title: Tmem175-/- B16-F10 lung metastatic model 3

city: Chengdu

last: Zhang

address: No. 17, Block 3, Southern Renmin Road

institute: West China Hospital, Sichuan University

description: Library name: KO3

data_processing:
The demultiplexing, barcoded processing, gene counting was made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mouse GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

extract_protocol:
Lungs were digested to create single cell suspension. Then the rate of live cells were calculated. Novogene then complete the following extraction steps.
Single-cell RNA sequencing (scRNA-seq) libraries were constructed using the 10x Chromium Single Cell 5’ platform (10X Genomics, Pleasanton, CA, USA) according to the manufacturer’s protocol. Briefly, single-cell suspensions were loaded onto a Chro-mium microfluidic chip to generate single-cell Gel Beads in Emulsion (GEMs). The scRNA-seq libraries were then prepared using the Chromium Single Cell 5’ Reagent Kit v2(10X Genomics, Pleasanton, CA, USA). Library quality was assessed using the Ag-ilent 2100 Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA), and se-quencing was performed on the Illumina NovaSeq X Plus platform (Illumina, San Di-ego, CA, USA) with a sequencing depth of at least 50,000 reads per cell.

value: lung

tag: cell line_injected

value: primary cells

tag: mouse genotype


title: Tmem175-/- B16-F10 lung metastatic model 2

status: Public on Jan 19 2026

type: SRA

first: Ziqi

state: Sichuan

department: National Clinical Research Center for Geriatrics,

country: China

description: Library name: KO2

library_source: transcriptomic single cell

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type


title: TG_MOC1_female_rep3

city: Kingston

first: Sebastien

last: Talbot

state: ON

address: 18 Stuart st

department: DBMS

country: Canada

institute: Queen's University

description: Library name: TG_MOC1_female3

library_source: transcriptomic

data_processing:
Sequences   were trimmed using Trimmomatic v0.35. Filtered reads were aligned to the mouse reference genome GRCm38 (mm10) using STAR v2.7.1a with strand-specific parameters. Gene-level expression quantification was performed using STAR and RSEM. Downstream analyses and visualization were performed in RStudio.
Assembly: GRCm38 (mm10)
Supplementary files format and content: CSV files containing raw readcounts from each sample

source_name: Trigeminal ganglion neuron

extract_protocol:
bilateral TGs were harvested, dissociated, and cell viability was assessed by microscopy. DiI⁺ neurons were sorted directly into 500 µL TRIzol reagent and stored at −80 °C until RNA extraction using TRIzol protocol.
RNA extraction, library construction and sequencing were performed at the IRIC Genomics Platform (Université de Montréal). RNA integrity was confirmed with an Agilent Bioanalyzer. Poly(A)+ RNA was enriched from total RNA and sequencing libraries were prepared using the KAPA RNA HyperPrep Kit with Poly(A) selection following the manufacturer’s instructions. Libraries were sequenced on an Illumina NextSeq 500 platform with single-end reads generated over 75 sequencing cycles (maximum read length 1×85 nt).

value: Trigeminal ganglion neuron


title: TG_MOC1_male_rep1

description: Library name: TG_MOC1_male1


title: Cy4C_13G (MS251_201)

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: Library name: Sample56

data_processing:
The genome sequence and transcript annotation (MacFas5.0) were downloaded from the NCBI ftp site.
SC3-seq read only the 3’ end of the transcripts, so that the expression levels were calculated as genes (Entrez genes) but not mRNAs.
Read trimming, mapping, and estimation of expression levels were performed using cutadapt (v1.18), tophat2 (v2.1.1), and HTseq (v0.11.0), as described previously (Mizuta et al., 2022; Nakamura et al., 2016).
Expression levels in reads per million mapped reads (RPM) were used for the analysis.
Assembly: MacFas5.0
Supplementary files format and content: tab-delimited text files include RPM values for each Sample

molecule: polyA RNA

organism: Macaca fascicularis

source_name: Ovary

growth_protocol: For in vitro growth culture (IVG), secondary or preantral follicles were mechanically isolated from ovaries in handling medium under a stereomicroscope, and using a glass capillary, transferred onto a Millicell membrane insert (Merck, PICM03050) in a 35-mm dish with 2 ml follicle culture medium outside of the membrane and 1 ml on the membrane.  Follicles were cultured in aMEM (GIBCO, 12571063) supplemented with 6% Quinn’s Advantage Serum Protein Substitute (CooperSurgical, ART-3011) or 5% FBS, 0.1 U/ml human urinary follicle stimulating hormone (uFSH; ASKA, 123-16188-6), 2 mM L-glutamine (GIBCO, 25030081), 150 mM Ascorbic Acid (Sigma-Aldrich, A4403), 1x Insulin-Transferrin-Selenium (GIBCO, 41400045), 1x MEM Non-Essential Amino Acids Solution (GIBCO, 11140050), 1 mM Sodium Pyruvate (GIBCO, 11360070), 0.5 mg/ml bovine fetuin (Sigma-Aldrich, F2379), 100 U/mL penicillin, and 0.1 mg/mL streptomycin (GIBCO, 15070063), and 2% polyvinylpyrrolidone (Wako, 162-17042Follicles were cultured at 37℃, 5% CO2 and 95% air in an incubator, and half of the volume of medium were changed every two days under stereomicroscope.  The collagenase treatment was performed on day3-4 to remove the tissue outside the basal lamina for improving the survival of the follicles. 　For collagenase treatment, follicles were incubated in collagenase solution [L-15 (Sigma-Aldrich, L5520) containing 30% FBS, 0.1% Collagenase I (Worthington Biochemicals, LS004294), 100 U/mL penicillin, and 0.1 mg/mL streptomycin]. 　The incubation was terminated by wash with L-15 handling medium [L-15 containing 5% FBS, 100 U/mL penicillin, and 0.1 mg/mL streptomycin], and follicles were transferred into follicle isolation medium [L-15 containing 0.4% polyvinylpyrrolidone, 100 U/mL penicillin, and 0.1 mg/mL streptomycin] for mechanical trimming of tissue outside the basal lamina with 27G needle or fine tungsten needle (FST, 10130-05).

extract_protocol:
Collected cy ovaries, COCs and cultured follicles were placed in handling medium [DMEM/F-12 with HEPES (GIBCO, 11330057) containing 10% FBS (GIBCO, 10437028), 100 U/mL penicillin, and 0.1 mg/mL streptomycin (GIBCO, 15070063)].  For isolating small follicles (primordial ~ preantral follicles) from cy ovaries, the ovarian cortical pieces were cut into 1 mm pieces after removal of medullary tissues. Then the tissue pieces were digested by a mixed digestion medium [aMEM (GIBCO, 12571063), 0.04 mg/ml Liberase DH (Roche, 5401054001), 10 IU/ml DNase I (Sigma-Aldrich, DN25)] for 20-75 min on a shaker at 37℃.  The incubation was terminated by wash with handling medium, and small follicles were manually collected.  Isolated follicles and COCs were photographed, followed by the dissociation process of oocytes and Granulosa cell.  Follicles and COCs were individually placed in 30 ml Accutase (Sigma-Aldrich, A6964) drops on a dish warmed by 37℃ plate, and oocytes and Granulosa cell were dissociated by pipetting up and down in a pulled fine glass capillary (Sutter Instrument, B100-75-10) with 30-120 mm in diameter, depending on the oocyte size.  For each follicle, about 15 Granulosa cell in the immediate vicinity of the oocyte were collected because of low abundancy of mRNA in these cells.  For primordial follicles, 15 Granulosa cell may not be obtained from a single follicle, in which case two or three primordial follicle-derived Granulosa cell were added together to make one sample.  At last, zona pellucida of GV/MII oocytes were removed by treating with acidic Tyrode's solution (Sigma-Aldrich, T1788) to obtain naked oocytes without contamination of Granulosa cell.  The removal of surrounding Granulosa cell from oocytes was confirmed under stereomicroscope (Leica, S8 APO) and inverted microscope (Olympus, IX71).  Dissociated oocytes and Granulosa cell from follicle grown in vivo and in vitro were manually picked up using glass capillaries under a stereomicroscope, and were used for SC3-seq.
The cDNA synthesis and amplification were performed as described previously (Kurimoto et al., 2006; Kurimoto et al., 2007; Nakamura et al., 2016; Nakamura et al., 2015). The quality of the amplified cDNA was measured by a SYBR real-time PCR method (CFX384 Touch Real-Time PCR Detection System, BIO-RAD; Power SYBR Green PCR Master Mix, Applied Biosystems, 4367659) targeting the PPIA, GAPDH, DPPA3, DDX4, FOXL2, GJA1, and IGFBP7 genes. The SC3-seq libraries were constructed as described previously (Ishikura et al., 2021; Mizuta et al., 2022; Nakamura et al., 2016; Nakamura et al., 2015; Okamoto et al., 2021), and the sequencing was performed on the Illumina NextSeq 500/550 plat-form with a NextSeq 500/550 high output kit v.2 (75 cycles) (FC-404-2005; Illumina).

treatment_protocol: For collecting ovary samples from cynomolgus monkeys (cy), bilateral salpingo-oophorectomies were performed under isoflurane and ketamine-based general anesthesia.  To minimize the number of cy used, only those scheduled for hysterectomy in other experiments and those euthanized for other reasons were subjected to the procedure.  For collecting the cy mature COCs, ovarian stimulation and oocyte collection were carried out as previously described (Mizuta et al., 2022; Yamasaki et al., 2011).

value: Ovary

value: Granulosa cell

tag: genotype

value: wildtype

tag: group

value: Cy4, age6, cryo-thawed ovary, 10-20 granulosa cells, secondary follicle, cryo-thawed adult cynomolgus ovary (in pregnant E15)


title: TG_MOC1_female_rep2

description: Library name: TG_MOC1_female2


title: Tmem175-/- B16-F10 lung metastatic model 1

description: Library name: KO1


title: 0041-R2

type: genomic

city: Rotterdam

first: Youri

last: Hoogstrate

address: Wytemaweg 80

department: Neurology

country: Netherlands

institute: Erasmus MC

description: tumor genomic DNA from patient 0041: Oligodendroglioma, WHO grade 2, resection #2

hyb_protocol: Bisulphite converted DNA was amplified, fragmented to human Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol

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

data_processing:
Minfi and R 4.4
GLASS-OD_processed_M-values.txt processed value definition: M-value

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: cell-free DNA was extracted from glial tumor tissue using QIAamp DNA FFPE Tissue Kit according to standard instructions

tag: Sex

value: female

value: Oligodendroglioma

tag: grade

value: WHO grade 2

tag: resection

value: resection #2

tag: set

value: GLASS-OD


title: 0040-R2

description: tumor genomic DNA from patient 0040: Oligodendroglioma, WHO grade 3, resection #2

value: WHO grade 3


title: 0039-R1

description: tumor genomic DNA from patient 0039: Oligodendroglioma, WHO grade 2, resection #1

value: male

value: resection #1


title: TG_MOC1_female_rep1

description: Library name: TG_MOC1_female1


title: 0038-R1

description: tumor genomic DNA from patient 0038: Oligodendroglioma, WHO grade 2, resection #1


title: Cy4C_12G (MS252_210)

description: Library name: Sample54

value: Cy4, age6, cryo-thawed ovary, granulosa cells were gained from a pair of oocyte, 10-20 granulosa cells, primordial follicle, cryo-thawed adult cynomolgus ovary (in pregnant E15)


title: 0038-R2

description: tumor genomic DNA from patient 0038: Oligodendroglioma, WHO grade 2, resection #2


title: Cy4C_12Ob (MS205_038)

description: Library name: Sample53

value: Oocyte

value: Cy4, age6, cryo-thawed ovary, oocyte, primordial follicle, cryo-thawed adult cynomolgus ovary (in pregnant E15)


title: BMDC_FD+LPS_2

city: München

first: Thomas

middle: M

last: Conlon

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Zentrum München

description:
Library name: 25_0FBT_01X4Helmholtz_25-Cow-2-dose-LPS-2-Back-up_ATAC_mm10_i40-29
25_25-Cow-2-dose-LPS-2-Back-up_ATAC_mm10

library_source: genomic

data_processing:
The paired-end 42 bp sequencing reads (PE42) were mapped to the genome using the BWA algorithm with default settings. Only reads that pass Illumina’s purity filter, align with no more than two mismatches, and map uniquely to the genome were used in the subsequent analysis. In addition, duplicate reads (“PCR duplicates”) are removed. Alignments were extended in silico at their 3′-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. Genomic regions with high levels of transposition/tagging events were determined using the MACS3 narrow peak-calling algorithm (53).  Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed. Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations. For differential analysis, reads were counted in all merged peak regions (using Subread), and the replicates for each condition were compared using DESeq2.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

source_name: Bone marrow

growth_protocol: BMDM: Bone marrow was isolated from C57BL/6J mice and cultured at a density of 3 x 10^6 bone marrow cells in 3ml of complete medium (RPMI 1640, 10% heat-inactivated fetal calf serum, penicillin, streptomycin, and 2-mercaptoethanol) supplemented with 20 ng/ml M-CSF (ImmunoTools #12343115) in 6 well plates. On day 3 and 6, half of the medium was removed and replaced with fresh medium containing 40 ng/ml M-CSF. On days 7, total medium was changed and replaced with medium containing 10ng/m M-CSF. Macrophages were used for experiments from day 8 onwards. BMDM differentiation efficacy was assessed by flow cytometry staining for CD11b and F4/80, reaching 90-95% purity. BMDC: Bone marrow was isolated from C57BL/6J mice and cultured at a density of 4 x 10^6 bone marrow cells per petri dish in 10 ml of complete medium (RPMI 1640, 10% heat-inactivated fetal calf serum, penicillin, streptomycin, and 2-mercaptoethanol) supplemented with 20 ng/ml GM-CSF (ImmunoTools #12343127). On day 3, 10 ml of fresh medium containing 20 ng/ml GM-CSF was added to each petri dish. On day 6, half of the medium was removed and replaced with fresh medium containing 20 ng/ml GM-CSF. On days 8 and 10, half of the medium was again removed and replaced with fresh medium containing 10 ng/ml GM-CSF. On day 12, non-adherent cells and loosely adherent cells were harvested by gentle washing with PBS and pooled cells are ready for further experiments

extract_protocol:
About 100,000 BMDM and BMDCs  were sent to Active Motif (Carlsbad, CA) for ATAC-Seq analysis, after cryopreserving the cells as described in the ATAC-Seq sample preparation guidelines supplied by the company
Cell nuclei were used for tagmentation with Tn5 and libraries were prepared using Active Motif’s kit (ActiveMotif, Cat No. 53150). Barcoded libraries were sequenced 42 bp paired-end on NovaSeq6000 (Illumina, San Diego, CA, USA).

treatment_protocol: BMDMs and BMDCs were differentiated and treated with 100 µg/ml FD or PBS twice over a 24-hour period. Following treatment, BMDMs were incubated with 10 ng/ml LPS for 6 hours and cryopreserved.

value: Bone marrow

value: Bone-marrow derived dendritic cell

tag: strain

tag: age

value: Female

tag: treatment

value: FD+LPS


title: 0040-R1

description: tumor genomic DNA from patient 0040: Oligodendroglioma, WHO grade 2, resection #1


title: WT B16-F10 lung metastatic model 3

description: Library name: WT3

value: lung

value: primary cells

value: WT


title: Cy4C_13O (MS205_040)

description: Library name: Sample55

value: Ovary

value: wildtype

value: Cy4, age6, cryo-thawed ovary, oocyte, secondary follicle, cryo-thawed adult cynomolgus ovary (in pregnant E15)


title: WT B16-F10 lung metastatic model 1

description: Library name: WT1


title: aal_D7

city: Wuhan

first: Han

last: Xia

state: Hubei

department: Key Laboratory of pathogenic Viruses and Biosafety

institute: Wuhan Institute of Virology, CAS

description: Library name: sample2

data_processing:
Raw reads were qualified, demultiplexed, mapped to the reference library of midgut cells of mosquitoes,  barcode counting, gene counting and data aggregation using with celescope
Assembly: AaegL5.0, AalbF5, TS_CPP_V2
Supplementary files format and content: Tab-seperated value files and matrix files

organism: Aedes albopictus

source_name: midgut

extract_protocol:
For each sample, an appropriate number of midguts were dissected from female mosquitoes, then washed and temporarily stored in Schneider’s Drosophila Medium (SDM) within a microcentrifuge tube on ice. After dissection, the medium was discarded, and the midguts were finely minced and then 300 μl of dissociation buffer was added, followed by further mincing. The tissue fragments were resuspended in 700 μl of dissociation buffer and then incubated in a 28 °C water bath for 15-25 min. The suspension was mixed and the cell concentration, viability and aggregation were measured by staining with 0.4% trypan blue every five minutes. Once the quality control  requirements were met, the suspension was loaded into a 50 ml centrifuge tube equipped with a pre-wetted 40 μm filter to remove larger cell debris, and then washed with 1× PBS until the final volume reached 15 ml. The resulting filter was centrifuged at 350× g, 4 °C for 5 min. A viable cell band could be found near or at the bottom of the tube and 100-200 μl of the supernatant was retained to avoid disturbing the pellet. The cell pellet was suspended, followed by a second counting with 0.4% trypan blue. Cell suspension samples with viability ≥ 80% and were used for subsequent scRNA-seq.
According to the manufacturer’s guidelines, the single-cell suspension was adjusted to appropriate concentration prior to loading onto a microfluidic microwell SCOPE-chip. The cDNA synthesis of captured cells and sequencing library construction were performed with GEXSCOPE Single Cell RNA Library Kit.

value: midgut

value: Jiangsu

value: female

tag: developmental stage

value: adult


title: 0044-R2

description: tumor genomic DNA from patient 0044: Oligodendroglioma, WHO grade 3, resection #2

value: Oligodendroglioma

value: WHO grade 3

value: resection #2

value: GLASS-OD


title: Cy4C_11Ob (MS205_035)

description: Library name: Sample50

value: Oocyte

value: Cy4, age6, cryo-thawed ovary, oocyte, primordial follicle, cryo-thawed adult cynomolgus ovary (in pregnant E15)


title: 0036-R2

description: tumor genomic DNA from patient 0036: Oligodendroglioma, WHO grade 2, resection #2

value: WHO grade 2


title: BMDC_FD_1

description:
Library name: 22_0FBR_01X4Helmholtz_22-Cow-2-dose-1-Back-up_ATAC_mm10_i38-27
22_22-Cow-2-dose-1-Back-up_ATAC_mm10

value: Bone marrow

value: Bone-marrow derived dendritic cell

value: Female

value: FD


title: 0036-R1

description: tumor genomic DNA from patient 0036: Oligodendroglioma, WHO grade 2, resection #1

value: resection #1


title: Cy4C_12Oa (MS205_037)

description: Library name: Sample52

value: Ovary

value: wildtype


title: HK-2 cells, siNAT10, Cisplatin, cell1

first: Yuting

last: Zhu

address: 1277 Jiefang Avenue

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: Library name: sample 4

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36).
Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing.
The de-duplicated consensus sequences were used for standard RNA-seq analysis. They were mapped to the reference genome of Homo sapiens from GRCh38_release110 using STAR software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). A p-value cutoff of 0.05 and Fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Assembly: GRCh38
Supplementary files format and content: raw gene counts for all samples.

extract_protocol:
Total RNA was extracted with RNAiso Plus reagent (Takara).2 μg total RNAs were used for stranded RNA sequencing library preparation.
RNA sequencing library was prepared using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

tag: cell line

value: human proximal tubular cells

value: Cisplatin and NAT10 siRNA


title: HK-2 cells, siNAT10, Cisplatin, cell2

description: Library name: sample 5


title: BMDC_LPS_1

description:
Library name: 16_0FBL_01X4Helmholtz_LPS-1-Back-up_ATAC_mm10_i32-21
16_LPS-1-Back-up_ATAC_mm10

value: LPS


title: HK-2 cells, siNC, Cisplatin, cell3

description: Library name: sample 3

value: Cisplatin and NC siRNA


title: 0035-R5

description: tumor genomic DNA from patient 0035: Oligodendroglioma, WHO grade 3, resection #5

value: male

value: Oligodendroglioma

value: WHO grade 3

value: resection #5


title: BMDC_Control_2

description:
Library name: 15_0FBK_01X4Helmholtz_CTRL-2-Back-up_ATAC_mm10_i31-20
15_CTRL-2-Back-up_ATAC_mm10

value: PBS


title: 0035-R4

description: tumor genomic DNA from patient 0035: Oligodendroglioma, WHO grade 3, resection #4

value: resection #4

value: GLASS-OD


title: Cy4C_11G (MS252_209)

description: Library name: Sample51

value: Granulosa cell

value: Cy4, age6, cryo-thawed ovary, granulosa cells were gained from a pair of oocyte, 10-20 granulosa cells, primordial follicle, cryo-thawed adult cynomolgus ovary (in pregnant E15)


title: BMDC_Control_1

description:
Library name: 14_0FBJ_01X4Helmholtz_CTRL-1-Back-up_ATAC_mm10_i30-19
14_CTRL-1-Back-up_ATAC_mm10

value: Bone marrow

value: Bone-marrow derived dendritic cell

value: Female


title: BMDC_LPS_2

description:
Library name: 17_0FBM_01X4Helmholtz_LPS-2-Back-up_ATAC_mm10_i33-22
17_LPS-2-Back-up_ATAC_mm10


title: Cy4C_10G (MS252_208)

description: Library name: Sample48

value: Ovary

value: wildtype


title: 0037-R1

description: tumor genomic DNA from patient 0037: Oligodendroglioma, WHO grade 2, resection #1

value: WHO grade 2

value: resection #1


title: Cy4C_11Oa (MS205_034)

description: Library name: Sample49

value: Oocyte

value: Cy4, age6, cryo-thawed ovary, oocyte, primordial follicle, cryo-thawed adult cynomolgus ovary (in pregnant E15)


title: BMDC_FD+LPS_1

description:
Library name: 24_0EQW_01X4Helmholtz_11-Cow-2-dose-LPS-1_ATAC_mm10_i45-44
24_11-Cow-2-dose-LPS-1_ATAC_mm10

value: FD+LPS


title: WT B16-F10 lung metastatic model 2

description: Library name: WT2

value: lung

value: primary cells

value: WT


title: 0035-R3

description: tumor genomic DNA from patient 0035: Oligodendroglioma, WHO grade 3, resection #3

value: male

value: Oligodendroglioma

value: WHO grade 3

value: resection #3


title: BMDC_FD_2

description:
Library name: 23_0EKZ_01X4Helmholtz_10-Cow-2-dose-2_ATAC_mm10_i41-21
23_10-Cow-2-dose-2_ATAC_mm10

value: Bone marrow

value: FD


title: BMDM_FD+LPS_1

description:
Library name: 12_0EWL_023MHelmholtz_Cow-2-Dose-LPS-1_ATAC_mm10_i33-40
12_Cow-2-Dose-LPS-1_ATAC_mm10

value: Bone-marrow derived macrophage

value: Female


title: 0035-R2

description: tumor genomic DNA from patient 0035: Oligodendroglioma, WHO grade 2, resection #2

value: resection #2

value: GLASS-OD


title: BMDM_FD+LPS_2

description:
Library name: 13_0EWM_023MHelmholtz_Cow-2-Dose-LPS-2_ATAC_mm10_i34-42
13_Cow-2-Dose-LPS-2_ATAC_mm10


title: Cy4C_10Ob (MS205_032)

description: Library name: Sample47

value: Ovary

value: wildtype


title: 0034-R1

description: tumor genomic DNA from patient 0034: Oligodendroglioma, WHO grade 3, resection #1

value: resection #1


title: 0037-R2

description: tumor genomic DNA from patient 0037: Oligodendroglioma, WHO grade 2, resection #2

value: WHO grade 2


title: HK-2 cells, siNC, Cisplatin, cell2

description: Library name: sample 2

value: human proximal tubular cells

value: Cisplatin and NC siRNA


title: HK-2 cells, siNC, Cisplatin, cell1

description: Library name: sample 1


title: Cy4C_10Oa (MS205_031)

description: Library name: Sample46

value: Oocyte

value: Cy4, age6, cryo-thawed ovary, oocyte, primordial follicle, cryo-thawed adult cynomolgus ovary (in pregnant E15)


title: Cy4C_08G (MS252_207)

description: Library name: Sample43

value: Granulosa cell

value: Cy4, age6, cryo-thawed ovary, granulosa cells were gained from a pair of oocyte, 10-20 granulosa cells, primordial follicle, cryo-thawed adult cynomolgus ovary (in pregnant E15)


title: 0033-R1

description: tumor genomic DNA from patient 0033: Oligodendroglioma, WHO grade 3, resection #1

value: female

value: Oligodendroglioma

value: WHO grade 3


title: Cy4C_09O (MS205_029)

description: Library name: Sample44


title: HK-2 cells, siNAT10, Cisplatin, cell3

description: Library name: sample 6

value: Cisplatin and NAT10 siRNA


title: Cy4C_09G (MS205_030)

description: Library name: Sample45


title: BMDM_FD_1

description:
Library name: 10_0EWJ_023MHelmholtz_Cow-2-Dose-1_ATAC_mm10_i31-38
10_Cow-2-Dose-1_ATAC_mm10

value: Bone marrow

value: Bone-marrow derived macrophage

value: Female

value: FD


title: 9904796106_R06C02

city: Sydney

first: Sarah

last: Williams

state: NSW

address: 384 Victoria St, Darlinghurst

country: Australia

institute: The Garvan Institute of Medical Research

description: Breast tumour tissue

hyb_protocol: Bisulfite converted DNA was amplified, fragmentsed and hybridised to the Illumina HumanMethylation 450K BeadChip following manufacturer's instructions

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: minfi package (v 1.48.) in the R environment (v 4.3.1)

label: Cy5 and Cy3

source_name: Breast

extract_protocol: DNA was extracted from FFPET with the Gentra Puregene Tissue Kit (Qiagen)

value: Breast

tag: tumour subtype

value: TNBC

tag: cohort

value: NBCF

tag: mortality

tag: follow up time (months)

tag: disease specific death


title: Cy4C_08Oa (MS205_026)

description: Library name: Sample41

tag: tissue

value: Ovary

tag: cell type

value: wildtype


title: 0033-R2

description: tumor genomic DNA from patient 0033: Oligodendroglioma, WHO grade 3, resection #2

value: resection #2

value: GLASS-OD


title: BMDM_LPS_1

description:
Library name: 04_0EWD_023MHelmholtz_LPS-1_ATAC_mm10_i24-31
04_LPS-1_ATAC_mm10

value: LPS


title: 0031-R2

description: tumor genomic DNA from patient 0031: Oligodendroglioma, WHO grade 3, resection #2


title: 0032-R1

description: tumor genomic DNA from patient 0032: Oligodendroglioma, WHO grade 3, resection #1

value: resection #1


title: BMDM_FD_2

description:
Library name: 11_0EWK_023MHelmholtz_Cow-2-Dose-2_ATAC_mm10_i32-39
11_Cow-2-Dose-2_ATAC_mm10


title: Cy4C_07G (MS252_205)

description: Library name: Sample40

value: Granulosa cell

tag: genotype

tag: group

value: Cy4, age6, cryo-thawed ovary, granulosa cells were gained from a pair of oocyte, 10-20 granulosa cells, primordial follicle, cryo-thawed adult cynomolgus ovary (in pregnant E15)


title: 0031-R1

description: tumor genomic DNA from patient 0031: Oligodendroglioma, WHO grade 2, resection #1

tag: Sex

value: female

value: Oligodendroglioma

tag: grade

value: WHO grade 2


title: Cy4C_07Ob (MS205_024)

description: Library name: Sample39

value: Oocyte

value: Cy4, age6, cryo-thawed ovary, oocyte, primordial follicle, cryo-thawed adult cynomolgus ovary (in pregnant E15)


title: 9904796106_R06C01

description: Breast tumour tissue

value: Female


title: Cy4C_08Ob (MS205_027)

description: Library name: Sample42


title: BMDM_Control_2

description:
Library name: 03_0EWC_023MHelmholtz_Control-2_ATAC_mm10_i23-30
03_Control-2_ATAC_mm10

value: Bone marrow

value: Bone-marrow derived macrophage

value: PBS


title: BMDM_Control_1

description:
Library name: 02_0EWB_023MHelmholtz_Control-1_ATAC_mm10_i22-29
02_Control-1_ATAC_mm10


title: Cy4C_06O (MS205_022)

description: Library name: Sample37

value: Ovary


title: 9904796106_R04C02

description: Breast tumour tissue

value: Breast

value: TNBC

value: NBCF


title: Cy4C_07Oa (MS205_023)

description: Library name: Sample38

value: wildtype


title: 0030-R2

description: tumor genomic DNA from patient 0030: Oligodendroglioma, WHO grade 2, resection #2

value: male

tag: resection

value: resection #2

tag: set

value: GLASS-OD


title: BMDM_LPS_2

description:
Library name: 05_0EWE_023MHelmholtz_LPS-2_ATAC_mm10_i25-32
05_LPS-2_ATAC_mm10

tag: strain

tag: age

value: LPS


title: 0029-R2

description: tumor genomic DNA from patient 0029: Oligodendroglioma, WHO grade 2, resection #2

value: Oligodendroglioma


title: Cy4C_05G (MS205_021)

description: Library name: Sample36

value: Granulosa cell

value: Cy4, age6, cryo-thawed ovary, granulosa cells were gained from a pair of oocyte, 10-20 granulosa cells, primordial follicle, cryo-thawed adult cynomolgus ovary (in pregnant E15)


title: 0029-R1

description: tumor genomic DNA from patient 0029: Oligodendroglioma, WHO grade 2, resection #1

value: WHO grade 2

value: resection #1


title: X0703_G09 (MS238_133)

description: Library name: Sample165

data_processing:
The genome sequence and transcript annotation (GRCm38.p6) were downloaded from the NCBI ftp site.
SC3-seq read only the 3’ end of the transcripts, so that the expression levels were calculated as genes (Entrez genes) but not mRNAs.
Read trimming, mapping, and estimation of expression levels were performed using cutadapt (v1.18), tophat2 (v2.1.1), and HTseq (v0.11.0), as described previously (Mizuta et al., 2022; Nakamura et al., 2016).
Expression levels in reads per million mapped reads (RPM) were used for the analysis.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include RPM values for each Sample

extract_protocol:
Collected mouse ovaries were placed in handling medium [DMEM/F-12 with HEPES (GIBCO, 11330057) containing 10% FBS (GIBCO, 10437028), 100 U/mL penicillin, and 0.1 mg/mL streptomycin (GIBCO, 15070063)].  For isolating small follicles (primordial ~ preantral follicles) from mouse ovaries, whole ovaries were cut into 1 mm pieces. Then the tissue pieces were digested by a mixed digestion medium [aMEM (GIBCO, 12571063), 0.04 mg/ml Liberase DH (Roche, 5401054001), 10 IU/ml DNase I (Sigma-Aldrich, DN25)] for 20-75 min on a shaker at 37℃.  The incubation was terminated by wash with handling medium, and small follicles were manually collected.  Isolated follicles and COCs were photographed, followed by the dissociation process of oocytes and Granulosa cell.  Follicles and COCs were individually placed in 30 ml Accutase (Sigma-Aldrich, A6964) drops on a dish warmed by 37℃ plate, and oocytes and Granulosa cell were dissociated by pipetting up and down in a pulled fine glass capillary (Sutter Instrument, B100-75-10) with 30-120 mm in diameter, depending on the oocyte size.  For each follicle, about 15 Granulosa cell in the immediate vicinity of the oocyte were collected because of low abundancy of mRNA in these cells.  For primordial follicles, 15 Granulosa cell may not be obtained from a single follicle, in which case two or three primordial follicle-derived Granulosa cell were added together to make one sample.  At last, zona pellucida of GV/MII oocytes were removed by treating with acidic Tyrode's solution (Sigma-Aldrich, T1788) to obtain naked oocytes without contamination of Granulosa cell.  The removal of surrounding Granulosa cell from oocytes was confirmed under stereomicroscope (Leica, S8 APO) and inverted microscope (Olympus, IX71).  Dissociated oocytes and Granulosa cell from follicle grown in vivo and in vitro were manually picked up using glass capillaries under a stereomicroscope, and were used for SC3-seq.
The cDNA synthesis and amplification were performed as described previously (Kurimoto et al., 2006; Kurimoto et al., 2007; Nakamura et al., 2016; Nakamura et al., 2015). The quality of the amplified cDNA was measured by a SYBR real-time PCR method (CFX384 Touch Real-Time PCR Detection System, BIO-RAD; Power SYBR Green PCR Master Mix, Applied Biosystems, 4367659) targeting the Arbp, Ppia, Ddx4, Stella, Dazl, Foxl2, and Gja1 genes. The SC3-seq libraries were constructed as described previously (Ishikura et al., 2021; Mizuta et al., 2022; Nakamura et al., 2016; Nakamura et al., 2015; Okamoto et al., 2021), and the sequencing was performed on the Illumina NextSeq 500/550 plat-form with a NextSeq 500/550 high output kit v.2 (75 cycles) (FC-404-2005; Illumina).

treatment_protocol: To collect immature follicles from mice, ovaries were obtained from 6 or 7-week-old female B6D2F1.   To collect fully-grown antral follicles including germinal vesicle (GV)-stage oocytes, ovaries were obtained from 6-week-old female B6D2F1 mice 20 hours after 5 IU pregnant mare serum gonadotropin (PMSG; ASKA, SEROTROPIN®) injection.  To collect metaphase II (MII)-stage oocytes and adjacent GCs, 6-weeks-old female B6D2F1 mice were treated with 5 IU PMSG, 48 hour later with 5 IU human chorionic gonadotropin (hCG; ASKA, 123-00078-9), and salpingectomy was performed 15.5 hours after hCG injection.

value: 10-20 granulosa cells, GV, adult mouse ovary


title: X0703_G08 (MS238_131)

description: Library name: Sample163


title: 9904796106_R04C01

description: Breast tumour tissue

value: Female


title: 0028-R1

description: tumor genomic DNA from patient 0028: Oligodendroglioma, WHO grade 2, resection #1


title: Cy4C_05Ob (MS205_020)

description: Library name: Sample35

value: Oocyte

value: Cy4, age6, cryo-thawed ovary, oocyte, primordial follicle, cryo-thawed adult cynomolgus ovary (in pregnant E15)


title: X0703_G07 (MS238_129)

description: Library name: Sample161

value: Ovary


title: X0703_G04 (MS238_125)

description: Library name: Sample157


title: X0703_G06 (MS238_127)

description: Library name: Sample159


title: Cy4C_05Oa (MS205_019)

description: Library name: Sample34


title: 9904796106_R05C02

description: Breast tumour tissue

value: Breast

value: TNBC


title: 0025-R1

description: tumor genomic DNA from patient 0025: Oligodendroglioma, WHO grade 3, resection #1

value: female

value: WHO grade 3


title: Cy4C_04O (MS205_018)

description: Library name: Sample33

value: wildtype


title: 0024-R2

description: tumor genomic DNA from patient 0024: Oligodendroglioma, WHO grade 3, resection #2

value: male

value: resection #2

value: GLASS-OD


title: 9904796039_R02C02

description: Breast tumour tissue

value: NBCF


title: Cy4C_03G (MS205_017)

description: Library name: Sample32

value: Granulosa cell

value: Cy4, age6, cryo-thawed ovary, 10-20 granulosa cells, secondary follicle, cryo-thawed adult cynomolgus ovary (in pregnant E15)


title: 0111-R2

description: tumor genomic DNA from patient 0111: Oligodendroglioma, WHO grade 3, resection #2

value: Oligodendroglioma


title: X0703_G03 (MS238_123)

description: Library name: Sample155

value: 10-20 granulosa cells, GV, adult mouse ovary


title: Cy4C_03O (MS205_016)

description: Library name: Sample31

value: Cy4, age6, cryo-thawed ovary, oocyte, secondary follicle, cryo-thawed adult cynomolgus ovary (in pregnant E15)


title: X0703_G02 (MS238_121)

description: Library name: Sample153


title: 9829118164_R01C02

description: Breast tumour tissue

value: Female


title: Cy4C_02G (MS205_015)

description: Library name: Sample30


title: 0023-R2

description: tumor genomic DNA from patient 0023: Oligodendroglioma, WHO grade 3, resection #2


title: 9904796106_R01C01

description: Breast tumour tissue


title: 0023-R1

description: tumor genomic DNA from patient 0023: Oligodendroglioma, WHO grade 2, resection #1

value: WHO grade 2

value: resection #1


title: 0022-R2

description: tumor genomic DNA from patient 0022: Oligodendroglioma, WHO grade 2, resection #2


title: X0625_G10 (MS238_119)

description: Library name: Sample152

value: Ovary

value: 10-20 granulosa cells, M2, adult mouse ovary, BDF1(6w6d-7w1d)


title: Cy4C_02O (MS205_014)

description: Library name: Sample29

value: Oocyte


title: X0625_O10 (MS238_118)

description: Library name: Sample151

value: oocyte, M2, adult mouse, BDF1(6w6d-7w1d)


title: 9904796039_R06C01

description: Breast tumour tissue

value: Breast

value: TNBC


title: Cy4C_01G (MS205_013)

description: Library name: Sample28

value: wildtype


title: 9904796106_R02C01

description: Breast tumour tissue


title: X0703_G10 (MS238_134)

description: Library name: Sample166


title: X0625_G09 (MS238_117)

description: Library name: Sample150


title: 9904796108_R04C01

description: Breast tumour tissue


title: 0021-R2

description: tumor genomic DNA from patient 0021: Oligodendroglioma, WHO grade 2, resection #2

value: male

value: resection #2

value: GLASS-OD


title: Cy4C_01O (MS205_012)

description: Library name: Sample27


title: 0030-R1

description: tumor genomic DNA from patient 0030: Oligodendroglioma, WHO grade 2, resection #1


title: 0022-R1

description: tumor genomic DNA from patient 0022: Oligodendroglioma, WHO grade 2, resection #1


title: 9829118164_R05C02

description: Breast tumour tissue

value: NBCF


title: Cy4F_14O (MS192_032)

description: Library name: Sample24

value: oocyte, primary follicle, adult cynomolgus ovary (in pregnant E15), Cy4, age6, fresh ovary


title: X0625_G07 (MS238_113)

description: Library name: Sample146

value: Granulosa cell


title: 9829118164_R02C01

description: Breast tumour tissue


title: Cy4F_15O (MS192_034)

description: Library name: Sample26

value: oocyte, secondary follicle, adult cynomolgus ovary (in pregnant E15), Cy4, age6, fresh ovary


title: 9904796027_R03C01

description: Breast tumour tissue

value: Female


title: 0021-R1

description: tumor genomic DNA from patient 0021: Oligodendroglioma, WHO grade 2, resection #1

value: Oligodendroglioma

value: WHO grade 2


title: 9829118153_R02C02

description: Breast tumour tissue


title: X0625_G08 (MS238_115)

description: Library name: Sample148

value: Ovary


title: X0625_O09 (MS238_116)

description: Library name: Sample149


title: 0020-R2

description: tumor genomic DNA from patient 0020: Oligodendroglioma, WHO grade 2, resection #2

value: female


title: Cy4F_14G (MS192_033)

description: Library name: Sample25

value: oocyte, primordial follicle, adult cynomolgus ovary (in pregnant E15), Cy4, age6, fresh ovary


title: 9904796039_R01C01

description: Breast tumour tissue


title: Cy4F_13G (MS192_031)

description: Library name: Sample23


title: 9904796039_R03C02

description: Breast tumour tissue


title: X0625_O08 (MS238_114)

description: Library name: Sample147

value: Oocyte

value: oocyte, M2, adult mouse, BDF1(6w6d-7w1d)


title: 9829118164_R01C01

description: Breast tumour tissue

value: Breast

value: TNBC


title: X0625_G05 (MS238_085)

description: Library name: Sample142

value: wildtype

value: 10-20 granulosa cells, M2, adult mouse ovary, BDF1(6w6d-7w1d)


title: X0625_G04 (MS238_083)

description: Library name: Sample140


title: Cy4F_13O (MS192_030)

description: Library name: Sample22

value: 5 granulosa cells, secondary follicle, adult cynomolgus ovary (in pregnant E15), Cy4, age6, fresh ovary


title: 0018-R2

description: tumor genomic DNA from patient 0018: Oligodendroglioma, WHO grade 3, resection #2

value: male

value: WHO grade 3

value: resection #2

value: GLASS-OD


title: 9829118164_R05C01

description: Breast tumour tissue

value: Female

value: NBCF


title: X0625_G06 (MS238_087)

description: Library name: Sample144

value: Granulosa cell


title: 0018-R3

description: tumor genomic DNA from patient 0018: Oligodendroglioma, WHO grade 2, resection #3

value: Oligodendroglioma

value: WHO grade 2

value: resection #3


title: 9904796027_R01C01

description: Breast tumour tissue


title: X0625_G03 (MS238_081)

description: Library name: Sample138

value: Ovary


title: 9829118153_R01C02

description: Breast tumour tissue


title: Cy4F_11G (MS192_027)

description: Library name: Sample19

value: oocyte, secondary follicle, adult cynomolgus ovary (in pregnant E15), Cy4, age6, fresh ovary


title: 9904796027_R05C01

description: Breast tumour tissue

value: Breast


title: 0017-R3

description: tumor genomic DNA from patient 0017: Oligodendroglioma, WHO grade 3, resection #3


title: X0625_G01 (MS238_077)

description: Library name: Sample134


title: 0016-R2

description: tumor genomic DNA from patient 0016: Oligodendroglioma, WHO grade 3, resection #2

value: female


title: X0525_G15 (MS234_086)

description: Library name: Sample125

value: wildtype

value: 10-20 granulosa cells, primordial follicle, fresh adult mouse ovary,6wBDF1


title: Cy4F_12O (MS192_028)

description: Library name: Sample20

value: Oocyte

value: 5 granulosa cells, secondary follicle, adult cynomolgus ovary (in pregnant E15), Cy4, age6, fresh ovary


title: 9829118153_R01C01

description: Breast tumour tissue

value: TNBC


title: 0017-R2

description: tumor genomic DNA from patient 0017: Oligodendroglioma, WHO grade 2, resection #2

value: male

value: resection #2


title: 9829118164_R02C02

description: Breast tumour tissue

value: Female


title: Cy4F_12G (MS192_029)

description: Library name: Sample21


title: Cy4F_09O (MS192_023)

description: Library name: Sample15

value: oocyte, primordial follicle, adult cynomolgus ovary (in pregnant E15), Cy4, age6, fresh ovary


title: Cy4F_11O (MS192_026)

description: Library name: Sample18

value: 5 granulosa cells, primordial follicle, adult cynomolgus ovary (in pregnant E15), Cy4, age6, fresh ovary


title: X0625_G02 (MS238_079)

description: Library name: Sample136

value: Granulosa cell

value: 10-20 granulosa cells, M2, adult mouse ovary, BDF1(6w6d-7w1d)


title: 0016-R1

description: tumor genomic DNA from patient 0016: Oligodendroglioma, WHO grade 2, resection #1

value: Oligodendroglioma

value: WHO grade 2

value: resection #1

value: GLASS-OD


title: 0014-R2

description: tumor genomic DNA from patient 0014: Oligodendroglioma, WHO grade 3, resection #2

value: WHO grade 3


title: 0018-R1

description: tumor genomic DNA from patient 0018: Oligodendroglioma, WHO grade 3, resection #1


title: Cy4F_10O (MS192_025)

description: Library name: Sample17

value: Ovary

value: wildtype


title: 9904796100_R04C02

description: Breast tumour tissue

value: Breast

value: NBCF


title: 9904796055_R03C01

description: Breast tumour tissue

value: TNBC


title: Cy4F_09G (MS192_024)

description: Library name: Sample16

value: 6 granulosa cells, primordial follicle, adult cynomolgus ovary (in pregnant E15), Cy4, age6, fresh ovary


title: 0015-R2

description: tumor genomic DNA from patient 0015: Oligodendroglioma, WHO grade 2, resection #2

value: female

value: resection #2


title: 0015-R1

description: tumor genomic DNA from patient 0015: Oligodendroglioma, WHO grade 2, resection #1


title: Cy4F_08O (MS192_022)

description: Library name: Sample14

value: Oocyte

value: 5 granulosa cells, primary follicle, adult cynomolgus ovary (in pregnant E15), Cy4, age6, fresh ovary


title: Cy4F_07G (MS192_021)

description: Library name: Sample13

value: Granulosa cell

value: oocyte, primary follicle, adult cynomolgus ovary (in pregnant E15), Cy4, age6, fresh ovary


title: 0013-R3

description: tumor genomic DNA from patient 0013: Oligodendroglioma, WHO grade 3, resection #3

value: male

value: Oligodendroglioma

value: resection #3


title: X0525_G07 (MS234_070)

description: Library name: Sample109

value: 10-20 granulosa cells, primordial follicle, fresh adult mouse ovary,6wBDF1


title: 9904796108_R01C01

description: Breast tumour tissue

value: Female


title: X0525_G14 (MS234_085)

description: Library name: Sample124

value: Ovary


title: X0525_G09 (MS234_075)

description: Library name: Sample114

value: wildtype


title: 0013-R2

description: tumor genomic DNA from patient 0013: Oligodendroglioma, WHO grade 3, resection #2

value: WHO grade 3

value: GLASS-OD


title: 9904796100_R01C02

description: Breast tumour tissue

value: Breast

value: TNBC

value: NBCF


title: 0014-R1

description: tumor genomic DNA from patient 0014: Oligodendroglioma, WHO grade 3, resection #1

value: resection #1


title: X0525_O07 (MS234_069)

description: Library name: Sample108

value: Oocyte

value: oocyte, primordial follicle, fresh adult mouse ovary,6wBDF1


title: 9904796108_R03C02

description: Breast tumour tissue


title: 0012-R3

description: tumor genomic DNA from patient 0012: Oligodendroglioma, WHO grade 3, resection #3


title: X0521_O24 (MS234_056)

description: Library name: Sample95

value: oocyte, secondary follicle, fresh adult mouse ovary,7wBDF1


title: Cy4F_06O (MS192_018)

description: Library name: Sample10

value: 5 granulosa cells, primary follicle, adult cynomolgus ovary (in pregnant E15), Cy4, age6, fresh ovary


title: 9904796027_R03C02

description: Breast tumour tissue


title: X0521_O23 (MS234_055)

description: Library name: Sample94


title: X0521_O22 (MS234_054)

description: Library name: Sample93


title: 0011-R2

description: tumor genomic DNA from patient 0011: Oligodendroglioma, WHO grade 2, resection #2

value: female

value: WHO grade 2

value: resection #2


title: Cy4F_05O (MS192_016)

description: Library name: Sample8


title: 9829118153_R02C01

description: Breast tumour tissue


title: X0521_O13 (MS234_037)

description: Library name: Sample76

value: oocyte, primary follicle, fresh adult mouse ovary,7wBDF1


title: Cy4F_05G (MS192_017)

description: Library name: Sample9

value: Granulosa cell

value: oocyte, primary follicle, adult cynomolgus ovary (in pregnant E15), Cy4, age6, fresh ovary


title: X0521_G11 (MS234_036)

description: Library name: Sample75

value: Ovary

value: wildtype

value: 10-20 granulosa cells, transitional follicle, fresh adult mouse ovary,7wBDF1


title: X0525_O08b (MS234_072)

description: Library name: Sample111


title: 0013-R1

description: tumor genomic DNA from patient 0013: Oligodendroglioma, WHO grade 2, resection #1

value: male

value: Oligodendroglioma

value: GLASS-OD


title: 9829118164_R06C01

description: Breast tumour tissue

value: Breast

value: Female

value: TNBC

value: NBCF


title: 0010-R2

description: tumor genomic DNA from patient 0010: Oligodendroglioma, WHO grade 2, resection #2


title: Cy4F_03G (MS192_014)

description: Library name: Sample6

value: 5 granulosa cells, primordial follicle, adult cynomolgus ovary (in pregnant E15), Cy4, age6, fresh ovary


title: 9904796055_R02C01

description: Breast tumour tissue


title: Cy4F_04O (MS192_015)

description: Library name: Sample7

value: Oocyte


title: 9904796027_R05C02

description: Breast tumour tissue


title: Cy4F_07O (MS192_020)

description: Library name: Sample12

value: 6 granulosa cells, primary follicle, adult cynomolgus ovary (in pregnant E15), Cy4, age6, fresh ovary


title: 0010-R1

description: tumor genomic DNA from patient 0010: Oligodendroglioma, WHO grade 2, resection #1

value: female

value: WHO grade 2

value: resection #1


title: X0521_O10 (MS234_034)

description: Library name: Sample73

value: oocyte, transitional follicle, fresh adult mouse ovary,7wBDF1


title: 0009-R2

description: tumor genomic DNA from patient 0009: Oligodendroglioma, WHO grade 3, resection #2

value: WHO grade 3

value: resection #2


title: 0009-R1

description: tumor genomic DNA from patient 0009: Oligodendroglioma, WHO grade 3, resection #1


title: X0521_G08 (MS234_032)

description: Library name: Sample71

value: Ovary

value: Granulosa cell

value: wildtype

value: 10-20 granulosa cells, transitional follicle, fresh adult mouse ovary,7wBDF1


title: 9904796108_R06C02

description: Breast tumour tissue

value: Breast


title: X0521_G09 (MS234_033)

description: Library name: Sample72


title: Cy4F_01G (MS192_010)

description: Library name: Sample2

value: 4 granulosa cells, primordial follicle, adult cynomolgus ovary (in pregnant E15), Cy4, age6, fresh ovary


title: X0521_G07 (MS234_031)

description: Library name: Sample70

value: 10-20 granulosa cells, primordial follicle, fresh adult mouse ovary,7wBDF1


title: Cy4F_03O (MS192_013)

description: Library name: Sample5

value: oocyte, primordial follicle, adult cynomolgus ovary (in pregnant E15), Cy4, age6, fresh ovary


title: Cy4F_02G (MS192_012)

description: Library name: Sample4

value: 6 granulosa cells, primordial follicle, adult cynomolgus ovary (in pregnant E15), Cy4, age6, fresh ovary


title: 9904796108_R01C02

description: Breast tumour tissue

value: Female

value: TNBC

value: NBCF


title: Cy4F_02O (MS192_011)

description: Library name: Sample3

value: Oocyte


title: 9904796027_R04C02

description: Breast tumour tissue


title: 9829118153_R04C02

description: Breast tumour tissue


title: 0008-R2

description: tumor genomic DNA from patient 0008: Oligodendroglioma, WHO grade 3, resection #2

value: female

value: Oligodendroglioma

value: GLASS-OD


title: X0521_G05 (MS234_028)

description: Library name: Sample67


title: 9904796100_R02C02

description: Breast tumour tissue


title: 0008-R1

description: tumor genomic DNA from patient 0008: Oligodendroglioma, WHO grade 3, resection #1

value: WHO grade 3

value: resection #1


title: Cy4F_06G (MS192_019)

description: Library name: Sample11

value: Ovary

value: Granulosa cell

value: oocyte, primary follicle, adult cynomolgus ovary (in pregnant E15), Cy4, age6, fresh ovary


title: 9904796004_R03C02

description: Breast tumour tissue

value: Breast


title: Cy4F_01O (MS192_009)

description: Library name: Sample1

value: wildtype


title: 0007-R1

description: tumor genomic DNA from patient 0007: Oligodendroglioma, WHO grade 2, resection #1

value: WHO grade 2


title: 0007-R2

description: tumor genomic DNA from patient 0007: Oligodendroglioma, WHO grade 3, resection #2

value: resection #2


title: ex-Zinc, scRNA-seq

city: shanghai

first: xuan

last: wang

address: 1239 Siping Road

institute: TONGJI UNIVERSITY

description: DNBelab C4

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the DNBelab_C4_scRNA_v2.3
Assembly: GRCH38
Supplementary files format and content: Tap-separated values files and matrix files

source_name: hES-derived islet organoid

extract_protocol:
SC-islets were dissociated into single cells with TrypLE and resuspended with DPBS with 0.5% fat-acid -free BSA. Added DNase I to eliminate the DNA released form the dead cells to prevent cell caking and placed the tubes containing cells on ice for preservation.
DNBelab C Series High-throughput Single-Cell RNA Library (MGI, #940-000047-00) was utilized for scRNA-seq library preparation. In brief, the single-cell suspensions were converted to barcoded scRNA-seq libraries through steps including droplet encapsulation, emulsion breakage, mRNA captured beads collection, reverse transcription, cDNA amplification and purification. cDNA production was sheared to short fragments with 250-400 bp, and indexed sequencing libraries were constructed according to the manufacturer’s protocol. Qualification was performed using Qubit ssDNA Assay Kit (Thermo Fisher Scientific) and Agilent Bioanalyzer 2100. All libraries were further sequenced by the MGISEQ-2000RS with pair-end sequencing. The sequencing reads contained 30-bp read 1 (including the 10-bp cell barcode 1, 10-bp cell barcode 2 and 10-bp unique molecular identifiers (UMI)), 100-bp read 2 for gene sequences and 10-bp barcodes read for sample index.

value: hES-derived islet organoid

value: WT


title: 0006-R2

description: tumor genomic DNA from patient 0006: Oligodendroglioma, WHO grade 2, resection #2

value: male


title: X0521_G02 (MS234_023)

description: Library name: Sample62

value: 10-20 granulosa cells, preantral follicle, fresh adult mouse ovary,7wBDF1


title: CT, scRNA-seq

description: DNBelab C4


title: X0521_G01 (MS234_022)

description: Library name: Sample61


title: 9904796004_R02C02

description: Breast tumour tissue

value: Female

value: TNBC

value: NBCF


title: Regenerating zebrafish caudal fin, DMSO, 24h, rep B3

city: Lisobon

first: António

last: Jacinto

address: Campus de Campolide

country: Portugal

institute: NIMSB - NOVA Institute for Medical Systens Biology

description: Library name: DMSO.B3

data_processing:
STAR-2.7.10a, default parameters
Assembly: GRCz11
Supplementary files format and content: Tab-delimited file includes CPM normalized raw counts for each Sample, Ensembl gene ids, official gene symbols and gene names

organism: Danio rerio

source_name: caudal fin

growth_protocol: Wild-type (WT) AB (obtained from ZIRC in 2019 and refreshed in 2024) zebrafish were maintained in a circulating system with a 14 hour/day and 10 hour/night cycle at 28°C.Fish housing and husbandry were performed according to standard protocols with feeding adjustments: L-type rotifers were provided as live feed until 60 days post-fertilization (dpf), followed by Artemia sp. nauplii thereafter. Dry feed consisted of a 1:1 mixture of GemmaMicro (Skretting) and Zebrafeed (Sparos) up to sexual maturation (60–90 dpf), followed by Zebrafeed only. The AB colony was maintained using a multiple paired-cross scheme to raise at least two stocks per generation. Equal numbers of embryos from 15–30 clutches of distinct pairs were pooled to establish each new stock, and the procedure was repeated over two consecutive weeks. Subsequent generations were produced by crossing females and males from different stocks.  All experiments were performed in 3-12 months-old fish, in equal amounts of male and females.

extract_protocol:
Caudal fin composed of the regenerated tissue and one bony-ray segment proximal to the amputation plane were collected. Pools from 10 caudal fins were used per biological replicate, and three biological replicates were used per condition. Briefly, samples were homogenized in Trizol reagent for cell disruption and RNA extraction. Chloroform was added, and the homogenate allowed to separate into a clear upper aqueous layer. RNA was precipitated and purified from the aqueous phase by adding an equal amount of 100% ethanol and loading the mixture into a Zymo-Spin IC Column (ZYMO Research). The remaining procedure was done following the Quick-RNA Microprep Kit manufacturer’s protocol.
The library construction of cDNA molecules was carried out using a Stranded mRNA Library Preparation Kit (Roche/KAPA mRNA HyperPrep kit).

treatment_protocol: Caudal fin amputations were performed in fish subjected to analgesia with 4 mg/L Lidocaine 2% Braun (Braun) and anesthetized with 160 mg/mL MS-222 (Sigma), using a sterile scalpel. Amputations were made 1 or 2 segments below the first bone-segment bifurcation, removing approximately one half of the fin, as previously described. Fish were left to regenerate in an incubator at 33°C with water from the circulating system and fins collected at predetermined time-points post-amputation. Regenerated fins were collected from anaesthetized fish. For pharmacological treatments fish were subjected to intraperitoneal (IP) injections at designated time-points with either Galloflavin (0,12 mg/g diluted in DMSO) or the corresponding vehicle (DMSO). IP injections were performed with an insulin syringe U-100 G 0,3 mL and a 30 G needle (BD Micro-fine) inserted close to the pelvic girdle. For all experiments water was replaced daily and fish left to regenerate until the desired time-point.

value: caudal fin

tag: treatment

value: caudal fin regeneration

tag: batch


title: X0514_G18 (MS234_013)

description: Library name: Sample52

tag: cell line

value: 10-20 granulosa cells, preantral follicle, fresh adult mouse ovary,6wBDF1


title: X0514_G21 (MS234_017)

description: Library name: Sample56

value: Ovary

value: 10-20 granulosa cells, primary follicle, fresh adult mouse ovary,6wBDF1


title: Regenerating zebrafish caudal fin, Galloflavin, 24h, rep B3

description: Library name: GLLO.B3


title: 9829118153_R06C02

description: Breast tumour tissue

tag: tumour subtype

tag: cohort


title: 0011-R1

description: tumor genomic DNA from patient 0011: Oligodendroglioma, WHO grade 2, resection #1

value: female

value: Oligodendroglioma

value: resection #1

value: GLASS-OD


title: X0514_G19 (MS234_014)

description: Library name: Sample53

value: Granulosa cell

value: wildtype


title: Regenerating zebrafish caudal fin, Galloflavin, 24h, rep B2

description: Library name: GLLO.B2

value: WT


title: 0005-R3

description: tumor genomic DNA from patient 0005: Oligodendroglioma, WHO grade 2, resection #3

value: WHO grade 2

value: resection #3


title: 9904796100_R05C01

description: Breast tumour tissue

value: Breast

value: Female

tag: mortality

tag: follow up time (months)


title: 9904796108_R04C02

description: Breast tumour tissue

tag: tissue

value: TNBC

value: NBCF

tag: disease specific death


title: 0005-R2

description: tumor genomic DNA from patient 0005: Oligodendroglioma, WHO grade 2, resection #2

value: resection #2


title: 0004-R1

description: tumor genomic DNA from patient 0004: Oligodendroglioma, WHO grade 3, resection #1

value: male

value: WHO grade 3


title: X0514_O11 (MS234_003)

description: Library name: Sample42

value: Ovary

tag: cell type

value: Oocyte

tag: genotype

value: oocyte, transitional follicle, fresh adult mouse ovary,6wBDF1


title: X0514_O09 (MS234_001)

description: Library name: Sample40

tag: group


title: 9904796100_R04C01

description: Breast tumour tissue

tag: Sex


title: X0514_G13 (MS234_004)

description: Library name: Sample43

value: 10-20 granulosa cells, primary follicle, fresh adult mouse ovary,6wBDF1


title: 9904796100_R02C01

description: Breast tumour tissue


title: 0005-R1

description: tumor genomic DNA from patient 0005: Oligodendroglioma, WHO grade 2, resection #1

value: female

value: Oligodendroglioma

tag: grade

tag: resection

value: resection #1

value: GLASS-OD


title: 0003-R3

description: tumor genomic DNA from patient 0003: Oligodendroglioma, WHO grade 3, resection #3

tag: set


title: 9829118164_R06C02

description: Breast tumour tissue


title: 0004-R2

description: tumor genomic DNA from patient 0004: Oligodendroglioma, WHO grade 3, resection #2


title: dpCoA-Seedling-NUDT11_rep2

city: Beijing

last: Wang

address: No.5 Yiheyuan Road

institute: Peking University

description: Library name: dpCoA-Seedling-NUDT11_rep2

data_processing:
The sequencing data were processed to remove adaptors (AGATCGGAAGAG) using cutadapt1 v4.9 with default parameters. Reads longer than 20 bp were retained for downstream analysis. The trimmed reads were then mapped to the TAIR10 genomic coordinates using the STAR aligner2 v2.7.11b with parameters ‘--alignIntronMax 5000 --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outFilterMismatchNoverLmax 0.1’. Subsequent analyses were conducted using custom scripts. First, teast 1 were retained as filtered sites. Next, all alignment sites were binned into 10-bp intervals. The CPM and total reads count were calculated for each bin using custom scripts. Bins with a CPM of at least 1 and a reads count of at least 1 were selected. The R package edgeR3 v4.0.16 was then used to calculate the changes in each bin between positive and negative samplhe 5' end positions of reads from the BAM file, which aligned with the genome, were extracted and converted into BED files, representing all alignment sites. The reads count and CPM (counts per million) were calculated for each nucleotide. Sites with a CPM of at least 1 and a reads count of at les. Bins with a log2 fold change of at least 1 and a p value less than 0.01 were identified as upregulated bins. The filtered sites overlapping with upregulated bins were obtained using bedtools4 v2.31.1 intersect function and were considered as candidate dpCoA-sites. Finally, bins that overlapped with genes were identified using bedtools intersect, with gene annotation based on Araport11. Finally, custom scripts were employed to select the sites with the highest CPM as dpCoA-sites. PCA analysis and pearson correlation analysis were both conducted based on CPM of each 10 bp bin. PCA analysis was performed using the base R function prcomp() with parameter ‘center = TRUE, scale. = TRUE’. Pearson correlation analysis was performed using the base R function cor(). Motif identification of dpCoA-sites around sequence is proceeded by online tool STREME v5.5.7, with a p value threshold of 0.05.
Assembly: Araport11
Supplementary files format and content: Mapping status of dpCoA-seq reads on the reference genome.

organism: Arabidopsis thaliana

source_name: seedling

extract_protocol:
Total RNA from all species except yeast was isolated using the TransZol Up reagent (TransGen Biotech) following manufacturer’s instructions. For bacterial RNA extraction, pellets obtained from 300 mL of culture were first pretreated. The bacterial pellet was thawed on ice and resuspended in 6 mL of 2 mg/mL lysozyme solution, then incubated at 37 °C for 5 min to initiate cell wall digestion, followed by cooling on ice for 30 min. Subsequent RNA extraction was performed using the TransZol Up reagent. Arabidopsis and mouse tissues were flash-frozen in liquid nitrogen and homogenized using a pre-chilled mortar and pestle, while monolayer-adherent human cells were washed with 1×PBS and subsequently lysed using TransZol Up. Yeast total RNA extraction employed a phenol-based lysis method. Yeast cell pellets were resuspended in 12 mL of TES buffer (10 mM Tris-HCl pH 7.5, 10 mM EDTA, 0.5% SDS), followed by immediate mixing with 12 mL of phenol through vigorous vortexing for 30 seconds. The mixture was incubated at 65 °C for 1 h to facilitate cell lysis. After incubation, the samples were centrifuged at 12,000 g for 5 minutes at 4 °C, and the aqueous phase was carefully collected. The remaining purification steps were carried out following the standard TransZol Up protocol, following manufacturer's instructions. Following total RNA isolation, all samples were treated with 1 unit/μg of DNase I (Roche) at 37 °C for 1 h to remove genomic DNA contamination. RNA was then purified by phenol/chloroform extraction and ethanol precipitation. For all species except bacteria, poly(A) RNAs were isolated from total RNA using Oligo d(T)₂₅ Magnetic Beads (New England Biolabs) according to manufacturer’s guidelines.
Subsequently, 20 units RNase H (New England Biolabs) was added, and incubation continued at 37 °C for 40 min. To isolate the cDNA, 30 μL of 2 × RNA loading dye was added to the sample, which was then resolved in a 7 M urea/1 × TBE/10% polyacrylamide gel. The gel was stained with SYBR Gold nucleic acid gel stain (Invitrogen) and visualized under UV transillumination. Gel fragments corresponding to 150–-450 nt cDNA were excised and broken to pieces in 1.5 mL tubes using RNase-free pipette tips. The gel pieces were mixed with 600 μL 0.4 M NaCl and incubated overnight at 4 °C to elute the cDNA. The cDNA was then ethanol-precipitated and resuspended in RNase-free water. PCR amplification was performed using 11.25 μL of the cDNA as a template in a 25 μL total reaction volume. The library was then constructed using the NEBNext® Multiplex Small RNA Library Prep Set, following the manufacturer’s recommended cycling conditions (15 cycles). The amplified products were mixed with 6 × DNA loading dye, then resolved in a 1 × TBE/10 % polyacrylamide gel, stained with SYBR Gold, and visualized under UV transillumination. Library fragments spanning 150–-450 bp were excised, gel-extracted, and resuspended in 15 μL of TE buffer. The libraries were then sequenced on an Illumina NovaSeq 4000 system (paired-end, 150 bp) at Berry Genomics (Beijing).Subsequently, 20 units RNase H (New England Biolabs) was added, and incubation continued at 37 °C for 40 min. To isolate the cDNA, 30 μL of 2 × RNA loading dye was added to the sample, which was then resolved in a 7 M urea/1 × TBE/10% polyacrylamide gel. The gel was stained with SYBR Gold nucleic acid gel stain (Invitrogen) and visualized under UV transillumination. Gel fragments corresponding to 150–-450 nt cDNA were excised and broken to pieces in 1.5 mL tubes using RNase-free pipette tips. The gel pieces were mixed with 600 μL 0.4 M NaCl and incubated overnight at 4 °C to elute the cDNA. The cDNA was then ethanol-precipitated and resuspended in RNase-free water. PCR amplification was performed using 11.25 μL of the cDNA as a template in a 25 μL total reaction volume. The library was then constructed using the NEBNext® Multiplex Small RNA Library Prep Set, following the manufacturer’s recommended cycling conditions (15 cycles). The amplified products were mixed with 6 × DNA loading dye, then resolved in a 1 × TBE/10 % polyacrylamide gel, stained with SYBR Gold, and visualized under UV transillumination. Library fragments spanning 150–-450 bp were excised, gel-extracted, and resuspended in 15 μL of TE buffer. The libraries were then sequenced on an Illumina NovaSeq 4000 system (paired-end, 150 bp) at Berry Genomics (Beijing).

value: seedling


title: 0012-R2

description: tumor genomic DNA from patient 0012: Oligodendroglioma, WHO grade 3, resection #2


title: X0514_O10 (MS234_002)

description: Library name: Sample41

value: wildtype


title: 0003-R2

description: tumor genomic DNA from patient 0003: Oligodendroglioma, WHO grade 3, resection #2


title: Regenerating zebrafish caudal fin, DMSO, 24h, rep B1

description: Library name: DMSO.B1

value: caudal fin

value: WT

value: caudal fin regeneration


title: dpCoA-Seedling-NUDT11_rep3

description: Library name: dpCoA-Seedling-NUDT11_rep3


title: 9904796004_R04C01

description: Breast tumour tissue

value: Breast

value: Female

value: TNBC

value: NBCF


title: 9829118153_R03C02

description: Breast tumour tissue


title: X0408_G02 (MS233_029)

description: Library name: Sample21

value: Ovary

value: Granulosa cell

value: 10-20 granulosa cells, antral follicle, fresh adult mouse ovary


title: 0002-R1

description: tumor genomic DNA from patient 0002: Oligodendroglioma, WHO grade 2, resection #1

value: WHO grade 2


title: Regenerating zebrafish caudal fin, Galloflavin, 24h, rep B1

description: Library name: GLLO.B1


title: dpCoA-Seedling-NUDT11_rep1

description: Library name: dpCoA-Seedling-NUDT11_rep1


title: 9904796100_R01C01

description: Breast tumour tissue


title: X0402_G04 (MS233_019)

description: Library name: Sample11


title: 9829118164_R03C02

description: Breast tumour tissue


title: N2

city: Cheongju

first: Chaelin

last: You

address: Chungdae-ro 1, Seowon-Gu

country: South Korea

institute: Chungbuk National University

hyb_protocol: DNA methylation profiles were generated using the Illumina HumanMethylation EPIC array platform.

scan_protocol: Illumina iScan

data_processing: The raw IDAT files were processed using Illumina GenomeStudio V2011.1 software.

source_name: Nasal mucosa

extract_protocol: DNA was extracted from tumor specimens in accordance with the QIAamp DNA Mini kit (Qiagen). Briefly, tumor specimens were dissociated into small pieces, placed in a 1.5 mL microcentrifuge tube, and 180 µL of Buffer ATL was added. 20 µL proteinase K was added to the specimens, mixed by vortexing, and incubated at 56°C until the tissue was completely lysed, then centrifuged to remove drops. 4 µL RNase A (100 mg/mL) was added to the specimens, mixed by pulse-vortexing for 15 s, incubated for 2 min at room temperature, and centrifuged to remove drops. 200 µL Buffer AL was added to the sample, mixed again by pulse-vortexing for 15 s, incubated at 70°C for 10 min, and centrifuged to remove drops. 200 µL ethanol (96–100%) was added to the sample, mixed by pulse-vortexing for 15 s, and centrifuged to remove drops. The mixture was carefully applied to the QIAamp Mini spin column and centrifuged. The QIAamp Mini spin column was placed in a clean 2 mL collection tube, and the tube containing the filtrate was discarded. 500 µL Buffer AW1 was added to the QIAamp Mini spin column and centrifuged. 500 µL Buffer AW2 was added to the QIAamp Mini spin column and centrifuged. 200 µL Buffer AE was added to the QIAamp Mini spin column, incubated at room temperature for 1 min, and then centrifuged.

value: Nasal mucosa


title: N6


title: X0327_O03 (MS233_004)

description: Library name: Sample4

value: Oocyte

value: oocyte, antral follicle, fresh adult mouse ovary


title: N3


title: dpCoA-Seedling-mock_rep2

description: Library name: dpCoA-Seedling-mock_rep2


title: Regenerating zebrafish caudal fin, DMSO, 24h, rep B2

description: Library name: DMSO.B2


title: mRNA-rep3

description: Library name: mRNA-rep3

data_processing:
The mRNA-seq data were processed in the same manner as dpCoA-seq data for adaptor removal and mapping to the TAIR10 genome. Subsequently, featureCounts5 v2.0.6 was employed to calculate the reads count and FPKM for each Arabidopsis gene. GO analysis of genes with FPKM >125 was preformed using the R package clusterProfiler6 v4.12.6. Total gene decay rate data were obtained from Sorenson et al, 20187. For the permutation test, we first identified dpCoA genes with FPKM > 125 from the total gene dataset. Among these dpCoA genes, decay rate values were available for 309 genes in the total dataset. Next, we randomly selected 309 genes from the total gene pool and calculated their median FPKM. This process was repeated 1,000 times to generate a distribution of median FPKM values for comparison.
Assembly: Araport11
Supplementary files format and content: Count


title: X0327_G02 (MS233_003)

description: Library name: Sample3


title: X0327_G03 (MS233_005)

description: Library name: Sample5


title: X0327_O02 (MS233_002)

description: Library name: Sample2


title: 9904796108_R02C02

description: Breast tumour tissue


title: DOX47h02

status: Public on Jan 18 2026

city: Bangkok

first: Jakkrit

last: Khamjerm

address: 270 Rama VI Rd, Thung Phaya Thai, Ratchathewi

country: Thailand

institute: Faculty of Medicine Ramathibodi Hospital

description: Library name: Sample12

data_processing:
CLC Genomics Workbench 23.0.5
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes normalized counts for all Sample

source_name: TNBC organoids from primary breast tumors

extract_protocol:
RNA was harvested using Trizol reagent
Libraries were prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina)

value: Doxorubicin

value: 47 hr


title: DOX47h01

description: Library name: Sample11

value: TNBC organoids from primary breast tumors


title: dpCoA-Seedling-mock_rep3

description: Library name: dpCoA-Seedling-mock_rep3

value: seedling


title: CA5

source_name: SNSCC tumor

value: SNSCC tumor


title: 9829118164_R04C02

description: Breast tumour tissue


title: 9829118153_R04C01

description: Breast tumour tissue


title: DOX23h01

description: Library name: Sample9

value: 23 hr


title: X0402_G07 (MS233_024)

description: Library name: Sample16

value: wildtype


title: mRNA-rep2

description: Library name: mRNA-rep2


title: CTR23h02

description: Library name: Sample6

value: Control


title: CA1


title: 9829118153_R05C01

description: Breast tumour tissue

value: Breast

value: Female

value: TNBC


title: X0327_G01 (MS233_001)

description: Library name: Sample1

value: Ovary

value: Granulosa cell


title: BTZ47h02

description: Library name: Sample4

value: Bortezomib


title: BTZ47h01

description: Library name: Sample3


title: 9829118164_R04C01

description: Breast tumour tissue

value: NBCF


title: 9904796004_R02C01

description: Breast tumour tissue


title: BTZ23h01

description: Library name: Sample1


title: 9904796027_R02C01

description: Breast tumour tissue


title: DOX23h02

description: Library name: Sample10


title: siFXR1-LNA,rep2

city: Milwaukee

first: Masaki

last: Lin

state: Wisconsin

address: 8701 W Watertown Plank Rd

country: USA

institute: Medical College of Wisconsin

description:
Library name: libF2
10x Genomics

data_processing:
Single cell RNAseq: The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Ascites

extract_protocol:
Ascites samples were collected in 50-ml conical tubes (BD), followed by centrifugation for 10 min at 400g at 4degree. The supernatant was aspirated and the remaining pellet was resuspended with 5 mL of ACK lysis buffer (Life technologies) and incubated for 5 min. 30 ml of PBS was used to quench the lysis buffer followed by centrifugation for 10 min at 400g at 4degree. The concentration of single-cell suspensions was adjusted to about 500–1,200 cells per μl.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics)

value: Ascites

tag: age

value: 6 weeks post tumor cell injection

tag: strain

value: FVB

value: female


title: mRNA-rep1

description: Library name: mRNA-rep1


title: CTR23h01

description: Library name: Sample5

value: TNBC organoids from primary breast tumors

tag: treatment

tag: batch


title: 9904796004_R03C01

description: Breast tumour tissue

tag: tumour subtype


title: 9904796108_R02C01

description: Breast tumour tissue

tag: cohort


title: FACS-purified MG and their neuronal progeny 1 month after NMDA and Adezmapimod (MAPK14 inhibitor) treatment

city: Hengyang

first: Houjian

state: Hunan

address: Shigu District Chuanshan Road

institute: The First Affiliated Hospital of University of South China

description:
Library name: Sample 1
10x Genomics

data_processing:
The raw sequencing data were processed using 10x Genomics' official analysis software, Cell Ranger, which performed data filtering, genome alignment, transcript quantification, and cell identification. This pipeline ultimately generated the gene expression matrix for each individual cell.
Subsequent analysis was performed using Seurat for further cell filtering, standardization of cell expression quantification, cell subpopulation classification, differential gene expression analysis across subpopulations, and marker gene screening.
Assembly: Mus musculus GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: retina

extract_protocol:
Cell quality control adjust the cell concentration to the optimal level, typically 1000 cells/μL. 10X Barcoding of cDNA Fragments Gel beads carrying barcode information are combined with a mixture of cells and enzymes, then encapsulated by oil-surfactant droplets within a microfluidic system to form GEMs. The GEMs flow into a collection reservoir, where the gel beads dissolve to release the barcode sequences. Reverse transcription is performed to generate cDNA fragments, and samples are labeled. The gel beads are then disrupted and the oil droplets are broken. Using the cDNA as a template, PCR amplification is carried out. The products from all GEMs are pooled to construct a standard sequencing library.
The cDNA is enzymatically fragmented into segments of approximately 200–300 bp. This is followed by traditional second-generation sequencing library preparation steps, such as the addition of sequencing adapters and primers. Finally, PCR amplification is performed to obtain the DNA library.

value: retina

value: Muller glia

value: GlastCreERT2+/tg; ROSA26R-tdTomato+/tg

value: NMDA and Adezmapimod treatment


title: RUUO_UUO_Spleen_3

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

institute: University Hospital Regensburg

description: Library name: Sample 6

data_processing:
UMI-barcoded and paired TCR-sequencing reads were processed using MIXCR (v4.7.0). Mapped TCR-seq data were further analysed using the immunarch package (v.0.9.1) in R (v4.4.2) to generate clonotype count tables and calculate repertoire diversities.
Assembly: GRCm38 (mm10)
Supplementary files format and content: clonotype count tables generated by MIXCR4.
Library strategy: TCR-Seq

source_name: spleen

extract_protocol:
CD4+ T cells were isolated from the kidneys of RUUO+UUO donor mice in two steps, first with a CD4+ T cell negative isolation kit (Miltenyi) and then with CD4 (L3T4) microbeads (Miltenyi). CD4+ T cells were isolated from the spleens of RUUO+UUO donor mice with CD4 (L3T4) microbeads (Miltenyi). Subsequently FACS-sorting of CD4+ T cells was performed.
Total RNA from FACS-sorted CD4+ T cell populations was used for 5’ RACE PCR of the TCR-beta chain. For cDNA generation, we introduced a template-switching oligo (TSO, Bio-GGGCUCGGAGAUGUGUAUAAGAGACAGUNNNNUNNNNUNNNNUrGrGrG) that included a unique molecular identifier (UMI). Following reverse transcription, excess TSO was digested using Uracil-DNA Glycosylase (UDG) (New England Biolabs). PCR was performed using the Advantage 2 PCR Kit (Takara) for 20 cycles along with primers specific for the constant region of the Trbc locus (GAAGCCCCTGGCCAAGCACACGAG) as well as a universal forward primer specific for the TSO sequence (GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGT). The PCR products were purified with AMPure XP beads (Beckman Coulter) and reactions were split into technical replicates for the successive extension PCR (15 cycles) using the Advantage 2 PCR Kit (Takara) and TSO (GTCTCGTGGGCTCGGAGATGTG) and another Tcrb-specific primer (TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGTTGATGGCTCAAACAAGGAG). Barcoding was performed in a third PCR using IDT for Illumina DNA/RNA UD Indexes (10 cycles). Libraries were purified using AMPure XP beads (Beckman Coulter), concentrations were measured with the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific) and fragment size profiles were assessed using the High Sensitivity D1000 or D5000 ScreenTape Assay (Agilent). Sequencing (paired-end 300bp) was performed on the Illumina NextSeq 2000 system.

treatment_protocol: Reversible unilateral ureteral obstruction  (RUUO) was performed using a displaceable clip (Fine Science Tools, Heidelberg, Germany). This clip was placed on the right ureter on day 0, shifted in position on days 2 and 4 to avoid strictures, and removed on day 6. As control, sham surgery was performed without placing a clip. On day 17, the left ureter was ligated through a low midline abdominal incision. Kidneys and spleens were harvested on day 22.

value: spleen

value: CD4+ T cells

value: C57BL/6 wildtype

value: Mice underwent reversible unilateral ureteral obstruction (RUUO) of the right kidney from day 0 to 6, followed by unilateral ureteral obstruction (UUO) of the left kidney from day 17 to 22.

value: mouse 3


title: siCont,rep2

description:
Library name: libC2
10x Genomics


title: RUUO_UUO_Spleen_2

description: Library name: Sample 5

value: mouse 2


title: 9904796027_R02C02

description: Breast tumour tissue

value: Breast

value: Female

value: TNBC

tag: mortality


title: siCont,rep1

description:
Library name: libC1
10x Genomics

value: Ascites

value: 6 weeks post tumor cell injection


title: CTR47h02

description: Library name: Sample8

value: Control

value: 47 hr


title: BTZ23h02

description: Library name: Sample2

value: TNBC organoids from primary breast tumors

value: Bortezomib

value: 23 hr


title: RUUO_UUO_Spleen_1

description: Library name: Sample 4

value: mouse 1


title: RUUO_UUO_Kidney_1

description: Library name: Sample 1

source_name: kidney

value: kidney


title: RUUO_UUO_Kidney_2

description: Library name: Sample 2

value: CD4+ T cells


title: RUUO_UUO_Kidney_3

description: Library name: Sample 3

value: C57BL/6 wildtype


title: B/T Day7 DataSet 2 Replicate 3

city: Boston

first: Nezihi Murat

last: Karabacak

state: Massachusetts

address: 51 Blossom St

institute: Massachusetts General Hospital

data_processing:
Raw sequencing reads were aligned to the mouse genome (UCSC mm9) using the Star Aligner (v. 2.7.10). Aligned reads were quantified using HTSEQ (v. 2.0.1).
Assembly: UCSC mm9
Supplementary files format and content: Tab separated value (tsv) matrix of RPM counts per gene for each sample.

source_name: cMPCs and blood cells

extract_protocol:
Whole blood was sorted using microfluidic iChip. RNA was purified from enriched blood sample using Qiagen micro kit.
Seqwell Rapid Kit was used according to manufacturer instructions

value: cMPCs and blood cells

value: wild type

value: Burn/tenotomy


title: CTR47h01

description: Library name: Sample7


title: B/T Day7 DataSet 2 Replicate 2


title: siFXR1-LNA,rep1

description:
Library name: libF1
10x Genomics

value: FVB

value: female


title: B/T 6h DataSet 2 Replicate 4


title: B/T 6h DataSet 2 Replicate 3


title: B/T 6h DataSet 2 Replicate 2


title: B/T Day7 DataSet 2 Replicate 4


title: B/T Day7 DataSet 2 Replicate 1


title: Replicate 2

description: 10X Genomics

data_processing:
10x Genomics Cell Ranger 7.1.0 (via 10x Genomics Cloud Analysis) was used to perform sample de-multiplexing, barcode processing, and single-cell gene counting (alignment, barcoding, and unique molecular identifier [UMI] count).  Reads were aligned to the mm10-2020-A reference genome as appropriate for the input dataset. Downstream analysis steps were performed using Seurat v5. Cells identified as poor libraries or resulting from doublet cells were filtered by eliminating cells on both ends of the distribution, as well as cells with unusually high percent mitochondrial transcripts. Normalization, scaling, and dimensional reductions using principal component analysis (PCA) and uniform manifold approximation and projection (UMAP) were performed using Seurat v5. Integrative analysis was performed using Harmony. Cell type labels were assigned based on characteristic relative marker gene expression levels between cell clusters using the FindAllMarkers function. Module scores were generated using the AddModuleScore function of Seurat to identify cell populations of interest. Module scores were calculated as the level of gene expression enrichment of a set gene list relative to a random control list, with higher module score values representing positive enrichment beyond background.
Assembly: mm10-2020-A
Supplementary files format and content: Gene expression matrix, barcodes and features in tab seperated files

extract_protocol:
Whole blood was sorted using microfluidic iChip. 10X was used to barcode single cells.
10x Genomics Chromium

value: burn/tenotomy


title: B/T 6h DataSet 2 Replicate 1


title: B/T Day1 DataSet 2 Replicate 3


title: B/T Day3 BAPN Replicate 5

description: Flash-seq

data_processing:
Raw sequencing reads were aligned to the mouse genome (UCSC mm9) using the RNA-Seq Alignment App (v2.0.2) on Basespace (Illumina, CA).
Assembly: UCSC mm9
Supplementary files format and content: Tab separated value (tsv) matrix of raw read counts per gene for each sample.
Supplementary files format and content: Gene IDs

value: Burn/tenotomy + BAPN


title: 9904796004_R01C02

description: Breast tumour tissue

value: Breast

value: Female

value: TNBC

value: NBCF

tag: follow up time (months)


title: B/T Day3 BAPN Replicate 1

description: Flash-seq


title: B/T Day3 BAPN Replicate 4

description: Flash-seq


title: B/T Day1 DataSet 2 Replicate 2


title: dpCoA-Seedling-mock_rep1

description: Library name: dpCoA-Seedling-mock_rep1

tag: tissue

value: seedling


title: B/T Day3 BAPN Replicate 3

description: Flash-seq


title: B/T Day1 DataSet 2 Replicate 4


title: B/T Day7 Replicate 6

description: Flash-seq


title: B/T Day1 DataSet 2 Replicate 1


title: MIO-M1 cells, siControl for siMapk8+9_2, Day 3

description:
Library name: Sample 8
Column name in siControl vs siMapk8+9_read_count_fpkm_tpm_All_Samples.xlsx

data_processing:
The raw sequencing data were filtered using SOAPnuke.
Clean data were aligned to the reference gene set using Bowtie2 (v2.3.4.3). Gene expression quantification was performed with RSEM (v1.3.1), and the expression levels of genes across different samples were visualized as a clustered heatmap using the pheatmap package (v1.0.8). Differential gene expression analysis was conducted with DESeq2 (v1.4.5) [6] (or alternatively with DEGseq or PoissonDis).
Assembly: Homo_sapiens_9606.NCBI.GCF_000001405.40_GRCh38.p14.v2201
Supplementary files format and content: Xlsx files include read_count, fpkm and tpm value

extract_protocol:
Total RNA was extracted from cells or retinal tissues with  TRIzol reagent. Following assessment of quality, samples with an RNA integrity number (RIN) greater than 7.5 were selected for library construction.
Capture mRNA with polyA tails using magnetic beads conjugated with Oligo(dT). RNA Fragmentation and Reverse Transcription: Fragment the obtained mRNA using a fragmentation buffer. Perform reverse transcription with random N6 primers to synthesize the first cDNA strand, followed by second-strand cDNA synthesis to generate double-stranded DNA. Double-Stranded DNA Processing and Ligation: Blunt-end and phosphorylate (5'-end) the double-stranded DNA, and create a 3'-end overhang with a single adenine ("A") base. Then ligate a bubble-shaped adapter that has a 3'-end overhang with a single thymine ("T") base. PCR Amplification and Circularization: Amplify the ligation product by PCR using specific primers. The PCR product is then heat-denatured into single strands. A bridge primer is used to circularize the single-stranded DNA, resulting in a single-stranded circular DNA library. Library Quality Assessment and Sequencing: The constructed library undergoes quality control. Once it passes quality inspection, it is ready for sequencing.

value: retina

tag: cell line

value: Muller glia

value: WT

value: siRNA treatment


title: MIO-M1 cells, siMapk8+9_1, Day 3

description:
Library name: Sample 10
Column name in siControl vs siMapk8+9_read_count_fpkm_tpm_All_Samples.xlsx

tag: cell type


title: B/T Day7 Replicate 4

description: Flash-seq

tag: genotype


title: MIO-M1 cells, siControl for siMapk8+9_3, Day 3

description:
Library name: Sample 9
Column name in siControl vs siMapk8+9_read_count_fpkm_tpm_All_Samples.xlsx


title: B/T Day3 BAPN Replicate 2

description: Flash-seq


title: MIO-M1 cells, siControl for siMapk8+9_1, Day 3

description:
Library name: Sample 7
Column name in siControl vs siMapk8+9_read_count_fpkm_tpm_All_Samples.xlsx


title: B/T Day3 Replicate 4

description: Flash-seq


title: MIO-M1 cells, siMapk14_3, Day 3

description:
Library name: Sample 6
Column name in siControl vs siMapk14_read_count_fpkm_tpm_All_Samples.xlsx


title: B/T Day3 Replicate 1

description: Flash-seq


title: B/T Day7 Replicate 5

description: Flash-seq


title: MIO-M1 cells, siControl for siMapk14_3, Day 3

description:
Library name: Sample 3
Column name in siControl vs siMapk14_read_count_fpkm_tpm_All_Samples.xlsx


title: B/T Day7 Replicate 2

description: Flash-seq


title: B/T Day1 Replicate 4

description: Flash-seq


title: K562 cells, sh-DUSP9,D3

city: zhengzhou

first: Li

last: Xudong

state: Henan

address: No. 1, Jianshe East Road, Erqi District

institute: The First Affiliated Hospital of Zhengzhou University

description:
Library name: D3
Column name in raw_counts_all_samples.txt: D3

data_processing:
Data was aligned to using hg38p14 using Rsubread (v2.18.0)
A count matrix was generated, genes were annotated using useMart(v2.60.1)
A DESeqDataSet was generated using DESeq2(v1.44.0).
Assembly: HG38p14
Supplementary files format and content: norm_counts_all is a comma separated file containing the normalized counts for the gene names per sample

source_name: cell lines

growth_protocol: K562 cells were maintained in 1640 supplemented with 10% fetalbovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme, RC112-01)
After enrichment, mRNA was fragmented using fragmentation buffer, followed by reverse transcription using random N5 primers to synthesize cDNA double strands. The synthesized double-stranded DNA was then end-repaired and 5' phosphorylated, with a protruding 'A' at the 3'end forming a blunt end, followed by ligation of a  bubble-shaped adapter with a protruding 'T' at the 3' end. The ligation producs were PCR amplified using specific primers. The PCR products were denatrued to single strands, and then single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality-checked and seuenced after passing the quality control. (BGI's DNB-seq protocol)

value: cell lines

value: Human leukemia cell line

value: DUSP9 knock down


title: B/T Day1 Replicate 3

description: Flash-seq

value: cMPCs and blood cells

value: wild type

value: Burn/tenotomy


title: B/T Day1 Replicate 1

description: Flash-seq


title: K562 cells, sh-control,NC2

description:
Library name: NC2
Column name in raw_counts_all_samples.txt: NC2

value: sh-control


title: K562 cells, sh-control,NC3

description:
Library name: NC3
Column name in raw_counts_all_samples.txt: NC3


title: MIO-M1 cells, siMapk8+9_3, Day 3

last: Zhang

description:
Library name: Sample 12
Column name in siControl vs siMapk8+9_read_count_fpkm_tpm_All_Samples.xlsx


title: B/T Day3 Replicate 3

description: Flash-seq


title: B/T Day7 Replicate 3

description: Flash-seq


title: MIO-M1 cells, siControl for siMapk14_1, Day 3

description:
Library name: Sample 1
Column name in siControl vs siMapk14_read_count_fpkm_tpm_All_Samples.xlsx


title: B/S Day3 Replicate 6

description: Flash-seq

value: Burn/sham incision


title: B/T Day1 Replicate 5

description: Flash-seq


title: MIO-M1 cells, siControl for siMapk14_2, Day 3

description:
Library name: Sample 2
Column name in siControl vs siMapk14_read_count_fpkm_tpm_All_Samples.xlsx


title: B/S Day3 Replicate 5

description: Flash-seq


title: MIO-M1 cells, siMapk14_1, Day 3

description:
Library name: Sample 4
Column name in siControl vs siMapk14_read_count_fpkm_tpm_All_Samples.xlsx


title: NC (CUT&Tag)

city: Zhengzhou

first: Peng

address: Science Avenue

institute: Zhengzhou University

description: Library name: Sample 5

data_processing:
Raw low-quality reads and reads contaminated with adapter sequences were filtered out using fastp (version 0.12.4). The remaining reads were aligned to GRCm39 genome using Bowtie2 (version 2.5.5). SAM files were converted to sorted BAM files using samtools (version 1.13), and duplicate fragments were removed using Picard Tools MarkDuplicates (version 2.25.5). Genome browser track files were generated from the deduplicated BAM files using deeptools bamCoverage (version 3.5.1), with parameters set to --normalizeUsing RPKM --binSize 10. Broad peaks were called using macs2 callpeak (2.2.7.1) with the following settings: -f BAMPE -g mm --nomodel --broad. Heatmaps and aggregate plots were created with deeptools plotHeatmap and plotProfile (version 3.5.1). Differential binding analysis was conducted using DiffBind (version 3.12.0), applying thresholds of |fold change| ≥ 2 and an adjusted p-value (FDR) < 0.05. Peak annotation was performed with the annotatePeak function from the R package ChIPseeker (version 1.38.0), defining promoter regions as ±2 kb from the transcription start site (TSS).
Assembly: GRCm39
Supplementary files format and content: BW
Library strategy: CUT&Tag

source_name: Spleen

extract_protocol:
CUT&Tag was performed on sorted Treg cells form Foxp3YFP-CreKmt2dfl/fl(cKO) and Foxp3YFP-CreKmt2d+/+ mice to profile H3K4me3-enriched DNA fragments, following the NovoNGS CUT&Tag 4.0 High-Sensitivity Kit (for Illumina) (Cat. No.: N259-YH01; Novoprotein, Shanghai, China).
Briefly, 1 × 106 Treg cells were harvested and incubated with NovoNGS ConA Beads for 10 minutes. The bead-bound cells were subsequently incubated overnight at 4°C with a primary antibody against H3K4me3 (Cell Signaling Technology), followed by a 1-hour incubation at room temperature with a secondary antibody while rotating. Tagmentation was initiated by adding a diluted ChiTag transposome and incubating for 1 hour at room temperature with rotation. Tagmentation Buffer was then added, and the mixture was incubated statically at 37°C for 1 hour. The reaction was terminated by adding Stop Buffer with vigorous vortexing, followed by a 10-minute incubation at 55°C. The resulting DNA libraries were purified using Tagment DNA Extract Beads; a two-volume equivalent of resuspended beads was added to the sample and incubated for 5 minutes at room temperature for DNA binding. The bead-bound DNA was captured magnetically, and the supernatant was discarded. The beads were washed twice with freshly prepared 80% ethanol. After air-drying, the purified DNA was eluted in Elution Buffer. These final library samples were undergoing PCR amplification to construct next-generation sequencing libraries, which were subsequently sequenced using the Illumina Novaseq X Plus platform. Two biological repeats were sequenced.

value: Spleen

value: Treg cells


title: K562 cells, sh-DUSP9,D2

description:
Library name: D2
Column name in raw_counts_all_samples.txt: D2


title: B/T Day7 Replicate 1

description: Flash-seq


title: MIO-M1 cells, siMapk8+9_2, Day 3

description:
Library name: Sample 11
Column name in siControl vs siMapk8+9_read_count_fpkm_tpm_All_Samples.xlsx


title: B/T Day1 Replicate 2

description: Flash-seq


title: MIO-M1 cells, siMapk14_2, Day 3

description:
Library name: Sample 5
Column name in siControl vs siMapk14_read_count_fpkm_tpm_All_Samples.xlsx


title: WT, replicate 2 (CUT&Tag)

description: Library name: Sample 2


title: B/S Day1 Replicate 6

description: Flash-seq


title: CA8

value: SNSCC tumor


title: B/T Day3 Replicate 2

description: Flash-seq


title: B/S Day3 Replicate 1

description: Flash-seq


title: B/S Day1 Replicate 5

description: Flash-seq


title: K562 cells, sh-control,NC1

description:
Library name: NC1
Column name in raw_counts_all_samples.txt: NC1


title: cKO, replicate 1 (CUT&Tag)

description: Library name: Sample 3


title: B/S Day3 Replicate 3

description: Flash-seq


title: L1MKG2203280-MIR18

city: Hong Kong

first: Yiwen

last: Pan

address: Pokfulam Road

country: Hong Kong

institute: The University Of Hong Kong

description: Library name: Sample10

data_processing:
Raw paired-end RNA-seq reads were quality filtered and adapter trimmed using fastp with default parameters to obtain clean reads.
Clean reads were aligned to the mouse reference genome (GRCm39) using HISAT2 in orientation mode with default settings.
Gene-level read counts and transcript abundances were quantified using RSEM, and expression levels were normalized as transcripts per million (TPM).
Differential gene expression analysis between miR-130a-3p overexpression and control groups was performed using DESeq2. Genes with adjusted P value (FDR) < 0.01 and |log2 fold change| ≥ 1 were defined as differentially expressed genes.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text files containing normalized gene expression values (TPM) for each sample with gene annotations.

source_name: medial prefrontal cortex

extract_protocol:
Mouse brains were rapidly collected and dissected, and the medial prefrontal cortex (mPFC) was identified using a mouse brain atlas and isolated by tissue punching (1-mm diameter). Total RNA was extracted using FreeZol reagent (Vazyme, #R711) following the manufacturer’s instructions, and RNA concentration was measured using a NanoDrop spectrophotometer. RNA quality was assessed using an Agilent 5300 Bioanalyzer; samples meeting library construction criteria (OD260/280 = 1.8–2.2, OD260/230 ≥ 2.0, RIN ≥ 6.5, 28S:18S ≥ 1.0, and >1 µg total RNA) were used for sequencing library preparation.
RNA-seq libraries were constructed using the Illumina Stranded mRNA Prep, Ligation kit according to the manufacturer’s protocol, including poly(A) mRNA enrichment, cDNA synthesis, adapter ligation, size selection, and PCR amplification.

value: medial prefrontal cortex

value: mixed cell types


title: B/S Day3 Replicate 7

description: Flash-seq


title: B/S Day3 Replicate 2

description: Flash-seq


title: L1MKG2203276-MIR13

description: Library name: Sample6


title: cKO, replicate 2 (CUT&Tag)

description: Library name: Sample 4


title: B/S Day3 Replicate 4

description: Flash-seq


title: CF_P56_Cre+_rep2 [ATAC-Seq]

city: Milan

first: Paola

last: Cattaneo

address: Via Fantoli 16/15

department: Institute of Genetic and Biomedical Research

country: Italy

institute: National Research Council of Italy

data_processing:
Differentially expressed peaks were selected based on the following parameters: FDR ≤0.05, and Log Fold Change ≤ -0.5 for peaks downregulated and ≥ 0.5 for peaks upregulated
bigWig were generated with wigToBigWig command starting from Signal.Unique.str.out.wig file generated after STAR mapping.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Postnatal day P56

extract_protocol:
Cardiac fibroblasts (75000 sorted cells) were isolated using collagenase enzymatic reaction and FACS sorted based on the GFP fluorescence from  Col1a1-GFP allele and on the tdTomato fluorescence driven by the LepR-Cre. Purified Cardiac fibroblasts  were collected in Storing Buffer (10mM HEPES, 2mM MgCl2, 25mM KCl, 250mM Sucrose, 70% Glycerol) and stored at -80C.
Tagmentation, PCR-amplification and Libraries  were generated using the ATAC-seq kit (Active Motif# 53150) according to the manufacturer’s protocol and sequenced on Nextseq 550 System (Illumina)

value: Postnatal day P56

value: primary cardiac fibroblasts


title: L1MKG2203278-MIR15

description: Library name: Sample8

value: WT


title: L1MKG2203277-MIR14

description: Library name: Sample7


title: WT, replicate 1 (CUT&Tag)

description: Library name: Sample 1


title: L1MKG2203272-CON7

description: Library name: Sample4


title: B/S Day1 Replicate 1

description: Flash-seq


title: B/S Day1 Replicate 3

description: Flash-seq


title: B/S Day1 Replicate 4

description: Flash-seq


title: B/S Day1 Replicate 2

description: Flash-seq


title: L1MKG2203279-MIR17

description: Library name: Sample9


title: CF_P56_Cre+_rep1 [ATAC-Seq]


title: L1MKG2203270-CON4

description: Library name: Sample2


title: L1MKG2203273-CON9

description: Library name: Sample5


title: L1MKG2203271-CON5

description: Library name: Sample3


title: K562 cells, sh-DUSP9,D1

description:
Library name: D1
Column name in raw_counts_all_samples.txt: D1