title: HEK293T_IscB_omegaRNA_ALDH1A3_Tg5.rep1

description:
Library name: HEK293T_IscB_omegaRNA_ALDH1A3_Tg5.rep1
Target.HEK293T.editing_frequency.txt


title: Hs10_O09 (MS251_026)

status: Public on Jan 19 2026

type: SRA

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: Sample234

library_source: transcriptomic

data_processing:
The genome sequence and transcript annotation (GRCh38.p12) 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: GRCh38.p12
Supplementary files format and content: tab-delimited text files include RPM values for each Sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Ovary

growth_protocol: For in vitro growth culture (IVG), some of the human ovaries were used after informed consent from participants undergoing ovariectomy for clinical indication.  Under a stereomicroscope, secondary or preantral follicles were mechanically isolated from ovaries in handling medium, 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 human 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 human 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 GCs.  Follicles and COCs were individually placed in 30 ml Accutase (Sigma-Aldrich, A6964) drops on a dish warmed by 37℃ plate, and oocytes and GCs 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 GCs in the immediate vicinity of the oocyte were collected because of low abundancy of mRNA in these cells.  For primordial follicles, 15 GCs may not be obtained from a single follicle, in which case two or three primordial follicle-derived GCs 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 GCs.  The removal of surrounding GCs from oocytes was confirmed under stereomicroscope (Leica, S8 APO) and inverted microscope (Olympus, IX71).  Dissociated oocytes and GCs 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, DDX4, DAZL, FOXL2, GJA1, and AMHR2 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: Human ovaries were collected after informed consent from participants undergoing ovariectomy for clinical indication.  To retrieve COCs from antral follicles, COCs were aspirated with 27G needles or extruded from the incision of follicles with micro scissors.

tag: tissue

value: Ovary

tag: cell type

value: Oocyte

tag: genotype

value: wildtype

tag: group

value: oocyte, primary  follicle, adult human ovary, Hs10, age23, gender identity disorder (testosterone medication until 6w before operation)


title: Hs10_G04 (MS251_017)

description: Library name: Sample225

value: Granulosa cell

value: 10-20 granulosa cells, secondary follicle, adult human ovary, Hs10, age23, gender identity disorder (testosterone medication until 6w before operation)


title: HEK293T_IscB_omegaRNA_ALDH1A3_Tg1.rep2

city: Hohhot

first: Lei

last: Yang

state: Inner Mongolia Autonomous Region

address: 24 Zhaojun Rd.

department: State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock

country: China

institute: Inner Mongolia University

description:
Library name: HEK293T_IscB_omegaRNA_ALDH1A3_Tg1.rep2
Target.HEK293T.editing_frequency.txt

library_source: genomic

data_processing:
Data analysis was performed using CRISPResso2. The editing efficiencies were quantified as the percentage of total sequencing reads containing indels.
Assembly: GRCh38,MM39
Supplementary files format and content: the average and SD values of the running results of CRISPResso, which are grouped statistics based on the running results of CRISPResso

molecule: genomic DNA

source_name: Kidney

extract_protocol:
the genomic DNA was extracted from transfected cells, infected embryos, and cattle ear-tips using the TIANamp Genomic DNA Kit (Tiangen) or QIAamp DNA Mini Kit (Qiagen) according to the manufacturer’s instructions.
Genomic sites of interest were amplified using unique barcoding primer pairs with Phanta Max Super-Fidelity DNA Polymerase (Vazyme) for deep sequencing. The PCR products were pooled by common amplicons and sequenced with pair-end 150 bp on the HiSeq 4000 system (Illumina).

value: Kidney

tag: cell line

value: Human embryonic kidney cells

tag: sample group


title: Hs10_O08 (MS251_024)

description: Library name: Sample232


title: Hs10_O07 (MS251_022)

description: Library name: Sample230

value: oocyte, primordial~primary  follicle, adult human ovary, Hs10, age23, gender identity disorder (testosterone medication until 6w before operation)


title: Hs10_G07 (MS251_023)

description: Library name: Sample231

value: 10-20 granulosa cells, primordial~primary follicle, adult human ovary, Hs10, age23, gender identity disorder (testosterone medication until 6w before operation)


title: Hs10_O12 (MS251_032)

description: Library name: Sample240

value: oocyte, primordial  follicle, adult human ovary, Hs10, age23, gender identity disorder (testosterone medication until 6w before operation)


title: Hs10_G03 (MS251_015)

description: Library name: Sample223


title: WT.rep3

description:
Library name: WT.rep3
TYR.editing_frequency.txt

organism: Mus musculus

source_name: Tail tip

value: Tail tip

value: Mouse tail tip cells

value: WT


title: Hs10_G05 (MS251_019)

description: Library name: Sample227


title: Hs10_O06 (MS251_020)

description: Library name: Sample228

value: oocyte, preantral  follicle, adult human ovary, Hs10, age23, gender identity disorder (testosterone medication until 6w before operation)


title: WT.rep2

description:
Library name: WT.rep2
TYR.editing_frequency.txt


title: Hs10_G08 (MS251_025)

description: Library name: Sample233

value: 10-20 granulosa cells, primary follicle, adult human ovary, Hs10, age23, gender identity disorder (testosterone medication until 6w before operation)


title: Hs10_O05 (MS251_018)

description: Library name: Sample226

value: oocyte, secondary  follicle, adult human ovary, Hs10, age23, gender identity disorder (testosterone medication until 6w before operation)


title: TYR9.rep3

description:
Library name: TYR9.rep3
TYR.editing_frequency.txt


title: HEK293T_IscB_omegaRNA_ALDH1A3_Tg1.rep3

description:
Library name: HEK293T_IscB_omegaRNA_ALDH1A3_Tg1.rep3
Target.HEK293T.editing_frequency.txt


title: Hs10_O03 (MS251_014)

description: Library name: Sample222

value: Ovary


title: HEK293T_IscB_omegaRNA_ALDH1A3_Tg3.rep2

description:
Library name: HEK293T_IscB_omegaRNA_ALDH1A3_Tg3.rep2
Target.HEK293T.editing_frequency.txt


title: HEK293T_IscB_omegaRNA_ALDH1A3_Tg2.rep1

description:
Library name: HEK293T_IscB_omegaRNA_ALDH1A3_Tg2.rep1
Target.HEK293T.editing_frequency.txt


title: WT.rep1

description:
Library name: WT.rep1
TYR.editing_frequency.txt


title: TYR9.rep2

description:
Library name: TYR9.rep2
TYR.editing_frequency.txt


title: HEK293T_IscB_omegaRNA_ALDH1A3_Tg2.rep3

description:
Library name: HEK293T_IscB_omegaRNA_ALDH1A3_Tg2.rep3
Target.HEK293T.editing_frequency.txt


title: Hs10_O04 (MS251_016)

description: Library name: Sample224

value: Oocyte


title: Hs9_G16 (MS257_202)

description: Library name: Sample215

value: wildtype

value: 10-20 granulosa cells, secondary follicle, adult human ovary, Hs9, age36, cervical cancer (post chemotherapy:TP 2cycle)


title: Hs9_G17 (MS251_009)

description: Library name: Sample217

value: Granulosa cell

value: 10-20 granulosa cells, primary follicle, adult human ovary, Hs9, age36, cervical cancer (post chemotherapy:TP 2cycle)


title: Hs10_G02 (MS251_013)

description: Library name: Sample221

value: 10-20 granulosa cells, COC aspirated from large antral follicle, adult human ovary, Hs10, age23, gender identity disorder (testosterone medication until 6w before operation)


title: Hs10_G01 (MS251_011)

description: Library name: Sample219


title: TYR9.rep1

description:
Library name: TYR9.rep1
TYR.editing_frequency.txt


title: TYR7.rep3

description:
Library name: TYR7.rep3
TYR.editing_frequency.txt


title: HS11_G01 (MS251_035)

description: Library name: Sample243

value: 10-20 granulosa cells, COC isolated from about 1mm antral follicle, adult human ovary, Hs11, age25, gender identity disorder (testosterone medication until 6w before operation)


title: TYR8.rep1

description:
Library name: TYR8.rep1
TYR.editing_frequency.txt


title: TYR8.rep3

description:
Library name: TYR8.rep3
TYR.editing_frequency.txt


title: Hs9_O15 (MS251_004)

description: Library name: Sample212

value: oocyte, primary  follicle, adult human ovary, Hs9, age36, cervical cancer (post chemotherapy:TP 2cycle)


title: TYR6.rep3

description:
Library name: TYR6.rep3
TYR.editing_frequency.txt


title: Hs10_O01 (MS251_010)

description: Library name: Sample218

value: oocyte, COC aspirated from large antral follicle, adult human ovary, Hs10, age23, gender identity disorder (testosterone medication until 6w before operation)


title: Hs9_G13 (MS251_001)

description: Library name: Sample209


title: Hs9_O17 (MS251_008)

description: Library name: Sample216


title: Hs9_O14 (MS251_002)

description: Library name: Sample210


title: Hs9_O16 (MS251_006)

description: Library name: Sample214

value: oocyte, secondary  follicle, adult human ovary, Hs9, age36, cervical cancer (post chemotherapy:TP 2cycle)


title: TYR7.rep1

description:
Library name: TYR7.rep1
TYR.editing_frequency.txt

value: Tail tip


title: Hs10_O02 (MS251_012)

description: Library name: Sample220


title: Hs9_G14 (MS257_201)

description: Library name: Sample211


title: TYR7.rep2

description:
Library name: TYR7.rep2
TYR.editing_frequency.txt

value: Mouse tail tip cells


title: Hs9_O12 (MS252_162)

description: Library name: Sample206


title: TYR5.rep2

description:
Library name: TYR5.rep2
TYR.editing_frequency.txt


title: Hs9_O13 (MS252_164)

description: Library name: Sample208


title: TYR6.rep2

description:
Library name: TYR6.rep2
TYR.editing_frequency.txt


title: HEK293T_IscB_omegaRNA_ALDH1A3_Tg1.rep1

description:
Library name: HEK293T_IscB_omegaRNA_ALDH1A3_Tg1.rep1
Target.HEK293T.editing_frequency.txt

value: Kidney

value: Human embryonic kidney cells


title: Hs9_G10 (MS257_224)

description: Library name: Sample203

value: 10-20 granulosa cells, primordial~primary follicle, adult human ovary, Hs9, age36, cervical cancer (post chemotherapy:TP 2cycle)


title: Hs9_O11 (MS252_160)

description: Library name: Sample204


title: TYR5.rep3

description:
Library name: TYR5.rep3
TYR.editing_frequency.txt


title: TYR4.rep3

description:
Library name: TYR4.rep3
TYR.editing_frequency.txt


title: Hs9_O10 (MS252_158)

description: Library name: Sample202

value: oocyte, primordial~primary  follicle, adult human ovary, Hs9, age36, cervical cancer (post chemotherapy:TP 2cycle)


title: TYR4.rep1

description:
Library name: TYR4.rep1
TYR.editing_frequency.txt


title: TYR4.rep2

description:
Library name: TYR4.rep2
TYR.editing_frequency.txt


title: Hs9_O09 (MS252_156)

description: Library name: Sample200

value: Ovary


title: TYR3.rep3

description:
Library name: TYR3.rep3
TYR.editing_frequency.txt


title: TYR2.rep3

description:
Library name: TYR2.rep3
TYR.editing_frequency.txt


title: TYR3.rep2

description:
Library name: TYR3.rep2
TYR.editing_frequency.txt


title: Hs9_G12 (MS252_163)

description: Library name: Sample207


title: TYR3.rep1

description:
Library name: TYR3.rep1
TYR.editing_frequency.txt


title: TYR6.rep1

description:
Library name: TYR6.rep1
TYR.editing_frequency.txt


title: Hs9_O08 (MS252_154)

description: Library name: Sample198

value: Oocyte


title: TYR2.rep1

description:
Library name: TYR2.rep1
TYR.editing_frequency.txt


title: TYR8.rep2

description:
Library name: TYR8.rep2
TYR.editing_frequency.txt


title: Hs9_G11 (MS252_161)

description: Library name: Sample205

value: wildtype


title: Hs9_O07 (MS252_152)

description: Library name: Sample196


title: Hs9_G08 (MS257_223)

description: Library name: Sample199


title: Hs9_G15 (MS251_005)

description: Library name: Sample213


title: Hs9_G06 (MS257_221)

description: Library name: Sample195


title: TYR5.rep1

description:
Library name: TYR5.rep1
TYR.editing_frequency.txt


title: TYR2.rep2

description:
Library name: TYR2.rep2
TYR.editing_frequency.txt


title: Hs9_O05 (MS257_219)

description: Library name: Sample192

value: oocyte, primordial  follicle, adult human ovary, Hs9, age36, cervical cancer (post chemotherapy:TP 2cycle)


title: Hs9_O06 (MS252_150)

description: Library name: Sample194


title: TYR1.rep3

description:
Library name: TYR1.rep3
TYR.editing_frequency.txt


title: Hs9_O04 (MS252_146)

description: Library name: Sample190


title: Hs9_G09 (MS252_157)

description: Library name: Sample201

value: Granulosa cell


title: TYR13.rep2

description:
Library name: TYR13.rep2
TYR.editing_frequency.txt


title: TYR14.rep3

description:
Library name: TYR14.rep3
TYR.editing_frequency.txt


title: Hs9_G04 (MS252_147)

description: Library name: Sample191

value: 10-20 granulosa cells, primordial follicle, adult human ovary, Hs9, age36, cervical cancer (post chemotherapy:TP 2cycle)


title: Hs9_G07 (MS257_222)

description: Library name: Sample197


title: Hs9_G05 (MS257_220)

description: Library name: Sample193


title: TYR14.rep1

description:
Library name: TYR14.rep1
TYR.editing_frequency.txt


title: Hs9_O03 (MS252_144)

description: Library name: Sample188


title: TYR12.rep3

description:
Library name: TYR12.rep3
TYR.editing_frequency.txt


title: Hs9_G02 (MS252_143)

description: Library name: Sample187

value: 10-20 granulosa cells, secondary follicle, adult human ovary, Hs9, age36, cervical cancer (post chemotherapy:TP 2cycle)


title: TYR12.rep1

description:
Library name: TYR12.rep1
TYR.editing_frequency.txt


title: TYR12.rep2

description:
Library name: TYR12.rep2
TYR.editing_frequency.txt


title: TYR14.rep2

description:
Library name: TYR14.rep2
TYR.editing_frequency.txt


title: TYR13.rep1

description:
Library name: TYR13.rep1
TYR.editing_frequency.txt


title: TYR1.rep2

description:
Library name: TYR1.rep2
TYR.editing_frequency.txt


title: TYR13.rep3

description:
Library name: TYR13.rep3
TYR.editing_frequency.txt


title: Hs9_G03 (MS252_145)

description: Library name: Sample189


title: Hs9_O02 (MS252_142)

description: Library name: Sample186


title: Hs9_O01 (MS252_140)

description: Library name: Sample184

value: oocyte, preantral  follicle, adult human ovary, Hs9, age36, cervical cancer (post chemotherapy:TP 2cycle)


title: Hs8_O12 (MS239_050)

description: Library name: Sample182

value: Hs8, age39, ovarian cancer (sample from intact side), oocyte, primary  follicle, adult human ovary


title: TYR11.rep2

description:
Library name: TYR11.rep2
TYR.editing_frequency.txt


title: TYR11.rep3

description:
Library name: TYR11.rep3
TYR.editing_frequency.txt


title: TYR11.rep1

description:
Library name: TYR11.rep1
TYR.editing_frequency.txt


title: Hs9_G01 (MS252_141)

description: Library name: Sample185

value: 10-20 granulosa cells, preantral follicle, adult human ovary, Hs9, age36, cervical cancer (post chemotherapy:TP 2cycle)


title: Hs8_G10 (MS239_048)

description: Library name: Sample180

value: Hs8, age39, ovarian cancer (sample from intact side), 10-20 granulosa cells, primary follicle, adult human ovary


title: Hs8_G11 (MS239_049)

description: Library name: Sample181

value: Hs8, age39, ovarian cancer (sample from intact side), 10-20 granulosa cells, early secondary follicle, adult human ovary


title: Hs8_G09 (MS239_046)

description: Library name: Sample178


title: TYR10.rep3

description:
Library name: TYR10.rep3
TYR.editing_frequency.txt

value: Tail tip

value: Mouse tail tip cells


title: TYR1.rep1

description:
Library name: TYR1.rep1
TYR.editing_frequency.txt


title: Hs8_O09 (MS239_045)

description: Library name: Sample177

value: Hs8, age39, ovarian cancer (sample from intact side), oocyte, early secondary  follicle, adult human ovary


title: OVA_sensi_challe_dust_preve_2

city: München

first: Thomas

middle: M

last: Conlon

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Zentrum München

description:
Library name: muc30249
10x Genomics

library_source: transcriptomic single cell

data_processing:
Following sequencing, the generation of count matrices was performed by using the Drop-seq core computational pipeline. The processing of next-generation sequencing reads of the scRNA-seq data was performed as previously described (54). Briefly, the Drop-seq computational pipeline was used (version 2.3.0, STAR version 2.5.3a) for the alignment of reads to the mm10 reference genome (provided by the Drop-seq group, GSE63269). For barcode filtering, we excluded barcodes with less than 200 detected genes.
During preprocessing we assessed the quality of our libraries and applied suitable filter criteria motivated by previously described best practices (55) with slight adjustments. We kept the top barcodes based on UMI count per cell, guided by the number of estimated cells per sample. After exploration of UMI counts and genes per cell for the combined count matrices, we retained barcodes with count numbers in the range of 400 to 6000 counts per cell and genes detected in at least three cells. A high proportion (>20%) of transcript counts derived from mitochondria-encoded genes may indicate low cell quality, and we removed such unqualified cells. The expression matrices were normalized using scran’s size factor-based approach and log-transformed via scanpy’s pp.log1p() function. In an additional step to mitigate the effects of unwanted sources of cell-to-cell variation, we regressed out the number of UMI counts and cell cycle scores for each cell. Genes variable in at least four samples were used as input for principal component analysis (PCA). Clustering was performed via Seurat Louvain method at resolution 2 and cell types manually annotated by using known marker genes.
Assembly: mm10
Supplementary files format and content: RDS, Seurat object

molecule: total RNA

source_name: Lung

extract_protocol:
Murine lobes were removed, minced, and digested for 20–30 min at 37 °C in an enzymatic mix containing dispase (50 caseinolytic U/ml), collagenase (2 mg/ml), elastase (1 mg/ml), and DNase (30 μg/ml). Single cells were harvested by straining through a 70-micron strainer. After centrifugation at 300×g for 5 min, single cells were taken up in 1 ml of PBS (with 10% fetal calf serum), counted, and critically assessed for single-cell separation and overall cell viability. Cells were aliquoted in PBS supplemented with 0.04% of bovine serum albumin at a final concentration of 100 cells/μl.
Drop-seq experiments were performed according to the original protocol (54). Briefly, single cells (100/μl) were co‐encapsulated in droplets with barcoded beads (120/μl, ChemGenes Corporation, Wilmington, MA) at rates of 4000 μl/hr. Droplet emulsions were collected for 10–20 min/each prior to droplet breakage by perfluorooctanol (Sigma‐Aldrich). After breakage, beads were harvested and the hybridized mRNA transcripts were reverse transcribed (Maxima RT, Thermo Fisher). Unused primers were removed by the addition of exonuclease I (New England Biolabs), following which, beads were washed, counted, and aliquoted for pre‐amplification (2000 beads/reaction, equals ca. 100 cells/reaction) with 12 PCR cycles. For each sample, 1 ng of pre‐amplified cDNA from an estimated 1000 cells was tagmented by Nextera XT (Illumina) with a custom P5‐primer (Integrated DNA Technologies). Single‐cell libraries were sequenced in a 100 bp paired‐end run on the Illumina HiSeq4000 using 0.2 nM denatured sample and 5% PhiX spike‐in.

value: Lung

tag: strain

value: BALB/c

tag: age

tag: Sex

value: Female

tag: treatment

value: OVA+FD


title: Hs8_G08 (MS239_044)

description: Library name: Sample176

value: Ovary

value: wildtype


title: TYR10.rep1

description:
Library name: TYR10.rep1
TYR.editing_frequency.txt


title: OVA_sensi_challe_dust_preve_3

description:
Library name: muc30251
10x Genomics


title: TYR10.rep2

description:
Library name: TYR10.rep2
TYR.editing_frequency.txt


title: Hs8_G07 (MS252_212)

description: Library name: Sample174

value: Granulosa cell

value: Hs8, age39, ovarian cancer (sample from intact side), 10-20 granulosa cells, secondary follicle, adult human ovary


title: OVA_sensi_challe_1

description:
Library name: muc30240
10x Genomics

value: OVA


title: OVA_sensi_challe_3

description:
Library name: muc30243
10x Genomics


title: Hs8_O08 (MS239_043)

description: Library name: Sample175

value: Oocyte


title: Hs8_O10 (MS239_047)

description: Library name: Sample179

value: Hs8, age39, ovarian cancer (sample from intact side), oocyte, primary  follicle, adult human ovary


title: OVA_sensi_challe_dust_preve_1

description:
Library name: muc30248
10x Genomics


title: PBS_sensi_2

description:
Library name: muc30233
10x Genomics

value: PBS


title: Hs8_O06 (MS239_040)

description: Library name: Sample172

value: Hs8, age39, ovarian cancer (sample from intact side), oocyte, secondary  follicle, adult human ovary


title: Hs8_G06 (MS252_211)

description: Library name: Sample173


title: PBS_sensi_1

description:
Library name: muc30232
10x Genomics


title: Hs8_G05 (MS239_039)

description: Library name: Sample171


title: Hs8_G03 (MS239_035)

description: Library name: Sample167

value: Hs8, age39, ovarian cancer (sample from intact side), 10-20 granulosa cells, preantral follicle, adult human ovary


title: Hs8_O05 (MS239_038)

description: Library name: Sample170


title: OVA_sensi_challe_2

description:
Library name: muc30242
10x Genomics


title: Hs8_G04 (MS239_037)

description: Library name: Sample169


title: Hs8_O04 (MS239_036)

description: Library name: Sample168


title: aae_bl_D14

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: sample5

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 aegypti

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: Rockefeller

value: female

tag: developmental stage

value: adult


title: aae_denv_D14

description: Library name: sample7


title: Hs8_G12 (MS239_051)

description: Library name: Sample183

value: Hs8, age39, ovarian cancer (sample from intact side), 10-20 granulosa cells, primary follicle, adult human ovary


title: Hs6_G19 (MS234_129)

description: Library name: Sample161

value: 10-20 granulosa cells, primary follicle, fresh human ovary ,Hs6, 38y, fresh ovary


title: her1, stigma, α-H3K9me2, replicate 2, Cut&Tag

city: Chengdu

first: Daiming

last: Guo

state: Sichuan

address: 211 Huimin Road, Wenjiang

department: Rice Research Institute

institute: Sichuan Agricultural University

data_processing:
Fastp was used to remove sequencing adapters and low-quality data.
clean reads were aligned to the reference genome (MSU7.0, rice.uga.edu) using BWA.
SAMtools was used to obtain high quality alignments and  potential PCR duplicates were removed by GATK MarkDuplicates.
MACS2 software was used to call peaks.
Peaks distributions were visualized using deepTools.
Assembly: MSU7
Supplementary files format and content: track file (tdf file)
Library strategy: Cut&Tag

organism: Oryza sativa

source_name: stigma

growth_protocol: All rice materials were grown in field conditions.

extract_protocol:
About 50,000 cell was harvested and incubated with concanavalin A coated magnetic beads for 15 min at RT. Then, bead-bound cells was resuspended and incubated with the appropriate primary antibody overnight at 4℃. Afterwards, secondary antibody was added to this mixture for 30 min at RT. The magnet stand was used to remove unbound antibodies.pA-Tn5 adapter complex was added at this step at RT for 1 h,then,remove unbound pA-Tn5 protein.Next,cells were resuspended in tagmentation buffer at 37℃ for 1 h. After that, immunoprecipitated DNA was saved.
To amplify libraries, 21 µL DNA was mixed with 2 µL of a universal i5 and a uniquely barcoded i7 primer, using a different barcode for each sample. A volume of 25 µL NEBNext HiFi 2× PCR Master mix was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and hold at 8 °C. Library was sequenced on Illumina novaseq 6000 with PE 150 method.

value: stigma

tag: cultivar

value: Loss of function of HER1


title: her1, stigma, α-IgG, replicate 2, Cut&Tag


title: Hs6_O17 (MS234_125)

description: Library name: Sample157

value: Ovary

value: wildtype

value: oocyte, primary follicle, fresh human ovary ,Hs6, 38y, fresh ovary


title: Hs6_G18 (MS234_128)

description: Library name: Sample160

value: Granulosa cell


title: Hs6_O18 (MS234_127)

description: Library name: Sample159

value: Oocyte


title: Hs8_G02 (MS239_033)

description: Library name: Sample165


title: WT, stigma, α-H3K9me2, replicate 2, Cut&Tag

value: WT


title: her1, stigma, α-IgG, replicate 1, Cut&Tag


title: her1, stigma, α-H3K9me2, replicate 1, Cut&Tag


title: Hs6_G17 (MS234_126)

description: Library name: Sample158


title: Hs8_O03 (MS239_034)

description: Library name: Sample166

value: Hs8, age39, ovarian cancer (sample from intact side), oocyte, preantral  follicle, adult human ovary


title: Hs8_G01 (MS239_031)

description: Library name: Sample163


title: WT, stigma, α-HER1, replicate 1, Cut&Tag


title: her1, stigma, replicate 2, RNA-seq

data_processing:
Fastp was used to remove sequencing adapters and low-quality data.
clean reads were aligned to the reference genome (MSU7.0, rice.uga.edu) using Hisat2.
Reads mapped to the genome were preserved and SAMtools was used to obtain high quality alignments.
FeatureCounts was used to calculate the number of reads mapped to each gene, analyzing the gene expression levels across the entire genome.
Differentially expressed genes between WT and her1 were detected using edgeR.
Assembly: MSU7
Supplementary files format and content: raw readcount data (xlsx file)
Supplementary files format and content: FPKM data (xlsx file)

extract_protocol:
RNA was extracted using an RNAprep pure Plant Kit (DP432, Tiangen Biotech).
The RNA-seq libraries were constructed using theVAHTS mRNA-seq V3 Library Prep Kit (Illumina), according to the manufacturer’s instructions.


title: her1, stigma, replicate 3, RNA-seq


title: Hs8_O01 (MS239_030)

description: Library name: Sample162


title: Hs6_O16 (MS234_123)

description: Library name: Sample155


title: Hs6_G16 (MS234_124)

description: Library name: Sample156


title: Hs6_G15 (MS234_122)

description: Library name: Sample154


title: aae_D7

description: Library name: sample1


title: WT, stigma, α-IgG, replicate 2, Cut&Tag


title: Hs8_O02 (MS239_032)

description: Library name: Sample164


title: her1, stigma, replicate 1, RNA-seq


title: WT, stigma, replicate 3, RNA-seq


title: WT, stigma, α-HER1, replicate 2, Cut&Tag


title: Hs6_G14 (MS234_120)

description: Library name: Sample152


title: WT, stigma, replicate 2, RNA-seq


title: Hs6_G13 (MS234_118)

description: Library name: Sample150

value: 10-20 granulosa cells, primordial follicle, fresh human ovary ,Hs6, 38y, fresh ovary


title: Hs6_O13a (MS234_116)

description: Library name: Sample148

value: oocyte, primordial follicle, fresh human ovary ,Hs6, 38y, fresh ovary


title: Hs6_G12 (MS234_115)

description: Library name: Sample147


title: Hs6_O13b (MS234_117)

description: Library name: Sample149


title: Cy15D23_04G2 (MS293_057)

description: Library name: Sample300

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

organism: Macaca fascicularis

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: IVG culture for 23 days

value: 15 Cumulus cells, 23 days cultured preantral follicle (follicle No.4), Cy16 ( 6y, dead due to intestinal lymphoma)


title: Hs6_O14 (MS234_119)

description: Library name: Sample151


title: Cy15D23_06O (MS305_212)

description: Library name: Sample304

value: Oocyte (103 um), 23 days cultured preantral follicle (follicle No.6), Cy16 ( 6y, dead due to intestinal lymphoma)


title: Hs6_G09 (MS234_109)

description: Library name: Sample141


title: Hs6_O12b (MS234_114)

description: Library name: Sample146


title: Hs6_O12a (MS234_113)

description: Library name: Sample145


title: Cy15D23_05G2 (MS293_060)

description: Library name: Sample303

value: 15 Cumulus cells, 23 days cultured preantral follicle (follicle No.5), Cy16 ( 6y, dead due to intestinal lymphoma)


title: Hs6_O11b (MS234_111)

description: Library name: Sample143


title: Cy15D23_04O (MS305_210)

description: Library name: Sample298

value: Oocyte (100 um), 23 days cultured preantral follicle (follicle No.4), Cy16 ( 6y, dead due to intestinal lymphoma)


title: Cy15D23_06G1 (MS293_062)

description: Library name: Sample305

value: 15 Cumulus cells, 23 days cultured preantral follicle (follicle No.6), Cy16 ( 6y, dead due to intestinal lymphoma)


title: Cy15D23_03G2 (MS293_054)

description: Library name: Sample297

value: 15 Cumulus cells, 23 days cultured preantral follicle (follicle No.3), Cy16 ( 6y, dead due to intestinal lymphoma)


title: Cy15D23_03G1 (MS293_053)

description: Library name: Sample296


title: Hs6_G07 (MS234_104)

description: Library name: Sample136

value: 10-20 granulosa cells, secondary follicle, fresh human ovary ,Hs6, 38y, fresh ovary


title: Hs6_O09 (MS234_108)

description: Library name: Sample140

value: Ovary


title: Hs6_O07 (MS234_103)

description: Library name: Sample135

value: wildtype

value: oocyte, secondary follicle, fresh human ovary ,Hs6, 38y, fresh ovary


title: Cy15D23_03O (MS305_209)

description: Library name: Sample295

value: Oocyte (111 um), 23 days cultured preantral follicle (follicle No.3), Cy16 ( 6y, dead due to intestinal lymphoma)


title: Hs6_G06 (MS234_102)

description: Library name: Sample134

value: Granulosa cell


title: Cy15D23_04G1 (MS293_056)

description: Library name: Sample299


title: Hs6_O06 (MS234_101)

description: Library name: Sample133

value: Oocyte


title: Cy15D23_02G2 (MS293_051)

description: Library name: Sample294

value: 15 Cumulus cells, 23 days cultured preantral follicle (follicle No.2), Cy16 ( 6y, dead due to intestinal lymphoma)


title: Hs6_O08b (MS234_106)

description: Library name: Sample138


title: Hs6_G08 (MS234_107)

description: Library name: Sample139

value: 10-20 granulosa cells, primordial follicle, fresh human ovary ,Hs6, 38y, fresh ovary


title: WT, stigma, replicate 1, RNA-seq

value: stigma

value: WT


title: Cy15D23_01G1 (MS293_048)

description: Library name: Sample291

value: IVG culture for 23 days

value: 15 Cumulus cells, 23 days cultured preantral follicle (follicle No.1), Cy16 ( 6y, dead due to intestinal lymphoma)


title: Hs6_G05 (MS234_100)

description: Library name: Sample132


title: Cy15D23_01O (MS305_208)

description: Library name: Sample290

value: Oocyte (124 um), 23 days cultured preantral follicle (follicle No.1), Cy16 ( 6y, dead due to intestinal lymphoma)


title: Cy15D23_07G2 (MS293_066)

description: Library name: Sample309

value: 15 Cumulus cells, 23 days cultured preantral follicle (follicle No.7), Cy16 ( 6y, dead due to intestinal lymphoma)


title: Hs6_G04 (MS234_098)

description: Library name: Sample130


title: Hs6_O05 (MS234_099)

description: Library name: Sample131


title: WT, stigma, α-H3K9me2, replicate 1, Cut&Tag


title: Cy15D23_01G2 (MS293_049)

description: Library name: Sample292


title: Cy14D16_06G1 (MS293_043)

description: Library name: Sample288

value: IVG culture for 16 days

value: 15 Cumulus cells, 16 days cultured preantral follicle (follicle No.6), Cy14 ( 8y, E17 pregnant)


title: Hs6_O03 (MS234_096)

description: Library name: Sample128


title: Hs6_G03 (MS234_097)

description: Library name: Sample129

value: 10-20 granulosa cells, secondary follicle, fresh human ovary ,Hs6, 38y, fresh ovary


title: Cy14D16_06O (MS305_207)

description: Library name: Sample287

value: Ovary

value: Oocyte (119 um), 16 days cultured preantral follicle (follicle No.6), Cy14 ( 8y, E17 pregnant)


title: Cy14D16_06G2 (MS293_044)

description: Library name: Sample289

value: wildtype


title: Cy14D16_05G2 (MS293_039)

description: Library name: Sample286

value: 15 Cumulus cells, 16 days cultured preantral follicle (follicle No.5), Cy14 ( 8y, E17 pregnant)


title: Hs4_O21 (MS232_124)

description: Library name: Sample124

value: oocyte, transitional follicle, Hs4, Age13, Hodgikin lymphoma (before chemotherapy)


title: Cy14D16_05O (MS293_037)

description: Library name: Sample284

value: Oocyte

value: Oocyte (110 um), 16 days cultured preantral follicle (follicle No.5), Cy14 ( 8y, E17 pregnant)


title: Hs6_O08a (MS234_105)

description: Library name: Sample137

value: oocyte, primordial follicle, fresh human ovary ,Hs6, 38y, fresh ovary


title: Cy14D16_04G2 (MS293_034)

description: Library name: Sample283

value: Granulosa cell

value: 15 Cumulus cells, 16 days cultured preantral follicle (follicle No.4), Cy14 ( 8y, E17 pregnant)


title: Cy14D16_04O (MS321_215)

description: Library name: Sample281

value: Oocyte (120 um), 16 days cultured preantral follicle (follicle No.4), Cy14 ( 8y, E17 pregnant)


title: Cy14D16_03G2 (MS293_029)

description: Library name: Sample280

value: 15 Cumulus cells, 16 days cultured preantral follicle (follicle No.3), Cy14 ( 8y, E17 pregnant)


title: Hs4_G19 (MS232_121)

description: Library name: Sample121

value: 10-20 granulosa cells, transitional follicle, Hs4, Age13, Hodgikin lymphoma (before chemotherapy)


title: Hs6_G02 (MS234_095)

description: Library name: Sample127


title: Hs6_G01 (MS234_094)

description: Library name: Sample126


title: Cy14D16_03G1 (MS293_028)

description: Library name: Sample279


title: Cy14D16_03O (MS305_205)

description: Library name: Sample278

value: Oocyte (121 um), 16 days cultured preantral follicle (follicle No.3), Cy14 ( 8y, E17 pregnant)


title: Hs4_O19 (MS232_120)

description: Library name: Sample120


title: Hs4_G20 (MS232_123)

description: Library name: Sample123


title: Hs4_G18 (MS232_119)

description: Library name: Sample119


title: Hs4_O18 (MS232_118)

description: Library name: Sample118


title: Cy14D16_04G1 (MS293_033)

description: Library name: Sample282

value: IVG culture for 16 days


title: Cy14D16_01G1 (MS293_020)

description: Library name: Sample275

value: 15 Cumulus cells, 16 days cultured preantral follicle (follicle No.1), Cy14 ( 8y, E17 pregnant)


title: Hs4_G17 (MS232_117)

description: Library name: Sample117


title: Cy14D16_02O (MS305_204)

description: Library name: Sample276

value: Oocyte (118 um), 16 days cultured preantral follicle (follicle No.2), Cy14 ( 8y, E17 pregnant)


title: Cy14D16_02G1 (MS293_024)

description: Library name: Sample277

value: Ovary

value: 15 Cumulus cells, 16 days cultured preantral follicle (follicle No.2), Cy14 ( 8y, E17 pregnant)


title: Hs4_O17 (MS232_116)

description: Library name: Sample116

value: wildtype


title: Hs4_G16 (MS232_115)

description: Library name: Sample115


title: Cy15D23_05G1 (MS293_059)

description: Library name: Sample302

value: IVG culture for 23 days

value: 15 Cumulus cells, 23 days cultured preantral follicle (follicle No.5), Cy16 ( 6y, dead due to intestinal lymphoma)


title: Hs4_O09 (MS232_113)

description: Library name: Sample113

value: Oocyte

value: oocyte, early secondary follicle, Hs4, Age13, Hodgikin lymphoma (before chemotherapy)


title: Hs4_O15 (MS232_114)

description: Library name: Sample114

value: oocyte, transitional follicle, Hs4, Age13, Hodgikin lymphoma (before chemotherapy)


title: Cy14D16_01O (MS305_203)

description: Library name: Sample274

value: Oocyte (110 um), 16 days cultured preantral follicle (follicle No.1), Cy14 ( 8y, E17 pregnant)


title: Hs6_O11a (MS234_110)

description: Library name: Sample142

value: oocyte, primordial follicle, fresh human ovary ,Hs6, 38y, fresh ovary


title: Cy9F_23G (MS251_112)

description: Library name: Sample271

value: Granulosa cell

value: 10-20 granulosa cells,  early secondary follicle, fresh adult cynomolgus ovary (in pregnant E59), Cy9, age11, fresh ovary


title: Cy9F_24G (MS251_114)

description: Library name: Sample273


title: Cy9F_23O (MS251_111)

description: Library name: Sample270

value: oocyte, early secondary follicle, fresh adult cynomolgus ovary (in pregnant E59), Cy9, age11, fresh ovary


title: Hs4_G07 (MS232_110)

description: Library name: Sample110

value: 10-20 granulosa cells, antral follicle, Hs4, Age13, Hodgikin lymphoma (before chemotherapy)


title: Cy9F_22G (MS257_214)

description: Library name: Sample269

value: 10-20 granulosa cells,  primary-secondary follicle, fresh adult cynomolgus ovary (in pregnant E59), Cy9, age11, fresh ovary


title: Hs4_G06 (MS232_108)

description: Library name: Sample108


title: Hs4_G08 (MS232_112)

description: Library name: Sample112


title: Cy15D23_02G1 (MS293_050)

description: Library name: Sample293

value: 15 Cumulus cells, 23 days cultured preantral follicle (follicle No.2), Cy16 ( 6y, dead due to intestinal lymphoma)


title: Hs4_O06 (MS232_107)

description: Library name: Sample107

value: oocyte, antral follicle, Hs4, Age13, Hodgikin lymphoma (before chemotherapy)


title: Cy9F_21G (MS251_108)

description: Library name: Sample267

value: Ovary


title: WT, stigma, α-IgG, replicate 1, Cut&Tag

value: stigma

value: WT


title: Cy9F_22O (MS251_109)

description: Library name: Sample268

value: wildtype

value: oocyte, primary-secondary follicle, fresh adult cynomolgus ovary (in pregnant E59), Cy9, age11, fresh ovary


title: Cy9F_20G (MS257_213)

description: Library name: Sample265


title: Hs4_G05 (MS232_106)

description: Library name: Sample106

value: 10-20 granulosa cells, early secondary follicle, Hs4, Age13, Hodgikin lymphoma (before chemotherapy)


title: Cy9F_21O (MS251_107)

description: Library name: Sample266

value: Oocyte


title: Cy9F_20O (MS251_105)

description: Library name: Sample264


title: Hs4_O07 (MS232_109)

description: Library name: Sample109


title: Hs4_G04 (MS232_104)

description: Library name: Sample104


title: Cy9F_19G (MS257_212)

description: Library name: Sample263

value: 10-20 granulosa cells,  primary follicle, fresh adult cynomolgus ovary (in pregnant E59), Cy9, age11, fresh ovary


title: Hs4_O05 (MS232_105)

description: Library name: Sample105

value: oocyte, early secondary follicle, Hs4, Age13, Hodgikin lymphoma (before chemotherapy)


title: Hs4_O04 (MS232_103)

description: Library name: Sample103


title: Hs4_O08 (MS232_111)

description: Library name: Sample111


title: Hs4_O03 (MS232_101)

description: Library name: Sample101


title: Cy9F_18O (MS251_101)

description: Library name: Sample260

value: oocyte, primary follicle, fresh adult cynomolgus ovary (in pregnant E59), Cy9, age11, fresh ovary


title: Hs4_G02 (MS232_100)

description: Library name: Sample100

value: Granulosa cell


title: Hs4_O01 (MS232_097)

description: Library name: Sample97


title: Cy9F_18G (MS257_211)

description: Library name: Sample261


title: Hs4_G03 (MS233_124)

description: Library name: Sample102


title: Cy9F_16G (MS257_210)

description: Library name: Sample258

value: 10-20 granulosa cells,  antral follicle, fresh adult cynomolgus ovary (in pregnant E59), Cy9, age11, fresh ovary


title: Cy9F_15G (MS251_097)

description: Library name: Sample256


title: Cy9F_16O (MS251_098)

description: Library name: Sample257

value: oocyte, antral follicle, fresh adult cynomolgus ovary (in pregnant E59), Cy9, age11, fresh ovary


title: Hs4_O02 (MS232_099)

description: Library name: Sample99


title: Hs3_G21 (MS232_096)

description: Library name: Sample96

value: 10-20 granulosa cells, transitional follicle, Hs3, age40, ovarian seromucinous borderline tumor (sample from intact ovary)


title: Cy9F_14G (MS251_095)

description: Library name: Sample254


title: Cy9F_15O (MS251_096)

description: Library name: Sample255


title: Hs6_O15 (MS234_121)

description: Library name: Sample153

value: oocyte, primary follicle, fresh human ovary ,Hs6, 38y, fresh ovary


title: Hs3_O21 (MS232_095)

description: Library name: Sample95

value: oocyte, transitional follicle, Hs3, age40, ovarian seromucinous borderline tumor (sample from intact ovary)


title: Cy9F_17G (MS251_100)

description: Library name: Sample259

value: 10-20 granulosa cells,  secondary follicle, fresh adult cynomolgus ovary (in pregnant E59), Cy9, age11, fresh ovary


title: Hs3_G20 (MS232_094)

description: Library name: Sample94

value: Ovary

value: 10-20 granulosa cells, early secondary follicle, Hs3, age40, ovarian seromucinous borderline tumor (sample from intact ovary)


title: Cy15D23_06G2 (MS293_063)

description: Library name: Sample306

value: IVG culture for 23 days

value: 15 Cumulus cells, 23 days cultured preantral follicle (follicle No.6), Cy16 ( 6y, dead due to intestinal lymphoma)


title: Cy9F_24O (MS251_113)

description: Library name: Sample272

value: wildtype

value: oocyte, early secondary follicle, fresh adult cynomolgus ovary (in pregnant E59), Cy9, age11, fresh ovary


title: Cy9F_13G (MS251_093)

description: Library name: Sample252


title: Cy9F_14O (MS251_094)

description: Library name: Sample253

value: Oocyte


title: Cy15D23_05O (MS305_211)

description: Library name: Sample301

value: Oocyte (113 um), 23 days cultured preantral follicle (follicle No.5), Cy16 ( 6y, dead due to intestinal lymphoma)


title: Hs4_G01 (MS232_098)

description: Library name: Sample98

value: 10-20 granulosa cells, early secondary follicle, Hs4, Age13, Hodgikin lymphoma (before chemotherapy)


title: Hs3_O20 (MS232_093)

description: Library name: Sample93

value: oocyte, early secondary follicle, Hs3, age40, ovarian seromucinous borderline tumor (sample from intact ovary)


title: Cy15D23_07G1 (MS293_065)

description: Library name: Sample308

value: Granulosa cell

value: 15 Cumulus cells, 23 days cultured preantral follicle (follicle No.7), Cy16 ( 6y, dead due to intestinal lymphoma)


title: Cy9F_13O (MS251_092)

description: Library name: Sample251

value: oocyte, antral follicle, fresh adult cynomolgus ovary (in pregnant E59), Cy9, age11, fresh ovary


title: Hs6_G11 (MS234_112)

description: Library name: Sample144

value: 10-20 granulosa cells, primordial follicle, fresh human ovary ,Hs6, 38y, fresh ovary


title: Hs4_O20 (MS232_122)

description: Library name: Sample122

value: oocyte, transitional follicle, Hs4, Age13, Hodgikin lymphoma (before chemotherapy)


title: Hs3_G18 (MS232_090)

description: Library name: Sample90

value: 10-20 granulosa cells, primary follicle, Hs3, age40, ovarian seromucinous borderline tumor (sample from intact ovary)


title: Hs3_G19 (MS232_092)

description: Library name: Sample92


title: Hs3_O19 (MS232_091)

description: Library name: Sample91

value: oocyte, primary follicle, Hs3, age40, ovarian seromucinous borderline tumor (sample from intact ovary)


title: Cy9F_11G (MS257_209)

description: Library name: Sample248

value: Ovary

value: 10-20 granulosa cells,  preantral follicle, fresh adult cynomolgus ovary (in pregnant E59), Cy9, age11, fresh ovary


title: Cy9F_12G (MS251_091)

description: Library name: Sample250


title: Hs3_O18 (MS232_089)

description: Library name: Sample89


title: Hs3_O17 (MS232_087)

description: Library name: Sample87


title: Cy9F_11O (MS251_088)

description: Library name: Sample247

value: oocyte, preantral follicle, fresh adult cynomolgus ovary (in pregnant E59), Cy9, age11, fresh ovary


title: Hs3_G17 (MS232_088)

description: Library name: Sample88


title: Hs3_G15 (MS232_084)

description: Library name: Sample84

value: 10-20 granulosa cells, transitional follicle, Hs3, age40, ovarian seromucinous borderline tumor (sample from intact ovary)


title: Hs3_G16 (MS232_086)

description: Library name: Sample86

value: wildtype


title: Cy9F_08O (MS251_082)

description: Library name: Sample241

value: oocyte, secondary follicle, fresh adult cynomolgus ovary (in pregnant E59), Cy9, age11, fresh ovary


title: Cy9F_10O (MS251_086)

description: Library name: Sample245

value: Oocyte


title: Cy9F_09G (MS251_085)

description: Library name: Sample244

value: 10-20 granulosa cells,  secondary follicle, fresh adult cynomolgus ovary (in pregnant E59), Cy9, age11, fresh ovary


title: Hs3_G14 (MS232_082)

description: Library name: Sample82


title: Cy9F_09O (MS251_084)

description: Library name: Sample243


title: Hs3_O14 (MS232_081)

description: Library name: Sample81

value: oocyte, transitional follicle, Hs3, age40, ovarian seromucinous borderline tumor (sample from intact ovary)


title: Cy9F_08G (MS251_083)

description: Library name: Sample242


title: Cy9F_12O (MS251_090)

description: Library name: Sample249


title: Hs3_G13 (MS232_080)

description: Library name: Sample80


title: Cy9F_07G (MS257_206)

description: Library name: Sample240

value: 10-20 granulosa cells,  transitional follicle, fresh adult cynomolgus ovary (in pregnant E59), Cy9, age11, fresh ovary


title: Hs3_O16 (MS232_085)

description: Library name: Sample85


title: Cy9F_06O (MS251_079)

description: Library name: Sample238

value: oocyte, transitional follicle, fresh adult cynomolgus ovary (in pregnant E59), Cy9, age11, fresh ovary


title: Cy9F_05G (MS251_078)

description: Library name: Sample237

value: Granulosa cell


title: Cy9F_06G (MS263_243)

description: Library name: Sample239


title: Hs3_O12 (MS232_077)

description: Library name: Sample77


title: Cy9F_04G (MS251_076)

description: Library name: Sample235

value: 10-20 granulosa cells,  primordial follicle, fresh adult cynomolgus ovary (in pregnant E59), Cy9, age11, fresh ovary


title: Cy9F_05O (MS251_077)

description: Library name: Sample236


title: Hs3_O15 (MS232_083)

description: Library name: Sample83


title: Hs3_O11c (MS232_075)

description: Library name: Sample75

value: oocyte, primordial follicle, Hs3, age40, ovarian seromucinous borderline tumor (sample from intact ovary)


title: Hs3_O11b (MS232_074)

description: Library name: Sample74

value: 10-20 granulosa cells, primordial follicle, Hs3, age40, ovarian seromucinous borderline tumor (sample from intact ovary)


title: Hs3_G12 (MS232_078)

description: Library name: Sample78


title: Hs3_G11 (MS232_076)

description: Library name: Sample76


title: Hs3_O13 (MS232_079)

description: Library name: Sample79


title: Hs3_G10 (MS232_072)

description: Library name: Sample72


title: Hs3_O11a (MS232_073)

description: Library name: Sample73


title: Cy9F_02O (MS251_072)

description: Library name: Sample232

value: oocyte, primordial follicle, fresh adult cynomolgus ovary (in pregnant E59), Cy9, age11, fresh ovary


title: Cy9F_03G (MS263_240)

description: Library name: Sample233


title: Cy9F_04O (MS251_075)

description: Library name: Sample234


title: CyDF_11G (MS251_070)

description: Library name: Sample230

value: CyD, age8, 10-20 granulosa cells, M2 COC picked up from adult monkey


title: CyDF_09G (MS251_066)

description: Library name: Sample226

value: Ovary


title: Hs3_G08 (MS232_068)

description: Library name: Sample68

value: 10-20 granulosa cells, late secondary follicle, Hs3, age40, ovarian seromucinous borderline tumor (sample from intact ovary)


title: Hs3_O09 (MS232_069)

description: Library name: Sample69

value: oocyte, late secondary follicle, Hs3, age40, ovarian seromucinous borderline tumor (sample from intact ovary)


title: Cy9F_01O (MS251_071)

description: Library name: Sample231


title: Cy15D23_07O (MS321_220)

description: Library name: Sample307

value: IVG culture for 23 days

value: Oocyte (117 um), 23 days cultured preantral follicle (follicle No.7), Cy16 ( 6y, dead due to intestinal lymphoma)


title: Hs3_G07 (MS232_066)

description: Library name: Sample66

value: wildtype


title: CyDF_10O (MS251_067)

description: Library name: Sample227

value: Oocyte

value: CyD, age8, oocyte, M2 COC picked up from adult monkey


title: CyDF_11O (MS251_069)

description: Library name: Sample229


title: Hs3_G09 (MS232_070)

description: Library name: Sample70


title: Hs3_O10 (MS232_071)

description: Library name: Sample71


title: CyDF_07G (MS251_062)

description: Library name: Sample222


title: Hs3_G05 (MS232_062)

description: Library name: Sample62

value: 10-20 granulosa cells, early secondary follicle, Hs3, age40, ovarian seromucinous borderline tumor (sample from intact ovary)


title: Hs3_G06 (MS232_064)

description: Library name: Sample64


title: Hs3_O07 (MS232_065)

description: Library name: Sample65


title: Hs3_O06 (MS232_063)

description: Library name: Sample63


title: CyDF_10G (MS251_068)

description: Library name: Sample228


title: CyDF_08G (MS251_064)

description: Library name: Sample224

value: CyD, age8, 10-20 granulosa cells, GV COC picked up from adult monkey


title: Hs3_O08 (MS232_067)

description: Library name: Sample67


title: CyDF_07O (MS251_061)

description: Library name: Sample221


title: CyDF_04G (MS251_059)

description: Library name: Sample219

value: CyD, age8, 10-20 granulosa cells, M1 COC picked up from adult monkey


title: Hs3_G04 (MS232_060)

description: Library name: Sample60

value: Granulosa cell


title: CyDF_08O (MS251_063)

description: Library name: Sample223

value: CyD, age8, oocyte, GV COC picked up from adult monkey


title: CyDF_02G (MS251_055)

description: Library name: Sample215


title: Hs3_O04 (MS232_059)

description: Library name: Sample59

value: oocyte, early secondary follicle, Hs3, age40, ovarian seromucinous borderline tumor (sample from intact ovary)


title: CyDF_03G (MS251_057)

description: Library name: Sample217


title: CyDF_03O (MS251_056)

description: Library name: Sample216


title: Hs3_G02 (MS232_056)

description: Library name: Sample56

value: 10-20 granulosa cells, COC from large antral follicle, Hs3, age40, ovarian seromucinous borderline tumor (sample from intact ovary)


title: Hs3_O05 (MS232_061)

description: Library name: Sample61


title: Hs3_O03 (MS232_057)

description: Library name: Sample57


title: Hs3_G03 (MS232_058)

description: Library name: Sample58


title: Hs3_G01 (MS232_054)

description: Library name: Sample54


title: CyDF_02O (MS251_054)

description: Library name: Sample214


title: Hs3_O02 (MS232_055)

description: Library name: Sample55

value: oocyte, COC from large antral follicle, Hs3, age40, ovarian seromucinous borderline tumor (sample from intact ovary)


title: CyDF_01G (MS251_053)

description: Library name: Sample213


title: Hs3_O01 (MS232_053)

description: Library name: Sample53


title: CyCF_03G (MS239_057)

description: Library name: Sample211

value: CyC, age8, OPU, 10-20 granulosa cells, M1 COC piked up from adult monkey


title: CyDF_01O (MS251_052)

description: Library name: Sample212

value: Ovary


title: CyDF_04O (MS251_058)

description: Library name: Sample218

value: CyD, age8, oocyte, M1 COC picked up from adult monkey


title: Hs2_G19 (MS232_052)

description: Library name: Sample52

value: 10-20 granulosa cells, early secondary follicle, Hs2, age15, Acute lymphoblastic leukemia (post chemotherapy; JPLSG ALL-B12 protocol)


title: CyDF_05O (MS251_060)

description: Library name: Sample220


title: CDXX brain 6

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

description: Library name: 1213_2024

data_processing:
Adapters from reads were removed using TrimGalore with degault parameters.
Reads were aligned to the dm6 version of dmelanogaster using STAR (v.2.7.10a) with default parameters
Count matrix was generated using the featureCounts function from the Rsubread R package  using the enembl gene annotation
Assembly: dm6
Supplementary files format and content: Count matrix in excel format

organism: Drosophila melanogaster

source_name: Brain

growth_protocol: All the organisms were maintained in BDSC Standard Cornmeal Medium (https://bdsc.indiana.edu/information/recipes/bloomfood.html). Larvae were maintained at 25 ºC before dissection.

extract_protocol:
1) Thaw lysis buffer (Functional Genomics Core Facility, FGCF) and confirm there are no precipitated salts. If so, vortex and spin. 2) Add 45 μL of lysis buffer into each Eppendorf (1.5 mL RNAse-free Eppendorf). Maintain the tube embebed in ice. 3) Select the larvae of interest and keep them in PBS in a well on ice.4) Dissect the tissue from the larvae in PBS and place the tissue fragment in the lysis buffer. Homogenize the tissue 5-10 times with the pipette. 5) Close the lid of the tube, perform a quick spin and incubate for 15 min at 65ºC in heat-block or a water bath. 6) After the incubation, spin down the tubes to recover condensates. 7) Save immediately the tubes at -20ºC/ -80ºC for submission to the FGCF.
RNA libraries were prepared for sequencing using the kits NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat# E7490) and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (Cat#E7770), following manufacturer´s instructions and 13 cycles of amplification

value: Brain

value: CDXX

tag: batch


title: Hs2_G18 (MS232_050)

description: Library name: Sample50

value: wildtype

value: 10-20 granulosa cells, primary follicle, Hs2, age15, Acute lymphoblastic leukemia (post chemotherapy; JPLSG ALL-B12 protocol)


title: T2L brain 6

description: Library name: 1211_2024


title: CDXY brain 6

description: Library name: 1212_2024

value: CDXY


title: C2L brain 6

description: Library name: 1210_2024


title: CyCF_01G (MS252_214)

description: Library name: Sample207

value: CyC, age8, OPU, 10-20 granulosa cells, GV COC piked up from adult monkey


title: Hs2_G16 (MS232_048)

description: Library name: Sample48


title: CyCF_02O (MS239_054)

description: Library name: Sample208

value: Oocyte

value: CyC, age8, OPU, oocyte, M2 COC piked up from adult monkey


title: CyCF_03O (MS239_056)

description: Library name: Sample210

value: CyC, age8, OPU, oocyte, M1 COC piked up from adult monkey


title: CyCF_02G (MS239_055)

description: Library name: Sample209

value: Granulosa cell

value: CyC, age8, OPU, 10-20 granulosa cells, M2 COC piked up from adult monkey


title: Hs2_G15 (MS232_047)

description: Library name: Sample47


title: CDX/X BRAIN 5

description: Library name: 0937_2024


title: T2L BRAIN 5

description: Library name: 0939_2024


title: Hs2_O19 (MS232_051)

description: Library name: Sample51

value: oocyte, early secondary follicle, Hs2, age15, Acute lymphoblastic leukemia (post chemotherapy; JPLSG ALL-B12 protocol)


title: C2L BRAIN 5

description: Library name: 0938_2024


title: Ore brain 6

description: Library name: 1209_2024

value: Oregon


title: CyCF_01O (MS239_052)

description: Library name: Sample206

value: CyC, age8, OPU, oocyte, GV COC piked up from adult monkey


title: CDX/Y BRAIN 5

description: Library name: 0936_2024


title: Hs2_O17 (MS232_049)

description: Library name: Sample49

value: Ovary

value: oocyte, primary follicle, Hs2, age15, Acute lymphoblastic leukemia (post chemotherapy; JPLSG ALL-B12 protocol)


title: CyBF_15G (MS239_029)

description: Library name: Sample205

value: CyB, age6, OPU, 10-20 granulosa cells, GV COC piked up from adult monkey


title: Hs4_G21 (MS232_125)

description: Library name: Sample125

value: 10-20 granulosa cells, transitional follicle, Hs4, Age13, Hodgikin lymphoma (before chemotherapy)


title: ORE BRAIN 5

description: Library name: 0935_2024

value: Brain


title: Hs2_O15 (MS232_046)

description: Library name: Sample46

value: wildtype


title: CyBF_15O (MS239_028)

description: Library name: Sample204

value: CyB, age6, OPU, oocyte, GV COC piked up from adult monkey


title: T2L BRAIN 4

description: Library name: 0922_2024


title: CDX/X BRAIN 4

description: Library name: 0920_2024

value: CDXX


title: Hs2_G06 (MS232_045)

description: Library name: Sample45

value: 10-20 granulosa cells, COC from unknown follicle, Hs2, age15, Acute lymphoblastic leukemia (post chemotherapy; JPLSG ALL-B12 protocol)


title: Hs2_G05 (MS232_044)

description: Library name: Sample44

value: 10-20 granulosa cells, antral follicle, Hs2, age15, Acute lymphoblastic leukemia (post chemotherapy; JPLSG ALL-B12 protocol)


title: CyBF_14G (MS252_206)

description: Library name: Sample203


title: C2L BRAIN 4

description: Library name: 0921_2024


title: Hs2_O05 (MS232_043)

description: Library name: Sample43

value: Oocyte

value: oocyte, antral follicle, Hs2, age15, Acute lymphoblastic leukemia (post chemotherapy; JPLSG ALL-B12 protocol)


title: CyBF_14O (MS239_026)

description: Library name: Sample202


title: ctrl brain 5

description: Library name: 0933_2024

growth_protocol: All the organisms where maintained in BDSC Standard Cornmeal Medium (https://bdsc.indiana.edu/information/recipes/bloomfood.html). Larvae were maintained at 29 ºC before dissection.

value: ctrl


title: CIN brain 5

description: Library name: 0934_2024

value: CIN


title: ctrl brain 6

description: Library name: 1224_2024


title: ORE BRAIN 4

description: Library name: 0918_2024


title: Cy14D16_05G1 (MS293_038)

description: Library name: Sample285

value: Granulosa cell

value: IVG culture for 16 days

value: 15 Cumulus cells, 16 days cultured preantral follicle (follicle No.5), Cy14 ( 8y, E17 pregnant)


title: Hs2_G04 (MS232_042)

description: Library name: Sample42

value: Ovary


title: CyBF_13O (MS239_024)

description: Library name: Sample200

value: CyB, age6, OPU, oocyte, M1 COC piked up from adult monkey


title: CDX/Y BRAIN 4

description: Library name: 0919_2024

value: CDXY


title: Hs2_O04 (MS232_041)

description: Library name: Sample41


title: CyBF_12O (MS239_022)

description: Library name: Sample199

value: CyB, age6, OPU, oocyte, M2 COC piked up from adult monkey


title: CIN brain 4

description: Library name: 0917_2024

value: Brain


title: RPMI 2650 Hypoxia ATAC-seq 3

city: Cheongju

first: Chaelin

last: You

address: Chungdae-ro 1, Seowon-Gu

country: South Korea

institute: Chungbuk National University

description: Library name: Hypoxia 3

data_processing:
Raw ATAC-seq reads were trimmed using Trim Galore with default parameters to ensure data quality. The trimmed reads were then aligned to the human reference genome (hg38) using Bowtie2. To identify open chromatin regions (peaks) over background signals, HOMER software was utilized, employing the makeTagDirectory and findPeaks commands. Bigwig files were generated using the bamCoverage command from deepTools.
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: peaks.txt

source_name: Nasal squamous cell carcinoma

growth_protocol: RPMI 2650 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. The cells were maintained in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
RPMI 2650 cells (hypoxic/normoxic) were washed with PBS and harvested using TrypLE Express. For nuclei isolation, 60,000 counted cells were resuspended in 50 μL cold lysis buffer (RSB with 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin). Lysis was performed on ice for 3 min. Nuclei were then washed with 1 mL of RSB with 0.1% Tween-20, followed by centrifugation at 500 × g for 10 min at 4°C.
Isolated nuclei were resuspended in 50 μL of transposition mix (Illumina TD Tagment DNA Buffer and TDE1 Tagment DNA Enzyme, with DPBS, digitonin, Tween-20, and nuclease-free water). Transposition was performed at 37°C for 30 min with shaking at 1000 RPM. Transposed DNA was cleaned up using the MinElute Reaction Cleanup Kit. Libraries were pre-amplified for 5 cycles using NEBNext® High-Fidelity 2X PCR Master Mix (NEB) with Illumina/Nextera adapter primers. Optimal additional cycles were determined by amplification profile assessment. Final libraries were purified using AMPure XP beads. Library quality was validated via Agilent High Sensitivity D1000 kit prior to high-throughput sequencing on an Illumina NovaSeq 6000 Sequencer.

treatment_protocol: RPMI 2650 cells were exposed to normoxic and hypoxic conditions for 24 hours.

value: Nasal squamous cell carcinoma

value: RPMI 2650

value: Epithelial cell

value: Hypoxia for 24 hours


title: ctrl brain 4

description: Library name: 0916_2024


title: Hs2_O02 (MS232_039)

description: Library name: Sample39

value: wildtype

value: oocyte, COC from unknown follicle, Hs2, age15, Acute lymphoblastic leukemia (post chemotherapy; JPLSG ALL-B12 protocol)


title: CyBF_13G (MS239_025)

description: Library name: Sample201

value: CyB, age6, OPU, 10-20 granulosa cells, M1 COC piked up from adult monkey


title: Hs2_O01 (MS232_038)

description: Library name: Sample38

value: Oocyte


title: RPMI 2650 Normoxia ATAC-seq 3

description: Library name: Normoxia 3

value: Normoxia for 24 hours


title: CyBF_10G (MS239_019)

description: Library name: Sample196

value: Granulosa cell

value: CyB, age6, OPU, 10-20 granulosa cells, M2 COC piked up from adult monkey


title: CyDF_09O (MS251_065)

description: Library name: Sample225

value: CyD, age8, oocyte, M2 COC picked up from adult monkey


title: Hs2_G03 (MS232_040)

description: Library name: Sample40

value: Ovary

value: 10-20 granulosa cells, COC from unknown follicle, Hs2, age15, Acute lymphoblastic leukemia (post chemotherapy; JPLSG ALL-B12 protocol)


title: CyBF_11O (MS239_020)

description: Library name: Sample197

value: CyB, age6, OPU, oocyte, M1 COC piked up from adult monkey


title: RPMI 2650 Hypoxia RNA-seq 2

description: Library name: Hypoxia 2

data_processing:
The raw data were processed by trimming with Trim Galore, and the reads were subsequently aligned to the human reference genome hg38 using the STAR aligner with default parameters. Gene expression levels in each sample were normalized using fragments per kilobase of transcript per million mapped reads (FPKM).
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA was extracted using the Ribospin II kit following the manufacturer’s protocol.
Following RNA extraction, sequencing libraries were constructed using the Illumina TruSeq RNA Library Prep Kit following the manufacturer’s guidelines.


title: CyBF_11G (MS252_204)

description: Library name: Sample198


title: Hs1_G18 (MS232_035)

description: Library name: Sample35

value: 10-20 granulosa cells, secondary follicle, Hs1, age1, EBV-associated lymphoproliferativedisorders (post chemotherapy; modified CHOP)


title: RPMI 2650 Hypoxia ATAC-seq 1

description: Library name: Hypoxia 1


title: RPMI 2650 Hypoxia RNA-seq 1

description: Library name: Hypoxia 1


title: CyBF_09G (MS239_017)

description: Library name: Sample194


title: Hs1_G19 (MS232_037)

description: Library name: Sample37


title: RPMI 2650 Normoxia ATAC-seq 2

description: Library name: Normoxia 2


title: CyBF_10O (MS239_018)

description: Library name: Sample195

value: CyB, age6, OPU, oocyte, M2 COC piked up from adult monkey


title: RPMI 2650 Normoxia ATAC-seq 1

description: Library name: Normoxia 1

value: Nasal squamous cell carcinoma


title: RPMI 2650 Hypoxia ATAC-seq 2

description: Library name: Hypoxia 2

value: RPMI 2650


title: Hs1_O19 (MS232_036)

description: Library name: Sample36

value: oocyte, secondary follicle, Hs1, age1, EBV-associated lymphoproliferativedisorders (post chemotherapy; modified CHOP)


title: RPMI 2650 Normoxia RNA-seq 3

description: Library name: Normoxia 3

value: Epithelial cell


title: RPMI 2650 Normoxia RNA-seq 1

description: Library name: Normoxia 1


title: RPMI 2650 Normoxia RNA-seq 2

description: Library name: Normoxia 2


title: Hs1_O18 (MS232_034)

description: Library name: Sample34

value: wildtype


title: CyBF_09O (MS239_016)

description: Library name: Sample193


title: CA8

data_processing:
The raw data were processed by trimming with Trim Galore, and the reads were subsequently aligned to the human reference genome hg38 using the STAR aligner71 with default parameters. Gene expression levels in each sample were normalized using fragments per kilobase of transcript per million mapped reads (FPKM).
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample

source_name: SNSCC tumor

extract_protocol:
RNA was extracted from tumor specimens in accordance with the RNeasy® Mini kit (Qiagen). Briefly, tumor specimens were dissociated in Buffer RLT and homogenized. The lysate was centrifuged, the supernatant was carefully removed by pipetting, and it was transferred to a new microcentrifuge tube. One volume of 70% ethanol was added to the cleared lysate, and the sample was transferred to a RNeasy spin column placed in a 2 ml collection tube and centrifuged, and the supernatant was discarded. For DNase digestion of RNA, 350 µl Buffer RW1 was added to the RNeasy spin column and centrifuged, and the supernatant was discarded. 10 µl DNase I stock solution was added to 70 µl Buffer RDD and mixed by gently inverting the tube. The DNase I incubation mix (80 µl) was added directly to the RNeasy spin column membrane and placed on the benchtop (20–30°C) for 15 min, then 350 µl Buffer RW1 was added to the RNeasy spin column and centrifuged, and the supernatant was discarded. 500 µl Buffer RPE was added to the RNeasy spin column, centrifuged to wash the spin column membrane and discard the flow-through. The RNeasy spin column was placed in a new 1.5 ml collection tube, and 50 µl RNAse-free water was added directly to the spin column membrane and centrifuged to elute the RNA. RNA concentration was quantified by measuring UV absorbance at 260 nm with a spectrophotometer and RNA integrity was checked using an Agilent Technologies 2100 Bioanalyzer with an RNA Integrity Number (RIN) value greater than or equal to 7.0.
Following RNA extraction, sequencing libraries were constructed using the Illumina TruSeq RNA Library Prep Kit following the manufacturer’s guidelines.

value: SNSCC tumor


title: CA9


title: CyBF_08G (MS239_015)

description: Library name: Sample192

value: CyB, age6, OPU, 10-20 granulosa cells, GV COC piked up from adult monkey


title: CA7


title: Hs1_O17 (MS232_032)

description: Library name: Sample32

value: Oocyte

value: oocyte, primary follicle, Hs1, age1, EBV-associated lymphoproliferativedisorders (post chemotherapy; modified CHOP)


title: Hs1_G17 (MS232_033)

description: Library name: Sample33

value: Granulosa cell

value: 10-20 granulosa cells, primary follicle, Hs1, age1, EBV-associated lymphoproliferativedisorders (post chemotherapy; modified CHOP)


title: RPMI 2650 Hypoxia RNA-seq 3

description: Library name: Hypoxia 3

value: Hypoxia for 24 hours


title: Hs1_G16 (MS232_031)

description: Library name: Sample31

value: Ovary


title: CyBF_08O (MS239_014)

description: Library name: Sample191

value: CyB, age6, OPU, oocyte, GV COC piked up from adult monkey


title: CA5


title: CA1


title: N11

source_name: Nasal mucosa

value: Nasal mucosa


title: N9


title: Hs1_O16 (MS232_030)

description: Library name: Sample30


title: CA2


title: N3


title: N7


title: CA6


title: N10


title: Hs1_G15 (MS232_029)

description: Library name: Sample29


title: Hs1_G14 (MS232_027)

description: Library name: Sample27


title: CyBF_07G (MS252_203)

description: Library name: Sample190


title: N6


title: CyBF_07O (MS239_012)

description: Library name: Sample189


title: CyBF_06G (MS239_011)

description: Library name: Sample188


title: Cy9F_19O (MS251_103)

description: Library name: Sample262

value: oocyte, primary follicle, fresh adult cynomolgus ovary (in pregnant E59), Cy9, age11, fresh ovary


title: N2


title: Hs1_O15 (MS232_028)

description: Library name: Sample28


title: CyBF_05G (MS239_009)

description: Library name: Sample186

value: CyB, age6, OPU, 10-20 granulosa cells, M2 COC piked up from adult monkey


title: SW620, 1H5_5

city: Brooklyn

first: Pargol

last: Mashati

state: New York

address: 2100 Bedford ave, BSB 2-95

country: USA

institute: SUNY Downstate

description: Library name: Sample 11

data_processing:
Raw sequencing reads were quality-checked using FastQC. Adapter sequences and low-quality bases were trimmed before alignment. Clean reads were aligned to the human reference genome (GRCh38) using HISAT2, a graph-based splice-aware aligner optimized for RNA-seq data. Gene-level read counts were generated using the featureCounts program from the Subread package. Count matrices were imported into R for downstream normalization and differential expression analysis
Assembly: GRCh38
Supplementary files format and content: CSV file contain normalized expression values (FPKM).

source_name: human colorectal cancer cell line

extract_protocol:
used Rneasy mini kit for RNA extraction
RNA samples were processed by Novogene using their standard Illumina-compatible stranded mRNA-seq workflow. Poly-A mRNA was enriched with oligo-dT beads, fragmented, and reverse-transcribed to synthesize first- and second-strand cDNA (dUTP method for strand specificity). After end repair, A-tailing, and ligation of indexed Illumina adapters, libraries were PCR-amplified, size-selected, and quality-checked using the Agilent Bioanalyzer/Tapestation before sequencing on the Illumina NovaSeq platform.

value: human colorectal cancer cell line

value: epithelial

value: ADAM10-targeting monoclonal antibody 1H5 (40 μg/mL) for 48 h


title: Hs1_G13 (MS232_025)

description: Library name: Sample25


title: SW620, 1H5_6

description: Library name: Sample 12


title: CyBF_06O (MS239_010)

description: Library name: Sample187


title: CyBF_05O (MS239_008)

description: Library name: Sample185

value: CyB, age6, OPU, oocyte, M2 COC piked up from adult monkey


title: SW620, 1H5_4

description: Library name: Sample 10


title: Cy9F_10G (MS251_087)

description: Library name: Sample246

value: wildtype

value: 10-20 granulosa cells,  preantral follicle, fresh adult cynomolgus ovary (in pregnant E59), Cy9, age11, fresh ovary


title: Hs1_O14 (MS232_026)

description: Library name: Sample26


title: CyBF_04G (MS252_202)

description: Library name: Sample184


title: SW620, CNT_1

description: Library name: Sample 7

value: vehicle control


title: Hs1_G12 (MS232_023)

description: Library name: Sample23


title: DLD-1, 1H5_2

description: Library name: Sample 5


title: CyBF_04O (MS239_006)

description: Library name: Sample183

value: Oocyte


title: DLD-1, 1H5_3

description: Library name: Sample 6


title: Hs1_O12 (MS232_022)

description: Library name: Sample22

value: oocyte, primary follicle, Hs1, age1, EBV-associated lymphoproliferativedisorders (post chemotherapy; modified CHOP)


title: SW620, CNT_3

description: Library name: Sample 9


title: SW620, CNT_2

description: Library name: Sample 8


title: CyBF_03O (MS239_004)

description: Library name: Sample181


title: Hs1_O13 (MS232_024)

description: Library name: Sample24


title: Hs1_G11 (MS232_021)

description: Library name: Sample21

value: Granulosa cell

value: 10-20 granulosa cells, transitional follicle, Hs1, age1, EBV-associated lymphoproliferativedisorders (post chemotherapy; modified CHOP)


title: DLD-1, 1H5_1

description: Library name: Sample 4


title: Hs1_O11 (MS232_020)

description: Library name: Sample20

value: oocyte, transitional follicle, Hs1, age1, EBV-associated lymphoproliferativedisorders (post chemotherapy; modified CHOP)


title: 0128-R1

type: genomic

city: Rotterdam

first: Youri

last: Hoogstrate

address: Wytemaweg 80

department: Neurology

country: Netherlands

institute: Erasmus MC

description: tumor genomic DNA from patient 0128: Oligodendroglioma, WHO grade 3, resection #1

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

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

value: male

value: Oligodendroglioma

tag: grade

value: WHO grade 3

tag: resection

value: resection #1

tag: set

value: GLASS-OD validation set


title: CyBF_03G (MS239_005)

description: Library name: Sample182

value: Ovary

value: CyB, age6, OPU, 10-20 granulosa cells, M2 COC piked up from adult monkey


title: CyBF_02G (MS252_201)

description: Library name: Sample180


title: DLD-1, CNT_3

description: Library name: Sample 3

value: human colorectal cancer cell line

value: epithelial


title: DLD-1, CNT_1

description: Library name: Sample 1


title: 0106-R1

description: tumor genomic DNA from patient 0106: Oligodendroglioma, WHO grade 3, resection #1

value: female


title: 0129-R1

description: tumor genomic DNA from patient 0129: Oligodendroglioma, WHO grade 3, resection #1


title: 0127-R3

description: tumor genomic DNA from patient 0127: Oligodendroglioma, WHO grade 3, resection #3

value: resection #3

value: GLASS-OD


title: 0126-R1

description: tumor genomic DNA from patient 0126: Oligodendroglioma, WHO grade 2, resection #1

value: WHO grade 2


title: Hs1_O09 (MS232_019)

description: Library name: Sample19

value: Oocyte

value: wildtype


title: DLD-1, CNT_2

description: Library name: Sample 2

value: vehicle control


title: Hs1_O08 (MS232_017)

description: Library name: Sample17

value: oocyte, transitional follicle, Hs1, age1, EBV-associated lymphoproliferativedisorders (post chemotherapy; modified CHOP)


title: CyBF_01O (MS239_001)

description: Library name: Sample178

value: CyB, age6, OPU, oocyte, M2 COC piked up from adult monkey


title: Cy2C_23G (MS251_222)

description: Library name: Sample176

value: Granulosa cell

value: 10-20 granulosa cells, early secondary follicle, cryo-thawed adult cynomolgus ovary (in pregnant E16), Cy2, age6, cryo-thawed ovary


title: Hs1_G08 (MS232_018)

description: Library name: Sample18

value: 10-20 granulosa cells, transitional follicle, Hs1, age1, EBV-associated lymphoproliferativedisorders (post chemotherapy; modified CHOP)


title: 0130-R2

description: tumor genomic DNA from patient 0130: Oligodendroglioma, WHO grade 3, resection #2

value: male

value: Oligodendroglioma

value: WHO grade 3

value: resection #2


title: 0126-R2

description: tumor genomic DNA from patient 0126: Oligodendroglioma, WHO grade 2, resection #2


title: Cy2C_24G (MS251_223)

description: Library name: Sample177

value: Ovary


title: 0124-R1

description: tumor genomic DNA from patient 0124: Oligodendroglioma, WHO grade 2, resection #1

value: resection #1


title: Hs1_G07 (MS232_016)

description: Library name: Sample16

value: 10-20 granulosa cells, primordial follicle, Hs1, age1, EBV-associated lymphoproliferativedisorders (post chemotherapy; modified CHOP)


title: CyBF_02O (MS239_002)

description: Library name: Sample179


title: Hs1_O07a (MS232_014)

description: Library name: Sample14

value: oocyte, primordial follicle, Hs1, age1, EBV-associated lymphoproliferativedisorders (post chemotherapy; modified CHOP)


title: 0125-R2

description: tumor genomic DNA from patient 0125: Oligodendroglioma, WHO grade 2, resection #2

value: WHO grade 2

value: GLASS-OD


title: 0123-R1

description: tumor genomic DNA from patient 0123: Oligodendroglioma, WHO grade 2, resection #1


title: 0125-R1

description: tumor genomic DNA from patient 0125: Oligodendroglioma, WHO grade 2, resection #1


title: Cy2C_22G (MS251_221)

description: Library name: Sample174

value: wildtype


title: Hs1_O07b (MS232_015)

description: Library name: Sample15

value: Oocyte


title: 0124-R2

description: tumor genomic DNA from patient 0124: Oligodendroglioma, WHO grade 3, resection #2


title: Cy2C_23O (MS238_176)

description: Library name: Sample175

value: oocyte, early secondary follicle, cryo-thawed adult cynomolgus ovary (in pregnant E16), Cy2, age6, cryo-thawed ovary


title: 0122-R1

description: tumor genomic DNA from patient 0122: Oligodendroglioma, WHO grade 2, resection #1

value: female


title: 0122-R2

description: tumor genomic DNA from patient 0122: Oligodendroglioma, WHO grade 2, resection #2


title: 0123-R2

description: tumor genomic DNA from patient 0123: Oligodendroglioma, WHO grade 2, resection #2


title: 0120-R2

description: tumor genomic DNA from patient 0120: Oligodendroglioma, WHO grade 2, resection #2


title: Hs1_O06a (MS232_012)

description: Library name: Sample12


title: CIN brain 6

description: Library name: 1225_2024

value: Brain

value: CIN


title: Cy2C_22O (MS238_174)

description: Library name: Sample173


title: 0121-R2

description: tumor genomic DNA from patient 0121: Oligodendroglioma, WHO grade 2, resection #2


title: Cy2C_20G (MS251_219)

description: Library name: Sample170

value: Granulosa cell

value: 10-20 granulosa cells, primordial follicle, cryo-thawed adult cynomolgus ovary (in pregnant E16), Cy2, age6, cryo-thawed ovary


title: 0120-R1

description: tumor genomic DNA from patient 0120: Oligodendroglioma, WHO grade 2, resection #1

value: male

value: Oligodendroglioma


title: 0119-R1

description: tumor genomic DNA from patient 0119: Oligodendroglioma, WHO grade 2, resection #1


title: Hs1_O06b (MS232_013)

description: Library name: Sample13


title: 0121-R1

description: tumor genomic DNA from patient 0121: Oligodendroglioma, WHO grade 2, resection #1


title: 0121-R3

description: tumor genomic DNA from patient 0121: Oligodendroglioma, WHO grade 3, resection #3

value: WHO grade 3

value: resection #3


title: Cy2C_21O (MS238_172)

description: Library name: Sample171

value: Ovary

value: oocyte, primordial follicle, cryo-thawed adult cynomolgus ovary (in pregnant E16), Cy2, age6, cryo-thawed ovary


title: Hs1_O05a (MS232_009)

description: Library name: Sample9

value: oocyte, primordial follicle, Hs1, age1, EBV-associated lymphoproliferativedisorders (post chemotherapy; modified CHOP)


title: Hs1_O04b (MS232_007)

description: Library name: Sample7


title: Cy2C_21G (MS251_220)

description: Library name: Sample172


title: 0119-R2

description: tumor genomic DNA from patient 0119: Oligodendroglioma, WHO grade 3, resection #2

value: resection #2


title: 0117-R3

description: tumor genomic DNA from patient 0117: Oligodendroglioma, WHO grade 3, resection #3

value: GLASS-OD


title: Cy2C_18G (MS238_167)

description: Library name: Sample166

value: wildtype


title: 0117-R1

description: tumor genomic DNA from patient 0117: Oligodendroglioma, WHO grade 2, resection #1

value: WHO grade 2

value: resection #1


title: 0115-R2

description: tumor genomic DNA from patient 0115: Oligodendroglioma, WHO grade 2, resection #2

value: female


title: 0116-R2

description: tumor genomic DNA from patient 0116: Oligodendroglioma, WHO grade 3, resection #2


title: Hs1_O05b (MS232_010)

description: Library name: Sample10

value: Oocyte


title: 0114-R2

description: tumor genomic DNA from patient 0114: Oligodendroglioma, WHO grade 3, resection #2


title: Hs1_G05 (MS232_011)

description: Library name: Sample11

value: 10-20 granulosa cells, primordial follicle, Hs1, age1, EBV-associated lymphoproliferativedisorders (post chemotherapy; modified CHOP)


title: 0116-R1

description: tumor genomic DNA from patient 0116: Oligodendroglioma, WHO grade 2, resection #1


title: 0118-R3

description: tumor genomic DNA from patient 0118: Oligodendroglioma, WHO grade 3, resection #3


title: 0118-R4

description: tumor genomic DNA from patient 0118: Oligodendroglioma, WHO grade 3, resection #4

value: resection #4


title: Hs1_O03 (MS232_004)

description: Library name: Sample4


title: 0114-R1

description: tumor genomic DNA from patient 0114: Oligodendroglioma, WHO grade 3, resection #1


title: Cy2C_20O (MS238_170)

description: Library name: Sample169


title: 0113-R2

description: tumor genomic DNA from patient 0113: Oligodendroglioma, WHO grade 2, resection #2


title: 0112-R2

description: tumor genomic DNA from patient 0112: Oligodendroglioma, WHO grade 3, resection #2


title: Cy2C_19O (MS251_217)

description: Library name: Sample167


title: 0112-R1

description: tumor genomic DNA from patient 0112: Oligodendroglioma, WHO grade 2, resection #1


title: 0118-R2

description: tumor genomic DNA from patient 0118: Oligodendroglioma, WHO grade 2, resection #2


title: 0117-R2

description: tumor genomic DNA from patient 0117: Oligodendroglioma, WHO grade 3, resection #2


title: Hs1_G04 (MS232_008)

description: Library name: Sample8

value: Granulosa cell


title: Hs1_G03 (MS232_005)

description: Library name: Sample5


title: Hs1_O01 (MS232_001)

description: Library name: Sample1

value: oocyte, secondary follicle, Hs1, age1, EBV-associated lymphoproliferativedisorders (post chemotherapy; modified CHOP)


title: 0115-R1

description: tumor genomic DNA from patient 0115: Oligodendroglioma, WHO grade 2, resection #1

value: Oligodendroglioma


title: 0109-R2

description: tumor genomic DNA from patient 0109: Oligodendroglioma, WHO grade 2, resection #2

value: male


title: Hs1_O04a (MS232_006)

description: Library name: Sample6


title: Female adult, Abx Morphine 5

city: Winston-Salem

first: Rebecca

last: Hofford

state: NC

address: 115 S Chestnut St

department: Translational Neuroscience

institute: Wake Forest School of Medicine

description: Library name: FMatD5

data_processing:
Reads were removed if they contained adaptor contamination, when nucleotides were uncertain for 10% or more of the read, or the base quality was less than 5 for 50% of the reads.
Aligned using STAR v2.7.10a
Normalized using DESeq2
Differential expression of genes using ExpressAnalyst
Assembly: mm10
Supplementary files format and content: HoffordZeroFemale.csv
Supplementary files format and content: Read counts for all female samples

extract_protocol:
Rneasy Mini Kit (Qiagen)
Fast RNA-seq Library Prep Kit V2 (abclonal Technology)

value: Brain

value: All

value: wild type

value: Female adult, Abx Morphine 5


title: Female adult, Abx Morphine 4

description: Library name: FMatD4

value: Female adult, Abx Morphine 4


title: Cy2C_17G (MS251_216)

description: Library name: Sample164

value: Ovary

value: 10-20 granulosa cells, transitional follicle, cryo-thawed adult cynomolgus ovary (in pregnant E16), Cy2, age6, cryo-thawed ovary


title: 0108-R1

description: tumor genomic DNA from patient 0108: Oligodendroglioma, WHO grade 3, resection #1

value: WHO grade 3

value: GLASS-OD


title: Cy2C_13G (MS251_213)

description: Library name: Sample158

value: wildtype


title: 0110-R2

description: tumor genomic DNA from patient 0110: Oligodendroglioma, WHO grade 3, resection #2

value: female

value: resection #2


title: Cy2C_13O (MS238_157)

description: Library name: Sample157

value: Oocyte

value: oocyte, transitional follicle, cryo-thawed adult cynomolgus ovary (in pregnant E16), Cy2, age6, cryo-thawed ovary


title: Cy2C_16O (MS238_163)

description: Library name: Sample162


title: Cy2C_18O (MS238_166)

description: Library name: Sample165

value: oocyte, primordial follicle, cryo-thawed adult cynomolgus ovary (in pregnant E16), Cy2, age6, cryo-thawed ovary


title: Cy2C_16G (MS251_215)

description: Library name: Sample163

value: Granulosa cell


title: Female adult, Abx Morphine 3

description: Library name: FMatD3

value: Female adult, Abx Morphine 3


title: Hs1_G02 (MS232_003)

description: Library name: Sample3

value: 10-20 granulosa cells, secondary follicle, Hs1, age1, EBV-associated lymphoproliferativedisorders (post chemotherapy; modified CHOP)


title: 0107-R1

description: tumor genomic DNA from patient 0107: Oligodendroglioma, WHO grade 2, resection #1

value: Oligodendroglioma

value: WHO grade 2

value: resection #1


title: Cy2C_15O (MS238_161)

description: Library name: Sample161


title: 0113-R1

description: tumor genomic DNA from patient 0113: Oligodendroglioma, WHO grade 2, resection #1

value: male


title: 0109-R1

description: tumor genomic DNA from patient 0109: Oligodendroglioma, WHO grade 2, resection #1


title: 0108-R3

description: tumor genomic DNA from patient 0108: Oligodendroglioma, WHO grade 3, resection #3

value: resection #3


title: Cy2C_14G (MS251_214)

description: Library name: Sample160

value: Ovary

value: 10-20 granulosa cells, transitional follicle, cryo-thawed adult cynomolgus ovary (in pregnant E16), Cy2, age6, cryo-thawed ovary


title: 0105-R2

description: tumor genomic DNA from patient 0105: Oligodendroglioma, WHO grade 2, resection #2

value: GLASS-OD


title: 0108-R4

description: tumor genomic DNA from patient 0108: Oligodendroglioma, WHO grade 3, resection #4

value: WHO grade 3

value: resection #4


title: Female adult, Abx Morphine 1

description: Library name: FMatD1

value: Brain

value: All

value: wild type

value: Female adult, Abx Morphine 1


title: Spleen lymphotytes cultured with Tmem175-/- BMDMs with tumor antigen and IL-18 3

first: Ziqi

last: Zhang

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

department: National Clinical Research Center for Geriatrics,

institute: West China Hospital, Sichuan University

description: Library name: KOB16-F10-OVAIL-183

data_processing:
We applied fastp with default parameter filtering the adaptor sequence and removed the low quality reads.
Assembly: Mouse GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: spleen and bone marrow

extract_protocol:
RNA was harvested by Trizol (Invitrogen). NovelBio performed the extraction.
RNA libraries for RNA-seq were prepared via poly A.

value: spleen and bone marrow

value: immune cells


title: Cy2C_11G (MS251_211)

description: Library name: Sample155

value: Granulosa cell

value: wildtype

value: 10-20 granulosa cells, primary follicle, cryo-thawed adult cynomolgus ovary (in pregnant E16), Cy2, age6, cryo-thawed ovary


title: Spleen lymphotytes cultured with Tmem175-/- BMDMs with tumor antigen and IL-18 1

description: Library name: KOB16-F10-OVAIL-181


title: Female adult, H2O Morphine 5

description: Library name: FMatC5

value: Female adult, H2O Morphine 5


title: Hs1_G01 (MS232_002)

description: Library name: Sample2

value: 10-20 granulosa cells, secondary follicle, Hs1, age1, EBV-associated lymphoproliferativedisorders (post chemotherapy; modified CHOP)


title: 0107-R2

description: tumor genomic DNA from patient 0107: Oligodendroglioma, WHO grade 3, resection #2

value: female

value: Oligodendroglioma

value: resection #2


title: Spleen lymphotytes cultured with Tmem175-/- BMDMs with tumor antigen and IL-1beta 3

description: Library name: KOB16-OVAIL-13


title: Female adult, Abx Morphine 2

description: Library name: FMatD2

value: Female adult, Abx Morphine 2


title: Female adult, H2O Morphine 3

description: Library name: FMatC3

value: Female adult, H2O Morphine 3


title: Cy2C_09G (MS251_210)

description: Library name: Sample153

value: Ovary


title: Spleen lymphotytes cultured with Tmem175-/- BMDMs with tumor antigen and IL-1beta 2

description: Library name: KOB16-OVAIL-12


title: Cy2C_08O (MS238_149)

description: Library name: Sample152

value: Oocyte

value: oocyte, preantral follicle, cryo-thawed adult cynomolgus ovary (in pregnant E16), Cy2, age6, cryo-thawed ovary


title: 0104-R1

description: tumor genomic DNA from patient 0104: Oligodendroglioma, WHO grade 2, resection #1

value: male

value: WHO grade 2

value: resection #1

value: GLASS-OD