title: DNMT3Amut_55

description: Library name: Sample55


title: DNMT3Amut_54

status: Public on May 19 2025

type: SRA

city: Taipei

first: Sao-Chih

last: Ni

address: Heping E. Rd

country: Taiwan

institute: National Taiwan University Hospital

description: Library name: Sample54

library_source: transcriptomic

data_processing:
Trimming of adaptor sequences and removal of reads of low quality were performed using cutadapt (v2.3).
Quantified reads were aligned to the human genome (GRCh38.p12) by STAR (v2.6.1 a)(24) and then gene-level read counts were generated based on the annotations of Gencode (v28).
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: bone marrow

extract_protocol:
Total RNA were extracted using RNeasy kit (Qiagen) and reverse trasncribed using Superscript II RT (Invitrogen).
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer's recommendations.

tag: tissue

value: bone marrow

tag: cell type

value: bone marrow mononuclear cells

tag: treatment

value: pretreatment diagnostic


title: Nipbl +/+; Isl1 +/+ 10

city: Irvine

first: Anne

last: Calof

state: CA

address: Biological Sciences III, 519 Ring Rd

department: Developmental & Cell Biology

country: USA

institute: University of California, Irvine

data_processing:
Reads were mapped onto the GRCm38 mm10 mouse reference genome using STAR. Reads that mapped to genes were counted using featureCounts to generate a raw read count matrices for every sample.
Assembly: mm10
Supplementary files format and content: raw-counts-all-samples.txt contains a raw read count matrix for all samples in comma delimited format.

organism: Mus musculus

source_name: Heart

extract_protocol:
Total RNA was extracted from mouse E10.5 hearts using New England Biolabs' Monarch Total RNA Miniprep Kit (Catalog #: T2010S).
RNA libraries were constructed using New England Biolabs' NEBNext Ultra II RNA Library Prep Kit for Illumina (Catalog #: E7765).

tag: developmental stage

value: Embryonic day E10.5

value: Heart

tag: genotype

value: Nipbl +/+; Isl1 +/+


title: DNMT3Amut_52

description: Library name: Sample52


title: DNMT3Amut_53

description: Library name: Sample53


title: Nipbl +/+; Isl1 +/+ 9


title: DNMT3Amut_51

description: Library name: Sample51


title: DNMT3Amut_63

description: Library name: Sample63


title: Nipbl +/+; Isl1 +/+ 7


title: Nipbl +/+; Isl1 +/+ 5


title: DNMT3Amut_49

description: Library name: Sample49


title: Isl1 +/- 7


title: DNMT3Amut_48

description: Library name: Sample48


title: Nipbl +/+; Isl1 +/+ 4


title: Nipbl +/-; Isl1 +/- 1

value: Nipbl +/-; Isl1 +/-


title: DNMT3Amut_47

description: Library name: Sample47


title: DNMT3Amut_46

description: Library name: Sample46


title: Nipbl +/+; Isl1 +/+ 3


title: Nipbl +/+; Isl1 +/+ 2


title: DNMT3Amut_45

description: Library name: Sample45


title: DNMT3Amut_44

description: Library name: Sample44


title: DNMT3Amut_43

description: Library name: Sample43


title: control, PD7 testes

city: Hangzhou

first: Lin-Yu

last: Lu

state: Zhejiang

address: 268 Kaixuan Road, North Central Building, Room 536

country: China

institute: Zhejiang University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The raw sequencing data were aligned to the mouse reference genome mm10 (10× Genomics pre-built, version refdata-gex-mm10-2020-A), and count matrices were generated using the 10× Genomics Cell Ranger Pipeline (version 6.0.2). Subsequently, these matrices were imported into R (version 4.2.3) via RStudio (version 2023.03.0 Build 386). R Package Seurat (version 4.3.0.1) was utilized for downstream scRNA-seq analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: testes

extract_protocol:
Testes of PD7 control and Brca1 vKO mice were isolated and digested into single cells by two continuous steps with collagenase IV (Sangon Biotech) and TrypLE Express (Thermo Fisher).
The single-cell suspensions were loaded onto the 10× Genomics Chromium platform to partition into Gel Bead-In-Emulsions (GEMs), followed by barcoded reverse transcription and PCR amplification of cDNA for library construction according to the manufacturer’s instructions. The single-cell libraries were sequenced by an MGISEQ-2000RS sequencer (MGI Tech).

value: testes

value: control


title: Brca1 vKO, PD7 testes

description: 10x Genomics

value: Brca1 vKO


title: DNMT3Amut_42

description: Library name: Sample42


title: Nipbl +/+; Isl1 +/+ 8


title: RNA_KO_organoids_IL13_RANKL_4days_rep3

city: Beijing

first: Xiaohuan

last: Guo

address: Hai Dian

department: Institute for Immunology

institute: Tsinghua University

description:
TPM_bulk_allsamples.txt
KO_IL-13_RANKL-rep3

data_processing:
bulk RNA-seq: aligned to mm10 with Bowtie2(v2.2.5) with default parameters
bulk RNA-seq: gene expression profiles were harvested with RSEM(V1.2.8, p 8, forward prob 0.5, paired end)
scRNA-seq: Raw reads were processed to generate gene expression profiles using CeleScope v1.5.2 (SingleronBiotechnologies) with default parameters.
sc-RNA-seq: Trimmed reads were aligned against the GRCm38 (mm10) transcriptome using STAR(v2.6.1b).
sc-RNA-seq: Uniquely mapped reads were then assigned to exons with FeatureCounts(v2.0.1).
Assembly: mm10
Supplementary files format and content: For bulk RNA-seq data: tab-delimited text files include TPM values for each sample.
Supplementary files format and content: For scRNA-seq data: mtx, a gene by cell count matrix in the sparse matrix market format
Supplementary files format and content: For scRNA-seq data: barcodes.tsv, cell names (colname names of the count matrix)
Supplementary files format and content: For scRNA-seq data: genes.tsv, gene names (row names of the count matrix)

source_name: intestinal organoids

growth_protocol: For bulk RNA-seq, intestinal organoids were cultured in ENR medium with or without 4-OHT(1 μM) for 3 days, Then the passaged organoids were treated with 20ng/ml IL-13 and with or without 50ng/ml RANKL for 4 days.

extract_protocol:
Single-cell suspensions were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System.
The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits.

value: intestinal organoids

value: Vil-creERT2; Rank fl/fl mice

value: ENR medium, 4-OHT, IL-13, RANKL for 4 days


title: DNMT3Amut_40

description: Library name: Sample40


title: RNA_KO_organoids_IL13_RANKL_4days_rep2

description:
TPM_bulk_allsamples.txt
KO_IL-13_RANKL_rep2


title: DNMT3Amut_41

description: Library name: Sample41


title: RNA_KO_organoids_IL13_4days_rep3

description:
TPM_bulk_allsamples.txt
KO_IL-13_rep3

value: ENR medium, 4-OHT, IL-13 in vitro for 4 days


title: Nipbl +/+; Isl1 +/+ 6


title: DNMT3Amut_39

description: Library name: Sample39


title: DNMT3Amut_50

description: Library name: Sample50


title: DNMT3Amut_38

description: Library name: Sample38


title: RNA_KO_organoids_IL13_4days_rep2

description:
TPM_bulk_allsamples.txt
KO_IL-13_rep2


title: RNA_KO_organoids_IL13_4days_rep1

description:
TPM_bulk_allsamples.txt
KO_IL-13_rep1


title: DNMT3Amut_35

description: Library name: Sample35


title: RNA_WT_organoids_IL13_RANKL_4days_rep2

description:
TPM_bulk_allsamples.txt
WT_IL13_RANKL_rep2

value: ENR medium, DMSO, IL-13, RANKL for 4 days


title: Nipbl +/+; Isl1 +/+ 1


title: DNMT3Amut_33

description: Library name: Sample33


title: DNMT3Amut_34

description: Library name: Sample34


title: RNA_WT_organoids_IL13_4days_rep3

description:
TPM_bulk_allsamples.txt
WT_IL13_rep3

value: ENR medium, DMSO, IL-13 in vitro for 4 days


title: RNA_WT_organoids_IL13_RANKL_4days_rep3

description:
TPM_bulk_allsamples.txt
WT_IL13_RANKL_rep3


title: RNA_WT_organoids_IL13_RANKL_4days_rep1

description:
TPM_bulk_allsamples.txt
WT_IL13_RANKL_rep1


title: DNMT3Amut_36

description: Library name: Sample36


title: DNMT3Amut_32

description: Library name: Sample32


title: DNMT3Amut_31

description: Library name: Sample31


title: RNA_WT_organoids_IL13_4days_rep1

description:
TPM_bulk_allsamples.txt
WT_IL13_rep1


title: RNA_WT_organoids_IL13_4days_rep2

description:
TPM_bulk_allsamples.txt
WT_IL13_rep2


title: DNMT3Amut_30

description: Library name: Sample30


title: DNMT3Amut_37

description: Library name: Sample37


title: DNMT3Amut_29

description: Library name: Sample29


title: DNMT3Amut_26

description: Library name: Sample26


title: Vieceral adipose tissue, human with normal weight3

city: nanjing

first: Hao

last: Zhu

address: 300 guangzhou road

institute: nanjing medical university

description: Library name: sample6

library_source: genomic

data_processing:
Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS)
Assembly: hg38
Supplementary files format and content: xls files include peaks detected for each Sample

molecule: genomic DNA

source_name: visceral adipose tissue

extract_protocol:
Fresh tissue sample is flash frozen by liquid nitrogen and then ground completely. The transposition reactions are initiated by adding transposase.
The library was validated on an Agilent Technologies 2100 bioanalyzer for quality control.The final library was amplified with phi29 (Thermo Fisher Scientific, MA, USA) to generate DNA nanoballs (DNBs), which had more than 300 copies of one molecule. DNBs were loaded into the patterned nanoarray, and single-end 50-base reads were generated on the BGISEQ500 platform (BGI-Shenzhen, China).

value: visceral adipose tissue

value: visceral adipocyte


title: DNMT3Amut_28

description: Library name: Sample28

value: bone marrow

value: bone marrow mononuclear cells


title: DNMT3Amut_25

description: Library name: Sample25

value: pretreatment diagnostic


title: Vieceral adipose tissue, human with obesity3

description: Library name: sample3


title: DNMT3Amut_27

description: Library name: Sample27


title: RNA_KO_organoids_IL13_RANKL_4days_rep1

description:
TPM_bulk_allsamples.txt
KO_IL-13_RANKL_rep1


title: DNMT3Amut_24

description: Library name: Sample24


title: Vieceral adipose tissue, human with normal weight1

description: Library name: sample4


title: Vieceral adipose tissue, human with obesity1

description: Library name: sample1


title: N7 cell-derived EV small RNA

city: Seongnam

first: Jae Hyun

last: Park

state: Gyeonggi-do

address: 335, Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-

country: South Korea

institute: CHA University

description: Library name: N7_cell_EV_smallRNA

data_processing:
Reads were mapped to GRCh38 using subread aligner
Readcount extraction was performed using featureCounts with miRBase v22.1 human annotation
Assembly: GRCh38
Supplementary files format and content: tab-delimited txt file includes raw counts

source_name: human fetal brain-derived astrocytes

extract_protocol:
total RNA and small RNA were extracted using BGI protocols
RNA libraries were prepared for sequencing using BGI protocols

value: human fetal brain-derived astrocytes


title: Vieceral adipose tissue, human with normal weight2

description: Library name: sample5


title: Vieceral adipose tissue, human with obesity2

description: Library name: sample2


title: DNMT3Amut_23

description: Library name: Sample23


description: Library name: sample6

data_processing:
The data of sequencing were screened with SOAPnuke (v1.5.2) by the following steps: (1) erasing reads having sequencing adapters; (2) removing reads that had base ratio of low-quality (base quality equal to or less than 5) more than 20%; and (3) deleting reads that had an unknown base ('N' base) more than 5% ratio. Then, we obtained and saved the clean reads in FASTQ format. HISAT2 (v2.0.4) were used to map the clean reads to the reference genome.
Assembly: hg38
Supplementary files format and content: xlsx files include FPKM values of differentially expressed genes for each Sample

extract_protocol:
Total RNA was extracted with TRIzol from tissue weigh approximately 60 mg following the manufacturer’s instructions
The library was validated on an Agilent Technologies 2100 bioanalyzer for quality control.The final library was amplified with phi29 (Thermo Fisher Scientific, MA, USA) to generate DNA nanoballs (DNBs), which had more than 300 copies of one molecule. DNBs were loaded into the patterned nanoarray, and single-end 50-base reads were generated on the BGISEQ500 platform (BGI-Shenzhen, China).


title: DNMT3Amut_22

description: Library name: Sample22


description: Library name: sample4


description: Library name: sample5


title: DNMT3Amut_19

description: Library name: Sample19


title: DNMT3Amut_20

description: Library name: Sample20


description: Library name: sample3


description: Library name: sample2


title: DNMT3Amut_17

description: Library name: Sample17


title: DNMT3Amut_18

description: Library name: Sample18


description: Library name: sample1


title: DNMT3Amut_16

description: Library name: Sample16


title: Mouse 33 (E14.5), Sample 33-2 (LTT3b), Lower trunk and tail, E7.5 tdTomato-virus (pMR671), GEX

city: Vienna

first: Sergey

last: Isaev

address: Spitalgasse, 4

department: Department of Neuroimmunology

country: Austria

institute: Medical University of Vienna

description:
Library name: LTT3b
Gene expression library

data_processing:
In the course of the experiments, one to three libraries were generated for each sample: (1) 10x v3 Gene Expression, and (2-3) viral barcode-containing cDNA libraries (two in the case of double injection). Detailed descriptions of each sample, corresponding libraries, and FP sequences are provided in Supplementary Table X. Reads from experiments (1) and (2) were aligned to a chimeric mm39 and FP genome reference using Cell Ranger 7.0.1.
Clonal barcodes were identified using an algorithm suggested in [PMID: 35210624] with modifications available at https://github.com/serjisa/TREX.modified. Firstly, barcode sequence corrections were performed individually for each cell, enhancing robustness against artificial merging but slightly increasing clonal dropout rates.
Assembly: Chimeric mm39 with FP-CloneID contigs added
Supplementary files format and content: h5-containers, h5ad-containers and comma-separated values

molecule: polyA RNA

source_name: Ectodermal and mesodermal derivatives

extract_protocol:
The embryos were removed from the uterus, sacrificed, and placed into a petri dish containing Hank’s Balanced Salt Solution (HBSS) on ice. Embryos were screened for expression of Tomato or GFP using a benchtop fluorescence stereoscope. Limbs, liver, and the ventral skin were removed. Body regions, primarily lower trunk, middle trunk, and cranial regions, were dissected separately and placed into a small Petri dish containing 2.5 mL of a cell dissociation buffer consisting of 2mg/mL Collagenase P (Roche, Sigma-Aldrich), 1X TrypLE, and 1uL/mL DNASe I, fully dissolved in HBSS (without phenol red, including Ca2+ and Mg2+). Tissue was chopped finely with a scalpel and forceps under control of stereomicroscope and transferred to 15mL falcon tubes. The tissue pieces were triturated 10X using a transfer pipette, and then 10X using a 1mL pipette. Samples were then incubated for 20 minutes at 37 C in a preheated shaking incubator set at 150 RPM, with the tubes tilted to ~60 degrees. During this time every 6-8 minutes, the samples were vortexed and triturated using a 1mL pipette. After the tissue clumps disappeared, 12.5 mL of 2% Fetal Bovine Serum (FBS) diluted in ice-cold HBSS (without phenol red, without Ca2+ and Mg2+, H6648 SIGMA) was added. The samples were centrifuged in a cold centrifuge (4C) for 15 minutes at 500 g. The supernatant was carefully removed and the pellet was resuspended in 1mL HBSS + 2% FBS and kept on ice thereafter. After centrifugation and resuspension, the cells were filtered into round-bottom polypropylene test tubes (Falcon) using a cell strainer with a 40 micrometer woven polyethylene terephthalate mesh (pluriSelect pluriStrainer SKU 43-10040-40) for downstream cell sorting.
Cells were loaded into the Chromium machine (aiming for ~10,000 cells per reaction) using the V3.1 single-cell reagent kit (10X Genomics). Following GEM creation and cell lysis, cDNA was synthesized by reverse transcription, then amplified by PCR for 12 cycles as per the manufacturer’s protocol (10X Genomics). A portion of the amplified cDNA was used to generate Gene expression libraries and then indexed using the Single Index Plate T Set A. CloneID enrichment from cDNA libraries was additionally performed based on Ratz et al 2022 to increase the retrieval of the barcodes by ~5-10%. Briefly, two nested PCR reactions were performed using Q5 error-correcting DNA polymerase to amplify the CloneID-containing region, and a third reaction was used for sample indexing using the Single Index Plate T Set A. In between each reaction, amplicons were purified by 0.8X AMPure beads using a DynaMag Magnetic separator. Indexed GE and CloneID-enrichment libraries were quantified using BioAnalyzer and/or Qubit, and then pooled prior to Illumina sequencing on a NovaSeq 6000 S2-200 v1.5 flow cell with read setup 28-8-0-166.

treatment_protocol: Injections for lentiviral gene delivery were performed according to previously published protocols. At embryonic day E7.5-E8.5, the females were anesthetized with isoflurane (4% induction, maintained at 1.5-2.5%) and placed on a heated plate for surgery. Depth of anesthesia was tested through pinching the paw. Eye gel was applied to prevent dehydration. Pain relief e.g. Buprenorphine 0.05-0.1 mg/kg was administered via subcutaneous injection 30 minutes before the first incision. All instruments were autoclaved and disinfected with chlorhexidine alcohol before surgery. The skin was disinfected with chlorhexidine alcohol, and the hair on the abdomen was removed with a shaver or hair removal agent such as Veet. A small incision was placed in the abdomen and the uterus was exposed and placed on top of gauze soaked in sterile NaCl solution, placed around the opening. The uterus was kept moist with warm NaCl solution (37C). Using a glass capillary, lentivirus (from 23-206 nL) was injected through the uterine wall into the amniotic cavity. After the embryos were injected, the uterus was brought back into the abdomen and the incisions in the muscle wall were sewn together with absorbent suture thread, and the skin was closed with suture thread or staples. The mice were taken off isoflurane and allowed to wake up in their own cage on a heating pad under supervision. Postoperative pain relief was given in the form of a subcutaneous injection of Buprenorphine (0.05-0.1 mg/kg). For embryo retrieval, the mother was euthanized via CO2 overdose and cervical dislocation, and the embryos were collected at E13.5 (or at E14.5 if this is labeled in the name of the sample) and euthanized via decapitation.

value: Ectodermal and mesodermal derivatives

tag: strain

value: Wild type


title: Sample 34 (three mice at E14.5), Sample 34-1 (3tail), Three tails combined, E7.5 tdTomato-virus (pMR671), GEX

description:
Library name: 3tail
Gene expression library


title: DNMT3Amut_12

description: Library name: Sample12


title: Mouse 32 (E14.5), Sample 32-2 (LTT2b), Lower trunk and tail, E7.5 tdTomato-virus (pMR671), GEX

description:
Library name: LTT2b
Gene expression library


title: Mouse 32 (E14.5), Sample 32-1 (LTT2a), Lower trunk and tail, E7.5 tdTomato-virus (pMR671), GEX

description:
Library name: LTT2a
Gene expression library


title: DNMT3Amut_14

description: Library name: Sample14


title: DNMT3Amut_11

description: Library name: Sample11


title: DNMT3Amut_13

description: Library name: Sample13


title: Mouse 33 (E14.5), Sample 33-1 (LTT3a), Lower trunk and tail, E7.5 tdTomato-virus (pMR671), GEX

description:
Library name: LTT3a
Gene expression library


title: ko3.fastq.gz

city: New York

first: Samie

last: Jaffrey

state: New York

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medicine

description: Library name: ko3.fastq.gz

library_source: other

data_processing:
OTTR monosome profiling dataset was processed as previously described. Briefly, the adaptor was trimmed and the unique molecular identifier and a single nucleotide at the beginning of the sequencing introduced during OTTR library preparation method were removed from the sequencing reads using cutadapt v4.1. Sequencing reads were further filtered for minimal 20 bp and quality score 10 using cutadapt v4.1. The pre-processed reads were first aligned to ribosomal RNAs. Reads that did not align to ribosomal RNAs were then aligned to the transcriptome in which a single transcript with the longest CDS was selected for each protein coding gene. Alignment to the transcriptome was performed using the following parameters: --sjdbOverhang 43 --alignSJoverhangMin 1 --alignSJDBoverhangMin 1 --seedSearchStartLmax 20 --outFilterMultimapNmax 1 --outFilterMismatchNmax 2 --alignEndsType EndToEnd. Aligned reads were further analyzed using riboWaltz v2.0. The length filter of 32-38 bp was applied to the libraries generated using P1 nuclease. Off-set to the A-site was determined using riboWaltz psite function with the default parameters. The mapped A-site was further analyzed using custom scripts in R v4.1.2.
Assembly: mm39
Supplementary files format and content: A list of P-sites mapped to the coding sequence of each transcript, the 5' and 3' extrimety of the read, read length, the start and stop codon for each transcript, the distance of the first nucleotide of the P-site relative to the start and the stop codon, and the genotype of the sample.
Library strategy: Ribo-Seq

molecule: other

source_name: mESC

growth_protocol: mESC cells were grown in KnockOut DMEM (ThermoFisher, 10829018) supplemented with 15% heat-inactivated FBS, 10 U/mL Penicillin-Streptomycin (ThermoFisher, 15140122), 1x GlutaMax (ThermoFisher, 35050061), 500 μM β-mercaptoethanol (ThermoFisher, 21985023), 1x Nonessential amino acids (ThermoFisher, 11140076), 103 U/mL LIF (MilliporeSigma, ESG1107), 3 μM CHIR99021 (ThermoFisher, 501013679), and 1 μM PD0325901 (ThermoFisher, 501013147). Cells were plated on plates coated with EmbryoMax™ 0.1% gelatin solution (MilliporeSigma, ES-006-B) and passaged daily using TrypLE Express (ThermoFisher, 12604039) according to the manufacturer’s instructions.

extract_protocol:
Cells were grown in a 150 mm dish to 70% confluency. Cells were washed with ice-cold PBS supplemented with 100 μg/mL cycloheximide and 100 μg/mL tigecycline. Cells were lysed in 300 μL lysis buffer [20 mM Tris-HCl, pH 7.4, 150 mM NaCl, 5 mM, MgCl2, 1 mM DTT, 1 % Triton X, 100 μg/mL cycloheximide, 100 μg/mL tigecycline, and 15 U/mL DNaeI (ThermoFisher, 89836)]. Lysates were passed through a 25-gauge needle five times, incubated on ice for 20 min, and clarified by centrifugation for 10 min at 20,000 x g at 4 °C.
OTTR ribosome profiling library was prepared using OTTR cDNA library construction kit (Karnateq, R2201001S). RNA in the lysate was quantified using Qubit™ RNA Broad Range kit (ThermoFisher, Q10211) on Qubit4 Fluorometer. 30 μg RNA was digested using 600 U P1 nuclease (NEB, M0660S) in 400 μL supplemented with 42 μL 0.2 M Bis-Tris, pH 6.0 (Life Technologies, J62686.AE) at 37 °C for 1 h. OTTR ribosome profiling libraries were prepared using mirRICH small RNA enrichment method according to the manufacturer’s instruction. Final library quality was assessed on Agilent TapeStation4200 using D1000 ScreenTape (Agilent, 5067-5582). Library was quantified on Qubit4 Fluorometer using Qubit 1X dsDNA HS Assay Kit (ThermoFisher, Q33231). Libraries were sequenced with single-end 100 cycles on Illumina NovaSeq 6000.

tag: cell line

value: mESC

value: Mettl14 knockout


title: DNMT3Amut_10

description: Library name: Sample10


title: ko2.fastq.gz

description: Library name: ko2.fastq.gz


title: Mouse 31, Sample 31-2 (LTT1b), Lower trunk and tail, E7.5 tdTomato-virus (pMR671), GEX

description:
Library name: LTT1b
Gene expression library


title: Mouse 31, Sample 31-1 (LTT1a), Lower trunk and tail, E7.5 tdTomato-virus (pMR671), GEX

description:
Library name: LTT1a
Gene expression library


title: DNMT3Amut_09

description: Library name: Sample9


title: DNMT3Amut_21

description: Library name: Sample21


title: DNMT3Amut_07

description: Library name: Sample7


title: ko1.fastq.gz

description: Library name: ko1.fastq.gz


title: DNMT3Amut_06

description: Library name: Sample6


title: wt2.fastq.gz

description: Library name: wt2.fastq.gz

value: wildtype


title: wt1.fastq.gz

description: Library name: wt1.fastq.gz


title: pmn deletion mouse lung (wt_pmn_deletion) 3

city: Shanghai

first: Jing

last: Wang

address: No. 227 South Chongqing Road, Shanghai

institute: Shanghai Jiao Tong University School of Medicine

description: Library name: 21_9_4_10

data_processing:
Raw reads of the fastq format were first processed using fastp, and the low-quality reads were removed to obtain clean reads.
The clean reads were mapped to the reference genome using HISAT2.
The FPKM of each gene was calculated, and the read counts of each gene were obtained by HTSeq count.
Assembly: mm10
Supplementary files format and content: csv files include FPKM values for each sample

source_name: lung

extract_protocol:
mRNA was isolated using PolyA tail enrichment, and was used for the construction of sequening libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA seq library preparation kit.

value: lung


title: DNMT3Amut_15

description: Library name: Sample15


title: pmn deletion mouse lung (wt_pmn_deletion) 2

description: Library name: 21_9_4_9


title: DNMT3Amut_04

description: Library name: Sample4


title: multiplexed elicited needles

city: Stanford

first: Conor

middle: James

last: McClune

address: 443 Via Ortega

institute: Stanford University

description:
Library name: elicited
mature and young needles with multiplexed perturbation ( subjected to chemical elicitors for 1-5 days prior to pooling and library preparation)

data_processing:
Reads were cleaned with trimmomatic and mapped to the genomes of Taxus chinensis with STARsolo (STAR ... --runThreadN 32 --alignIntronMax 10000 --soloUMIlen 12 --soloCellFilter EmptyDrops_CR --soloFeatures GeneFull --soloMultiMappers EM --soloType CB_UMI_Simple). Ambient RNA was removed with cellbender. Using the doubletdetection library, doublets were removed, as well as cells with outlier numbers of reads or where most reads were the most expressed genes (pct_counts_in_top_20_genes < 30). Genes were removed from analysis if expressed in fewer than 50 cells.
Assembly: reads were mapped to the Taxus chinensis genome (GCA_019776745.2)
Supplementary files format and content: preprocessed data are h5ad files contain the cell x gene metrices outputed by the final preprocessing step (cellbender)

molecule: nuclear RNA

organism: Taxus x media

source_name: mature and young needles

extract_protocol:
Nuclei extraction buffer (NIB) consisted of 5 mM MgCl2, 10 mM HEPES pH 7.6, 0.8 M sucrose, 0.1% Triton X and (for density matching to prevent nuclei settling during flow sorting) 1% Dextran T40 and 2% Ficoll. On the day of use, NIB was supplemented with 1 mM dithiothreitol. All nuclei extraction steps were conducted at 4°C and wide bore pipette tips were used when handling nuclei. Steps between tissue harvesting and loading into the Chromium device were completed within 90 minutes to avoid RNA loss. To isolate nuclei, approximately 1 g of Taxus media tissue was removed from the plant and immediately placed in a petri dish with 10mL NIB. Tissue was chopped by hand at ~200 rpm with a fresh razor blade for 5 minutes until most large tissue was broken down, and then gently rocked at 4°C for 15 minutes. To remove large debris, disrupted tissue was then passed through a pre-wet 100 μm cell strainer stacked atop a 40 μm cell strainer. Nuclei were gently pelleted at 300 g at 4°C for 5 minutes and resuspended in 1 mL NIB with 5 ng/μL 4,6-diamidino-2-phenylindole (DAPI, Thermo Fischer) and 5 ng/μL propidium iodide. Using a Sony SH800 cell sorter with a 70 μm chip, 140,000-200,000 nuclei were sorted into a tube containing 1 mL PBS+ (PBS, 0.1% bovine serum albumin, 20 U/mL Invitrogen Ribonuclease Inhibitor).  Nuclei were centrifuged at 300g at 4°C for 5 minutes, then gently resuspended in 40 μL PBS+. Nuclei were immediately loaded onto a 10x Genomics Chromium controller and libraries were generated using v3 chemistry.
Nuclei were immediately loaded onto a 10x Genomics Chromium controller and libraries were generated using v3 chemistry.  Libraries were sequenced on an Illumina NextSeq 3000.

treatment_protocol: For multiplexed elicitation experiment, Taxus needles were subjected to perturbation in deep-well 96-well plates with 200 μL MS media [7.5 g/L Murashige and Skoog macronutrients (Fischer), 3 g/L sucrose, pH 5.7] supplemented with elicitor. Two needles (biological replicates) each from two developmental stages (young and mature) were treated with each elicitation condition (17 conditions listed in Table S2) for each time point (1, 2, 3 and 4 days), resulting in 272 tissue samples (two replicates of 136 perturbations). To minimize contamination, needles were washed thoroughly in sterile water before moving to MS plates, which were sealed with breathable rayon film (VWR) and placed under 18 hour light cycles. Tissue elicitation was started at staggered times so all tissues could be harvested simultaneously. To extract nuclei from elicited tissues, all tissues were combined in a wire mesh, washed with water, and subjected to the above nuclei extraction protocol.

value: mature and young needles

value: multiplexed chemical perturbation


title: mature tissues (needles, stems, bud scales)

description:
Library name: mature
mature arial tissues (needles, stems, bud scales)


title: EF5

type: RNA

city: Boston

first: William

last: Crisler

state: Massachusetts

address: 221 Longwood Ave

department: Dermatology

institute: Brigham & Women's Hospital

description: Samples were run using the nanostring panel NS_Hs_AI_Pro_v1.1

hyb_protocol: 100 ng of total RNA was hybridized to the reporter and capture probes in 30 μL reaction volume for 20 hours at 65°C.

scan_protocol: The captured targets were  immobilized on the nCounter cartridge on the NanoString PrepStation. The cartridge was scanned at 555 fields of view (FOV) on the nCounter Digital Analyzer. Images were processed into a digital format (RCC files). All samples were analyzed using a single lot of reagents.

data_processing:
Raw data appraisal, quality control, processing, and normalization were all performed using nSolver analysis software V4.0. Background subtraction was performed using the module's negative controls. Samples were then normalized using internal positive controls and housekeeping genes included in the module. For hierarchical clustering and heatmap generation, raw counts were normalized according to nSolver guidelines. nSolver V4.0 was further used to analyze differentially expressed genes (DEGs).
Log2 transformed normalized counts are in the matrix tables. One matrix table depicts Log2 transformed normalized counts for morphea vs. normal skin. A second matrix table shows Log2 transformed normalized counts for eosinophilic fasciitis vs. normal skin.

label: Nanostring reporter probes

source_name: Esoinophilic fasciitis lesional skin

label_protocol: We used the NanoString nCounter Human Autoimmune Profiling Panel with probes representing 750 genes. Samples were processed on the NanoString nCounter Analysis System according to the manufacturer’s protocol (NanoString Technologies).

extract_protocol: RNA was extracted from six consecutive 10um sections from FFPE skin biopsies (8 normal skin, 10 morphea, and 6 eosinophilic fasciitis). Deparaffinization with xylene and RNA extraction were carried out using the RNeasy FFPE Kit (Qiagen). RNA concentration and purity were measured with a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific), and RNA quality was assessed using the 260/280 nm absorbance ratio.

tag: gender

value: Female

tag: age

tag: race

value: White, non-Hispanic


title: DNMT3Amut_02

description: Library name: Sample2


title: pmn deletion mouse lung (wt_pmn_deletion) 1

description: Library name: 21_9_4_6


title: EF6


title: EF3

value: Male


title: DNMT3Amut_03

description: Library name: Sample3


title: DNMT3Amut_08

description: Library name: Sample8


title: EF4


title: wt mouse lung (wt_pmn_deletion) 3

description: Library name: 21_9_4_3


title: EF1


title: Morphea10

source_name: Morphea lesional skin


title: wt mouse lung (wt_pmn_deletion) 2

description: Library name: 21_9_4_2


title: EF2


title: Morphea9

value: Black, Hispanic


title: Parse sequencing, PC3cisplatin sublibrary8 (contains all samples)

city: Baltimore

first: Sarah

middle: R

last: Amend

state: MD

address: 600 N Wolfe St

department: Brady Urological Institute

institute: Johns Hopkins University

description: Library name: PC_sublibrary8

data_processing:
RNA barcodes were filtered on Total UMI Count ( > 500 UMIs), feature count ( > 350 features), and percentage of mitochondrial genes ( < 25%). Seurat v4.3.057 was used for handling of normalization, identification of variable genes, scaling, principal component analysis, UMAP dimensional reduction, and SNN generation followed by Leiden clustering.
Assembly: Human GRCh38/hg38
Supplementary files format and content: matrix files

growth_protocol: RPMI medium supplemented with 10%FBS and 1% penicilin/streptomycin

extract_protocol:
Cells were collected on timepoint day using tubes pre-coated with bovine serum albumin (BSA). Cell fixation was performed on timepoint day using Parse Biosciences Fixation kit (Parse Biosciences) according to manufacturer protocol, except for no cell filtering steps were performed. No cell filtering steps were performed during barcoding and library prep to prevent loss of the large cells surviving chemotherapy.
Barcoding and library prep for PC3 cells untreated and surviving cisplatin was done using the Evercode Whole Transcriptome Mega kit according to manufacturer protocol (V2, Parse Biosciences). Sequencing was performed on an Illumina NovaSeq 6000 and alignment done using v0.7.2p alignment pipeline (Parse Biosciences). Barcoding and library prep for PC3 cells untreated and surviving docetaxel was done using the Evercode Whole Transcriptome Mega kit according to manufacturer protocol (V2, Parse Biosciences). Sequencing was performed on an Illumina NovaSeq X and alignment done using v1.0.6p alignment pipeline (Parse Biosciences).

value: untreated, 1, 5, and 10 DPT


title: wt mouse lung (wt_pmn_deletion) 1

description: Library name: 21_9_4_1


title: Morphea7


title: cko mouse peripheral blood (wt_cko) 2

description: Library name: PB_Piezol_cko2

source_name: peripheral blood

value: peripheral blood


title: Parse sequencing, PC3cisplatin sublibrary7 (contains all samples)

description: Library name: PC_sublibrary7


title: DNMT3Amut_05

description: Library name: Sample5

value: bone marrow

value: bone marrow mononuclear cells


title: Morphea6


title: young needles and buds

description:
Library name: young
young needles and buds

source_name: young needles and buds

value: young needles and buds


title: Parse sequencing, PC3cisplatin sublibrary6 (contains all samples)

description: Library name: PC_sublibrary6


title: cko mouse peripheral blood (wt_cko) 1

description: Library name: PB_Piezol_cko1


title: Morphea5


title: Morphea4

value: Other, Hispanic


title: wt mouse peripheral blood (wt_cko) 2

description: Library name: PB_WT2


title: DNMT3Amut_01

description: Library name: Sample1

value: pretreatment diagnostic


title: Morphea2


title: Morphea3


title: Morphea1


title: wt mouse peripheral blood (wt_cko) 1

description: Library name: PB_WT1


title: Parse sequencing, PC3cisplatin sublibrary4 (contains all samples)

description: Library name: PC_sublibrary4


title: Parse sequencing, PC3cisplatin sublibrary3 (contains all samples)

description: Library name: PC_sublibrary3


title: cko mouse lung (wt_cko) 2

description: Library name: lung_Piezol_cko2


title: NL8

source_name: Normal adult skin

value: de-identified


title: Morphea8


title: Parse sequencing, PC3cisplatin sublibrary2 (contains all samples)

description: Library name: PC_sublibrary2


title: NL6


title: cko mouse lung (wt_cko) 1

description: Library name: lung_Piezol_cko1


title: NL3


title: NL4


title: wt mouse lung (wt_cko) 1

description: Library name: lung_WT1


title: Parse sequencing, PC3cisplatin sublibrary1 (contains all samples)

description: Library name: PC_sublibrary1


title: shPDK1_2_3

city: Gifu

first: Kazuya

last: Tokumura

address: 1-25-4 Daigakunishi

department: Bioactive Molecules

country: Japan

institute: Gifu Pharmaceutical University

description: Library name: shPDK1_2_3

data_processing:
Trimming was conducted using “Trimmomatic” (ver. 0.39), followed by quality checks with “FASTQC” (ver 0.12.1). Alignment to the Homo sapiens genome (GRCh38.p14) was performed using “STAR” (ver. 2.7.11a), and expression levels were calculated from the resulting BAM files using “RSEM” (ver. 1.3.3).
Assembly: GRCh38
Supplementary files format and content: csv file of raw count for each sample

source_name: Bone

extract_protocol:
Cells were lysed and total RNA was extracted using FastGene RNA Premium Kit (NIPPON Genetics, Tokyo, Japan) per the manufacturer’s instructions
NEBNext Ultra RNA Library Prep Kit for Illumina

value: Bone

value: osteosarcoma


title: NL1


title: wt mouse bone marrow 3

description: Library name: BM_3


title: shPDK1_2_2

description: Library name: shPDK1_2_2


title: FFPE_ATAC_Human_thymus_10um

city: philadelphia

first: Pengfei

state: PA

address: 422 Curie Boulevard, Stellar Chance Labs, 711-712 (lab), philadelphia

institute: University of Pennsylvania

description:
Library name: Sample 17
ATAC-seq

data_processing:
Linkers 1 and 2 are used for targeted filtering of read 2, aligning utilizing BWA followed by sorting and indexing via Samtools to facilitate efficient data handling and retrieval. This reformatting process assigned genome sequences to the first read and incorporated barcodes A and B into the second read. We aligned these fastq files against mouse (GRCm38) or human (GRCh38) reference genomes. The conversion produced tsv-like fragments files, enriched with spatial and genomic information through the integration of barcode pairs, facilitating comprehensive downstream analysis.
Assembly: GRCm38, GRCh38
Supplementary files format and content: TSV files for downstream analysis. The tsv file contains tissue location info (barcode A x barcode B) and fragments info on the genome.
Library strategy: Spatial ATAC-seq

source_name: Human thymus

extract_protocol:
The workflow is summarized in Fig. 1a and Extended Data Fig. 1. Initially, FFPE tissues underwent antigen retrieval (AR) to break crosslinks, followed by in situ Tn5 transposition, where adapters were inserted into accessible genomic regions. Next, spatial barcodes (A1-50 and B1-50) were ligated onto the genomic DNA through two rounds of ligation, facilitated by microfluidic channels. Tissue slides were then imaged to link the spatial barcodes to tissue morphology. After tissue lysis, the barcoded DNA fragments were amplified for library preparation.
After antigen retrieval, tissue was washed twice with 1 ml of 1× DPBS and cleaned with ddH2O. The sequential order for spatial ATAC profiling is as follows: 1. ATAC-seq; 2. Ligation of barcode A; 3. Ligation of barcode B; 4. Reverse crosslink; 5. Library construction; 6. Library QC and sequencing.

value: Human thymus


title: Parse sequencing, PC3cisplatin sublibrary5 (contains all samples)

description: Library name: PC_sublibrary5


title: shPDK1_2_1

description: Library name: shPDK1_2_1


title: FFPE_ATAC_Human_thymus_50um_replicate_2

description:
Library name: Sample 16
ATAC-seq


title: NL7


title: shPDK1_1_3

description: Library name: shPDK1_1_3


title: wt mouse bone marrow 2

description: Library name: BM_2

source_name: bone marrow


title: wt mouse bone marrow 1

description: Library name: BM_1


title: shPDK1_1_2

description: Library name: shPDK1_1_2


title: NL5


title: wt mouse peripheral blood 3

description: Library name: blood_3


title: TT-seq_U1AMO1

first: Ana

last: Fiszbein

state: MA

address: 24 Cummington Mall, LSE(Life Science and Engineering) Building

department: Biology

institute: Boston University

description:
Library name: TT-seq_U1AMO1
U1AMO_replicate 1

data_processing:
Read pairs were trimmed to eliminate adapter sequences, and low-quality 3’ bases were removed using Cutadapt 2.10. Subsequently, the trimmed reads were aligned to the reference genome GRCh38.99 using bowtie2. The resulting BAM files were merged and converted to bigwig files using a custom script.
Assembly: NCBI_RefSeq_GRCh38
Supplementary files format and content: bigwig

source_name: HeLa

growth_protocol: HeLa cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) under standard cell culture conditions at 37°C in a humidified atmosphere with 5% CO2. The DMEM medium was supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin antibiotics.

extract_protocol:
For 4-thiouridine (4SU) labeling, cells were treated with 1 mM of 4SU for 15 minutes. Cells were harvested with 4 ml of TRizol reagent and total RNA was isolated by conventional phenol:chloroform extraction method. Isolated RNA (200 µg) was mixed with 2 µg of yeast spike-in RNA in 100 µL of RNase-free water. The mixture was fragmentized and biotinylated to isolate 4SU labeled RNA. Biotinylated RNA was denatured at 65°C for 10 minutes and rapidly cooled on ice for 5 minutes. Subsequently, 100 µL of streptavidin MicroBeads were added and incubated for 15 minutes with rotation. The beads-conjugated RNA was captured using uColumn in a magnetic field. Purified newly transcribed RNA was eluted by adding 200 µL of 100 mM DTT solution. To clean up and concentrate the eluates, the Monarch PCR & DNA cleanup kit (New England Biolabs, #T1030) was used following the manufacturer’s instructions.
A total of 200 ng of purified RNA was used for library construction with the KAPA RNA HyperPrep Kit with RiboErase (KAPA Biosystems, #KR1351) and the KAPA Unique Dual-indexed Adapter Kit (KAPA Biosystems, #KR1736), as per the manufacturer’s instructions. Libraries were pooled and treated with Illumina free adapter blocking reagent (Illumina, #20024145).

value: HeLa


title: NL2


title: wt mouse lung (wt_cko) 2

description: Library name: lung_WT2

value: lung


title: wt mouse peripheral blood 2

description: Library name: blood_2


title: shCtrl_3

description: Library name: shCtrl_3

value: WT


title: TT-seq_Ctrl2

description:
Library name: TT-seq_Ctrl2
Control_replicate 2


title: wt mouse peripheral blood 1

description: Library name: blood_1


title: TT-seq_Ctrl1

description:
Library name: TT-seq_Ctrl1
Control_replicate 1


title: shPDK1_1_1

description: Library name: shPDK1_1_1


title: shCtrl_2

description: Library name: shCtrl_2


title: Human dermal fibroblasts with low MitoTracker level isolated from co-culture with A431, rep 3

city: Zurich

first: Sabine

last: Werner

address: Otto-Stern-Weg 7

department: Department of Biology

country: Switzerland

institute: ETHZ

data_processing:
Fastq files were trimmed using Trimmomatic (v0.36)
Trimmed files were pseudo-aligned using Salmon (v1.10.2)
Salmon-derived count matrix was processed using tximport.
Assembly: GRCh38
Supplementary files format and content: tab-delimited files give gene-level raw counts for each sample
Supplementary files format and content: tab-delimited files give gene-level TPM for each sample

source_name: primary human dermal fibroblasts

growth_protocol: A431-LifeACT cells and primary human dermal fibroblasts were maintained in Dulbecco`s modified Eagle`s Medium (DMEM)/10% FBS/1% P/S (complete DMEM).

extract_protocol:
each RNA sample was extracted from 300,000 cells using Total RNA Mini Kit (Tissue) (IBI SCIENTIFIC IB47303) and diluted to 100ng/µl concentration.
Illumina Truseq mRNA

treatment_protocol:
Equal numbers of A431 and fibroblasts were co-cultured for 24 hr to reach 100% confluency. Prior to co-culture, A431 were stained with MitoTracker Green dye and washed with PBS to remove unincorporated dye.
Viable primary human dermal fibroblasts with high and low MitoTracker Green fluorescence intensity were sorted from co-cultures by FACS.
Control fibroblasts was mono-cultured to reach 100% confluency and subjected to the same FACS-sorting procedure.

value: primary human dermal fibroblasts

value: co-cultured with A431

value: FACS-sorted for low MitoTracker intensity


title: Human dermal fibroblasts with low MitoTracker level isolated from co-culture with A431, rep 2


title: TT-seq_Ctrl3

description:
Library name: TT-seq_Ctrl3
Control_replicate 3


title: wt mouse lung 3

description: Library name: lung_3


title: OSC_3

description: Library name: OSC_3


title: Human dermal fibroblasts with low MitoTracker level isolated from co-culture with A431, rep 1


title: Human dermal fibroblasts with high MitoTracker level isolated from co-culture with A431, rep 3

value: FACS-sorted for high MitoTracker intensity


title: shCtrl_1

description: Library name: shCtrl_1


title: wt mouse lung 2

description: Library name: lung_2


title: Human dermal fibroblasts with high MitoTracker level isolated from co-culture with A431, rep 2


title: TT-seq_U1AMO3

description:
Library name: TT-seq_U1AMO3
U1AMO_replicate 3


title: wt mouse lung 1

description: Library name: lung_1


title: Human dermal fibroblasts, mono-culture control, rep 3

value: monoculture

value: FACS-sorted


title: LVCP, postnatal day 60 n=2

city: Stockholm

first: Mónica

middle: da Silva

last: Fernandes

address: Nobels väg 6

country: Sweden

institute: Karolinska Institutet

description: Library name: P60_n2

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were made using the CellRanger software (v5.0.1)
Assembly: mm10
Supplementary files format and content: h5 count matrix

source_name: 60 days postnatal healthy mouse

extract_protocol:
Single-cell RNA sequencing was performed on lateral ventricle choroid plexus (CP) samples from mice at postnatal days P2-3, P11, and young adults (10 weeks), while single-cell multiome included P11 and young adult mice. CPs were isolated from perfused mouse brains, pooled (3–4 CPs/sample from both sexes), and enzymatically and mechanically dissociated through a multi-step protocol with pronase (0.1 mg/ml)  for 15min, Enzyme P mix (adult brain dissociation kit, 130-107-677, Miltenyi Biotec) for 30 min, and trypsin (0.025%) for 15min, with mechanic digestion every 5min. Cells pellets were resuspended in PBS-2%BSA. The Chromium Next GEM Single Cell 3ʹ v3.1 kit (10x Genomics) was used for scRNA-seq, following the manufacturer’s guidelines.
10x Protocol for scRNA-seq

value: Choroid plexus

value: 60 days postnatal (P60)


title: CWR22Rv1 cells, FUT8 OE, biol rep 3

city: Newcastle Upon Tyne

first: Margarita

last: Orozco-Moreno

address: Newcastle University, International Centre for Life

department: Biosciences Institute

country: United Kingdom

institute: Newcastle University

description:
CWR22-FUT8-OE-S24
CWR22Rv1 FUT8 con-OE.tabular

data_processing:
Analysis was conducted in Galaxy version 22.01
Quality control was performed with FastQC
Reads were quantified using featureCounts
Differential gene expression analysis was performed with limma-voom
Assembly: hg38
Supplementary files format and content: raw read counts for each sample

source_name: Prostate cancer

extract_protocol:
RNEasy Kit following manufacturer's protocol (Qiagen)
TruSeq Stranded mRNA Sequencing Library Prep Kit following manufacturer's protocols.

value: Prostate cancer

value: FUT8 overexpression


title: CWR22Rv1 cells, OEControl, biol rep 2

description:
CWR22-FUT8-Control-S20
CWR22Rv1 FUT8 con-OE.tabular

value: Lenti-ORF control


title: TT-seq_U1AMO2

description:
Library name: TT-seq_U1AMO2
U1AMO_replicate 2


title: combo2

city: Warsaw

first: Karol

last: Jacek

address: Ludwika Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

description: Resolve smFISH

hyb_protocol: not provided

scan_protocol: not provided

data_processing: The raw tiff images were processed using Resolve Bioscience online data processing pipeline, resulitng in the txt files containing the cells' centroid cartesian location and the raw values of detected mRNA fragments. Further analysis was performed in Seurat 4.2.0 and Squdipy 1.21.1. The scripts to recreate this analysis will be available on github. The name of the github repository will be mentioned in the code availability section of the publication.

source_name: Brain, Tumor

label_protocol: not provided

extract_protocol: Tumor bearing brain was isolated and fixed

value: Brain, Tumor

tag: tumorcellline

tag: molecule type

value: RNA panel of 100 genes


title: OSC_2

description: Library name: OSC_2

value: Bone

value: osteosarcoma


title: LVCP, postnatal day 3, n=2

description: Library name: P3_n2

source_name: 3 days postnatal healthy mouse

value: 3 days postnatal (P3)


title: CPG1

description: Resolve smFISH


title: Human dermal fibroblasts, mono-culture control, rep 1


title: HCC1428 cells, C48 day 7, biol rep 3

city: San Diego

first: Marie

last: Classon

address: 10555 Science Center Dr

institute: Pfizer

description:
Library name: HCC1428 C48 d7 3
Column name in _.txt: L3_HCC1428_GNE_48_d7

data_processing:
FASTQ files were aligned to human GENCODE v28 transcriptome using STAR aligner (v.2.6.0c)
Assembly: hg38
Supplementary files format and content: Lau_RNA_log2TPM.txt

growth_protocol: HCC1428 breast adenocarcinoma cells were maintained in RPMI supplemented with 10% FBS, 1% penicillin/streptomycin, 4.5 g/L D-glucose in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen).
RNA was randomly primed (not polyA-selected), and rRNA depleted

treatment_protocol: Cells were either treated with DMSO as a control for 7 days or 2.5uM C48 for 2 or 7 days

value: breast adenocarcinoma cells

value: WT

tag: time

value: Day 7


title: HCC1428 cells, C48 day 7, biol rep 2

description:
Library name: HCC1428 C48 d7 2
Column name in _.txt: L2_HCC1428_GNE_48_d7


title: OSC_1

description: Library name: OSC_1


title: CWR22Rv1 cells, FUT8 OE, biol rep 2

description:
CWR22-FUT8-OE-S23
CWR22Rv1 FUT8 con-OE.tabular


title: non-OSC_3

description: Library name: non-OSC_3


title: LVCP, postnatal day 2, n=3

description: Library name: P2_n3

source_name: 2 days postnatal healthy mouse

value: 2 days postnatal (P2)


title: CWR22Rv1 cells, FUT8 OE, biol rep 1

description:
CWR22-FUT8-OE-S22
CWR22Rv1 FUT8 con-OE.tabular


title: CWR22Rv1 cells, OEControl, biol rep 3

description:
CWR22-FUT8-Control-S21
CWR22Rv1 FUT8 con-OE.tabular


title: non-OSC_2

description: Library name: non-OSC_2


title: LVCP, postnatal day 11, n=2

description: Library name: P11_n2

source_name: 11 days postnatal healthy mouse

value: 11 days postnatal (P11)


title: LVCP, postnatal day 11, n=1

description: Library name: P11_n1


title: CWR22Rv1 cells, OEControl, biol rep 1

description:
CWR22-FUT8-Control-S19
CWR22Rv1 FUT8 con-OE.tabular


title: non-OSC_1

description: Library name: non-OSC_1


title: PBS2

description: Resolve smFISH


title: combo1

description: Resolve smFISH


title: Human dermal fibroblasts with high MitoTracker level isolated from co-culture with A431, rep 1

value: primary human dermal fibroblasts

value: co-cultured with A431

value: FACS-sorted for high MitoTracker intensity


title: LVCP, postnatal day 3, n=1

description: Library name: P3_n1

value: Choroid plexus


title: Human dermal fibroblasts, mono-culture control, rep 2

value: monoculture

value: FACS-sorted


title: CPG2

description: Resolve smFISH


title: LVCP, postnatal day 60, n=3

description: Library name: P60_n3

value: 60 days postnatal (P60)


title: LVCP, postnatal day 60, n=1

description: Library name: P60_n1


title: aPD2

description: Resolve smFISH

value: Brain, Tumor


title: HCC1428 cells, C48 day 2, biol rep 3

description:
Library name: HCC1428 C48 d2 3
Column name in _.txt: K3_HCC1428_GNE_48_d2

value: Day 2


title: PBS1

description: Resolve Bioscience smFISH

value: RNA panel of 100 genes


title: HCC1428 cells, C48 day 7, biol rep 1

description:
Library name: HCC1428 C48 d7 1
Column name in _.txt: L1_HCC1428_GNE_48_d7


title: aPD1

description: Resolve smFISH


title: combo4 scRNA-seq

description:
Library name: COHP_49883
10X Genomics 3'

data_processing:
Raw files were processed using CellRanger v5.1.0  mkfastq and count functions using standard parameters and merged into adata_scRNA.rds seurat object using Seurat seurat 4.2.0.
Code to recreate the analysis will be available on the github repository mentioned in the publication's code availability section.
Assembly: mm10 (10X Genomics)
Supplementary files format and content: RDS files, whole dataset befor subsetting (adata_scRNA.rds), subsetted dataset for myeloid figure (myelo_05_11_2023.rds), subsetted dataset for lymphoid figure (rl__05_11_2023), subsetted dataset for nk figure (NK_19II2024.rds)

extract_protocol:
Tumor bearing hemisphere was isolated and dissociated using Adult Brain Dissociation Kit, mouse and rat (Miltenyi Biotec)
10X Genomics Single Cell 3' Gene Expression v4; according to 10X Genomics protocols

value: CpG-STAT3ASO + antiPD1


title: combo3 scRNA-seq

description:
Library name: COHP_49882
10X Genomics 3'


title: HCC1428 cells, C48 day 2, biol rep 2

description:
Library name: HCC1428 C48 d2 2
Column name in _.txt: K2_HCC1428_GNE_48_d2


title: 31_H1130_t0

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

description: Library name: lib91749

data_processing:
Proliferation screen FASTQs were processed using MAGeCK RRA (v0.5.9.5)45 to create gRNA readcount matrices using mageck -count. Differential gRNA enrichment was conducted using mageck test with --control-sgrna and --paired flags. Results were analyzed using MAGeCKFlute (2.2.0)8
Supplementary files format and content: Guide read counts matrix

source_name: primary human T cells

growth_protocol: 6e7 CD4+ T cells were activated in 30 mL of TCM for 24 hours. T cells were then infected with 2% v/v 100x concentrated dCas9-ZIM3-mCherry lentivirus. 24 hours later, the cells were infected again with 0.25% v/v 100x concentrated GW2 library lentivirus (MOI 0.5~1). At 1 day post-infection (dpi), cells were counted to ensure there were at least 30e6 live cells

extract_protocol:
Genomic DNA from cells (in 10M cell increments) were resuspended in 50 μl ChIP lysis buffer (1% SDS, 10 mM EDTA, in 50 mM Tris-HCl, pH 8.1) and pipetted up and down. Lysed cells were transfered to a 96-well plate or 8-well strip, then incubated at 65°C for 10 min. Then sample was cooled to 37°C, and 1 μl Rnase cocktail (Ambion, AM2286) was added, again mixed by pipetting and spun down followed by incubation at 37°C for 30 min. 5 μl proteinase K (NEB P8107) was added and the sample was mixed by pipetting. To isolate genomic DNA, we added 36.4μl Ampure XP to the sample, mixed thoroughly by pipetting, incubated for 5 min, and used a magnet to isolate genomic beads from the lysed sample. We pipetted off the supernatant and washed the sample 3 times with 80% ethanol while on the magnet. After drying the pellet for 5 min, gDNA was then eluted in 45 μl ddH2O, yielding on average 3-6 pg per cell.
We then used 0.6 μg of genomic DNA from each sample for qPCR to determine optimal PCR cycle number for library preparation. Each 10 μL qPCR reaction contained 5 μL of NEBNext Q5 Hotstart HiFi PCR master mix (NEB # M0543L), FwdInnerSeq and RevInnerSeq at 500 nM each (final concentration; Supplementary Table 30), 0.6 μg of genomic DNA, 1.7 μL of SYBR (diluted 1/10000), and added water to have a final volume of 10 μL. Once the optimal PCR cycle was determined, 50 μL PCR reactions were used to amplify the amplicon, and the number of reactions were scaled to the total available gDNA. The PCR reactions from each sample were pooled, and 50 μL was taken for amplicon purification. Amplicons were purified using a two-step Ampure XP method. 0.65x Ampure XP was added to the sample, followed by mixing via pipet, and incubating for 5 min. The sample was applied to the magnet and the supernatant was isolated for further purification. To the supernatant, an additional 1.0x Ampure XP was added to the sample to capture PCR amplicon. The sample was incubated for 5 minutes, and then magnetic beads were captured by magnet. The supernatant was removed and discarded, and the captured beads were washed 3 times with 80% ethanol. The sample was dried for 5 min and eluted with 25 μL of H2O. Samples were analyzed on a TapeStation to assess amplicon purity and size estimation, and the concentration of amplicon DNA was measured using Qubit. Samples were pooled based on the concentration of the specific target amplicon percentage and sequenced on a Nextseq 2000 with custom read1 primer hU6_R1 and custom index primer sgPuro_I.

treatment_protocol: 15e6 cells were collected as time zero control (day 2) of proliferation screens. For the remaining cells, fresh Th0 media (TCM with recombinant human IL-2 (final concentration 500 U/mL)) and puromycin (final concentration 2.5 μg/mL) was added to bring cells to 1e6 cells/mL. At 2 dpi, cells were harvested, spun down and resuspended at 0.5e6 cells/mL in Th0 media. Cells were maintained between 0.5-1e6 cells/mL until 10 dpi, when cells were harvested and live ZIM3-mCherry+ cells were FACS sorted (typically ~10-30% of total cells). Sorted ZIM3-mCherry+ cells were maintained at 0.5e6-1e6 cells/mL in Th0 media until day 21. At least 15M cells were then collected per donor and stored at -80°C until genomic DNA extraction.

value: primary human T cells

tag: donor id

value: donor H

tag: group

value: day 2

tag: donor

tag: library type

value: CRISPRi guide RNA library from primary human T cells


title: 12_G1121_pro

description: Library name: lib91746

value: donor G


title: 22_G1130_pro

description: Library name: lib91748


title: 32_H1130_pro

description: Library name: lib91750


title: 11_G1121_t0

description: Library name: lib91745


title: 21_G1130_t0

description: Library name: lib91747


title: HCC1428 cells, C48 day 2, biol rep 1

description:
Library name: HCC1428 C48 d2 1
Column name in _.txt: K1_HCC1428_GNE_48_d2

value: breast adenocarcinoma cells

value: WT


title: HCC1428 cells, DMSO day 7, biol rep 3

description:
Library name: HCC1428 DMSO 3
Column name in _.txt: J3_HCC1428_DMSO_d7

value: DMSO

value: Day 7


title: combo2 scRNA-seq

description:
Library name: COHP_49881
10X Genomics 3'

tag: tissue


title: 02_G1104_pro

description: Library name: lib91744

tag: cell type


title: CPG4 scRNA-seq

description:
Library name: COHP_49880
10X Genomics 3'

tag: treatment


title: HCC1428 cells, DMSO day 7, biol rep 2

description:
Library name: HCC1428 DMSO 2
Column name in _.txt: J2_HCC1428_DMSO_d7


title: SI73_YY_REP3

city: Copenhagen N

first: Jesper

last: Svejstrup

state: Denmark

address: Blegdamsvej 3, 18.6

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

data_processing:
Paired-end reads were demultiplexed using bcl2fastq (v2.20.0.422) and resultant FASTQ fileswere quality checked using MultiQC (v1.11).
Unique molecular identifiers (UMIs) present in R2 were appended to R1, and resulting FASTQ file was mapped to GRCh38/hg38 and sacCer3 genomes using hisat2 (v2.2.1) with standard single-end read settings.
Mapped reads in SAM format were converted to BAM (view), which were then sorted (sort) and indexed (index) using samtools (v1.20) with standard settings, and PCR duplicates were removed using UMI tools (v1.1.4) deduplication function (dedup).
For external reference normalisation using yeast spike-in material, reads mapping to hg38 and sacCer3 chromosomes were counted usingFeatureCounts from the subread package (v2.0.6; featureCounts -O -M -T 32 -s 0 -F SAF), afterwhich edgeR (v3.40.2) on Rstudio (v4.2.1) was used to determine scaling factors for BAM to bigWig file conversion using the bamCoverage function from the deeoptools package (v3.5.5, bamCoverage -of bigwig -bs 50 -p max --normalizeUsing CPM --smoothLength 150 --filterRNAstrand forward/reverse –scaleFactor X).
Assembly: GRCh38/hg38 and sacCer3
Supplementary files format and content: bigwig, scaled according to yeast spike-in material
Library strategy: Transient Transcriptome sequencing (TT-seq)

source_name: HEK293 FlpN TREX

growth_protocol: HEK293 FlpN TREX cells were maintained in DMEM supplemented with 10% (v/v) fetal bovine serum (FBS), penicillin(100U/ml) and streptomycin (100 μg/ml) in humidified atmosphere with 5% carbon dioxide at 37◦C

extract_protocol:
Nascent RNA was labelled using a 15-minute pulse of 4-thiouridine, after which the reaction was stopped by aspiration of media and addition of 1mL Trizol. For total RNA isolation, one-fifth of chloroform was added to lysates and shaken well, followed by addition of the upper aqueous phase and an equal volume of chloroform/isoamyl alcohol (24:1) to MaXtract high-density phase-lock tubes, that were previously prepared according to manufacturer’s instructions. Lysates were then centrifuged (12000g, 5 minutes at 4C) and upper aqueous phase was transferred to a new tube and 1.1X volumes of 100% isopropanol was added, followed by shaking for 30 seconds, incubation at room temperature for 20 minutes and centrifugation (12000g, 20 minutes at 4C). Supernatant was removed and RNA pellets were washed using 750µL 85% (v/v) ethanol, centrifuged (7500g, 5 minutes at 4C), air dried at room temperature and resuspended in 100µL Ultrapure DNase/RNase-free distilled water. As an external reference control, S.cerevisiae (strain BY4741, MATa, his3D1, leu2D0, met15D0, ura3D0) nascent RNA was spiked-in to each sample. Total RNA was then isolated using PureLink RNA Mini kit according to the manufacturer’s instruction for the enzymatic protocol. 500ng of S.cerevisiae total RNA was spiked-in to 100µg of H.sapiens total RNA, material was adjusted to 100µL and fragmented by the addition of 20µL 1M NaOH and incubation on ice for 20 minutes. Fragmentation was stopped by the addition of 80µL 1M Tris HCl pH 6.8 and material was purified twice using the Micro Bio-Spin P-30 Gel Columns according to manufacturer’s instructions. Thiol-specific biotinylation of RNA was performed using 10 mM Tris-HCl pH 7.4, 1 mM EDTA and 5 mg MTSEA biotin-XX linker in a final volume of 250µL and incubation at room temperature for 30 minutes in the dark. Biotinylated RNA was then purified by addition of 250μL of phenol/chloroform/isoamyl alcohol (25:24:1 (vol/vol)), followed by shaking and then addition to MaXtract high-density phase-lock tubes that were previously prepared according to manufacturers instructions. Upper aqueous phase was transferred to a new tube and biotinylated RNA was precipitated using one-tenth the volume 5M NaCl and 1.1X volume 100% isopropanol, followed by incubation room temperature for 10 minutes and centrifugation (20000g, 20 minutes at 4C). Supernatant was discarded and RNA pellet was washed using 500µL 85% (v/v) ethanol, centrifuged (20000g, 5 minutes at 4C), air dried at room temperature, resuspended in 50µL Ultrapure DNase/RNase-free distilled water and denatured by incubating for 10 minutes at 65°C in the dark. Biotinylated RNA was separated from the total RNA pool by addition of 200 μL μMACS Streptavidin MicroBeads and incubation for 15 minutes at room temperature with constant rotation. Beads were then applied to a μColumn pre-equilibrated with 100 µL nucleic acid equilibration buffer and immobilised on a magnetic stand, washed twice with pre-warmed (55°C) wash buffer (100 mM Tris HCl pH 7.4 10mM EDTA, 1M NaCl and 0.1% (v/v) Tween 20) and biotinylated RNA was eluted by two additions of 100μL 100 mM DTT 5 minutes apart. Purification of biotinylated RNA was performed using the RNeasy MinElute kit according to manufacturer’s instructions, where 1050 μL 100% ethanol and 750 μL RLT buffer was adder per 200μL reaction to precipitate RNA < 200 nt.
Sequencing libraries were prepared from biotinylated RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (without additional fragmentation) and NEBNextMultiplex Oligos for Illumina (Unique Dual Index UMI adapters RNA Set 1) and sequenced on the NextSeq 2000 (P3 50 kit).

treatment_protocol: HEK293 FlpN TREX cells were seeded at a density of XX cells in a 100mm plate. The next day XX µl of 20 µM control or CDC73-targeting siRNA were transfected with Lipofectamine RNAiMAX according to manufacturer’s instructions. Transfection was repeated 24 h later and cells were split for the experiment the next day, followed by the addition of

value: HEK293 FlpN TREX

value: pFRT::CDC73 YY/AA

value: CDC73 siRNA; 1μg/mL doxycycline 24 hours


title: CPG3 scRNA-seq

description:
Library name: COHP_49879
10X Genomics 3'


title: 01_G1104_t0

description: Library name: lib91743


title: HCC1428 cells, DMSO day 7, biol rep 1

description:
Library name: HCC1428 DMSO 1
Column name in _.txt: J1_HCC1428_DMSO_d7


title: PBS3 scRNA-seq

description:
Library name: COHP_49878
10X Genomics 3'

value: PBS (control)


title: SI73_YY_REP2


title: combo1 scRNA-seq

description:
Library name: COHP_49877
10X Genomics 3'

value: Brain, Tumor


title: SI73_WT_REP2

value: pFRT::CDC73 WT


title: SI73_YY_REP1


title: SI73_WT_REP3


title: SI73_WT_REP1


title: SI73_REP3

value: Parental


title: CPG2 scRNA-seq

description:
Library name: COHP_49876
10X Genomics 3'


title: HCC1428 cells, C48, S96, biol rep 2

description:
Library name: HCC1428 C48 2
Column name in merged_fraction_cts_HCC1428.csv: HCC_GNE_Y2

data_processing:
FASTQ files were aligned to hg38 and dm6 genome using Bowtie2 (v2.3.4.1).
To count reads aligning to repetitive elements, RepEnrich2 was utilized (https://github.com/nerettilab/RepEnrich2). Repeat reference was downloaded from UCSC Genome Browser (hg38; https://genome.ucsc.edu/)
Assembly: hg38
Supplementary files format and content: Lau_S96_merged_fraction_cts_HCC1428.csv includes raw counts that map to tranposable elements (TEs) for each sample.
Library strategy: CUT&Tag

extract_protocol:
Samples were processed according to CUT&Tag-IT R-loop Assay Kit (Active Motif 53167), with the addition of Drosophila spike-in nuclei and spike-in antibody: Drosophila spike-in nuclei CUT&Tag-IT® Spike-In Control, Anti-Mouse (Active Motif 53174). Spike-in nuclei were added to each sample at a ratio of 1:10 spike-in nuclei to cells, and each were added to ConA beads. Cells, nuclei and ConA beads were mixed by gentle pipetting and strip tubes containing the samples were placed on a room temperature nutator for 10 minutes.  Spike-in antibody was added to each sample according to the kit instructions at the same time as the primary antibody, S9.6 (included in R-loop Assay Kit). The CUT&Tag-IT R-loop Assay Kit protocol was followed as per the manufacturer’s instructions for all remaining steps for R-loop samples and CUT&Tag-IT Assay Kit, Anti-Rabbit for the H3K4me3 samples.
NGS libraries were evaluated on a TapeStation 4150 (Agilent, Santa Clara, CA) using High Sensitivity D1000 ScreenTapes (Agilent 5067-5584) and pooled for equal sequencing depths targeting approximately 30 million reads per sample. Sequencing was conducted on a NovaSeq6000

treatment_protocol: Cells were either treated with DMSO as a control or  2.5uM C48 for 2 or 5 days

value: Day 5


title: HCC1428 cells, C48, S96, biol rep 1

description:
Library name: HCC1428 C48 1
Column name in merged_fraction_cts_HCC1428.csv: HCC_GNE_Y1


title: SI73_REP2


title: HCC1428 cells, DMSO, S96, biol rep 2

description:
Library name: HCC1428 DMSO 2
Column name in merged_fraction_cts_HCC1428.csv: HCC_DMSO_Y2


title: HCC1428 cells, DMSO, S96, biol rep 1

description:
Library name: HCC1428 DMSO 1
Column name in merged_fraction_cts_HCC1428.csv: HCC_DMSO_Y1


title: CPG1 scRNA-seq

description:
Library name: COHP_49875
10X Genomics 3'


title: SI73_REP1


title: SI73_DELTA_REP3

value: pFRT::CDC73 {delta}KIM


title: HCC1428 cells, C48, H3K4me3, biol rep 2

description:
Library name: HCC1428 C48 2
Column name in Lau_H3K4me3_ctag_merged_annotatedpeaks_hcc1428.csv: HCC1428-GNE-rep2
Column name in merged_fraction_counts_HCC1428.csv: HCC_GNE2

data_processing:
FASTQ files were aligned to hg38 and dm6 genome using Bowtie2 (v2.3.4.1).
To find location of peaks in the genome, peak positions were first called per sample using Homer (http://homer.ucsd.edu/homer/), then merged into a set of consensus genomic positions. They were then annotated and peak scores were calculated per sample.
To count reads aligning to repetitive elements, RepEnrich2 was utilized (https://github.com/nerettilab/RepEnrich2). Repeat reference was downloaded from UCSC Genome Browser (hg38; https://genome.ucsc.edu/)
Assembly: hg38
Supplementary files format and content: Lau_H3K4me3_ctag_merged_annotatedpeaks_hcc1428.csv includes annotated peak counts for each sample, after normalization with Drosophila spike-in counts
Supplementary files format and content: Lau_H3K4me3_merged_fraction_counts_HCC1428.csv includes raw counts that map to tranposable elements (TEs) for each sample.
Library strategy: CUT&Tag

extract_protocol:
Samples were processed according to CUT&Tag-IT R-loop, Anti-Rabbit Kit (Active Motif 53160), with the addition of Drosophila spike-in nuclei and spike-in antibody: Drosophila spike-in nuclei CUT&Tag-IT® Spike-In Control, Anti-Rabbit (Active Motif 53168). Spike-in nuclei were added to each sample at a ratio of 1:10 spike-in nuclei to cells, and each were added to ConA beads. Cells, nuclei and ConA beads were mixed by gentle pipetting and strip tubes containing the samples were placed on a room temperature nutator for 10 minutes.  Spike-in antibody was added to each sample according to the kit instructions at the same time as the primary antibody, H3K4me3 (Active Motif 53160). The CUT&Tag-IT Assay Kit protocol was followed as per the manufacturer’s instructions for all remaining steps in CUT&Tag-IT Assay Kit.
NGS libraries were evaluated on a TapeStation 4150 (Agilent, Santa Clara, CA) using High Sensitivity D1000 ScreenTapes (Agilent 5067-5584) and pooled for equal sequencing depths targeting approximately 30 million reads per sample. Sequencing was conducted on a NovaSeq6000


title: PBS2 scRNA-seq

description:
Library name: COHP_49874
10X Genomics 3'


title: SI73_DELTA_REP1


title: CON_REP3

value: Control siRNA; 1μg/mL doxycycline 24 hours


title: PBS1 scRNA-seq

description:
Library name: COHP_49873
10X Genomics 3'


title: CON_REP1


title: M5_D_lymph.node_rep3

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

description:
Library name: S3_C379
sample has been sequenced on 3 runs

data_processing:
Unique Molecular Identifiers (UMIs) of first 12 nucleotides, serving as unique RNA molecule identifiers, were extracted from the sequencing reads using UMI-tools "extract" (version 1.1.4)
Read were trimmed with fastp (version 0.23.4) and aligned to the mouse reference genome (mm10) utilizing STAR (version 2.7.11a)
Post-alignment, deduplication of reads based on their UMI barcodes was executed using UMI-tools "dedup"
Gene-level quantification of reads was conducted with htseq (version 2.0.3)
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw count per gene

extract_protocol:
RNA was isolated using Rneasy Plus Kit according to the manufacturer's instructions. Samples were eluted with 80µl.
A total of 10 ng purified RNA was used for library preparation using the QIAseq UPX 3' Transcriptome Kit (QIAGEN) following the manufacturer's protocol.

value: Wildlings


title: HCC1428 cells, C48, H3K4me3, biol rep 1

description:
Library name: HCC1428 C48 1
Column name in Lau_H3K4me3_ctag_merged_annotatedpeaks_hcc1428.csv: HCC1428-GNE-rep1
Column name in merged_fraction_counts_HCC1428.csv: HCC_GNE1


title: HCC1428 cells, DMSO, H3K4me3, biol rep 2

description:
Library name: HCC1428 DMSO 2
Column name in Lau_H3K4me3_ctag_merged_annotatedpeaks_hcc1428.csv: HCC1428-DMSO-rep2
Column name in merged_fraction_counts_HCC1428.csv: HCC_DMSO2


title: CON_REP2


title: M4_D_lymph.node_rep3

description:
Library name: S3_C331
sample has been sequenced on 3 runs


title: RNA-seq_U1AMO2

description: U1 AMO_replicate 2

data_processing:
Read pairs were processed using Cutadapt 2.10 to remove adapter sequences and low-quality 3’ bases. Trimmed reads were aligned to the Ensembl reference genome GRCh38.99 using STAR version 2.7.9a.
Assembly: Ensembl reference genome GRCh38.99
Supplementary files format and content: bigwig

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, 74104). Purified RNA underwent DNaseI treatment (Thermo Scientific, EN0521) to eliminate any residual genomic DNA. RNA integrity was confirmed using the Agilent Bioanalyzer with RNA Pico Chips (Agilent Technologies, Cat#5067-1513).
Sequencing libraries were generated by the Boston University Medical Campus (BUMC) Microarray and Sequencing Resource.

value: HeLa

value: U1 AMO


title: HCC1428 cells, DMSO, H3K4me3, biol rep 1

description:
Library name: HCC1428 DMSO 1
Column name in Lau_H3K4me3_ctag_merged_annotatedpeaks_hcc1428.csv: HCC1428-DMSO-rep1
Column name in merged_fraction_counts_HCC1428.csv: HCC_DMSO1

value: breast adenocarcinoma cells


title: RNA-seq_U1AMO3

description: U1 AMO_replicate 3


title: RNA-seq_Ctrl1

description: Control AMO_replicate 1

value: Control AMO


title: M2_D_lymph.node_rep3

description:
Library name: S3_C235
sample has been sequenced on 3 runs


title: M3_D_lymph.node_rep3

description:
Library name: S3_C283
sample has been sequenced on 3 runs


title: RNA-seq_U1AMO1

description: U1 AMO_replicate 1


title: CARLIN allele, injection at E7.5 and E8.5, collection at P4, otocyst cells, bulk RNA sequencing

city: Houston

first: Joel

last: Nelson

email: Joel.Nelson@bcm.edu, joeln@bcm.edu

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description: Library name: CARLIN_early_bulk

data_processing:
Cell Ranger
Assembly: Mouse mm10
Supplementary files format and content: Processed data includes matrix (.mtx), barcodes, and features (.tsv) for single-cell experiment, and an analysis file (.mat) for the bulk experiment

source_name: postnatal inner ear tissue

extract_protocol:
Post natal mice were harvested in cold, sterile 1X CMF (Calcium Magnesium Free) PBS for each tissue extraction process. Following dissection of the inner ear, the tissue was dissociated via a 35-40 minute incubation period in 0.22 µm papain/ DNase solution at 37 deg C. Tissue was homogenized following dissociation by adding a 1:1 ratio of cold 1X CMF PBS + 4% FBS solution and pipetting up and down 150x per sample. Samples were centrifuged at 470 RCF for 5 min (at 4 deg), then supernatant was removed and replaced with fresh 1X CMF PBS + 4% FBS solution, re-suspending the pellet by pipetting. This process was repeated for more viscous samples. Cells then underwent a incubation step with a Apc-conjugated EpCAM antibody for 20 minutes at 4 deg, on a nutator. Finally, samples were filtered through 40 µm pluriSelect mini strainers into sterile 5 ml conical tubes. Purified APC+ cells from FACS were collected in 150 µl fresh 1X CMF PBS + 4% FBS solution per sample.
All libraries were prepared according to the 10X Genomics protocol (Chromium™ Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1). In summary, Gel Beads-in-emulsion (GEMS) were produced via mixing Single Cell 3' v3.1 Gel Beads with the cell solution master mix for each sample and Partitioning Oil, then loading these into the Chromium Chip G. The gel beads were lysed and combined with primers containing a Illumina TruSeq R1 primer, a 12 nt unique molecular identifier (UMI), 16 nt 10X Barcode, and 30 nt poly(dT) sequence for each GEM, as well as a reverse transcription Master Mix of reagents. Following production of pooled, barcoded full-length cDNA from the poly-adenylated mRNA of each cell, the cDNA was purified from this mixture using silane magnetic beads, then amplified by PCR. Appropriately sized fragments were selected for the library, and paired end P5 and P7 primers, the TruSeq R2 primer sequence, and a sample index were added in the later stages of library construction. The library and cDNA were then used to generate the single-cell and bulk RNAseq samples respectively.

treatment_protocol: Doxycycline injection via IP injection at E7.5 and E8.5 via retro-orbital injections with 25 ug/g of a 10 mg/mL solution.

value: postnatal inner ear tissue

value: CARLIN x KH2/iGas9

value: P4 inner ear cells

value: Doxyclicline injection at E7.5 and E8.5


title: GV (MS238_132)

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

description: Library name: Sample162

data_processing:
All read data were processed with cutadapt v1.18 and mapped with Tophat2 v2.1.1/bowtie2 v2.3.4.1 as described previously (Nakamura et.al.).
Read counts per genes were calculated using HTseq v0.11.0.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: Single-cell of oocyte, GV oocyte, fresh adult mouse ovary

extract_protocol:
For the SC3-seq samples, dissociated oocytes and granulosa cells from in vivo mouse ovarian follicles and in vitro oocyte-like cells were manually picked up using glass capillaries under a stereomicroscope (Leica, S8 APO).  The subsequent cDNA synthesis and amplification methods were as previously described (Kurimoto et al, 2006, 2007; Nakamura et al, 2015, 2016). and the 3’ termini of cDNA were subjected to sequencing on the Illumina NextSeq 500/550 platform with a NextSeq 500/550 high output kit v. 2 (75 cycles) (FC-404-2005; Illumina).
For the SC3-seq samples, the subsequent cDNA synthesis and amplification methods were as previously described (Kurimoto et al, 2006, 2007; Nakamura et al, 2015, 2016). and the 3’ termini of cDNA were subjected to sequencing on the Illumina NextSeq 500/550 platform with a NextSeq 500/550 high output kit v. 2 (75 cycles) (FC-404-2005; Illumina).

value: Adult ovary


title: SI73_DELTA_REP2

value: HEK293 FlpN TREX

value: CDC73 siRNA; 1μg/mL doxycycline 24 hours


title: M1_D_lymph.node_rep3

description:
Library name: S3_C187
sample has been sequenced on 3 runs


title: POBNCI_ACC004_PDX_ADCT_701_2

city: Bethesda

first: Nitin

last: Roper

address: 37 Convent Drive

department: Developmental Therapeutics Branch

institute: National Cancer Institute

description: Library name: POBNCI_ACC004_PDX_ADCT_701_2

data_processing:
Bulk RNA-seq
Samples were pooled and sequenced on NovaSeq 6000 SP.
Samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome and the annotated transcripts using STAR.
Gene expression quantification analysis was performed using STAR/RSEM tools.
RSEM generated read counts for each gene between samples were normalized using TMM method implemented in edgeR.
Assembly: hg19
Supplementary files format and content: TPM data file

source_name: PDX

extract_protocol:
RNA was extracted using an AllPrep DNA/RNA extraction kit according to the manufacturer’s protocol (Qiagen #80204).
RNA libraries for bulk RNA-seq were prepared using Illumina Total RNA Prep

value: PDX

value: adrencortical carcinoma


title: GV (MS238_126)

description: Library name: Sample159


title: GV (MS238_128)

description: Library name: Sample160


title: POBNCI_ACC004_PDX_ADCT_701_1

description: Library name: POBNCI_ACC004_PDX_ADCT_701_1


title: POBNCI_ACC004_PDX_ADCT_701_3

description: Library name: POBNCI_ACC004_PDX_ADCT_701_3


title: GV (MS238_124)

description: Library name: Sample158


title: GV (MS238_130)

description: Library name: Sample161


title: POBNCI_ACC004_PDX_saline_4

description: Library name: POBNCI_ACC004_PDX_saline_4

value: saline


title: M5_D_lymph.node_rep2

description:
Library name: S3_C183
sample has been sequenced on 3 runs


title: RNA-seq_Ctrl2

description: Control AMO_replicate 2


title: POBNCI_ACC004_PDX_saline_3

description: Library name: POBNCI_ACC004_PDX_saline_3


title: GV (MS238_122)

description: Library name: Sample157


title: M3_D_lymph.node_rep2

description:
Library name: S3_C087
sample has been sequenced on 3 runs


title: Rabbit IgG CUT&RUN, replicate 3

city: Oxford

first: Alexandra Maria

last: Bisia

address: S Parks Rd

department: Sir William Dunn School of Pathology

institute: University of Oxford

data_processing:
Paired-end sequencing fastq files were aligned to the mouse mm10 genome using Bowtie2 version 2.4.4.
Resulting sam files were converted to bam files, sorted, and mitochondrial reads removed with SAMtools version 1.14.
Files were downsampled to contain the same number of reads between test and control files using PICARD version 2.27.4.
Peaks were called using MACS2 version 2.2.7.1.
Assembly: GRCm38/mm10
Supplementary files format and content: Bigwig files of aligned bams normalised for read number.
Library strategy: CUT&RUN

source_name: Trophoblast stem cell

growth_protocol: Cultured on Matrigel-coated plates in TX defined medium (Kubaczka et al., 2014)

extract_protocol:
Cell nuclei were permeabilised in 0.02% digitonin solution and EOMES-bound chromatin fragments were cleaved by ProteinA-Mnase and released by diffusion through the permeabilised nuclei as described in Skene and Henikoff (2017).
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illunima (E7645).

value: Trophoblast stem cells

tag: antibody

value: IgG


title: Rabbit IgG CUT&RUN, replicate 2

tag: genotype


title: Rabbit IgG CUT&RUN, replicate 1


title: M2_D_lymph.node_rep2

description:
Library name: S3_C039
sample has been sequenced on 3 runs

value: Wildlings


title: EOMES CUT&RUN, replicate 2

value: Eomes


title: POBNCI_ACC004_PDX_saline_2

description: Library name: POBNCI_ACC004_PDX_saline_2


title: EOMES CUT&RUN, replicate 3


title: EOMES CUT&RUN, replicate 1

value: !Sample_source_name_ch1 = Trophoblast stem cell


title: ABDE3 TSCs, 48h dTAG-13 treatment 2

data_processing:
Paired-end reads were aligned to the mm10 mouse genome assembly using Bowtie2 with the very sensitive option.
Aligned reads were sorted, mitochondrial reads were discarded using SAMtools, and duplicate reads removed using Picard.
BigWig files were generated using deepTools version 3.5.1.
Biological replicates were randomly downsampled to contain the same number of reads for each individual sample, and peaks were called using MACS2 version 2.2.7.1.
MACS2-called peaks with a P-value of <10-3 were used in downstream analyses.
Notable changes in ATAC-seq datasets were identified using the DiffBind package on the Galaxy server, using bam files and a bed file of all identified peaks in each sample.
Assembly: GRCm38/mm10
Supplementary files format and content: Bigwig files of aligned and read-normalised bam files.

extract_protocol: Tagmentation and indexing of single-cell suspensions was performed as previously described (Buenrostro et al., 2013).

treatment_protocol: Addition to culture medium of 200nM dTAG-13 dissolved in DMSO, or 10uM BRM014 dissolved in DMSO, or DMSO only for control.

value: Trophoblast stem cell

value: Eomesdeg/deg


title: POBNCI_ACC004_PDX_saline_1

description: Library name: POBNCI_ACC004_PDX_saline_1


title: M1_D_lymph.node_rep2

description:
Library name: S3_C373
sample has been sequenced on 3 runs


title: M5_C_lymph.node_rep3

description:
Library name: S3_C139
sample has been sequenced on 3 runs

value: TXlab


title: E198K_patient, DIV 14 neurons_03

first: Randee

last: Young

address: 4 Blackfan st

department: Pediatrics

institute: Boston Children's Hospital

description:
Library name: E198K_03
E198K_03

data_processing:
Sequence reads were mapped to GRCh38 using STAR
Read count extraction and normalization were performed using featureCounts
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

source_name: E198K patient iPSCs

growth_protocol: E198K and E420K patient-derived and respective isogenic corrected control iPSCs were maintained in mTeSR Plus medium.

extract_protocol:
RNA was harvested from iPSC-derived neurons at 14 days in vitro using a standard TRIzol RNA extraction protocol and purified using the Zymo RNA-concentrator kit.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: Patient-derived iPSCs were directly induced into cortical neurons by induced NGN2 expression. Human iPSCs were dissociated into single cells with Accutase (Stem Cell Technologies) and plated onto Geltrex coated plates. On differentiation day -1, iPSCs were transduced with pLV-Ubi-rtTA and pLV-TetO-hNGN2-mCherry-Puro lentiviruses in the presence of polybrene (8 µg/mL, Sigma) overnight. Plasmids were provided by Ovid Therapeutics. The next day, NGN2 expression was induced using doxycycline (2 µg/mL, Millipore) and the media was changed to Neural Induction Media (NIM). On day 1, infected cells were then selected using puromycin (1 µg/mL, Invitrogen) and NIM was supplemented with doxycycline and puromycin was changed every day for 3-4 days or until the culture was homogenous with all cells containing neurites. Cells were then dissociated using Accutase and replated on poly-D-lysine and laminin coated coverslips in Cortical Neuron Media consisting of DMEM/F12, HEPES (Gibco) and Neurobasal Plus Medium (Gibco) supplemented with B27 Plus Supplement (Gibco), BDNF (10 ng/mL, Peprotech),  GDNF (10 ng/mL, Peprotech),  NT-3 (10 ng/mL, Peprotech), and 10 µm ascorbic acid (Sigma). Cortical Neuron Media was changed three days a week by removing half of the media and adding half fresh media and neurons were cultured for 14 days when total mRNA was extracted.

value: E198K patient iPSCs

value: iPSC derived cortical neurons

value: cortical neuron differentiation


title: ABDE3 TSCs, 48h dTAG-13 treatment 1


title: ABDE3 TSCs, 48h dTAG-13 treatment 3


title: M4_D_lymph.node_rep2

description:
Library name: S3_C135
sample has been sequenced on 3 runs


title: M4_C_lymph.node_rep3

description:
Library name: S3_C091
sample has been sequenced on 3 runs


title: ABDE3 TSCs, 48h BRG1 inhibition 3


title: E198K_patient, DIV 14 neurons_02

description:
Library name: E198K_02
E198K_02


title: ABDE3 TSCs, 48h BRG1 inhibition 1


title: M3_C_lymph.node_rep3

description:
Library name: S3_C043
sample has been sequenced on 3 runs


title: E198K_patient, DIV 14 neurons_01

description:
Library name: E198K_01
E198K_01


title: E198K_corrected, DIV14 neurons_03

description:
Library name: corE198K_03
corE198K_03

source_name: E198K corrected iPSCs

value: E198K corrected iPSCs


title: ABDE3 TSCs, 48h DMSO control 3


title: ABDE3 TSCs, 48h DMSO control 2


title: M2_C_lymph.node_rep3

description:
Library name: S3_C377
sample has been sequenced on 3 runs


title: ABDE3 TSCs, 48h DMSO control 1


title: M1_C_lymph.node_rep3

description:
Library name: S3_C329
sample has been sequenced on 3 runs


title: E198K_corrected, DIV14 neurons_02

description:
Library name: corE198K_02
corE198K_02


title: ABDE3 TSCs, 24h dTAG-13 treatment 2


title: ABDE3 TSCs, 24h dTAG-13 treatment 3


title: ABDE3 TSCs, 24h dTAG-13 treatment 1


title: M5_C_lymph.node_rep2

description:
Library name: S3_C325
sample has been sequenced on 3 runs


title: E198K_corrected, DIV14 neurons_01

description:
Library name: corE198K_01
corE198K_01


title: E420K_patient, DIV 14 neurons_03

description:
Library name: E420K_03
E420K_03

source_name: E420K patient iPSCs

value: E420K patient iPSCs


title: ABDE3 TSCs, 24h BRG1 inhibition 2


title: M3_C_lymph.node_rep2

description:
Library name: S3_C229
sample has been sequenced on 3 runs


title: ABDE3 TSCs, 24h DMSO control 3


title: ABDE3 TSCs, 24h BRG1 inhibition 1


title: ABDE3 TSCs, 48h BRG1 inhibition 2


title: E420K_patient, DIV 14 neurons_02

description:
Library name: E420K_02
E420K_02


title: ABDE3 TSCs, 24h DMSO control 2


title: M2_C_lymph.node_rep2

description:
Library name: S3_C181
sample has been sequenced on 3 runs


title: E420K_corrected, DIV14 neurons_03

description:
Library name: corE420K_03
corE420K_03

source_name: E420K corrected iPSCs

value: E420K corrected iPSCs


title: ABDE3 TSCs, 24h DMSO control 1


title: ABDE3 TSCs, 12h dTAG-13 treatment 3


title: M1_C_lymph.node_rep2

description:
Library name: S3_C133
sample has been sequenced on 3 runs


title: ABDE3 TSCs, 12h dTAG-13 treatment 1


title: ABDE3 TSCs, 12h dTAG-13 treatment 2


title: E420K_corrected, DIV14 neurons_02

description:
Library name: corE420K_02
corE420K_02


title: ABDE3 TSCs, 12h BRG1 inhibition 2


title: M5_B_lymph.node_rep3

description:
Library name: S3_C281
sample has been sequenced on 3 runs

value: TXwildlings


title: E420K_corrected, DIV14 neurons_01

description:
Library name: corE420K_01
corE420K_01


title: M4_C_lymph.node_rep2

description:
Library name: S3_C277
sample has been sequenced on 3 runs


title: ABDE3 TSCs, 24h BRG1 inhibition 3


title: ABDE3 TSCs, 12h BRG1 inhibition 1


title: ABDE3 TSCs, 12h DMSO control 3


title: PRO-seq_U1ASO3

description:
Library name: PRO-seq_U1ASO3
U1ASO_replicate 3

data_processing:
Read pairs for each group were trimmed using cutadapt 1.14 to remove adapter sequences (-O 1–match-read-wildcards-m 26), then aligned to the reference genome GRCh38.99 using bowtie2 (v2.5.1). Reads mapping to the reference genome were then sorted using samtools 1.3.1 (-n) and converted to bigwig files using Deeptools (v3.5.6) bamCoverage function. The coverage for each data was normalized with Drosophila spike-in factors and averaged for each group for visiaulization.
Assembly: NCBI_RefSeq_GRCh38
Supplementary files format and content: bigwig
Library strategy: PRO-Seq

source_name: HeLa

extract_protocol:
Cells were rinsed with room temperature 1X PBS, detached using trypsin (quenched with ice-cold DMEM + 10% FBS), and collected in 50 mL conical tubes. The cells were pelleted by centrifugation, washed with  cold 1X PBS, and centrifuged again under the same conditions. The cell pellets were then resuspended in wash buffer (10 mM Tris-Cl, 10 mM KCl, 250 mM Sucrose, 5 mM MgCl2, 1 mM EGTA, 0.5 mM DTT, 10 % Glycerol) to achieve a single-cell suspension, followed by the addition of 10 mL permeabilization buffer  (wash buffer with 0.1 % (v/v) Igepal CA-630 and 0.05 % Tween-20). After 5 minutes of incubation on ice for permeabilization, cells were centrifuged at 400 × g for 8 minutes at 4°C, and the supernatant was removed. The pellets were washed twice with wash buffer and finally resuspended in 200 µL of freeze buffer (50 mM Tris-Cl, 40 % (v/v) glycerol, 5 mM MgCl2, 1.1 mM EDTA, 0.5 mM DTT), followed by an additional rinse with 200 µL freeze buffer, to yield a total of 400 µL. The cells were snap-frozen in liquid nitrogen and stored at -80°C until further processing.
Libraries were prepared and sequenced by Nascent Transcriptomics Core at Harvard Medical School as described in Mimoso et al. 2023; https://doi.org/10.1002/cpz1.961

value: HeLa


title: M3_B_lymph.node_rep3

description:
Library name: S3_C185
sample has been sequenced on 3 runs


title: ABDE3 TSCs, 12h DMSO control 2


title: ABDE3 TSCs, 12h DMSO control 1


title: PRO-seq_U1ASO2

description:
Library name: PRO-seq_U1ASO2
U1ASO_replicate 2


title: E420K_patient, DIV 14 neurons_01

description:
Library name: E420K_01
E420K_01


title: ABDE3 TSCs, 1h BRG1 inhibition 3


title: M2_B_lymph.node_rep3

description:
Library name: S3_C137
sample has been sequenced on 3 runs


title: ABDE3 TSCs, 1h BRG1 inhibition 2


title: ABDE3 TSCs, 1h BRG1 inhibition 1


title: M1_B_lymph.node_rep3

description:
Library name: S3_C089
sample has been sequenced on 3 runs


title: PRO-seq_Ctrl3

description:
Library name: PRO-seq_Ctrl3
Control_replicate 3


title: ABDE3 TSCs, 12h BRG1 inhibition 3


title: ABDE3 TSCs, 1h DMSO control 2


title: M5_B_lymph.node_rep2

description:
Library name: S3_C085
sample has been sequenced on 3 runs


title: ABDE3 TSCs, 1h DMSO control 3


title: ABDE3 TSCs, 1h DMSO control 1


title: PRO-seq_Ctrl2

description:
Library name: PRO-seq_Ctrl2
Control_replicate 2


title: ABDE3 TSCs, untreated 3

value: Untreated


title: M4_B_lymph.node_rep2

description:
Library name: S3_C037
sample has been sequenced on 3 runs


title: M4_B_lymph.node_rep3

description:
Library name: S3_C233
sample has been sequenced on 3 runs


title: ABDE3 TSCs, untreated 2


title: PRO-seq_Ctrl1

description:
Library name: PRO-seq_Ctrl1
Control_replicate 1


title: ABDE3 TSCs, untreated 1


title: HEL24.3-Mab13, d0, scRNAseq

city: Turku

first: Johanna

last: Ivaska

address: Tykistökatu 6

country: Finland

institute: University of Turku

description: 10x Genomics

data_processing:
Demultiplexing, barcode processing, count matrix generation made using CellRanger 7.1.0 software
Assembly: hg38
Supplementary files format and content: Tan separated value files and matrix files

extract_protocol:
Cells were grown on Matrigel-coated 6-well plates and dissociated with TryPLE incubation. From each sample 3000-15000 cells were loaded on Chromium Next GEM Chip G and partitioned into droplets using a Chromium X instrument (10x Genomics)
10x Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index), following manufacturer’s instructions (Protocol number CG000315)

value: primed hiPSC


title: M2_B_lymph.node_rep2

description:
Library name: S3_C323
sample has been sequenced on 3 runs


title: c34DBF1 (MS378_071)

description: d4c34 oocyte-like cell, OSC-free cultured on m220

extract_protocol:
For the bulk RNA-seq samples, the mouse gonadal/ovarian cells were lysed and the total RNAs were purified using a NucleoSpin RNA XS (Takara Bio, U0902A) according to the manufacturer’s instructions. Biologically duplicated (E9.5, E10.5, E11.5, E12.5, E13.5, E16.5, E17.5, E18.5, P0, P1, ESCs, EpiLCs, c0, c3 , c5 ,c7, c11, c13) or triplicated (E14.5,E15.5) samples were prepared in each stage.1 ng of total RNAs from each sample was used for the synthesis and amplification of cDNAs. The cDNA synthesis and library construction were as described previously (Nakamura et al, 2015; Ishikura et al, 2016; Okamoto et al, 2021). The sequencing was performed on the Illumina NextSeq 500/550 platform with a NextSeq 500/550 high output kit v. 2 (75 cycles) (FC-404-2005; Illumina).
For the SC3-seq samples, dissociated oocytes and granulosa cells from in vivo mouse ovarian follicles and in vitro oocyte-like cells were manually picked up using glass capillaries under a stereomicroscope (Leica, S8 APO).  The subsequent cDNA synthesis and amplification methods were as previously described (Kurimoto et al, 2006, 2007; Nakamura et al, 2015, 2016). and the 3’ termini of cDNA were subjected to sequencing on the Illumina NextSeq 500/550 platform with a NextSeq 500/550 high output kit v. 2 (75 cycles) (FC-404-2005; Illumina).
For the bulk RNA-seq samples, 1 ng of total RNAs from each sample was used for the synthesis and amplification of cDNAs. The cDNA synthesis and library construction were as described previously (Nakamura et al, 2015; Ishikura et al, 2016; Okamoto et al, 2021). The sequencing was performed on the Illumina NextSeq 500/550 platform with a NextSeq 500/550 high output kit v. 2 (75 cycles) (FC-404-2005; Illumina).
For the SC3-seq samples, the subsequent cDNA synthesis and amplification methods were as previously described (Kurimoto et al, 2006, 2007; Nakamura et al, 2015, 2016). and the 3’ termini of cDNA were subjected to sequencing on the Illumina NextSeq 500/550 platform with a NextSeq 500/550 high output kit v. 2 (75 cycles) (FC-404-2005; Illumina).

value: Oocyte-like cell

tag: transgene

value: ovarian soma-free culture

value: day 34


title: c34DBF1 (MS378_070)

tag: cell line


title: HEL24.3, d0, scRNAseq

description: 10x Genomics


title: c34DBF1 (MS378_074)


title: c34DBF1 (MS378_065)


title: PRO-seq_U1ASO1

city: Boston

description:
Library name: PRO-seq_U1ASO1
U1ASO_replicate 1


title: 0.5-Mab13, d2, scRNAseq

description: 10x Genomics

value: naive hiPSC

value: 2 day capacitation +Mab13


title: M1_B_lymph.node_rep2

description:
Library name: S3_C275
sample has been sequenced on 3 runs


title: c34DBF1 (MS378_064)


title: c34 (MS417_006)


title: M5_A_lymph.node_rep3

description:
Library name: S3_C041
sample has been sequenced on 3 runs

value: Lab


title: 0.5, d2, scRNAseq

description: 10x Genomics

value: 2 day capacitation +None


title: c34 (MS417_005)


title: c34DBF1 (MS378_069)


title: 0.5-Mab13, d0, scRNAseq

description: 10x Genomics


title: M4_A_lymph.node_rep3

description:
Library name: S3_C375
sample has been sequenced on 3 runs


title: c34 (MS417_002)


title: M3_B_lymph.node_rep2

description:
Library name: S3_C371
sample has been sequenced on 3 runs


title: M3_A_lymph.node_rep3

description:
Library name: S3_C327
sample has been sequenced on 3 runs