h recovery rep3

description: Library name: RNAseq_REC48_reTSA_rep3

value: 100 ng/ml TSA re-treatment following 48h recovery from TSA treatment


title: Patient_10_Seminoma_2

description: Library name: S18_32334_1f

value: TESTICLE


title: Suspension_K93_Trim28sg1_Rep2

description: Library name: S93_T1_2


title: RNA-seq mESC re-treated with TSA after 48h recovery rep2

description: Library name: RNAseq_REC48_reTSA_rep2

value: mESC wt

value: Wild type


title: Suspension_K93_Trim28sg1_Rep1

description: Library name: S93_T1_1


title: RNA-seq mESC re-treated with TSA after 48h recovery rep1

description: Library name: RNAseq_REC48_reTSA_rep1


title: Patient_8_Seminoma

description: Library name: S18_23880_3c

source_name: PARA AORTIC MASS

value: RPLND

value: PARA AORTIC MASS

value: Chemo


title: Suspension_K93_NT_Rep1

description: Library name: S93_N_1


title: RNA-seq mESC 96h recovery after TSA washout rep3

description: Library name: RNAseq_REC96_expt3_rep3

value: 96h recovery from TSA treatment


title: RNA-seq mESC 48h recovery then 24h recovery after second TSA treatment rep2

description: Library name: RNAseq_REC48_reREC24_expt3_rep2


title: RNA-seq mESC 96h recovery after TSA washout rep2

description: Library name: RNAseq_REC96_expt3_rep2


title: ActB_Cre_Ctrl_1

source_name: Spleen

value: Spleen


title: Patient_7_Seminoma

description: Library name: S18_23132_1e

value: WT


title: B3GALT6_10_skin_fibroblast_male_324_months_rep2

type: RNA

city: Vandoeuvre-lès-Nancy

first: Sebastien

last: Hergalant

address: Faculté de Médecine. 9 avenue de la forêt de Haye

department: Bioinformatics

institute: INSERM

description: number of growth cycles: 4

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA was hybridized to GeneChip® Human Gene 2.0 ST (Affymetrix) at 45°C for 17 hours.

scan_protocol: After overnight hybridization, chips were washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G. The scanned images were then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls.

data_processing: Fluorescence values corresponding to raw expression data were extracted from Affymetrix CEL files (one file per sample) using the R oligo package (https://bioconductor.org/) with the corresponding platform definitions (pd.hugene.2.0.st). Positive and negative control probes were removed, leaving 44,629 probes corresponding to 33,898 unique gene annotations. LOWESS normalization was applied against a median profile of all samples. If needed, corrections for batch effects between microarrays were performed with Combat (package sva from Bioconductor) with batch and technical replicates as model covariates.

label: biotin

source_name: B3GALT6 patient 10, skin biopsy, male, 324 months, replicate

label_protocol: After purification according to Affymetrix protocol, 5.5 ug of Sens Target DNA were fragmented and biotin labelled.

growth_protocol: Control and spEDS fibroblasts were isolated from skin biopsies obtained from age and sex-matched individuals and spEDS patients and were cultured in Dulbecco′s Modified Eagle′s Medium with high glucose supplemented with 10% FBS, 1% glutamine, 1% penicillin/streptomycin and 1% non-essential amino acids until confluence.

extract_protocol: Total RNA was extracted from control and spEDS fibroblasts using TRIzol Plus RNA purification kit (Thermo Fisher Scientific). After validation of the RNA quality with Bioanalyzer 2100 (using Agilent RNA6000 Nano Chip kit), 100ng of total RNA was reverse transcribed following the GeneChip® WT Plus Reagent Kit (Affymetrix).

tag: condition

value: spEDS

value: skin fibroblast

tag: gender

value: M

tag: gene mutation

tag: protein mutation

tag: number of growth cycles

tag: b3galt6 mutations

value: homozygous


title: Suspension_K93_Trim28sg2_Rep1

description: Library name: S93_T2_1

value: Suspension K93

value: SCLC cell line


title: Adherent_K60_Trim28sg2_Rep2

description: Library name: A60_T2_2

source_name: Adherent K60

value: Adherent K60


title: RNA-seq mESC 96h recovery after TSA washout rep1

description: Library name: RNAseq_REC96_expt3_rep1


title: Patient_5_Mixed_NSGCT_or_GCNIS_2

description: Library name: S17_73124_1g

source_name: TESTICLE

value: orchiectomy

value: testicular cancer


title: Adherent_K60_Trim28sg2_Rep1

description: Library name: A60_T2_1


title: Adherent_K69_Trim28sg1_Rep2

description: Library name: A60_T1_2


title: Patient_5_Mixed_NSGCT_or_GCNIS_1

description: Library name: S17_73124_1f

value: TESTICLE


title: B3GALT6_11_skin_fibroblast_male_96_months_rep1

description: number of growth cycles: 3

source_name: B3GALT6 patient 11, skin biopsy, male, 96 months

value: Ala108Glyfs*163 + Asp207His

value: heterozygous


title: RNA-seq mESC 72h recovery after TSA washout rep3

description: Library name: RNAseq_REC72_expt3_rep3

value: mESC wt

value: Wild type

value: 72h recovery from TSA treatment


title: Adherent_K60_Trim28sg1_Rep1

description: Library name: A60_T1_1


title: Patient_6_Teratoma

description: Library name: S18_13686_6a

source_name: PARA AORTIC MASS AND LYMPH NODES

value: RPLND

value: PARA AORTIC MASS AND LYMPH NODES

value: Chemo


title: Suspension_K93_NT_Rep2

description: Library name: S93_N_2


title: RNA-seq mESC 72h recovery after TSA washout rep2

description: Library name: RNAseq_REC72_expt3_rep2


title: control_7_skin_fibroblast_male_93_months_rep1

description: number of growth cycles: 7

source_name: control patient 7, skin biopsy, male, 93 months

value: CTRL

value: skin fibroblast


title: B3GALT6_9_skin_fibroblast_female_36_months_rep1

description: number of growth cycles: 4

source_name: B3GALT6 patient 9, skin biopsy, female, 36 months

value: spEDS

value: F

value: homozygous


title: Patient_9_Seminoma

description: Library name: S18_28328_1d

value: WT


title: Patient_4_Teratoma

description: Library name: S17_6862_8b

source_name: PARA-AORTIC MASS AND LYMPH NODES

value: PARA-AORTIC MASS AND LYMPH NODES


title: control_8_skin_fibroblast_female_34_months_rep1

description: number of growth cycles: 5

source_name: control patient 8, skin biopsy, female, 34 months


title: B3GALT6_10_skin_fibroblast_male_324_months_rep1

description: number of growth cycles: 4

source_name: B3GALT6 patient 10, skin biopsy, male, 324 months

value: M


title: B3GALT6_6_skin_fibroblast_female_13_months_rep1

description: number of growth cycles: 4

source_name: B3GALT6 patient 6, skin biopsy, female, 13 months

value: Phe160Serfs*118 + Arg261His


title: RNA-seq mESC 72h recovery after TSA washout rep1

description: Library name: RNAseq_REC72_expt3_rep1


title: Adherent_K60_NT_Rep1

description: Library name: A60_N_1

value: Adherent K60

value: SCLC cell line


title: Patient_2_NonGCT

description: Library name: S17_6271_3a

source_name: LEFT SPERMATIC CORD AND PARA-AORTIC MASS

value: testicular cancer


title: NH4

first: Manoj

last: Bhasin

address: 101 Woodruff Cir

description: 10x Genomics

data_processing:
scRNA-Seq data after standard quality control was aligned to the reference genome (mm10) using the 10x Cell Ranger(v7.0.0) pipeline. Preprocessed and filtered normalized data were subjected to unsupervised analysis using principal component analysis (PCA) (Seurat v4.3 Bioconductor package) to identify principal components with significant variation that was used as input for UMAP analysis to determine overall relationship among cells.
Assembly: mm10
Supplementary files format and content: Comma-separated values files and matrix files

source_name: wound debridment

extract_protocol:
Tissue dissociation was initiated by transferring sample to a tissue digestion master mix: 0.25% Trypsin-EDTA Free (Gibco, 25200-05), 5 mg/ml Collagenase P (Roche, 1124002001), 5 mg/ml Dispase (Gibco, 17105-041), and 3 mg/ml Dnase-1 (STEMCELL, 07470). The tissue was mechanically minced with fine surgical scissors and incubated at 37oC for 40 minutes with shaking. Complete RPMI(Gibco,11875093) was added to the digested tissue, followed by filtration through a 70 mm pore-size cell strainer (BioLogix, 15-1070) and spinning at 500 g for 5 min at 4oC. The resulting cell pellet was then washed with ice-cold PBS and cell viability assessed and viably frozen in cell freezing media (Gibco, 12648-010) and stored at -80C till use.
ScRNA-seq libraries were prepared using the Next GEM Chromium single cell 3′ reagent kits V3.1 with feature barcode technology for cell surface protein (10x genomics) and sequenced using NextSeq 500 high output kits and Novaseq S4 PE100 kits (Illumina).

value: wound debridment

value: single cells isolated from wound

tag: race

value: African American


title: Adherent_K60_NT_Rep2

description: Library name: A60_N_2


title: Adherent_K93_Trim28sg2_Rep2

description: Library name: A93_T2_2

source_name: Adherent K93

value: Adherent K93


title: RNA-seq mESC 48h recovery after TSA washout rep3

description: Library name: RNAseq_REC48_expt3_rep3

value: mESC wt

value: Wild type

value: 48h recovery from TSA treatment


title: B3GALT6_4_skin_fibroblast_male_12_months_rep1

description: number of growth cycles: 2

source_name: B3GALT6 patient 4, skin biopsy, male, 12 months

value: spEDS

value: skin fibroblast

value: Tyr310Cys + Glu265Asp

value: heterozygous


title: control_5_skin_fibroblast_male_331_months_rep1

description: number of growth cycles: 2

source_name: control patient 5, skin biopsy, male, 331 months

value: CTRL


title: Patient_3_Embryonal_Carcinoma

description: Library name: S17_65404_1a

source_name: PARA AORTIC 'MASS' AND LYMPH NODES

value: RPLND

value: PARA AORTIC 'MASS' AND LYMPH NODES

value: WT


title: RNA-seq mESC 48h recovery after TSA washout rep2

description: Library name: RNAseq_REC48_expt3_rep2


title: Adherent_K93_Trim28sg2_Rep1

description: Library name: A93_T2_1

value: SCLC cell line


title: RNA-seq mESC 48h recovery after TSA washout rep1

description: Library name: RNAseq_REC48_expt3_rep1


title: Patient_1_Yolk_Sac_Tumor

description: Library name: S17_45968_1m

value: orchiectomy

value: TESTICLE

value: testicular cancer


title: Patient_1_Seminoma

description: Library name: S17_45968_1i


title: Adherent_K93_Trim28sg1_Rep2

description: Library name: A93_T1_2


title: RNA-seq mESC DMSO control expt3 rep3

description: Library name: RNAseq_DMSO_expt3_rep3


title: Patient_1_Teratoma

description: Library name: S17_45968_1e


title: NH2

description: 10x Genomics

value: single cells isolated from wound

value: diabetic foot ulcer (DFU)

value: African American


title: Patient MDS_12, CD4+ T cell sorted from bone marrow, bulk-ATAC-seq

city: Ulsan

first: Dayoung

last: Kim

address: 50 Unist-gil

country: South Korea

institute: UNIST

description: Library name: CD4ATAC_MDS_12

data_processing:
5 bp sequence at 5' end, and primer sequence at 3' end were trimmed using in-house script.
ATAC-seq reads were aligned to UCSC hg38 genome using Bowtie version 2.5.3.
MACS2 version 2.2.9.1 was used to call ATAC-seq narrowPeaks.
bigWig files were generated using genomicRanges R package.
Supplementary files format and content: narrowPeak files containing all MACS2 called peaks from each ATAC-seq mapped reads.
Supplementary files format and content: Normalized bigWig file to visualize the mapped read in genome-wide tracks.

source_name: Bone marrow

extract_protocol:
Cells were thawed using 37C CTL wash buffer, and apoptotic cells were discarded using MACS Annexin-V microbead Kit.
50,000 cells were used as starting material for Omni-ATAC-seq. For each library, the amplification cycle was determined using qPCR, but not to exceed 16 cycles in total. Before sequencing, the libraries were size selected at 200 bp or longer to remove excessive primer dimers.

value: Bone marrow

tag: individual

tag: disease state

value: high-risk myelodysplastic syndrome

tag: response group

value: Responder

value: CD4+ sorted cell (FACS)


title: Adherent_K93_Trim28sg1_Rep1

first: Yixiang

address: 450 Brookline Ave

description: Library name: A93_T1_1

value: Adherent K93


title: RNA-seq mESC DMSO control expt3 rep2

description: Library name: RNAseq_DMSO_expt3_rep2

value: mESC wt

value: Wild type


title: NH1

description: 10x Genomics

tag: tissue


title: control_3_skin_fibroblast_male_101_months_rep1

description: number of growth cycles: 4

source_name: control patient 3, skin biopsy, male, 101 months

value: CTRL

tag: cell type

value: skin fibroblast

value: M


title: control_1_skin_fibroblast_female_4_months_rep1

description: number of growth cycles: 3

source_name: control patient 1, skin biopsy, female, 4 months

value: F


title: Adherent_K93_NT_Rep2

description: Library name: A93_N_2

value: SCLC cell line

tag: genotype


title: control_2_skin_fibroblast_male_8_months_rep1

description: number of growth cycles: 4

source_name: control patient 2, skin biopsy, male, 8 months


title: Patient MDS_11, CD4+ T cell sorted from bone marrow, bulk-ATAC-seq

description: Library name: CD4ATAC_MDS_11

value: Non-responder


title: RNA-seq mESC DMSO control expt3 rep1

description: Library name: RNAseq_DMSO_expt3_rep1

tag: treatment


title: H4

description: 10x Genomics


title: H5

description: 10x Genomics

value: wound debridment

value: White-Hispanic


title: H3

description: 10x Genomics

value: single cells isolated from wound

value: diabetic foot ulcer (DFU)


title: Adherent_K93_NT_Rep1

description: Library name: A93_N_1

tag: batch


title: Patient MDS_06, CD4+ T cell sorted from bone marrow, bulk-ATAC-seq

description: Library name: CD4ATAC_MDS_06

value: Bone marrow


title: lung, Influenza A Virus, S4_HTO

first: Ruth

last: Franklin

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

description:
Library name: Sample_Set_004_HTO
10X Genomics

library_source: other

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline (v8.0.1) to generate gene expression matrices. Reference files for alignment and counting of 10x single-cell reads were prepared using GENCODE Release M33 (GRCm39), available from the GENCODE website, following build notes provided by 10x Genomics.
To create a custom reference genome, complete H1N1 segment cRNA sequences from the NCBI Nuccore database (accessions LC333182, LC333183, LC333184, LC333185, LC333186, LC333187, LC333188, and LC333189) were added to the primary GRCm39 assembly FASTA file. Matching GTF entries for these H1N1 segments were also generated and appended to the filtered GRCm39 GTF file. The modified GRCm39 reference files, now containing H1N1 segment information, were used to build the combined reference genome (GRCm39_GENCODEv33_H1N1) using cellranger mkref.
Gzipped FASTQ files containing gene and antibody hashtag data were aligned to this custom reference genome using Cell Ranger v8.0.1. Gene expression counts for samples S1–S4 were generated with the cellranger count command, followed by normalization and hashtag demultiplexing using Seurat.
Assembly: GRCm39 (Gencode M33)
Assembly: H1N1 segment cRNA sequences from LC333182, LC333183, LC333184, LC333185, LC333186, LC333187, LC333188, and LC333189 (https://www.ncbi.nlm.nih.gov/nuccore/)
Supplementary files format and content: Filtered matrix.mtx, barcodes.tsv and features.tsv files for each set of hashed samples.

molecule: protein

source_name: Whole Lung

extract_protocol:
Animals were euthanized by administration of a lethal dose of ketamine/xylazine mixture and perfused with 2mM EDTA in PBS. The trachea was exposed, nicked, and a 22g catheter was inserted. A 1mL-PBS-filled syringe was attached to the catheter and used to inflate then deflate lungs to collect cells present in BALF. The syringe was replaced with a 1mL-dispase-filled syringe and lungs were inflated. Inflated lungs were removed, and lung lobes were chopped and immersed in enzyme solution (100μg/mL DNAse and 83μg/mL Liberase in RPMI) and placed in a 37°C shaker for 40 minutes. BALF and lung digest cells were filtered through a 70μm cell strainer to obtain a single cell suspension and exposed to hypotonic lysis (ACK lysing buffer, ThermoFisher) to remove red blood cells.
Samples were prepared using a Chromium Next GEM Single Cell 3' Kit v3.1 according to the manufacturer’s instructions.

treatment_protocol: 30uls of PBS or 30uls PBS containing 225 pfu of influenza A virus (A/WSN/33;H1N1)

value: Whole Lung

value: WT and OsmtmWtsi/Osmtm1aWtsi (KO)

tag: Sex

value: Female

value: 225 pfu Influenza A virus in 30uLs of PBS i.n.

tag: age

tag: library type

value: HTO

tag: hto

value: Hashtag1 TotalSeq-B0301 anti-mouse (WT),  Hashtag2 TotalSeq-B0302 anti-mouse (KO)


title: Patient MDS_04, CD4+ T cell sorted from bone marrow, bulk-ATAC-seq

description: Library name: CD4ATAC_MDS_04

value: high-risk myelodysplastic syndrome

value: Responder

value: CD4+ sorted cell (FACS)


title: Patient MDS_05, CD4+ T cell sorted from bone marrow, bulk-ATAC-seq

description: Library name: CD4ATAC_MDS_05


title: lung, Influenza A Virus, S3_HTO

description:
Library name: Sample_Set_003_HTO
10X Genomics


title: RNA-seq mESC 16h recovery after TSA washout rep3

description: Library name: RNAseq_REC16_expt6_rep3

tag: cell line

value: mESC wt

value: Wild type

value: 16h recovery from TSA treatment


title: RNA-seq mESC 20h recovery after TSA washout rep3

description: Library name: RNAseq_REC20_expt6_rep3

value: 20h recovery from TSA treatment


title: RNA-seq mESC 20h recovery after TSA washout rep2

description: Library name: RNAseq_REC20_expt6_rep2


title: Patient MDS_03, CD4+ T cell sorted from bone marrow, bulk-ATAC-seq

description: Library name: CD4ATAC_MDS_03

value: Non-responder


title: lung, Influenza A Virus, S4_GEX

description:
Library name: Sample_Set_004_GEX
10X Genomics

value: mRNA


title: testis, ICR, RNA-seq, rep15

description:
Library name: sample15
piRNAcluster_normCounts_ICR_RNAseq.tsv

source_name: testis

value: testis

value: ICR


title: H1

description: 10x Genomics

value: single cells isolated from wound

value: diabetic foot ulcer (DFU)

value: African American


title: RNA-seq mESC 20h recovery after TSA washout rep1

description: Library name: RNAseq_REC20_expt6_rep1


title: lung, Influenza A Virus, S3_GEX

description:
Library name: Sample_Set_003_GEX
10X Genomics

value: Whole Lung

value: WT and OsmtmWtsi/Osmtm1aWtsi (KO)

value: Female

value: 225 pfu Influenza A virus in 30uLs of PBS i.n.


title: RNA-seq mESC 16h recovery after TSA washout rep2

description: Library name: RNAseq_REC16_expt6_rep2


title: Patient MDS_02, CD4+ T cell sorted from bone marrow, bulk-ATAC-seq

description: Library name: CD4ATAC_MDS_02

value: Bone marrow

value: high-risk myelodysplastic syndrome


title: testis, ICR, RNA-seq, rep14

description:
Library name: sample14
piRNAcluster_normCounts_ICR_RNAseq.tsv


title: lung, control, S2_HTO

description:
Library name: Sample_Set_002_HTO
10X Genomics

value: 30uL PBS i.n.

value: HTO

value: Hashtag1 TotalSeq-B0301 anti-mouse (WT),  Hashtag2 TotalSeq-B0302 anti-mouse (KO)


title: testis, ICR, RNA-seq, rep13

description:
Library name: sample13
piRNAcluster_normCounts_ICR_RNAseq.tsv


title: RNA-seq mESC 16h recovery after TSA washout rep1

description: Library name: RNAseq_REC16_expt6_rep1

value: mESC wt

value: Wild type

value: 16h recovery from TSA treatment


title: RNA-seq mESC DMSO control expt6 rep3

description: Library name: RNAseq_DMSO_expt6_rep3


title: testis, ICR, RNA-seq, rep12

description:
Library name: sample12
piRNAcluster_normCounts_ICR_RNAseq.tsv

value: testis


title: lung, control, S2_GEX

description:
Library name: Sample_Set_002_GEX
10X Genomics

value: mRNA


title: Healthy donor  HD_02, CD8+ T cell sorted from bone marrow, bulk-ATAC-seq

description: Library name: CD8ATAC_HD_02

value: CD8+ sorted cell (FACS)


title: lung, control, S1_HTO

description:
Library name: Sample_Set_001_HTO
10X Genomics


title: H2

description: 10x Genomics

value: single cells isolated from wound

value: diabetic foot ulcer (DFU)


title: RNA-seq mESC DMSO control expt6 rep2

description: Library name: RNAseq_DMSO_expt6_rep2


title: Healthy donor  HD_01, CD8+ T cell sorted from bone marrow, bulk-ATAC-seq

description: Library name: CD8ATAC_HD_01


title: testis, ICR, RNA-seq, rep11

description:
Library name: sample11
piRNAcluster_normCounts_ICR_RNAseq.tsv

value: ICR


title: Patient MDS_12, CD8+ T cell sorted from bone marrow, bulk-ATAC-seq

description: Library name: CD8ATAC_MDS_12

value: Responder


title: RNA-seq mESC DMSO control expt6 rep1

description: Library name: RNAseq_DMSO_expt6_rep1


title: testis, ICR, RNA-seq, rep10

description:
Library name: sample10
piRNAcluster_normCounts_ICR_RNAseq.tsv


title: ATAC-seq mESC after second 24h recovery rep2

description:
Library name: ATAC_reREC_rep2
ATAC_re24hREC_merged_calibrated.bw

data_processing:
Data were mapped using bowtie2 against mm10 and hg19 and duplicates reads were discarded. Unique mouse and human reads were discarded and a donwsampling factor for spike-in normalisation was calulated as in Fursova et al. (2019) and bigwigs were produced directly from deduplicated bam files. For detailed protocol see the Method section of the adjoining paper.
Assembly: mm10
Supplementary files format and content: Processed files are given as a spike-in normalised mouse bigwig file of the two merged replicates. Peak files correspond to individual replicates.

extract_protocol:
90.000 live mESCs and 10.000 like HEK cells were used for each condition accotding to Active Motif ATAC-seq kit manual.
Libraries were prepared according to Active Motif ATAC-seq kit manual.

treatment_protocol: DMSO: 0.01% DMSO for 4 hours; TSA: 100 ng/ml TSA for 4 hours; REC: 4 hours TSA (100 ng/ml) followed by 24 hours of recovery; reTSA: 4 hours TSA (100 ng/ml) re-treatment; following 24 hours of recovery; reREC: 24 hours of recovery following the second round of TSA treatment.

value: 24 h recovery following a second TSA pulse


title: lung, control, S1_GEX

description:
Library name: Sample_Set_001_GEX
10X Genomics

value: Whole Lung

value: WT and OsmtmWtsi/Osmtm1aWtsi (KO)

value: Female


title: Patient MDS_11, CD8+ T cell sorted from bone marrow, bulk-ATAC-seq

description: Library name: CD8ATAC_MDS_11

value: Bone marrow

value: high-risk myelodysplastic syndrome

value: Non-responder


title: testis, ICR, RNA-seq, rep9

description:
Library name: sample09
piRNAcluster_normCounts_ICR_RNAseq.tsv


title: Healthy donor  HD_03, CD8+ T cell sorted from bone marrow, bulk-ATAC-seq

description: Library name: CD8ATAC_HD_03


title: HS11286, ΔcpxR, biol rep3

city: Shanghai

first: Runze

last: Wang

address: School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, No.800, Dongchuan Road, Minhang District, Shanghai, People's Republic of China

institute: State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University

description:
Library name: HS11286, ΔcpxR, biol rep3
cpxR_3

data_processing:
Bowtie2 was used to build an index based on the HS11286 genome, followed by the alignment of sequencing reads to the reference genome. Read counts per gene were generated with featureCounts (v2.0.3) by utilizing the genome's annotated file. Differential expression analysis was performed using DESeq2 (v1.40.2) in R. Genes with a Benjamini-Hochberg adjusted p-value < 0.05 and absolute log2FoldChange > 1 were deemed significant.
Read counts per gene were generated with featureCounts (v2.0.3) by utilizing the genome's annotated file.
Genes with a Benjamini-Hochberg adjusted p-value < 0.05 and absolute log2FoldChange > 1 were deemed significant.
Assembly: NC_016845
Supplementary files format and content: A tab-delimited file containing FPKM values for all samples. Each column represents one sample and each row represents one gene.

organism: Klebsiella pneumoniae

source_name: bacteria

growth_protocol: The test bacterial strain was inoculated into LB liquid medium and cultured until the stationary phase. A 1:100 transfer was made into LB liquid medium. After culturing to the logarithmic phase, the bacterial cells were collected by centrifugation and washed three times with PBS. Each group was set up in triplicate. All samples are cultured at 37℃, 220 rpm.

extract_protocol:
Total bacterial RNA was extracted using the Trizol method, with RNA quality and integrity assessed by agarose gel electrophoresis, NanoDrop spectrophotometer, and Agilent 2100 Bioanalyzer. Ribosomal RNA (rRNA) was removed from total RNA using the Ribo-Zero rRNA Removal Kit (Illumina).
First-strand cDNA was synthesized using random oligonucleotides and SuperScript III, followed by second-strand cDNA synthesis employing DNA Polymerase I and RNase H, where dUTP replaced dTTP. Library quality was verified using Agilent 2100, DNA concentration measured with PicoGreen, effective concentration confirmed by qPCR.

tag: strain

tag: growth phase

value: logarithmic phase

value: bacteria

value: cpxR deletion


title: HS11286, ΔcpxR, biol rep2

description:
Library name: HS11286, ΔcpxR, biol rep2
cpxR_2


title: HS11286, ΔcpxR, biol rep1

description:
Library name: HS11286, ΔcpxR, biol rep1
cpxR_1


title: testis, ICR, RNA-seq, rep7

description:
Library name: sample07
piRNAcluster_normCounts_ICR_RNAseq.tsv

value: testis


title: HS11286, WT, biol rep3

description:
Library name: HS11286, WT, biol rep3
WT_3

value: wild-type


title: Patient MDS_06, CD8+ T cell sorted from bone marrow, bulk-ATAC-seq

description: Library name: CD8ATAC_MDS_06

value: CD8+ sorted cell (FACS)


title: ATAC-seq mESC after second TSA pulse rep1

description:
Library name: ATAC_reTSA_rep1
ATAC_reTSA_merged_calibrated.bw

value: mESC wt

value: Wild type

value: 24h recovery followed by 100 ng/ml TSA


title: testis, ICR, RNA-seq, rep8

description:
Library name: sample08
piRNAcluster_normCounts_ICR_RNAseq.tsv

value: ICR


title: ATAC-seq mESC after second 24h recovery rep1

description:
Library name: ATAC_reREC_rep1
ATAC_re24hREC_merged_calibrated.bw

value: 24 h recovery following a second TSA pulse


title: Patient MDS_05, CD8+ T cell sorted from bone marrow, bulk-ATAC-seq

description: Library name: CD8ATAC_MDS_05


title: ATAC-seq mESC after second TSA pulse rep2

description:
Library name: ATAC_reTSA_rep2
ATAC_reTSA_merged_calibrated.bw


title: Patient MDS_04, CD8+ T cell sorted from bone marrow, bulk-ATAC-seq

description: Library name: CD8ATAC_MDS_04

value: Responder


title: Patient MDS_03, CD8+ T cell sorted from bone marrow, bulk-ATAC-seq

description: Library name: CD8ATAC_MDS_03


title: ROMI_mC_rep2

description:
Library name: ROMI_mC_rep2
romidepsin treated WT ESC
mRomi_mm10.mcool

data_processing:
Micro-C data was processed using the HiC-Pro v3.1.0 pipeline (https://github.com/nservant/HiC-Pro). In brief, raw sequencing reads were mapped independently to the reference genome using Bowtie2 in local alignment mode and non-informative reads were removed using the default options. See adjoning paper for the detailed pipeline.
Assembly: mm10
Supplementary files format and content: Each processed .mcool file represent pairwise information of the observed genome contacts (produced by the cooler package https://cooler.readthedocs.io/en/latest/index.html). Loop files represent coodrinates of focal contacts idenitied by mustache v1.0 (https://github.com/ay-lab/mustache) with default parameters on ICE-balanced .mcool maps at 1 kb and 4 kb resolutions. Redundant loops between different resolutions were filtered in 20 kb windows, and in case of overlap loop coordinates were retained at the finer resolution.

extract_protocol:
Cell lysis, MNase digestion, ligation, biotin labeling and pulldown were preformed according to Dovetail Micro-C kit User Guide version 1.0.
DMSO, TSA, Romi and REC libraries were prepared as in the Dovetail Micro-C kit User Guide version 1.0, PCGF2 libraries were prepared with version 2.0; except that Dovetail reagents were replaced by reagents from the NEBNext Ultra II DNA Library Prep Kit for Illumina kit. For detailed protocol see adjoning paper.

treatment_protocol: DMSO: 0.01% DMSO for 4 hours; TSA: 100 ng/ml TSA for 4 hours; REC: 4 hours TSA (100 ng/ml) followed by 24 hours of recovery; Romi: 4 hours of0.03 nM romidepsin; PCGF2 UT DMSO: PCGF4-/- PCGF2fl/fl +0.01% DMSO; PCGF2 OHT DMSO: PCGF4-/- PCGF2fl/fl 72h 800 nM OHT +0.01% DMSO; PCGF2 OHT TSA: PCGF4-/- PCGF2fl/fl 72h 800 nM OHT +4h 100 ng/ml TSA; PCGF2 OHT REC: PCGF4-/- PCGF2fl/fl 96h 800 nM OHT and 24h recovery from TSA treatment;

value: 0.03 nM romidepsin


title: HS11286, WT, biol rep2

description:
Library name: HS11286, WT, biol rep2
WT_2


title: HS11286, WT, biol rep1

description:
Library name: HS11286, WT, biol rep1
WT_1


title: ROMI_mC_rep1

description:
Library name: ROMI_mC_rep1
romidepsin treated WT ESC
mRomi_mm10.mcool


title: Patient MDS_02, CD8+ T cell sorted from bone marrow, bulk-ATAC-seq

description: Library name: CD8ATAC_MDS_02


title: testis, ICR, RNA-seq, rep4

description:
Library name: sample04
piRNAcluster_normCounts_ICR_RNAseq.tsv


title: Healthy donor HD_03, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_HD_03

value: Whole bone marrow


title: PCGF2_OHT_REC_mC_rep1

description:
Library name: PCGF2_OHT_REC_mC_rep1
PCGF2 +96h OHT TSA-treated followed by 24 hours of recovery

value: mESC

value: PCGF4-/- PCGF2fl/fl

value: 100 ng/mlTSA followed by 24 hours of recovery +96h 800 nM OHT


title: Set 2 WT F

city: Newark

first: Tania

last: Wong Fok Lung

state: New Jersey

address: 205 South Orange Avenue

department: Department of Microbiology, Biochemistry & Molecular Genetics

institute: Center for Immunity and Inflammation, Rutgers NJ Medical School

data_processing:
Alignment using star
reads quantification using featurecounts
differential gene expression analysis using DEseq2 in R:Bioconductor
Assembly: Staphylococcus aureus
Supplementary files format and content: tab-delimited files with raw counts for each sample

organism: Staphylococcus aureus

growth_protocol: Bacteria were grown in Luria Bertani (LB) broth with and without fumarate to late exponential phase.

extract_protocol:
Bacterial pellets were incubated in lysis buffer (50 μM Tris-EDTA pH 7.5, 8 U ml−1mutanolysin (Sigma-Aldrich), 0.018 mg ml−1lysostaphin (Sigma-Aldrich), 0.05 mg ml−1lysozyme (Sigma-Aldrich)) at 37 °C for 45 min and TRK lysis buffer (Omega Bio-tek) was added. After 10 min at room temperature, 70% ethanol was added, and samples were transferred to E.Z.N.A. RNA isolation columns (Omega Bio-tek). RNA was isolated following the manufacturer’s instructions and treated with DNase using the DNA-free DNA removal kit (Invitrogen). The RNA was precipitated with 0.1 volume 3 M sodium acetate (Thermo Fisher, S209) and 3 volumes of 100% ethanol, recovered by centrifugation, and washed with ice cold 70% ethanol.
A ribosomal RNA-depleted cDNA library was prepared according to the manufacturer’s instructions using the Universal Prokaryotic RNA-Seq Prokaryotic AnyDeplete kit (NuGEN, 0363-32) and sequenced with Illumina HiSeq.

treatment_protocol: LB with and without 100 mM sodium fumarate, pH7 (Sigma, F1506).

value: WT USA300 LAC

value: Grown in Luria Bertani broth supplemented with 100 mM fumarate (pH7)


title: testis, ICR, RNA-seq, rep3

description:
Library name: sample03
piRNAcluster_normCounts_ICR_RNAseq.tsv


title: Set 1 WT F

value: bacteria


title: PCGF2_OHT_TSA_mC_rep1

description:
Library name: PCGF2_OHT_TSA_mC_rep1
PCGF2 +72h OHT TSA-treated

value: 100 ng/ml TSA +72h 800 nM OHT


title: testis, ICR, RNA-seq, rep2

description:
Library name: sample02
piRNAcluster_normCounts_ICR_RNAseq.tsv

value: testis


title: Set 2 WT

value: Grown in Luria Bertani broth


title: PCGF2_OHT_DMSO_mC_rep1

description:
Library name: PCGF2_OHT_DMSO_mC_rep1
PCGF2 +72h OHT DMSO control

value: DMSO +72h 800 nM OHT


title: Healthy donor HD_01, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_HD_01

value: Bone marrow


title: Set 1 WT


title: PCGF2_UT_DMSO_mC_rep1

description:
Library name: PCGF2_UT_DMSO_mC_rep1
PCGF2 untreated DMSO control


title: KO8_3

status: Public on Jul 09 2025

city: Shenzhen

first: Jin-Tang

state: Guangdong

address: 1088 Xueyuan Blvd.

institute: Southern University of Science  and Technology

description:
Library name: sample6
Column name in TPMs_all_Samples.txt: KO8_3

data_processing:
Illumina Casava1.7 software used for basecalling.
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively. Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI, which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12). Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited  text  file  includes  TPMs  for  each  Sample

extract_protocol:
Remove the supernatant and wash with PBS, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 150 bases reads were generated on MGI2000 platform (BGI-Shenzhen, China).

value: prostate cancer cells

value: ZFHX3 knockout


title: Wt_3

description:
Library name: sample3
Column name in TPMs_all_Samples.txt: Wt_3

value: Wt


title: KO8_2

description:
Library name: sample5
Column name in TPMs_all_Samples.txt: KO8_2


title: Wt_1

description:
Library name: sample1
Column name in TPMs_all_Samples.txt: Wt_1


title: testis, ICR, RNA-seq, rep6

description:
Library name: sample06
piRNAcluster_normCounts_ICR_RNAseq.tsv

value: ICR


title: Wt_2

description:
Library name: sample2
Column name in TPMs_all_Samples.txt: Wt_2


title: testis, ICR, RNA-seq, rep5

description:
Library name: sample05
piRNAcluster_normCounts_ICR_RNAseq.tsv


title: LCN2 KO-IMQ 3

city: Xi'an

first: Kaixuan

last: Ren

address: Huangcheng West Road

institute: Xi'an jiaotong University

description:
L1EHB2701291--KO_IMQ_3.R
raw_counts.txt

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using Hisat
Reads Per kilobase of exon per Megabase of library size (TPM) were calculated using a protocol from the standardized method developed by Wagner et al. (2012).
Assembly: mm8
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

source_name: skin

growth_protocol: All experimental animals were maintained in a specific pathogen-free (SPF) environment.

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using ribosome minus RNAseq protocols

treatment_protocol: To induce a psoriasis-like disease model, 5% imiquimod (IMQ) cream (Sichuan Mingxin Pharmaceuticals Co., China) or vehicle control was applied daily to the shaved back for a consecutive period of six days.

value: skin

value: LCN2 knockdown

value: IMQ