title: Spleen lymphotytes cultured with Tmem175-/- BMDMs with tumor antigen and IL-18 2

description: Library name: KOB16-F10-OVAIL-182

value: spleen and bone marrow

value: immune cells


title: Cy2C_14O (MS238_159)

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: Sample159

library_source: transcriptomic

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

molecule: polyA RNA

organism: Macaca fascicularis

source_name: Ovary

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

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

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

tag: tissue

value: Ovary

tag: cell type

value: Oocyte

tag: genotype

value: wildtype

tag: group

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


title: Cy2C_07O (MS238_147)

description: Library name: Sample150

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


title: Cy2C_11O (MS238_154)

description: Library name: Sample154

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


title: 0102-R2

type: genomic

city: Rotterdam

first: Youri

last: Hoogstrate

address: Wytemaweg 80

department: Neurology

country: Netherlands

institute: Erasmus MC

description: tumor genomic DNA from patient 0102: Oligodendroglioma, WHO grade 3, resection #2

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

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

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

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

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

tag: Sex

value: male

value: Oligodendroglioma

tag: grade

value: WHO grade 3

tag: resection

value: resection #2

tag: set

value: GLASS-OD


title: Female adult, Abx Saline 5

city: Winston-Salem

first: Rebecca

last: Hofford

state: NC

address: 115 S Chestnut St

department: Translational Neuroscience

country: USA

institute: Wake Forest School of Medicine

description: Library name: FMatB5

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

organism: Mus musculus

source_name: Brain

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

value: Brain

value: All

value: wild type

tag: treatment

value: Female adult, Abx Saline 5


title: 0095-R2

description: tumor genomic DNA from patient 0095: Oligodendroglioma, WHO grade 3, resection #2


title: 0101-R2

description: tumor genomic DNA from patient 0101: Oligodendroglioma, WHO grade 2, resection #2

value: WHO grade 2


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

city: Chengdu

first: Ziqi

last: Zhang

state: Sichuan

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

department: National Clinical Research Center for Geriatrics,

country: China

institute: West China Hospital, Sichuan University

description: Library name: KOB16-OVA1

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

tag: cell line

value: immune cells


title: Female adult, H2O Morphine 4

description: Library name: FMatC4

value: Female adult, H2O Morphine 4


title: Cy2C_06O (MS238_145)

description: Library name: Sample148

value: Ovary

value: Oocyte

value: wildtype


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

description: Library name: KOB16-OVAIL-11


title: Female adult, H2O Morphine 2

description: Library name: FMatC2

value: Female adult, H2O Morphine 2


title: Spleen lymphotytes cultured with Tmem175-/- BMDMs without tumor antigen 3

description: Library name: KO3


title: Cy2C_07G (MS251_209)

description: Library name: Sample151

value: Granulosa cell

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


title: Female adult, H2O Morphine 1

description: Library name: FMatC1

value: Female adult, H2O Morphine 1


title: 0100-R2

description: tumor genomic DNA from patient 0100: Oligodendroglioma, WHO grade 3, resection #2

value: female

value: Oligodendroglioma

value: WHO grade 3

value: resection #2


title: Female adult, Abx Saline 4

description: Library name: FMatB4

value: Brain

value: All

value: wild type

value: Female adult, Abx Saline 4


title: Cy2C_06G (MS251_208)

description: Library name: Sample149


title: 0099-R2

description: tumor genomic DNA from patient 0099: Oligodendroglioma, WHO grade 2, resection #2

value: male

value: WHO grade 2

value: GLASS-OD


title: 0095-R1

description: tumor genomic DNA from patient 0095: Oligodendroglioma, WHO grade 2, resection #1

value: resection #1


title: Spleen lymphotytes cultured with Tmem175-/- BMDMs with tumor antigen 2

description: Library name: KOB16-OVA2

value: spleen and bone marrow

value: immune cells


title: Female adult, Abx Saline 3

description: Library name: FMatB3

value: Female adult, Abx Saline 3


title: 0094-R2

description: tumor genomic DNA from patient 0094: Oligodendroglioma, WHO grade 2, resection #2


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

description: Library name: KOB16-OVA3


title: Cy2C_12G (MS251_212)

description: Library name: Sample156

value: Ovary

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: Cy2C_04G (MS238_142)

description: Library name: Sample145

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


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

description: Library name: WTB16-OVAIL-183

value: WT


title: 0094-R1

description: tumor genomic DNA from patient 0094: Oligodendroglioma, WHO grade 2, resection #1

value: Oligodendroglioma


title: Cy2C_05G (MS251_207)

description: Library name: Sample147

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


title: Cy2C_04O (MS238_141)

description: Library name: Sample144

value: Oocyte

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


title: Cy2C_05O (MS238_143)

description: Library name: Sample146

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


title: 0090-R3

description: tumor genomic DNA from patient 0090: Oligodendroglioma, WHO grade 3, resection #3

value: male

value: WHO grade 3

value: resection #3


title: 0091-R2

description: tumor genomic DNA from patient 0091: Oligodendroglioma, WHO grade 3, resection #2

value: female

value: resection #2

value: GLASS-OD


title: Female adult, H2O Saline 4

description: Library name: FMatA4

value: Brain

value: All

value: wild type

value: Female adult, H2O Saline 4


title: Spleen lymphotytes cultured with WT BMDMs with tumor antigen and IL-18 2

description: Library name: WTB16-OVAIL-182

value: spleen and bone marrow

value: immune cells


title: Female adult, Abx Saline 1

description: Library name: FMatB1

value: Female adult, Abx Saline 1


title: Spleen lymphotytes cultured with Tmem175-/- BMDMs without tumor antigen 1

description: Library name: KO1


title: Cy2C_03O (MS238_139)

description: Library name: Sample142

value: Ovary

value: wildtype


title: Female adult, Abx Saline 2

description: Library name: FMatB2

value: Female adult, Abx Saline 2


title: 0092-R3

description: tumor genomic DNA from patient 0092: Oligodendroglioma, WHO grade 3, resection #3

value: Oligodendroglioma


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

description: Library name: WTB16-OVAIL-13

value: WT


title: Cy2C_02G (MS251_205)

description: Library name: Sample141

value: Granulosa cell

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


title: Female adult, H2O Saline 2

description: Library name: FMatA2

value: Female adult, H2O Saline 2


title: 0092-R2

description: tumor genomic DNA from patient 0092: Oligodendroglioma, WHO grade 2, resection #2

value: female

value: WHO grade 2

value: resection #2


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

description: Library name: WTB16-OVAIL-181


title: Female adult, H2O Saline 1

description: Library name: FMatA1

value: Brain

value: All

value: Female adult, H2O Saline 1


title: 0090-R2

description: tumor genomic DNA from patient 0090: Oligodendroglioma, WHO grade 3, resection #2

value: male

value: WHO grade 3

value: GLASS-OD


title: Spleen lymphotytes cultured with Tmem175-/- BMDMs without tumor antigen 2

description: Library name: KO2

value: spleen and bone marrow

value: immune cells


title: Female adult, H2O Saline 5

description: Library name: FMatA5

value: wild type

value: Female adult, H2O Saline 5


title: Cy2C_03G (MS251_206)

description: Library name: Sample143

value: Ovary

value: wildtype


title: 0089-R3

description: tumor genomic DNA from patient 0089: Oligodendroglioma, WHO grade 2, resection #3

value: Oligodendroglioma

value: resection #3


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

description: Library name: WTB16-OVAIL-12

value: WT


title: Female adolescent, Abx Morphine 3

description: Library name: FAdoD3

value: Female adolescent, Abx Morphine 3


title: Cy2C_01O (MS238_135)

description: Library name: Sample138

value: Oocyte

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


title: 0089-R2

description: tumor genomic DNA from patient 0089: Oligodendroglioma, WHO grade 2, resection #2

value: female

value: WHO grade 2

value: resection #2


title: Spleen lymphotytes cultured with WT BMDMs with tumor antigen 2

description: Library name: WTB16-OVA2


title: Spleen lymphotytes cultured with WT BMDMs with tumor antigen 1

description: Library name: WTB16-OVA1


title: Cy2C_02O (MS238_137)

description: Library name: Sample140


title: Cy2C_01G (MS251_204)

description: Library name: Sample139

value: Granulosa cell

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


title: Female adolescent, Abx Morphine 4

description: Library name: FAdoD4

value: Brain

value: All

value: Female adolescent, Abx Morphine 4


title: 0088-R1

description: tumor genomic DNA from patient 0088: Oligodendroglioma, WHO grade 2, resection #1

value: resection #1

value: GLASS-OD


title: Female adolescent, Abx Morphine 5

description: Library name: FAdoD5

value: wild type

value: Female adolescent, Abx Morphine 5


title: Cy5C_16O (MS233_092)

description: Library name: Sample136

value: Ovary

value: wildtype

value: oocyte, early secondary follicle, cryo-thawed adult cynomolgus ovary,Cy5, age7, cryo-thawed ovary


title: Spleen lymphotytes cultured with WT BMDMs with tumor antigen and IL-1beta 1

description: Library name: WTB16-OVAIL-11

value: spleen and bone marrow

value: immune cells

value: WT


title: Female adult, H2O Saline 3

description: Library name: FMatA3

value: Female adult, H2O Saline 3


title: Spleen lymphotytes cultured with WT BMDMs with tumor antigen 3

description: Library name: WTB16-OVA3


title: Female adolescent, Abx Morphine 2

description: Library name: FAdoD2

value: Female adolescent, Abx Morphine 2


title: Spleen lymphotytes cultured with WT BMDMs without tumor antigen 3

description: Library name: WT3


title: 0088-R2

description: tumor genomic DNA from patient 0088: Oligodendroglioma, WHO grade 2, resection #2

value: female

value: Oligodendroglioma

value: WHO grade 2

value: resection #2


title: 0087-R2

description: tumor genomic DNA from patient 0087: Oligodendroglioma, WHO grade 2, resection #2

value: male


title: Female adolescent, H2O Morphine 5

description: Library name: FAdoC5

value: Brain

value: All

value: Female adolescent, H2O Morphine 5


title: Female adolescent, Abx Morphine 1

description: Library name: FAdoD1

value: wild type

value: Female adolescent, Abx Morphine 1


title: Cy5C_15G (MS233_091)

description: Library name: Sample135

value: Ovary

value: Granulosa cell

value: wildtype

value: 10-20 granulosa cells, primary follicle, cryo-thawed adult cynomolgus ovary (in pregnant E16),Cy5, age7, cryo-thawed ovary


title: 0087-R1

description: tumor genomic DNA from patient 0087: Oligodendroglioma, WHO grade 2, resection #1

value: resection #1

value: GLASS-OD


title: 0086-R2

description: tumor genomic DNA from patient 0086: Oligodendroglioma, WHO grade 3, resection #2

value: WHO grade 3


title: Cy5C_14G (MS233_090)

description: Library name: Sample134

value: oocyte, transitional follicle, cryo-thawed adult cynomolgus ovary,Cy5, age7, cryo-thawed ovary


title: Cy5C_18O (MS233_093)

description: Library name: Sample137

value: Oocyte

value: oocyte, early secondary follicle, cryo-thawed adult cynomolgus ovary,Cy5, age7, cryo-thawed ovary


title: Female adolescent, H2O Morphine 3

description: Library name: FAdoC3

value: Female adolescent, H2O Morphine 3


title: Mouse brain, Rc5d, rep3

city: Shanghai

first: Yang

last: Yang

address: 393 Middle Huaxia Road, Pudong, Shanghai

institute: ShanghaiTech University

description:
Library name: rl5d3
10x Genomics

library_source: transcriptomic single cell

data_processing:
The initial processing of sequencing reads, including alignment and the generation of digital expression matrices, was carried out using the 10X Genomics Cell Ranger (v7.0.1). Sequences were aligned to a custom mm10 2020 mouse reference genome, which was assembled to include the sequences of the mCherry and EGFP viruses for comprehensive mapping.
Assembly: mm10 assembled to include the sequences of the mCherry and EGFP viruses
Supplementary files format and content: Tab-separated value files and matrix files

molecule: total RNA

source_name: brain

extract_protocol:
The microdissected amygdala tissue pieces were transferred into 1 mL of papain digest solution (in aCSF, supplemented with 5% DNase). The tissue was digested for a total of approximately 40 min at 37 ℃. Following digestion, the tissue was sequentially triturated using large- and small-diameter fire-polished glass pipettes to generate a cell suspension. All collected cell suspension was pooled, filtered through an aCSF-equilibrated 35 μm cell strainer. The filtered cell suspension was pelleted by centrifugation at 300 g for 5 min at 4 ℃. The cell pellet was resuspended in 200 μL of aCSF supplemented with 2.5% DNase. For debris removal, the suspension was layered on top of 1 mL of 5% OptiPrep in aCSF, and centrifuged at 150 g for 10 min at 4 ℃. The final cell pellet was resuspended in 60 μL of aCSF.
The cells that have passed the test are washed and resuspended to prepare a suitable cell concentration of 700~1200 cells/ul for 10x Genomics ChromiumTM. The system is operated on the machine. GEMs (Gel Bead in Emulsion) were constructed for single cell separation according to the number of cells to be harvested. After GEMs were normally formed, GEMs were collected for reverse transcription in a PCR machine for labeling. The GEMs were oil-treated, and the amplified cDNA was purified by magnetic beads, and then subjected to cDNA amplification and quality inspection. The Gene Expression Library was constructed with the quality-qualified cDNA. After fragmentation,  adaptor ligation, sample index PCR, etc., the library is finally quantitatively examined. Sequencing: The final library pool was sequenced on the Illumina Nova 6000 instrument using 150-base-pair paired-end reads.

value: brain

value: WT

value: Sampling 5 d after reward conditioning


title: Female adolescent, H2O Morphine 4

description: Library name: FAdoC4

value: Brain

value: All

value: Female adolescent, H2O Morphine 4


title: Spleen lymphotytes cultured with WT BMDMs without tumor antigen 2

description: Library name: WT2

value: spleen and bone marrow

value: immune cells


title: Mouse brain, Rc5d, rep2

description:
Library name: rl5d2
10x Genomics


title: Cy5C_13Oa (MS233_088)

description: Library name: Sample132

value: Ovary

value: wildtype

value: oocyte, primordial follicle, cryo-thawed adult cynomolgus ovary,Cy5, age7, cryo-thawed ovary


title: 0086-R1

description: tumor genomic DNA from patient 0086: Oligodendroglioma, WHO grade 2, resection #1

value: female

value: Oligodendroglioma

value: WHO grade 2

value: resection #1

value: GLASS-OD


title: 0083-R1

description: tumor genomic DNA from patient 0083: Oligodendroglioma, WHO grade 2, resection #1

value: male


title: Cy5C_13Ob (MS233_089)

description: Library name: Sample133

value: Oocyte


title: Female adolescent, H2O Morphine 2

description: Library name: FAdoC2

value: wild type

value: Female adolescent, H2O Morphine 2


title: Female adolescent, H2O Morphine 1

description: Library name: FAdoC1

value: Brain

value: Female adolescent, H2O Morphine 1


title: 0082-R2

description: tumor genomic DNA from patient 0082: Oligodendroglioma, WHO grade 2, resection #2

value: resection #2


title: Cy5C_12Oc (MS233_086)

description: Library name: Sample130


title: 0082-R1

description: tumor genomic DNA from patient 0082: Oligodendroglioma, WHO grade 2, resection #1


title: Female adolescent, Abx Saline 5

description: Library name: FAdoB5

value: All

value: Female adolescent, Abx Saline 5


title: Cy5C_12G (MS233_087)

description: Library name: Sample131

value: Ovary

value: Granulosa cell

value: 10-20 granulosa cells, primordial follicle, cryo-thawed adult cynomolgus ovary (in pregnant E16),Cy5, age7, cryo-thawed ovary


title: Mouse brain, Rc2h, rep3

description:
Library name: rl2h3
10x Genomics

value: brain

value: WT

value: Sampling 2 h after reward conditioning


title: 0088-R3

description: tumor genomic DNA from patient 0088: Oligodendroglioma, WHO grade 3, resection #3

value: female

value: Oligodendroglioma

value: WHO grade 3

value: resection #3


title: 0083-R2

description: tumor genomic DNA from patient 0083: Oligodendroglioma, WHO grade 3, resection #2

value: male

value: GLASS-OD


title: Cy5C_12Oa (MS233_084)

description: Library name: Sample128

value: Oocyte

value: wildtype

value: oocyte, primordial follicle, cryo-thawed adult cynomolgus ovary,Cy5, age7, cryo-thawed ovary


title: Female adolescent, Abx Saline 4

description: Library name: FAdoB4

value: Brain

value: All

value: wild type

value: Female adolescent, Abx Saline 4


title: Cy5C_12Ob (MS233_085)

description: Library name: Sample129

value: Ovary


title: 0081-R2

description: tumor genomic DNA from patient 0081: Oligodendroglioma, WHO grade 3, resection #2

value: resection #2


title: Mouse brain, Rc2h, rep2

description:
Library name: rl2h2
10x Genomics

value: brain

value: WT


title: Spleen lymphotytes cultured with WT BMDMs without tumor antigen 1

description: Library name: WT1

value: spleen and bone marrow

value: immune cells


title: Mouse brain, Rc5d, rep1

description:
Library name: rl5d1
10x Genomics

value: Sampling 5 d after reward conditioning


title: Female adolescent, Abx Saline 3

description: Library name: FAdoB3

value: Female adolescent, Abx Saline 3


title: Mouse brain, Rc2h, rep1

description:
Library name: rl2h1
10x Genomics

value: Sampling 2 h after reward conditioning


title: 0081-R1

description: tumor genomic DNA from patient 0081: Oligodendroglioma, WHO grade 2, resection #1

value: female

value: Oligodendroglioma

value: WHO grade 2

value: resection #1

value: GLASS-OD


title: Cy5C_11G (MS233_083)

description: Library name: Sample127

value: Granulosa cell

value: wildtype

value: 10-20 granulosa cells, primordial follicle, cryo-thawed adult cynomolgus ovary (in pregnant E16),Cy5, age7, cryo-thawed ovary


title: Mouse brain, Fc5d, rep3

description:
Library name: fc5d5
10x Genomics

value: Sampling 5 d after fear conditioning


title: Female adolescent, Abx Saline 1

description: Library name: FAdoB1

value: Brain

value: All

value: wild type

value: Female adolescent, Abx Saline 1


title: Cy5C_11Ob (MS233_082)

description: Library name: Sample126

value: Ovary

value: Oocyte

value: oocyte, primordial follicle, cryo-thawed adult cynomolgus ovary,Cy5, age7, cryo-thawed ovary


title: Mouse brain, Fc5d, rep2

description:
Library name: fc5d4
10x Genomics

value: brain

value: WT


title: Female adolescent, H2O Saline 5

description: Library name: FAdoA5

value: Female adolescent, H2O Saline 5


title: Mouse brain, Fc5d, rep1

description:
Library name: fc5d3
10x Genomics


title: 0080-R2

description: tumor genomic DNA from patient 0080: Oligodendroglioma, WHO grade 2, resection #2

value: female

value: Oligodendroglioma

value: WHO grade 2

value: resection #2


title: Mouse brain, Fc2h, rep3

description:
Library name: fc2h5
10x Genomics

value: Sampling 2 h after fear conditioning


title: Cy5C_11Oa (MS233_081)

description: Library name: Sample125

value: wildtype


title: Female adolescent, H2O Saline 4

description: Library name: FAdoA4

value: Female adolescent, H2O Saline 4


title: Cy5C_10G (MS233_080)

description: Library name: Sample124

value: Granulosa cell

value: 10-20 granulosa cells, primordial follicle, cryo-thawed adult cynomolgus ovary (in pregnant E16),Cy5, age7, cryo-thawed ovary


title: 0079-R3

description: tumor genomic DNA from patient 0079: Oligodendroglioma, WHO grade 3, resection #3

value: male

value: WHO grade 3

value: resection #3

value: GLASS-OD


title: Female adolescent, H2O Saline 3

description: Library name: FAdoA3

value: Brain

value: All

value: wild type

value: Female adolescent, H2O Saline 3


title: Cy5C_10Oa (MS233_078)

description: Library name: Sample122

value: Ovary

value: Oocyte

value: oocyte, primordial follicle, cryo-thawed adult cynomolgus ovary,Cy5, age7, cryo-thawed ovary


title: 0079-R1

description: tumor genomic DNA from patient 0079: Oligodendroglioma, WHO grade 3, resection #1

value: Oligodendroglioma

value: resection #1


title: Cy2C_19G (MS251_218)

description: Library name: Sample168

value: wildtype

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


title: Mouse brain, Fc2h, rep2

description:
Library name: fc2h4
10x Genomics

value: brain

value: WT

value: Sampling 2 h after fear conditioning


title: Female adolescent, H2O Saline 2

description: Library name: FAdoA2

value: Female adolescent, H2O Saline 2


title: Cy5C_10Ob (MS233_079)

description: Library name: Sample123


title: 0078-R1

description: tumor genomic DNA from patient 0078: Oligodendroglioma, WHO grade 2, resection #1

value: male

value: WHO grade 2


title: 0078-R2

description: tumor genomic DNA from patient 0078: Oligodendroglioma, WHO grade 2, resection #2

value: resection #2

value: GLASS-OD


title: Cy5C_09G (MS233_077)

description: Library name: Sample121

value: Granulosa cell

value: 10-20 granulosa cells, primordial follicle, cryo-thawed adult cynomolgus ovary (in pregnant E16),Cy5, age7, cryo-thawed ovary


title: 0077-R3

description: tumor genomic DNA from patient 0077: Oligodendroglioma, WHO grade 3, resection #3

value: WHO grade 3

value: resection #3


title: 0080-R1

description: tumor genomic DNA from patient 0080: Oligodendroglioma, WHO grade 2, resection #1

value: female


title: Mouse brain, Fc2h, rep1

description:
Library name: fc2h3
10x Genomics


title: Female adolescent, Abx Saline 2

description: Library name: FAdoB2

value: Brain

value: All

value: wild type

value: Female adolescent, Abx Saline 2


title: Mouse brain, Control, rep3

description:
Library name: ctrl5
10x Genomics

value: brain


title: Mouse brain, Control, rep2

description:
Library name: ctrl4
10x Genomics

value: WT


title: 0075-R3

description: tumor genomic DNA from patient 0075: Oligodendroglioma, WHO grade 2, resection #3

value: Oligodendroglioma


title: Female adolescent, H2O Saline 1

description: Library name: FAdoA1

value: Female adolescent, H2O Saline 1


title: Cy5C_09Oa (MS233_075)

description: Library name: Sample119

value: Ovary

value: Oocyte

value: wildtype

value: oocyte, primordial follicle, cryo-thawed adult cynomolgus ovary,Cy5, age7, cryo-thawed ovary


title: Cy5C_07G (MS233_073)

description: Library name: Sample117

value: Granulosa cell

value: 10-20 granulosa cells, late secondary follicle, cryo-thawed adult cynomolgus ovary (in pregnant E16),Cy5, age7, cryo-thawed ovary


title: Cy5C_09Ob (MS233_076)

description: Library name: Sample120


title: omp2_1

city: Hohhot

first: xuxu

last: wang

address: Jinshan Campus, Inner Mongolia Medical University, Jinshan Economic and Technological Development Zone, Tumed Left Banner

department: School of Public Health

institute: Inner Mongolia Medical University

description:
Library name: omp2_1
OMP: Stimulated with OMP19 (mouse primary peritoneal macrophages)

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to DM 1-3 516 R44 (v6.1)  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: gene counts and fpkm for each sample

source_name: mouse primary peritoneal macrophages

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: mouse primary peritoneal macrophages

value: OMP:Stimulated with OMP19


title: 0074-R3

description: tumor genomic DNA from patient 0074: Oligodendroglioma, WHO grade 3, resection #3

value: male

value: WHO grade 3

value: resection #3

value: GLASS-OD


title: 0074-R2

description: tumor genomic DNA from patient 0074: Oligodendroglioma, WHO grade 2, resection #2

value: WHO grade 2

value: resection #2


title: SLAM-seq MYC-mAID auxin rep 3

city: Solna

first: Vladislav

last: Kuzin

state: Stockholm

address: Solnavägen 9

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institute

description: Library name: SLAM_AUX_3

library_source: genomic

data_processing:
Basecalls were performed using BclConvert_v4.4.6 at Illumina Basespace.
UMI extraction and trimming of FASTQ files were performed as suggested in the CORALL Data Analysis Pipeline (https://github.com/Lexogen-Tools/corall_analysis). Spesifically the trimming was done using the arguments -U 9 -m 20 --interleaved -n 3 --nextseq-trim 20 -a "$rd1Adapter" -A "N{12}$rd2Adapter;min_overlap=15;max_error_rate=0.045455" -G "XT{18}" -a "r1polyA=A{18}" -
SLAM-seq reads were aligned either to the ENCODE GRCh38.primary_assembly.genome.fa reference genome or to the ERCC92 reference genome using NextGenMap version 0.5.5 with the following settings: ngm -r "${ref_genome}" -1 "${rd1_trim_fq}" -2 "${rd2_trim_fq}" -t "${threads}" -o "${tmp_sam}"  --slam-seq 2 --rg-id "${rg_id:-$sample}" --rg-sm "${sm_tag}"  --rg-pl "${rg_pl}"
After deduplication with UMI_tools version 1.1.6, slamdunk filter was run with hg38 expressed protein-coding genes or ERCC genes as opposed to just the 3′ untranslated regions, followed by single-nucleotide polymorphism detection via slamdunk snp.
Nascent human reads with T > C conversions were counted using slamdunk count using a T > C conversion threshold of ≥ 2. Then T > C conversions separated from background reads using the alleyoop read-separator command from the slamdunk package.
Human T > C counts were normalised to ERCC filtered reads for each sample by applying a spike-in-based scaling factor defined as  (ERCC filtered reads in the lowest-ERCC sample) / (ERCC filtered reads in each sample).  Spike-in–normalized T > C counts per gene were then divided by gene length (kb) and log10-transformed after addition of a pseudocount (+1).
Assembly: hg38
Supplementary files format and content: T>C converted read counts

source_name: HCT116 MYC-mAID

growth_protocol: Cells were grown in DMEM (Thermo, 61965059) containing 10% FBS (Thermo, 10270106)supplied with 5% CO2.

extract_protocol:
Cells were washed twice with fresh medium and scraped stepwise in 2 × 0.5 ml of ice cold TRIzol LS Reagent (Invitrogen, 10296010) and proceeded immediately to the next step. For RNA isolation, we followed the manufacturer’s instructions of SLAM-seq Kinetics Kit-Anabolic Kinetics Module (Lexogen, 061.24) except for the following modifications: Samples were incubated for 5 min at 65°C and mixed with 200 μl of chloroform:isoamyl alcohol mix (24:1) (Sigma-Aldrich, 25666), before further incubation for 15 min at 65°C under strong agitation (2000 rpm) and repeated vortexing. RNA in the aqueous phase was separated by centrifugation at 16000g for 15min at 4°C, supplemented with reducing agent and again extracted with one amount of chloroform:isoamyl alcohol mix (24:1) before precipitation overnight at −80°C (in the presence of reducing agent). RNA was pelleted for 20 minutes at 16000g washed twice with 1 and 0.18 ml of 80% EtOH (plus reducing agent), respectively, and pelleted for 10 min at 7500g. Resuspension in the elution buffer (provided by the SLAM-seq Kinetics Kit) was facilitated by incubation for 15 min at 55°C, 10 min on ice and gentle pipetting to avoid fragmentation of RNA. RNA was quantified with the Qubit RNA HS Assay Kit (Invitrogen, Q32852) and its integrity was controlled using the RNA 6000 nano kit (Agilent, 5067-1511) on a Bioanalyzer 2100 (Agilent) . To facilitate normalization of the sequencing reads, the isolated RNA was mixed with ERCC RNA Spike In-Mix (Invitrogen, 4456740). Specifically, RNA (4.5 μg) was mixed with 2 μl of 1:10 diluted ERCC RNA Spike In-Mix and the elution buffer was added to fill up to 10 μl. Next 4.5 μg RNA mixed with ERCC was taken, the elution buffer added up to 15 μl and alkylation was performed by addition of iodoacetamide following the manufacturer’s instructions. Once again Qubit RNA HS Assay Kit (Invitrogen, Q32852) was used to quantify the RNA, and RNA integrity was controlled using the RNA 6000 nano kit (Agilent, 5067-1511) on a Bioanalyzer 2100 (Agilent). Ribosomal RNAs (rRNAs) were depleted from 950 ng of alkylated RNA using the RiboCop (HMR) kit (as part of the CORALL Total RNA Seq V2 12nt B1 UDI12B_0001-0024, Lexogen, 184.24) following the manufacturer’s instructions, except for increasing the volume for RNA elution to 16 μl. Removal of rRNAs was confirmed using the RNA 6000 Pico Kit (Agilent, 5067-1513) on a Bioanalyzer 2100 (Agilent).
To prepare cDNA libraries spanning the whole transcript length, the CORALL Total RNA Seq V2 12nt B1 UDI12B_0001-0024 (Lexogen, 184.24) was used, which includes reverse transcription with displacement stop primers. Ten microliters of the rRNA-depleted RNA was used as input material, and the final library was amplified by 15 PCR cycles as defined from the PCR Add-on and reamplification Kit V2 for Illumina (Lexogen, 208.96). DNA concentration and molarity were determined by Qubit dsDNA HS Assay Kit (Invitrogen, Q33231) and Bioanalyzer High Sensitivity DNA Kit (5067-4626) on a Bioanalyzer 2100 (Agilent), respectively. Libraries were pooled and sequenced using the NextSeq™ 1000/2000 P2 XLEAP-SBS™ Reagent Kit (100 Cycles) (Illumina, 20100987). The sequencing run was paired-end and dual index with 2 x 53-bp reads.

treatment_protocol: Cells were treated (in biological triplicates for the sequencing assays) with 0.1 mM Auxinole 24 hours before harvest, 500 µM Auxin 90 minutes before harvest. 100 μM 4-Thiouridine (S4U) was added to the medium of all samples in the dark 75 minutes before the harvest.

value: HCT116 MYC-mAID

value: Auxin, S4U


title: 0075-R2

description: tumor genomic DNA from patient 0075: Oligodendroglioma, WHO grade 3, resection #2

value: female

value: Oligodendroglioma


title: SLAM-seq MYC-mAID auxin rep 2

description: Library name: SLAM_AUX_2


title: SLAM-seq MYC-mAID auxinole (ctrl) rep 3

description: Library name: SLAM_OLE_3

value: Auxinole, S4U


title: omp2_2

description:
Library name: omp2_2
OMP: Stimulated with OMP19 (mouse primary peritoneal macrophages)


title: cpps_omp3_3

description:
Library name: cpps_omp3_3
CPPS+OMP: Stimulated with CPPS and OMP19 (mouse primary peritoneal macrophages)

value: CPPS+OMP:Stimulated with CPPS and OMP19


title: SLAM-seq MYC-mAID auxin rep 1

description: Library name: SLAM_AUX_1


title: Cy5C_08G (MS233_074)

description: Library name: Sample118

value: Ovary

value: wildtype

value: 10-20 granulosa cells, primordial follicle, cryo-thawed adult cynomolgus ovary (in pregnant E16),Cy5, age7, cryo-thawed ovary


title: omp2_3

description:
Library name: omp2_3
OMP: Stimulated with OMP19 (mouse primary peritoneal macrophages)

value: mouse primary peritoneal macrophages


title: Mouse brain, Control, rep1

description:
Library name: ctrl3
10x Genomics

value: brain

value: WT


title: 0077-R2

description: tumor genomic DNA from patient 0077: Oligodendroglioma, WHO grade 2, resection #2

value: male


title: TOP2cc MYC-mAID untreated rep 3

description: Library name: TOP2cc_MYC_untr_3

data_processing:
Basecalls were performed using BclConvert_v4_2_7 at Illumina Basespace.
CAD-seq reads were trimmed using Cutadapt v5.0 using --nextseq-trim 25 option, discarding reads left with < 30 bp
CAD-seq reads were aligned to the UCSC hg38 genome using Bowtie version 2.5.4 with default settings.
BigWig files were generated with bamCoverage from Deeptools v3.5.6 package.
To create average profiles and heatmaps, coverage matrices were generated  using computeMatrix from normalized bigwig files and plotted using plotProfile and plotHeatmap from Deeptools version 3.5.6.
Assembly: hg38
Supplementary files format and content: normalized bigWig

extract_protocol:
Cells were harvested by scraping in 5ml of Buffer M. Samples were sonicated with a Bandelin probe sonicator for 1 second at 20% amplitude. TOP2 cleavage complexes were precipitated by adding 2.5ml of 100% Ethanol, incubating overnight at -20C and spinning at 15000g for 10minutes at 4C. The pellet was then washed three times with wash buffer, dried and resuspended in EB+0.05%SDS + protein inhibitors + AEBSF. The samples were then fragmented with benzonase at 0.02U/µg. This material was then used for IP with TOP2A antibody using the standard ChIP protocol.
DNA from ChIP was quantified with the Qubit dsDNA HS Assay Kit (Thermo Fisher, Q33230). Sequencing libraries were created according to the ThruPLEX DNA-seq kit protocol (Takara, R400676). Size selection was performed in the range of 200-700bp with AMPure XP beads (Beckman, A63880) and confirmed using the Agilent High Sensitivity DNA Kit (Agilent, 5067-4626) on the Agilent 2100 Bioanalyzer. Libraries were pooled and sequenced using the NextSeq 1000/2000 P3 XLEAP-SBS™ Reagent Kit (100 Cycles) (Illumina, 20100990). The sequencing run was Paired End and Dual Index with 2x50 bp reads.

treatment_protocol: Cells were treated (in biological triplicates for the sequencing assays) with 500µM Auxin 1.5 hours before harvest, 10µM of MG132 36 minutes before harvest and 100µM Etoposide 6 minutes before harvest.

value: MG132, ETO


title: SLAM-seq MYC-mAID auxinole (ctrl) rep 1

description: Library name: SLAM_OLE_1


title: Cy5C_07O (MS233_072)

description: Library name: Sample116

value: Oocyte

value: oocyte, late secondary follicle, cryo-thawed adult cynomolgus ovary,Cy5, age7, cryo-thawed ovary


title: Cy5C_06G (MS233_071)

description: Library name: Sample115

value: Granulosa cell

value: 10-20 granulosa cells, late secondary follicle, cryo-thawed adult cynomolgus ovary (in pregnant E16),Cy5, age7, cryo-thawed ovary


title: Cy5C_05O (MS233_068)

description: Library name: Sample112


title: cpps_omp3_1

description:
Library name: cpps_omp3_1
CPPS+OMP: Stimulated with CPPS and OMP19 (mouse primary peritoneal macrophages)


title: Cy5C_06O (MS233_070)

description: Library name: Sample114


title: 0073-R2

description: tumor genomic DNA from patient 0073: Oligodendroglioma, WHO grade 3, resection #2

value: WHO grade 3

value: resection #2

value: GLASS-OD


title: SLAM-seq MYC-mAID auxinole (ctrl) rep 2

description: Library name: SLAM_OLE_2

value: HCT116 MYC-mAID

value: Auxinole, S4U


title: TOP2cc MYC-mAID untreated rep 2

description: Library name: TOP2cc_MYC_untr_2


title: con1_2

description:
Library name: con1_2
Control: Untreated (mouse primary peritoneal macrophages)


title: 0072-R3

description: tumor genomic DNA from patient 0072: Oligodendroglioma, WHO grade 3, resection #3

value: Oligodendroglioma

value: resection #3


title: cpps_omp3_2

description:
Library name: cpps_omp3_2
CPPS+OMP: Stimulated with CPPS and OMP19 (mouse primary peritoneal macrophages)

value: CPPS+OMP:Stimulated with CPPS and OMP19


title: Cy5C_04G (MS233_067)

description: Library name: Sample111

value: Ovary

value: wildtype


title: Cy5C_04O (MS233_066)

description: Library name: Sample110


title: con1_1

description:
Library name: con1_1
Control: Untreated (mouse primary peritoneal macrophages)

value: mouse primary peritoneal macrophages


title: TOP2cc MYC-mAID auxin rep 2

description: Library name: TOP2cc_MYC_auxin_2

value: Auxin, MG132, ETO


title: TOP2cc MYC-mAID auxin rep 1

description: Library name: TOP2cc_MYC_auxin_1


title: CRAB3

city: Suzhou

address: NO. 899, Pinghai Road

institute: the First Affiliated Hospital of Soochow University

description: Library name: Sample5

data_processing:
(1) Remove reads with adapters; (2) Remove paired reads when the N content in any sequencing read exceeds 10% of the base number of the read; (3) Remove paired reads when the number of low-quality (Q<=20) bases in any sequencing read exceeds 50% of the base number of the read.
Assembly: Mus_musculus.GRCm39.109
Supplementary files format and content: Differentially expressed genes
Supplementary files format and content: CRAB_vs_AB.diff.annot

source_name: Lung

extract_protocol:
Trizol
The mRNA was fragmented with fragmentation buffer, and short RNA fragments were used as templates for synthesizing the first strand of cDNA with random hexamer primers. The second strand of cDNA was then synthesized using buffer, dNTPs (dTTP, dATP, dGTP, and dCTP), and DNA polymerase I. The double-stranded cDNA was purified with DNA purification beads, followed by end-repair, A-tailing, and ligation with sequencing adapters. After selecting fragments of the appropriate size using DNA purification beads, the final cDNA library was enriched via PCR.

value: Lung


title: 0073-R1

description: tumor genomic DNA from patient 0073: Oligodendroglioma, WHO grade 2, resection #1

value: female

value: WHO grade 2

value: resection #1


title: 0072-R2

description: tumor genomic DNA from patient 0072: Oligodendroglioma, WHO grade 3, resection #2

value: male


title: Cy5C_03G (MS233_065)

description: Library name: Sample109

value: Granulosa cell

value: 10-20 granulosa cells, early secondary follicle, cryo-thawed adult cynomolgus ovary (in pregnant E16),Cy5, age7, cryo-thawed ovary


title: 0071-R3

description: tumor genomic DNA from patient 0071: Oligodendroglioma, WHO grade 3, resection #3

value: WHO grade 3

value: GLASS-OD


title: 0071-R2

description: tumor genomic DNA from patient 0071: Oligodendroglioma, WHO grade 2, resection #2

value: resection #2


title: Cy5C_05G (MS233_069)

description: Library name: Sample113

value: 10-20 granulosa cells, late secondary follicle, cryo-thawed adult cynomolgus ovary (in pregnant E16),Cy5, age7, cryo-thawed ovary


title: TOP2cc MYC-mAID untreated rep 1

description: Library name: TOP2cc_MYC_untr_1

value: HCT116 MYC-mAID

value: MG132, ETO


title: TOP2cc MYC-mAID auxin rep 3

description: Library name: TOP2cc_MYC_auxin_3


title: con1_3

description:
Library name: con1_3
Control: Untreated (mouse primary peritoneal macrophages)


title: 20-HCT116_tetD350A_NutlinandDoxy_input

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Library name: 20-HCT116_tetD350A_NutlinandDoxy_input_S61

data_processing:
Sequencing reads were quality checked with FASTQC (v0.11.9)  and aligned to the GRCh37 (hg19) genome using STAR (v2.7.9a). Homer and macs2 were used for peak call and diffbind for diffrential bind. Deeptool used for bigwigfiles.
Assembly: Hg19
Supplementary files format and content: CPM-normalized bigWig files were generated using Deeptools (v3.5.1). Score represents the normalized coverage of DNA fragment at a given coordinate.

growth_protocol: McCoy's 5A media, 10% tet-free FBS, 1%Penn/Strep

extract_protocol:
Non-histone samples were first crosslinked with EGS for 25 minutes. All cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, cells were sonicated with a Cavaris S220 Ultrasonicator.
Barcoded libraries were made using NEB Ultra II DNA Library Prep Kit for Illumina following manufacturer's instructions and quantified by Agilent 4200 Tapestation System.

treatment_protocol: Vehicle (DMSO), nutlin, or nutlin+doxycycline (24 hours)

value: colorectal cancer cell line

value: Nutlin+Doxycycline


title: Cy5C_02O (MS233_063)

description: Library name: Sample107

value: Ovary

value: Oocyte

value: wildtype

value: oocyte, late secondary follicle, cryo-thawed adult cynomolgus ovary,Cy5, age7, cryo-thawed ovary


title: 0070-R3

description: tumor genomic DNA from patient 0070: Oligodendroglioma, WHO grade 3, resection #3

value: Oligodendroglioma

value: resection #3


title: Cy5C_02G (MS233_064)

description: Library name: Sample108


title: 19-HCT116_tetPADI4_NutlinandDoxy_input

description: Library name: 19-HCT116_tetPADI4_NutlinandDoxy_input_S60


description: Library name: 18-HCT116_tetD350A_NutlinandDoxy_ChIP_p53_rep2_S59


title: AB2

description: Library name: Sample2

value: Lung


title: CRAB1

description: Library name: Sample4


title: 0070-R1

description: tumor genomic DNA from patient 0070: Oligodendroglioma, WHO grade 2, resection #1

value: male

value: WHO grade 2

value: resection #1


title: AB1

description: Library name: Sample1


title: AB3

description: Library name: Sample3


title: Cy5C_01O (MS233_061)

description: Library name: Sample105

value: oocyte, early secondary follicle, cryo-thawed adult cynomolgus ovary,Cy5, age7, cryo-thawed ovary


title: 0070-R2

description: tumor genomic DNA from patient 0070: Oligodendroglioma, WHO grade 2, resection #2

value: resection #2

value: GLASS-OD


title: 0071-R1

description: tumor genomic DNA from patient 0071: Oligodendroglioma, WHO grade 2, resection #1

value: female


title: Cy6C_08G (MS233_059)

description: Library name: Sample103

value: Granulosa cell

value: 10-20 granulosa cells, early secondary follicle, cryo-thawed adult cynomolgus ovary (in pregnant E17),Cy6, age5, cryo-thawed ovary


title: Cy6C_07G (MS233_058)

description: Library name: Sample102


title: 0069-R1

description: tumor genomic DNA from patient 0069: Oligodendroglioma, WHO grade 2, resection #1


title: 0069-R2

description: tumor genomic DNA from patient 0069: Oligodendroglioma, WHO grade 3, resection #2

value: WHO grade 3


description: Library name: 16-HCT116_tetD350A_untreated_ChIP_p53_rep2_S57

value: colorectal cancer cell line

value: Vehicle


title: Trmt6 KO rep2

city: Hangzhou

first: Aiwei

last: Wu

state: Zhejiang

address: 2318 Yuhangtang Road

department: School of Basic Medical Sciences

institute: Hangzhou Normal University

description: Library name: Sample5

data_processing:
Raw reads were trimmed using fastp, and mapped to mouse genome mm10 using HISAT2. Gene expression were evaluated by featureCounts.
Assembly: mm10
Supplementary files format and content: raw counts

source_name: intestinal tissue

extract_protocol:
Total RNA was extracted from using Quick-RNA Kits (ZYMO) and subjected to cDNA synthesis and amplification.
Sequencing libraries were generated from 500 pg cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) following the manufacturer’s instructions.

value: intestinal tissue


title: Cy5C_01G (MS233_062)

description: Library name: Sample106

value: Ovary

value: wildtype

value: 10-20 granulosa cells, early secondary follicle, cryo-thawed adult cynomolgus ovary (in pregnant E16),Cy5, age7, cryo-thawed ovary


title: 0068-R2

description: tumor genomic DNA from patient 0068: Oligodendroglioma, WHO grade 3, resection #2

value: Oligodendroglioma


title: Cy6C_07O (MS233_057)

description: Library name: Sample101

value: Oocyte

value: oocyte, early secondary follicle, cryo-thawed adult cynomolgus ovary,Cy6, age5, cryo-thawed ovary


title: Trmt6 KO rep3

description: Library name: Sample6


title: 17-HCT116_tetD350A_Nutlin_ChIP_p53_rep2

description: Library name: 17-HCT116_tetD350A_Nutlin_ChIP_p53_rep2_S58

value: Nutlin


description: Library name: 15-HCT116_tetD350A_NutlinandDoxy_ChIP_H3K27ac_rep2_S56

value: Nutlin+Doxycycline


title: 0068-R3

description: tumor genomic DNA from patient 0068: Oligodendroglioma, WHO grade 3, resection #3

value: male

value: resection #3


description: Library name: 14-HCT116_tetD350A_Nutlin_ChIP_H3K27ac_rep2_S55


title: Trmt6 KO rep1

description: Library name: Sample4


title: Cy6C_06G (MS233_056)

description: Library name: Sample100

value: 10-20 granulosa cells, primary follicle, cryo-thawed adult cynomolgus ovary (in pregnant E16),Cy6, age5, cryo-thawed ovary


title: WT rep3

description: Library name: Sample3

value: wild type


title: 0067-R2

description: tumor genomic DNA from patient 0067: Oligodendroglioma, WHO grade 2, resection #2

value: WHO grade 2

value: resection #2

value: GLASS-OD


title: Cy6C_10O (MS233_060)

description: Library name: Sample104


title: Cy6C_06O (MS233_055)

description: Library name: Sample99

value: oocyte, primary follicle, cryo-thawed adult cynomolgus ovary,Cy6, age5, cryo-thawed ovary


description: Library name: 11-HCT116_tetPADI4_Nutlin_ChIP_p53_sc_rep2_S52

value: colorectal cancer cell line


title: WT rep2

description: Library name: Sample2

value: intestinal tissue


description: Library name: 13-HCT116_tetD350A_untreated_ChIP_H3K27ac_rep2_S54

value: Vehicle


title: Cy6C_05O (MS233_054)

description: Library name: Sample98

value: Ovary

value: wildtype


title: 0065-R2

description: tumor genomic DNA from patient 0065: Oligodendroglioma, WHO grade 2, resection #2

value: female

value: Oligodendroglioma


description: Library name: 10-HCT116_tetPADI4_untreated_ChIP_p53_sc_rep2_S51


description: Library name: 9-HCT116_tetPADI4_NutlinandDoxy_ChIP_p53_sc_rep1_S50


title: E0771_Y238A_3

city: CHICAGO

first: Ekrem Emrah

last: Er

state: IL

address: 909 S  WOLCOTT AVE

department: Physiology and Biophysics

institute: The University of Illinois at Chicago

data_processing:
Reads were aligned to the GRCm38 genome (+ Human MRTFA) with STAR
Counts were generated from the BAM files using Feature Counts
Assembly: GRCm38 + Human MRTFA
Supplementary files format and content: raw counts table

extract_protocol:
Qiagen RNeasy
NuGen Universal Plus mRNA

value: mammary carcinoma

value: MRTFAY238A overexpression

value: 48hr 2ug/ml doxycycline


title: 0065-R1

description: tumor genomic DNA from patient 0065: Oligodendroglioma, WHO grade 2, resection #1

value: resection #1


title: 0064-R4

description: tumor genomic DNA from patient 0064: Oligodendroglioma, WHO grade 3, resection #4

value: WHO grade 3

value: resection #4


description: Library name: 12-HCT116_tetPADI4_NutlinandDoxy_ChIP_p53_sc_rep2_S53

value: Nutlin+Doxycycline


title: Cy6C_02G (MS233_050)

description: Library name: Sample94

value: Granulosa cell

value: 10-20 granulosa cells, primordial follicle, cryo-thawed adult cynomolgus ovary ,Cy6, age5, cryo-thawed ovary


title: Cy6C_03O (MS233_051)

description: Library name: Sample95

value: Oocyte

value: oocyte, early secondary follicle, cryo-thawed adult cynomolgus ovary,Cy6, age5, cryo-thawed ovary


title: E0771_pRetroX_3

value: empty pRetroX


title: 0064-R2

description: tumor genomic DNA from patient 0064: Oligodendroglioma, WHO grade 2, resection #2

value: WHO grade 2

value: resection #2

value: GLASS-OD


title: AT-3_Y238A_3


title: Cy6C_03G (MS233_052)

description: Library name: Sample96

value: Ovary

value: wildtype

value: 10-20 granulosa cells, early secondary follicle, cryo-thawed adult cynomolgus ovary (in pregnant E15),Cy6, age5, cryo-thawed ovary


title: 0066-R2

description: tumor genomic DNA from patient 0066: Oligodendroglioma, WHO grade 3, resection #2

value: male

value: Oligodendroglioma


description: Library name: 8-HCT116_tetPADI4_Nutlin_ChIP_p53_sc_rep1_S49

value: colorectal cancer cell line

value: Nutlin


title: Cy6C_04G (MS233_053)

description: Library name: Sample97

value: 10-20 granulosa cells, early secondary follicle, cryo-thawed adult cynomolgus ovary ,Cy6, age5, cryo-thawed ovary


title: E0771_MRTFA_3

value: mammary carcinoma

value: MRTFA WT overexpression

value: 48hr 2ug/ml doxycycline


description: Library name: 6-HCT116_tetPADI4_NutlinandDoxy_ChIP_p53_dc_rep3_S47

value: Nutlin+Doxycycline


description: Library name: 7-HCT116_tetPADI4_untreated_ChIP_p53_sc_rep1_S48

value: Vehicle


title: 0064-R3

description: tumor genomic DNA from patient 0064: Oligodendroglioma, WHO grade 3, resection #3

value: female

value: WHO grade 3

value: resection #3


title: WT rep1

description: Library name: Sample1

value: intestinal tissue

value: wild type


title: AT-3_MRTFA_3


description: Library name: 5-HCT116_tetPADI4_Nutlin_ChIP_p53_dc_rep3_S46


title: 0062-R4

description: tumor genomic DNA from patient 0062: Oligodendroglioma, WHO grade 3, resection #4

value: resection #4

value: GLASS-OD


title: Cy6C_01G (MS233_048)

description: Library name: Sample92

value: Ovary

value: Granulosa cell

value: wildtype


title: Cy6C_02O (MS233_049)

description: Library name: Sample93

value: Oocyte

value: oocyte, primordial follicle, cryo-thawed adult cynomolgus ovary,Cy6, age5, cryo-thawed ovary


title: 0062-R2

description: tumor genomic DNA from patient 0062: Oligodendroglioma, WHO grade 2, resection #2

value: male

value: Oligodendroglioma

value: WHO grade 2

value: resection #2


title: AT-3_pRetroX_3

value: mammary carcinoma

value: empty pRetroX

value: 48hr 2ug/ml doxycycline


title: E0771_Y238A_2

value: MRTFAY238A overexpression


title: 0061-R2

description: tumor genomic DNA from patient 0061: Oligodendroglioma, WHO grade 2, resection #2


title: Cy6F_11G (MS224_022)

description: Library name: Sample91

value: 16 granulosa cells, antral follicle picked up from adult cynomolgus ovary, Cy6, Fresh ovary, age5,euthanasia


title: E0771_pRetroX_2


title: 0060-R2

description: tumor genomic DNA from patient 0060: Oligodendroglioma, WHO grade 2, resection #2


title: E0771_MRTFA_2

value: MRTFA WT overexpression


title: Cy6F_11O (MS224_021)

description: Library name: Sample90

value: oocyte, antral follicle picked up from adult cynomolgus ovary, Cy6, Fresh ovary, age5,euthanasia


description: Library name: 4-HCT116_tetPADI4_untreated_ChIP_p53_dc_rep3_S45

value: colorectal cancer cell line

value: Vehicle


title: 0061-R1

description: tumor genomic DNA from patient 0061: Oligodendroglioma, WHO grade 2, resection #1

value: resection #1

value: GLASS-OD


title: Cy6F_10G (MS224_020)

description: Library name: Sample89

value: Ovary

value: Granulosa cell

value: wildtype

value: 15 granulosa cells, antral follicle picked up from adult cynomolgus ovary, Cy6, Fresh ovary, age5,euthanasia


title: Cy6F_10O (MS224_019)

description: Library name: Sample88

value: Oocyte


title: 0060-R1

description: tumor genomic DNA from patient 0060: Oligodendroglioma, WHO grade 2, resection #1

value: male

value: Oligodendroglioma

value: WHO grade 2


title: AT-3_MRTFA_2

value: mammary carcinoma

value: 48hr 2ug/ml doxycycline


description: Library name: 1-HCT116_tetPADI4_untreated_ChIP_H3K27ac_S42


description: Library name: 3-HCT116_tetPADI4_NutlinandDoxy_ChIP_H3K27ac_S44

value: Nutlin+Doxycycline


title: 0059-R3

description: tumor genomic DNA from patient 0059: Oligodendroglioma, WHO grade 3, resection #3

value: WHO grade 3

value: resection #3


title: Cy6F_9G (MS224_018)

description: Library name: Sample87


title: AT-3_pRetroX_2

value: empty pRetroX


title: CA8, ATAC

city: Cheongju

first: Chaelin

last: You

address: Chungdae-ro 1, Seowon-Gu

country: South Korea

institute: Chungbuk National University

data_processing:
Raw sequencing data (FASTQ files) were aligned to the hg38 reference genome and quantified using Cell Ranger ARC v2.0.2. cellranger-arc count pipeline produced barcoded count matrices for gene expression and ATAC data.
Assembly: hg38
Supplementary files format and content: Cell Ranger ARC output files: filtered_feature_bc_matrix.h5
Supplementary files format and content: Cell Ranger ARC output files: atac_fragments.tsv.gz

source_name: SNSCC tumor

extract_protocol:
Nuclei were isolated from solid tissues using a Singulator 100 system (S2 Genomics) following the manufacturer's protocol. Debris was removed using a Percoll gradient. Nuclei concentration was determined using a LUNA-FL™ Automated Fluorescence Cell Counter (Logos Biosystems), and morphology was examined by microscopy. The isolated nuclei were then incubated in a Transposition Mix containing Transposase.
Libraries were prepared using the Chromium controller (10x Genomics) according to the Chromium Single Cell Multiome ATAC + Gene Expression protocol (CG000338). Briefly, transposed nuclei were mixed with master mix and loaded with Single Cell Multiome gel beads and partitioning oil into a Chromium Chip J. The gel beads contained poly (dT) sequences for gene expression (GEX) library preparation and spacer sequences for assay for transposase-accessible chromatin (ATAC) library preparation.
Gel bead-in-emulsion (GEM) incubation resulted in 10x barcoded DNA from transposed DNA (for ATAC) and 10x barcoded cDNA from polyadenylated mRNA (for GEX). After pre-amplification, the PCR product was divided for separate ATAC and GEX library construction steps. For the ATAC library, P7 adapters and sample indices were added to pre-amplified transposed DNA during library construction via PCR. For the GEX library, pre-amplified cDNA underwent PCR amplification, followed by fragmentation, end repair, A-tailing, adapter ligation, and index PCR.
The purified libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide (KAPA Biosystems). Library quality was assessed using an Agilent Technologies 4200 TapeStation (Agilent technologies). Sequencing was performed on a HiSeq platform (Illumina) following the read length in the user guide.
OTHER: snMultiome-seq

value: SNSCC tumor


title: CA5, ATAC


title: Cy6F_8G (MS224_017)

description: Library name: Sample86


title: 2-HCT116_tetPADI4_Nutlin_ChIP_H3K27ac

description: Library name: 2-HCT116_tetPADI4_Nutlin_ChIP_H3K27ac_S43

value: colorectal cancer cell line

value: Nutlin


title: CA8, GEX

molecule: nuclear RNA


title: AT-3_Y238A_2

value: MRTFAY238A overexpression


title: E0771_Y238A_1


title: 0059-R2

description: tumor genomic DNA from patient 0059: Oligodendroglioma, WHO grade 3, resection #2

value: resection #2

value: GLASS-OD


title: Cy6F_6G (MS224_016)

description: Library name: Sample85

value: Ovary

value: Granulosa cell

value: wildtype

value: 15 granulosa cells, antral follicle picked up from adult cynomolgus ovary, Cy6, Fresh ovary, age5,euthanasia


title: E0771_MRTFA_1

value: MRTFA WT overexpression


title: CA5, GEX


title: 0058-R3

description: tumor genomic DNA from patient 0058: Oligodendroglioma, WHO grade 3, resection #3

value: male

value: Oligodendroglioma


title: E0771_pRetroX_1

value: mammary carcinoma

value: 48hr 2ug/ml doxycycline


title: Cy6F_5O (MS224_014)

description: Library name: Sample83

value: Oocyte

value: oocyte, antral follicle picked up from adult cynomolgus ovary, Cy6, Fresh ovary, age5,euthanasia


title: AT-3_Y238A_1


title: Cy6F_6O (MS224_015)

description: Library name: Sample84


title: 0058-R2

description: tumor genomic DNA from patient 0058: Oligodendroglioma, WHO grade 2, resection #2

value: WHO grade 2


title: HC1, ATAC

source_name: Nasal mucosa

value: Nasal mucosa


title: AT-3_MRTFA_1


title: HC2, ATAC


title: 0057-R1

description: tumor genomic DNA from patient 0057: Oligodendroglioma, WHO grade 2, resection #1

value: female

value: resection #1


title: Cy6F_2O (MS224_010)

description: Library name: Sample79


title: 0054-R3

description: tumor genomic DNA from patient 0054: Oligodendroglioma, WHO grade 3, resection #3

value: WHO grade 3

value: resection #3


title: 0057-R2

description: tumor genomic DNA from patient 0057: Oligodendroglioma, WHO grade 3, resection #2

value: resection #2

value: GLASS-OD


title: 0055-R2

description: tumor genomic DNA from patient 0055: Oligodendroglioma, WHO grade 3, resection #2


title: 0055-R1

description: tumor genomic DNA from patient 0055: Oligodendroglioma, WHO grade 2, resection #1


title: AT-3_pRetroX_1

value: empty pRetroX


title: Cy6F_3G (MS224_012)

description: Library name: Sample81

value: Ovary

value: Granulosa cell

value: wildtype

value: 16 granulosa cells, antral follicle picked up from adult cynomolgus ovary, Cy6, Fresh ovary, age5,euthanasia


title: Dental mesenchyme, E60, bio rep3

city: Beijing

first: Jiangyi

last: Wang

state: None Selected

address: NO. 4 Tiantanxili, Dongcheng District, Beijing, China

institute: Beijing Stomatological Hospital, Capital Medical University

data_processing:
Illumina HiSeq Xten (Illumina, USA)
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads.
Hisat2 (version:2.0.4) were used to map clean reads to the ssc10.2 reference genome.
Stringtie（version:1.3.0）was run with a reference annotation to generate FPKM values for known gene models.
Differentially expressed genes were identified using edgeR.
Assembly: ssc10.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Sus scrofa

source_name: Tooth germ

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (Cat# 74004, Qiagen) following the manufacturer’s instructions
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® following manufacturer's protocols.

value: Dental mesenchyme

value: Wild type

tag: developmental stage

value: Embryonic 60 day


title: Cy6F_4G (MS224_013)

description: Library name: Sample82

value: 18 granulosa cells, antral follicle picked up from adult cynomolgus ovary, Cy6, Fresh ovary, age5,euthanasia


title: Cy6F_1G (MS224_009)

description: Library name: Sample78

value: 15 granulosa cells, antral follicle picked up from adult cynomolgus ovary, Cy6, Fresh ovary, age5,euthanasia


title: aortic tissue of CA1 knockin ApoE-/- mice fed with high-fat food and simultaneously treated with methoxazolamide

city: Qingdao

first: XIAOTIAN

last: CHANG

state: Shandong

address: 1677 Wutaishan road

institute: The Affiliated Hospital of Qingdao University

description:
SampleD
aortic tissue of CA1 knockin ApoE-/- mice that were fed with high-fat food and simultaneously treated with methoxazolamide
10× Genomics

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: aortic tissues

extract_protocol:
The nuclear suspension preparation experiment was conducted on ice. Fresh or frozen tissue samples were chopped in 1ml of cell lysate (NST), which was divided into 0.1% NP40, 10mM Tris-HCl, 146mM NaCl, 1mM CaCl2, 21mM MgCl2 and 1U/μl RNase inhibitor. The cracking time was 7min. After the cells were completely lysed by Trypan blue microscopy, 1ml ST Wash buffer (10mM Tris-HCl, 146mM NaCl, 1mM CaCl2, 21mM MgCl2) was added. 0.01% BSA (NEB B9000S) and 40U/mL RNase inhibitor). Filtrate was transferred to a 15mL centrifuge tube through a 40µm cell sieve (BD). The filtrate was rinsed with an appropriate amount of ST Wash buffer and combined with the nuclear filtrate. Centrifuge the horizontal rotor 500g at 4℃ for 5 min. The nucleus was re-suspended with 5ml PBS+1%BSA, and after washing and centrifugation, 100µl PBS+1%BSA was re-suspended. Trypan blue staining, microscopic counting.
Nuclei were diluted to 700-1200/µl with PBS+1%BSA. Machine and cDNA libraries were amplified according to the operating instructions of 10×Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (1000268). The DNA library was constructed using Chromium™ single cell 3'/5' library construction kit (1000020). The constructed library was sequenced using the Illumina Nova 6000 platform in PE150 sequencing mode.

value: aortic tissues

value: CA1 knockin ApoE-/-

value: fed with high-fat food and simultaneously treated with methoxazolamide.


title: 0054-R1

description: tumor genomic DNA from patient 0054: Oligodendroglioma, WHO grade 2, resection #1

value: male

value: Oligodendroglioma

value: WHO grade 2

value: resection #1


title: Dental mesenchyme, E60, bio rep2


title: HC1, GEX

value: Nasal mucosa


title: HC2, GEX


title: aortic tissue of CA1 knockin ApoE-/- mice that were fed with high-fat food

description:
SampleB
10× Genomics

value: fed with high-fat food


title: CyAF_06G (MS205_011)

description: Library name: Sample77

value: Ovary

value: Granulosa cell

value: CyA, age7, 10-20granulosa cells, GV follicle picked up from adult cynomolgus ovary


title: aortic tissue of CA1 knockin ApoE-/- mice fed high-fat, methoxazolamide treated after atherosclerosis was established

description:
SampleC
aortic tissue of CA1 knockin ApoE-/- mice that were fed with high-fat food and treated with methoxazolamide after atherosclerosis was established
10× Genomics


title: 0052-R2

description: tumor genomic DNA from patient 0052: Oligodendroglioma, WHO grade 3, resection #2

value: female

value: WHO grade 3

value: resection #2

value: GLASS-OD


title: Dental mesenchyme, E60, bio rep1

value: Dental mesenchyme

value: Wild type

value: Embryonic 60 day


title: bone marrow-derived macrophages, WT, 3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using IlluQC_PRLL.pl of NGSQCToolkit
Trimmed sequence reads were mapped to Mus_musculus.GRCm38 using hisat2
Read count extraction and normalization were performed using featureCounts
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text files include gene counts for each Sample

source_name: primary bone marrow-derived macrophages

extract_protocol:
BMDMs were harvested and lysed in TRIzol (Invitrogen). The extraction and sequencing of RNA was performed by Novogene Bioinformatics Institute, Beijing, China.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: primary bone marrow-derived macrophages

value: WT


title: Dental epithelium, E60, bio rep3

value: Dental epithelium


title: Dental epithelium, E60, bio rep2


title: 0053-R1

description: tumor genomic DNA from patient 0053: Oligodendroglioma, WHO grade 2, resection #1

value: male

value: Oligodendroglioma

value: WHO grade 2


title: Dental epithelium, E60, bio rep1


title: Dental mesenchyme, E50, bio rep3

value: Embryonic 50 day


title: CyAF_05G (MS205_009)

description: Library name: Sample75

value: Ovary

value: wildtype


title: 0051-R2

description: tumor genomic DNA from patient 0051: Oligodendroglioma, WHO grade 3, resection #2


title: bone marrow-derived macrophages, Tmem175flox/flox Lyz2-Cre+/-, 3


title: CyAF_05O (MS205_008)

description: Library name: Sample74

value: Oocyte

value: CyA, age7, oocyte, GV follicle picked up from adult cynomolgus ovary


title: aortic tissue of CA1 knockin ApoE-/- mice without treatment

description:
SampleA
10× Genomics

value: aortic tissues

value: CA1 knockin ApoE-/-


title: Cy6F_2G (MS224_011)

description: Library name: Sample80

value: Granulosa cell

value: 17 granulosa cells, antral follicle picked up from adult cynomolgus ovary, Cy6, Fresh ovary, age5,euthanasia


title: bone marrow-derived macrophages, WT, 2


title: bone marrow-derived macrophages, WT, 1


title: 0051-R1

description: tumor genomic DNA from patient 0051: Oligodendroglioma, WHO grade 3, resection #1

value: WHO grade 3

value: resection #1

value: GLASS-OD


title: Dental mesenchyme, E50, bio rep1

value: Dental mesenchyme

value: Wild type


title: CyAF_04G (MS205_007)

description: Library name: Sample73

value: CyA, age7, 10-20granulosa cells, GV follicle picked up from adult cynomolgus ovary


title: 0052-R1

description: tumor genomic DNA from patient 0052: Oligodendroglioma, WHO grade 2, resection #1

value: female

value: Oligodendroglioma


title: 0048-R3

description: tumor genomic DNA from patient 0048: Oligodendroglioma, WHO grade 3, resection #3

value: male

value: resection #3


title: CyAF_06O (MS205_010)

description: Library name: Sample76

value: Ovary

value: wildtype


title: Dental mesenchyme, E50, bio rep2

value: Embryonic 50 day


title: Dental epithelium, E50, bio rep1

value: Dental epithelium


title: Dental epithelium, E50, bio rep2


title: Dental epithelium, E50, bio rep3


title: cxpip_D7

city: Wuhan

first: Han

last: Xia

state: Hubei

department: Key Laboratory of pathogenic Viruses and Biosafety

institute: Wuhan Institute of Virology, CAS

description: Library name: sample3

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: Culex pipiens pallens

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

tag: strain

value: Beijing

tag: age

value: adult


title: bone marrow-derived macrophages, Tmem175flox/flox Lyz2-Cre+/-, 1

value: primary bone marrow-derived macrophages


title: CyAF_02G (MS205_004)

description: Library name: Sample70

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

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).

value: Granulosa cell

value: CyA, age7, 10-20granulosa cells, M1 follicle picked up from adult cynomolgus ovary


title: CSC 3

type: RNA

city: San Franciscco

last: Xiao

state: CA

address: 155 5th Street

department: Biomedical Sciences

institute: Arthur A. Dugoni School of Dentistry, University of the Pacific

description: total RNA and miRNA

hyb_protocol: Hybridization was performed at 40°C for 16 hours on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://mirbase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.  The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry.  The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 L 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide.  After RNA hybridization, tag-conjugating Cy3 dye was circulated through the microfluidic chip for dye staining.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device).

data_processing:
Fluorescence images were digitized using Array-Pro image analysis software (Media Cybernetics).
Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression), which is provided in the *processed.xlsx file.

source_name: dental pulp stem cells

label_protocol: A strand-labeling reaction was carried out with total RNA (1 ug), control oligo-nucleotides, App-Cap3(5’-adenylated and 3’-dideoxy oligo-adaptor, Integrated DNA Technologies) and T4 RNA ligase (Rnl2tr-K227Q, New England BioLabs) in T4 RNA ligase buffer with PEG 8000 and RNase inhibitor (Promega).  The reaction mixture was incubated at 16ºC for 16 hours and stopped by adding equal volume of hybridization buffer.

growth_protocol: Dental pulp stem cells (DPSCs) were cultured in α-MEM (Fischer Scientific, IL) with 10% fetal bovine serum (Neuromics, MN), antibiotics and glutamate.

extract_protocol: Total RNA and miRNAs were collected from the DPSC lysate at the end of the 6-week of treatment with 100 μg/ml CSC using miRNeasy kit (Qiagen).

treatment_protocol: DPSCs were treated with100 μg/ml CSC for 6 weeks, trypsinized, counted and passed every week for 6 weeks.

value: dental pulp stem cells

value: cigarette smoke condensate


title: CyAF_04O (MS205_006)

description: Library name: Sample72

value: Oocyte

value: CyA, age7, oocyte, GV follicle picked up from adult cynomolgus ovary


title: 0048-R1

description: tumor genomic DNA from patient 0048: Oligodendroglioma, WHO grade 2, resection #1

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

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

value: Oligodendroglioma

value: WHO grade 2

value: resection #1

value: GLASS-OD


title: 0048-R2

description: tumor genomic DNA from patient 0048: Oligodendroglioma, WHO grade 3, resection #2

value: male

value: WHO grade 3

value: resection #2


title: bone marrow-derived macrophages, Tmem175flox/flox Lyz2-Cre+/-, 2


title: CyAF_03G (MS205_005)

description: Library name: Sample71

value: Ovary

value: wildtype

value: CyA, age7, coexisting oocyte was excluded due to contamination, 10-20granulosa cells, GV follicle picked up from adult cynomolgus ovary


title: 0046-R1

description: tumor genomic DNA from patient 0046: Oligodendroglioma, WHO grade 2, resection #1


title: CSC 1

description: total RNA and miRNA


title: 0047-R3

description: tumor genomic DNA from patient 0047: Oligodendroglioma, WHO grade 3, resection #3

value: female

value: resection #3


title: 0046-R2

description: tumor genomic DNA from patient 0046: Oligodendroglioma, WHO grade 3, resection #2


title: CyAF_02O (MS205_003)

description: Library name: Sample69

value: CyA, age7, oocyte, M1 follicle picked up from adult cynomolgus ovary


title: 0045-R2

description: tumor genomic DNA from patient 0045: Oligodendroglioma, WHO grade 3, resection #2


title: Sample 3: Mouse Lateral Septum Cells for snRNAseq (S6)

city: Cambridge

first: Mukund

last: Raj

state: Massachusetts

address: 415 Main St

institute: Broad Institute of MIT and Harvard

description: Library name: Sample 3 (S6): Mouse Lateral Septum Tissue for snRNAseq

data_processing:
Raw count matrices were analyzed using Seurat (v.4) with default parameters unless otherwise specified. Cells were first filtered based on the percent of mitochondrial transcripts (<15%), library size (between 750-5000 total reads), and unique genes detected (between 800 and 2,000 genes). Counts were normalized using SCTransform, while regressing out the percentage of mitochondrial transcripts. Dimensionality reduction was performed with principal component analysis (PCA), and batch effects across samples were corrected using Harmony integration. The first 30 Harmony-corrected principal components were used to construct a shared nearest neighbor graph, followed by clustering with the Louvain algorithm at a resolution of 0.5. For visualization, UMAP was computed using the first 20 Harmony-corrected principal components. Broad cell types were annotated based on the expression of canonical marker genes (e.g., Snap25 for neurons; Slc17a7 and Slc17a6 for glutamatergic neurons; Gad1, Gad2, and Slc32a1 for GABAergic neurons). Top marker genes for each broad cell type cluster were identified with Seurat’s FindAllMarkers() function (log2 fold-change >1), and the top 50 markers per cluster were retained. Glutamatergic neurons expressing Slc17a7 were excluded from further analyses. The dataset was then re-normalized with SCTransform, dimensionality reduction and batch correction were repeated using PCA and Harmony, and neighbor graph construction and Louvain clustering was again performed at a resolution of 0.5 to obtain our final broad cell type clusters. For subclustering, GABAergic neurons were subset and re-analyzed with SCTransform normalization, Harmony integration, and clustering using 40 Harmony dimensions and a k-nearest neighbor graph with k=30. This resulted in our final fine-resolution GABAergic cell type clusters. An identical workflow was used to subcluster Somatostatinergic neurons. UMAP visualizations were used for all cell type clustering results. Marker genes for each GABAergic or Somatostatinergic subcluster were identified using Seurat’s FindAllMarkers function, reporting only genes with positive log2 fold-change >1. The top 50 marker genes per cluster were exported. Heatmaps, dot plots, and UMAPs of various marker gene and genes of interest were used to visualize average and/or scaled expression patterns for broad, GABAergic, and Somatostatinergic cell type clusters.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated top 50 marker genes/values per cluster from processed data (.xlsx).

source_name: Lateral Septum Brain Dissection

growth_protocol: Not Applicable.

extract_protocol:
Tissue collection, preparation, sorting, and sequencing procedures were performed following previously published protocols. 8 naïve, adult (3 months old) male C57BL/6J littermates were used for tissue collection. Mice were allowed to acclimate in the lab in their homecages for ≥1 hr prior to being deeply anesthetized as above and perfused using an ice-cold (4 ºC) HEPES-sucrose solution (pH=7.4; in mM): 110 NaCl, 10 HEPES, 25 glucose, 75 sucrose, and 7.5 MgCl2·6H2O. Brain tissue was then immediately dissected and mounted on a vibratome, and 200 µm-thick coronal sections (spanning the broad anterior-posterior/dorsal-ventral extent of the LS) were collected and maintained in the HEPES-sucrose solution. 500 µm-wide circular punches across the anterior-posterior and dorsal-ventral axes of the LS from each mouse were made, and immediately flash frozen using liquid nitrogen. Care was taken to minimize the collection of any non-LS tissue; however, we recognize the possibility for the partial inclusion of some neighboring structures such as medial septum, triangular septum, prefrontal cortex, and/or striatum, given their proximity to the LS. Frozen septal tissues were immediately collected into Eppendorf tubes and maintained at -80 ºC until sequencing.
Sample preparation and nuclei isolation from the samples was performed using fluorescence-activated nuclei sorting (FANS) following previously published protocols. snRNAseq was then performed using the 10X Genomics (v.3) kit and using NextSeq or NovaSeq4000 (Illumina), following manufacturer’s protocols and instructions (three libraries were generated from pooled cells).

treatment_protocol: Not Applicable.

value: Lateral Septum Brain Dissection

value: Cells from Brain Tissue

value: C57BL/6J Littermates

tag: batch


title: Sample 2: Mouse Lateral Septum Cells for snRNAseq (S5)

description: Library name: Sample 2 (S5): Mouse Lateral Septum Tissue for snRNAseq


title: CyAF_01O (MS205_001)

city: Kyoto

institute: Kyoto University, Graduate school of medicine

description: Library name: Sample67

value: Oocyte

value: CyA, age7, oocyte, GV follicle picked up from adult cynomolgus ovary


title: CSC 2

description: total RNA and miRNA

value: dental pulp stem cells

value: cigarette smoke condensate


title: CyAF_01G (MS205_002)

description: Library name: Sample68

value: Granulosa cell

value: CyA, age7, 10-20granulosa cells, GV follicle picked up from adult cynomolgus ovary


title: Cy4C_18G (MS205_051)

description: Library name: Sample66

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


title: Control 2

description: total RNA and miRNA

value: control


title: Sample 1: Mouse Lateral Septum Cells for snRNAseq (S4)

description: Library name: Sample 1 (S4): Mouse Lateral Septum Tissue for snRNAseq

value: male


title: Control 1

description: total RNA and miRNA


title: 0043-R2

city: Rotterdam

institute: Erasmus MC

description: tumor genomic DNA from patient 0043: Oligodendroglioma, WHO grade 3, resection #2

value: Oligodendroglioma

value: WHO grade 3

value: resection #2

value: GLASS-OD


title: Control 3

description: total RNA and miRNA


title: Cy4C_16G (MS205_047)

description: Library name: Sample62

value: Ovary

value: wildtype


title: TG_Sham_male_rep1

city: Kingston

first: Sebastien

last: Talbot

state: ON

address: 18 Stuart st

department: DBMS

country: Canada

institute: Queen's University

description: Library name: TG_Sham_male1

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

source_name: Trigeminal ganglion neuron

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

value: Trigeminal ganglion neuron


title: 0045-R1

description: tumor genomic DNA from patient 0045: Oligodendroglioma, WHO grade 2, resection #1

value: WHO grade 2

value: resection #1


title: TG_Sham_male_rep3

description: Library name: TG_Sham_male3


title: 0044-R1

description: tumor genomic DNA from patient 0044: Oligodendroglioma, WHO grade 2, resection #1

value: female


title: TG_Sham_female_rep3

description: Library name: TG_Sham_female3


title: Cy4C_17O (MS205_048)

last: Yabuta

address: Yoshida-Konoe-cho, Sakyo-ku

description: Library name: Sample63

source_name: Ovary

value: Oocyte

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


title: TG_Sham_female_rep2

description: Library name: TG_Sham_female2


title: Cy4C_18O (MS205_050)

description: Library name: Sample65


title: MG1655 cells, disome fraction, rep2

city: Heidelberg

first: Günter

last: Kramer

address: Im Neuenheimer Feld 329

country: Germany

institute: Center for Molecular Biology of Heidelberg University (ZMBH)

description: Library name: DiSP_Disome_rep2

data_processing:
The 3' adaptor sequences were trimmed form demultiplexed raw read sequencing files with Cutadapt (v1.13) with the following command for NextSeq550 files: cutadapt --cores=4 -q20 -m23 --discard-untrimmed -O6 -a ATCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -o <path_to_output>.fastq.gz <path_to_input>.fastq.gz. For samples sequenced on HiSeq2000 the following command was used: cutadapt --cores=4 -q20 -m23 --discard-untrimmed -O6 -a CTGTAGGCACCATCAATTCGTATGCCGTCTTCTGCTTG -o <path_to_output>.fastq.gz <path_to_input>.fastq.gz
Unique molecular identifiers (UMIs) were extracted from each read for the downstream analysis using a custom Julia script (available as supplement information in Bertolini et al., 2021) with the following command: julia <path_to_script>/Script1.jl <path_to_input>.fastq.gz <path_to_output>.fastq.gz --umi3 5 --umi5 2. SeRP samples did not contain UMI sequences in the adaptors, therefore this step was not included.
Reads were aligned to the E. coli genome using bowtie.
All reads aligning to the coding sequence (CDS) were assigned to the p-site via a custom Julia script (available as supplement information in Bertolini et al., 2021). p-site assigned reads were used for all downstream analysis.
Assembly: NC_000913
Supplementary files format and content: HDF5 files containing raw reads assigned to ribosomal P-sites, organised by coding sequence (CDS). Depending on the library preparation method PCR duplicates are removed based on the unique molecular identifier (UMI).
Library strategy: Ribo-Seq

organism: Escherichia coli

source_name: bacterial cell

growth_protocol: Cells were grown in EZ RDM. For lacZ-mEYFP SeRP, expression was induced with 10 uM IPTG 15 min before harvesting. For DiSP, endogenous lacZ expression was induced with by lactose. Cells were harvested by rapid filtration through a 0.2 um nitrocellulose membrane, scraped of rapidly and plunged into liquid nitrogen.

extract_protocol:
Ribosomes were purifed by sucrose density ultracentrifugation (SeRP total sample), affinity purification (SeRP IP sample) or sucrose gradient ultracentrifugation (DiSP monosome and disome samples). RNA from ribosome fractions was extracted using the hot acid phenol method as previously described (DOI: 10.1038/s41596-019-0185-z)
SeRP libraries were prepared as previosly described (DOI: 10.1038/nprot.2013.133). DiSP libraries were prepared as previously publsihed (DOI: 10.1038/s41596-019-0185-z)

value: bacterial cell

value: wild type


title: MG1655 cells, monosome fraction, rep2

description: Library name: DiSP_Monosome_rep2


title: Cy4C_17G (MS252_213)

first: Yukihiro

description: Library name: Sample64

value: Granulosa cell

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


title: TG_Sham_female_rep1

description: Library name: TG_Sham_female1


title: Cy4C_16O (MS205_046)

description: Library name: Sample61


title: TG_MOC1_male_rep3

description: Library name: TG_MOC1_male3


title: 0043-R1

first: Youri

last: Hoogstrate

address: Wytemaweg 80

description: tumor genomic DNA from patient 0043: Oligodendroglioma, WHO grade 2, resection #1

value: male


title: Cy4C_15G (MS251_203)

description: Library name: Sample60

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


title: 0042-R2

description: tumor genomic DNA from patient 0042: Oligodendroglioma, WHO grade 2, resection #2

value: Oligodendroglioma


title: 0042-R3

description: tumor genomic DNA from patient 0042: Oligodendroglioma, WHO grade 3, resection #3

value: WHO grade 3

value: resection #3


title: Cy4C_15O (MS205_044)

description: Library name: Sample59

value: Ovary

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


title: cxtri_D7

description: Library name: sample4

organism: Culex tritaeniorhynchus

value: midgut

value: Yingcheng

value: adult


title: TG_MOC1_male_rep2

description: Library name: TG_MOC1_male2

value: Trigeminal ganglion neuron


title: cxtri_bl_D14

description: Library name: sample6

value: female


title: Cy4C_14G (MS251_202)

description: Library name: Sample58

value: wildtype


title: Cy4C_14O (MS205_042)

description: Library name: Sample57

value: Oocyte