title: HEK293-untreated-rep4

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

institute: F. Hoffmann - La Roche AG

data_processing:
Basecalls and sample de-multiplexing performed by bcl2fastq conversion with default parameters
Sequenced reads were quality check with fastqc default parameters and then mapped with STAR using default algorithm parameters against hg38
The resulting BAM files were processed with FeatureCounts (Subreads) to yield count data for RefSeq transcript annotations
Transcripts Per Million (TPM) were calculated.
RefSeq annotations from NCBI Homo sapiens Annotation Release 110
Assembly: hg38
Supplementary files format and content: ctrl_refseq_count.gct contains raw read counts per RefSeq gene (Entrezgene ID and gene symbol) in gct format
Supplementary files format and content: ctrl_refseq_tpm.gct contains normalized read counts per RefSeq gene (Entrezgene ID and gene symbol) in gct format

growth_protocol: HEK293 and U2OS were seeded one day before treatment, in order to reach 80% confluency after 4 days.

extract_protocol:
Total RNA was extracted from frozen cell pellets using Qiagen RNeasy Mini kit following manufacturer’s instructions (Qiagen, Catalog No. 74106). RNA samples were quantified using Qubit 4.0 Fluorometer (Thermo Fisher) and RNA integrity was checked with RNA Kit on Agilent 5300 Fragment Analyzer (Agilent Technologies). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (New England Biolabs, Catalog No. E7775) for Illumina following manufacturer’s instructions
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (New England Biolabs, Catalog No. E7775) for Illumina following manufacturer’s instructions

treatment_protocol: On the day of the treatment, medium containing  1uM of non-targetting ASO was added on the cells. 3 days later, cells were washed with PBS and detached with TripleE. Cell pellets were obtained by centrifugation (300 g for 5 minutes) and kept at -80C. Cell pellets were shipped to GENEWIZ Germany GmbH for subsequent processing. ASO seuqences are as follows : CTRL1 : 5'-CCAAATCTTATAATAACTAC-3'; CTRL2: 5'-CGTCAGTATGCGAATC-3'; CTRL3: 5'-GCAAATTCCTATTCCC-3'; SSO: 5'-ACTTACCTTAACCCAG-3'

value: embryonic kidney

value: Griptite HEK293-Cas9

value: WT


title: 0.5, d0, scRNAseq

status: Public on May 19 2025

type: SRA

city: Turku

first: Johanna

last: Ivaska

address: Tykistökatu 6

country: Finland

institute: University of Turku

description: 10x Genomics

library_source: transcriptomic single cell

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

molecule: total RNA

organism: Homo sapiens

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)

tag: cell line

tag: cell type

value: naive hiPSC

tag: treatment

tag: time


title: c34 (MS417_003)

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

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

library_source: transcriptomic

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

molecule: polyA RNA

organism: Mus musculus

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: c24 (MS305_092)

description: d4c24 oocyte-like cell, OSC-free cultured on m220

value: day 24


title: c34 (MS417_004)


title: c34 (MS330_047)


title: M2_A_lymph.node_rep3

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

description:
Library name: S3_C279
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.

tag: tissue

value: Lab


title: M5_A_lymph.node_rep2

description:
Library name: S3_C227
sample has been sequenced on 3 runs


title: c24 (MS305_088)


title: HEK293-untreated-rep2

country: Switzerland

tag: genotype


title: c24 (MS305_090)


title: c24 (MS305_087)


title: M1_A_lymph.node_rep3

description:
Library name: S3_C231
sample has been sequenced on 3 runs


title: c24 (MS305_086)


title: HEK293-untreated-rep1


title: M3_A_lymph.node_rep2

description:
Library name: S3_C131
sample has been sequenced on 3 runs


title: c24 (MS305_089)


title: RAc13 (MS236_061)

description: d4c13oocyte-like cells RAc0-c13BMP2c3-c13 Y10μmαMEM SC+, rep2

value: day 13


title: M4_A_lymph.node_rep2

description:
Library name: S3_C179
sample has been sequenced on 3 runs


title: c24 (MS305_084)


title: HEK293-CTRL3 ASO-3 days-rep4


title: RAc13 (MS236_060)

description: d4c13oocyte-like cells RAc0-c13BMP2c3-c13 Y10μmαMEM SC+, rep1


title: M2_A_lymph.node_rep2

description:
Library name: S3_C083
sample has been sequenced on 3 runs


title: c34 (MS417_001)


title: RAc11 (MS236_057)

description: d4c11oocyte-like cells RAc0-c11BMP2c3-c11 Y10μmαMEM SC+, rep2

value: day 11


title: HEK293-CTRL3 ASO-3 days-rep3


title: RAc11 (MS236_056)

description: d4c11oocyte-like cells RAc0-c11BMP2c3-c11 Y10μmαMEM SC+, rep1


title: M1_A_lymph.node_rep2

description:
Library name: S3_C035
sample has been sequenced on 3 runs


title: HEK293-CTRL3 ASO-3 days-rep2


title: RAc9 (MS236_053)

description: d4c9oocyte-like cells RAc0-c9BMP2c3-c9 Y10μmαMEM SC+, rep2

value: day 9


title: RAc7 (MS236_049)

description: d4c7oogonia-like cells RAc0-c7BMP2c3-c7 Y10μmαMEM SC+, rep2

value: day 7


title: RAc9 (MS236_052)

description: d4c9oocyte-like cells RAc0-c9BMP2c3-c9 Y10μmαMEM SC+, rep1


title: HEK293-CTRL3 ASO-3 days-rep1


title: HEK293-untreated-rep3


title: RAc7 (MS236_048)

description: d4c7oogonia-like cells RAc0-c7BMP2c3-c7 Y10μmαMEM SC+, rep1


title: M5_D_lung_rep3

description:
Library name: S12_C355
sample has been sequenced on 3 runs

source_name: lung

value: lung

value: Wildlings


title: c13SChigh (MS236_067)

description: d4c13oocyte-like cells RAc0-c2.5BMP2c3-c13 Y10μmαMEM SC high, rep2


title: c11 (MS378_061)

description: d4c11oocyte-like cells RAc0-c2.5BMP2c3-c11 Y10μmαMEM SC+, rep2


title: c13SChigh (MS236_066)

description: d4c13oocyte-like cells RAc0-c2.5BMP2c3-c13 Y10μmαMEM SC high, rep1


title: M3_D_lung_rep3

description:
Library name: S12_C259
sample has been sequenced on 3 runs


title: HEK293-CTRL2 ASO-3 days-rep4


title: c11 (MS236_055)

description: d4c11oocyte-like cells RAc0-c2.5BMP2c3-c11 Y10μmαMEM SC+, rep1


title: c9 (MS236_051)

description: d4c9oocyte-like cells RAc0-c2.5BMP2c3-c9 Y10μmαMEM SC+, rep2


title: c9 (MS236_050)

description: d4c9oocyte-like cells RAc0-c2.5BMP2c3-c9 Y10μmαMEM SC+, rep1


title: HEK293-CTRL2 ASO-3 days-rep3


title: HEK293-CTRL2 ASO-3 days-rep1


title: M1_D_lung_rep3

description:
Library name: S12_C163
sample has been sequenced on 3 runs


title: c5 (MS236_043)

description: d4c5PGCLCs RAc0-c2.5BMP2c3-c5 Y10μm αMEM SC+, rep2

value: day 5


title: M5_D_lung_rep2

description:
Library name: S12_C159
sample has been sequenced on 3 runs


title: M2_D_lung_rep3

description:
Library name: S12_C211
sample has been sequenced on 3 runs


title: HEK293-CTRL1 ASO-3 days-rep3


title: c5 (MS236_042)

description: d4c5PGCLCs RAc0-c2.5BMP2c3-c5 Y10μm αMEM SC+, rep1


title: c3 (MS236_039)

description: d4c3PGCLCs RAc0-c2.5 Y10μm αMEM SC+, rep2

value: PGCLC

value: day 3


title: M3_D_lung_rep2

description:
Library name: S12_C063
sample has been sequenced on 3 runs


title: M4_D_lung_rep3

description:
Library name: S12_C307
sample has been sequenced on 3 runs


title: M2_D_lung_rep2

description:
Library name: S12_C015
sample has been sequenced on 3 runs


title: c3 (MS236_038)

description: d4c3PGCLCs RAc0-c2.5 Y10μm αMEM SC+, rep1


title: EpiLC (MS087_049)

description: EpiLC, rep1

value: EpiLC


title: EpiLC (MS087_085)

description: EpiLC, rep2


title: HEK293-CTRL1 ASO-3 days-rep2

value: embryonic kidney

value: Griptite HEK293-Cas9

value: WT


title: M4_D_lung_rep2

description:
Library name: S12_C111
sample has been sequenced on 3 runs


title: HEK293-CTRL2 ASO-3 days-rep2


title: HEK293-CTRL1 ASO-3 days-rep1


title: ESC (MS087_082)

value: ESC


title: ESC (MS087_046)


title: c7 (MS378_060)

description: d4c7oogonia-like cells RAc0-c2.5BMP2c3-c7 Y10μmαMEM SC+, rep2

value: Oocyte-like cell

value: ovarian soma-free culture


title: U2OS-untreated-rep4

value: bone


title: M1_D_lung_rep2

description:
Library name: S12_C349
sample has been sequenced on 3 runs


title: c7 (MS236_047)

description: d4c7oogonia-like cells RAc0-c2.5BMP2c3-c7 Y10μmαMEM SC+, rep1


title: MII (MS238_086)

description: Single-cell of oocyte, M2, adult mouse, BDF1(6w6d-7w1d)

source_name: Adult ovary

value: Adult ovary


title: M5_C_lung_rep3

description:
Library name: S12_C115
sample has been sequenced on 3 runs

value: TXlab


title: MII (MS238_088)


title: HEK293-CTRL1 ASO-3 days-rep4


title: M4_C_lung_rep3

description:
Library name: S12_C067
sample has been sequenced on 3 runs


title: MII (MS238_084)


title: U2OS-untreated-rep2


title: MII (MS238_080)


title: MII (MS238_082)


title: M3_C_lung_rep3

description:
Library name: S12_C019
sample has been sequenced on 3 runs


title: U2OS-untreated-rep1


title: Antral cumulus (MS233_047)

description: Single-cell of 10-20 granulosa cells, antral follicle, fresh adult mouse ovary


title: M2_C_lung_rep3

description:
Library name: S12_C353
sample has been sequenced on 3 runs


title: U2OS-SSO-3 days-rep4


title: c34_H18_K4me3_1

library_source: genomic

data_processing:
Paired-end reads were processed using Trim-Galore! v0.4.1/cutadapt v1.9.1 (refs) to remove adaptor sequences.
The truncated reads were then aligned to (GRCm38.p3) using Bowtie2 v2.3.4.1 (refs) with the “-very-sensitive” option.  Reads aligned to chromosomes 1 to 19, X, and Y were converted to the BAM format by SAMtools v1.7 (refs).
In the samples sequenced in a paired-end manner, duplicated reads were removed using the MarkDuplicates command of Picard Tools v2.18.23 (https://broadinstitute.github.io/picard/).
BED files were obtained from the BAM format using the bamtobed command of BEDTools v2.29.2 (refs).
Assembly: mm10
Supplementary files format and content: bw files are bigwig files generated from the BAM files using bamcoverage for raw count with the “--normalizeUsing CPM -bs 100” option of deepTools v3.5.0.The blacklist regions (Amemiya et al, 2019) were excluded.
Supplementary files format and content: Due to the broad peak nature of epigenetic marks of H3K4m3, H3K27me3, and H3K36me3 in oocytes, the peaks enriched by these marks were identified using epic2 v0.0.41 (refs) with the “--bin-size” of 1kb for H3K4me3 and 10kb for H3K27me3 and H3K36me3. For H3K27ac peaks, MACS v2.1.1 (refs) was used with the “-q 0.01 --nomodel --keep-dup all --extsize 200” option.

molecule: genomic DNA

source_name: H18 Prdm1-mVenus; Dppa3-ECFP reporter

extract_protocol:
Briefly, cells were pelleted and resuspended in nuclear isolation buffer (10 mM Tris-HCl, pH8.0, 140 mM NaCl, 5 mM MgCl2, 0.6% NP-40, 0.1% Triton X-100, 0.1% deoxycholate, 1 x EDTA-free proteinase inhibitor cocktail and 1 mM PMSF). Chromatin was then fragmented with MNase (2 U/μl at 37 °C for 7.5 min) and diluted in NChIP immunoprecipitation buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 150 mM NaCl, 0.1% Triton X-100, 1 × EDTA-free protease inhibitor cocktail and 0.1 mM PMSF). Carrier DNA (30 ng) was added into the fragmented chromatin to reduce DNA loss during immunoprecipitation. The fragmented chromatin was then pre-cleared with 5 μl of Dynabeads Protein A/Protein G (ThermoFisher) and immunoprecipitated overnight at 4 °C with the pre-prepared antibody-beads complex, which contains 700 ng H3K4me3 antibody (Digagenode, 15410003) or H3K27me3 antibody (Merk, 07‐449), H3K36me3 (Active motif, 61101) and 5 μl Dynabeads Protein A/Protein G. After immunoprecipitation, beads were washed twice with 150 μl of low salt wash buffer (20 mM Tris-HCl, pH 8.0, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 1 x EDTA-free proteinase inhibitor cocktail, 0.1 mM PMSF, and 0.2 ng/μl carrier DNA) and twice with 150 μl of high salt wash buffer (20 mM Tris-HCl, pH 8.0, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 500 mM NaCl, 1 x EDTA-free proteinase inhibitor cocktail, 0.1 mM PMSF, and 0.2 ng/μl carrier DNA). Protein-DNA complexes were eluted from beads in 100 μl ChIP elution buffer (100 mM NaHCO3 and 1% SDS) for 2 h at 65 °C. Immunoprecipitated DNA was purified by phenol-chloroform extraction followed by ethanol precipitation.
Adaptor ligation was performed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, New England Biolabs), and library pre-amplification was performed by 9 cycles of PCR. The pre-amplified library was digested by I-SceI (5 U/μl; 2 h incubation at 37 °C followed by 20 min heat inactivation at 65 °C). Barcoded final libraries were generated by further amplification of the carrier-DNA-removed pre-amplification products.

value: H18 Prdm1-mVenus; Dppa3-ECFP reporter

value: d4c34 oocyte-like cell


title: Antral cumulus (MS233_045)


title: U2OS-SSO-3 days-rep3


title: c7_H18_Input_1

value: d4c7oogonia-like cells


title: Antral cumulus (MS233_043)


title: M5_C_lung_rep2

description:
Library name: S12_C301
sample has been sequenced on 3 runs

value: lung


title: U2OS-untreated-rep3


title: Antral cumulus (MS233_041)


title: U2OS-SSO-3 days-rep1


title: U2OS-SSO-3 days-rep2


title: MII (MS238_078)


title: M3_C_lung_rep2

description:
Library name: S12_C205
sample has been sequenced on 3 runs


title: U2OS-CTRL3 ASO-3 days-rep4


title: dietary intervention (HFD -> ND) 8

city: Leuven

first: Mitsugu

last: Shimobayashi

address: Herestraat 49

country: Belgium

institute: KU Leuven

description: Library name: GC144485

data_processing:
Reads of 50 basepairs were generated and an average of 4 million reads per sample was obtained and mapped against mouse genome (mm10)
Assembly: mus musculus reference genome (mm10)
Supplementary files format and content: tab-separated values text file (tsv) includes raw and normalized counts for each sample

source_name: sWAT

extract_protocol:
Tissue was homogenized and RNA extracted using Nucleozol reagent (Macherey-Nagel) according to the manufacturer’s protocol.
Libraries were generated with the LexoGen Quant Seq Library Preparation Kit and subsequently sequenced on the Illumina HiSeq 4000.

value: sWAT

value: dietary intervention (HFD -> ND)


title: dietary intervention (HFD -> ND) 7

description: Library name: GC144484


title: U2OS-CTRL3 ASO-3 days-rep3


title: Antral cumulus (MS233_035)


title: M2_C_lung_rep2

description:
Library name: S12_C157
sample has been sequenced on 3 runs


title: Antral cumulus (MS233_037)


title: dietary intervention (HFD -> ND) 6

description: Library name: GC144483


title: MII (MS238_076)


title: dietary intervention (HFD -> ND) 5

description: Library name: GC144482


title: Antral cumulus (MS233_033)


title: M1_C_lung_rep3

description:
Library name: S12_C305
sample has been sequenced on 3 runs


title: U2OS-CTRL3 ASO-3 days-rep2


title: dietary intervention (HFD -> ND) 4

description: Library name: GC144481


title: U2OS-CTRL3 ASO-3 days-rep1


title: Antral cumulus (MS233_031)


title: M5_B_lung_rep3

description:
Library name: S12_C257
sample has been sequenced on 3 runs

value: TXwildlings


title: M4_C_lung_rep2

description:
Library name: S12_C253
sample has been sequenced on 3 runs


title: Antral cumulus (MS233_028)


title: Antral cumulus (MS233_039)


title: M4_B_lung_rep3

description:
Library name: S12_C209
sample has been sequenced on 3 runs


title: M3_B_lung_rep3

description:
Library name: S12_C161
sample has been sequenced on 3 runs


title: dietary intervention (HFD -> ND) 2

description: Library name: GC144479


title: Antral cumulus (MS233_026)


title: dietary intervention (HFD -> ND) 1

description: Library name: GC144478


title: Antral cumulus (MS233_021)


title: U2OS-CTRL2 ASO-3 days-rep2


title: HFD-fed tirzepatide 8

description: Library name: GC144477

value: HFD-fed tirzepatide


title: M1_B_lung_rep3

description:
Library name: S12_C065
sample has been sequenced on 3 runs


title: Antral cumulus (MS233_018)


title: HFD-fed tirzepatide 7

description: Library name: GC144476


title: Antral cumulus (MS233_008)


title: M5_B_lung_rep2

description:
Library name: S12_C061
sample has been sequenced on 3 runs


title: U2OS-CTRL1 ASO-3 days-rep4


title: M4_B_lung_rep2

description:
Library name: S12_C013
sample has been sequenced on 3 runs


title: dietary intervention (HFD -> ND) 3

description: Library name: GC144480


title: Antral cumulus (MS233_023)


title: U2OS-CTRL2 ASO-3 days-rep4


title: M1_C_lung_rep2

description:
Library name: S12_C109
sample has been sequenced on 3 runs


title: HFD-fed tirzepatide 6

description: Library name: GC144475


title: M3_B_lung_rep2

description:
Library name: S12_C347
sample has been sequenced on 3 runs


title: HFD-fed tirzepatide 5

description: Library name: GC144474


title: U2OS-CTRL1 ASO-3 days-rep2


title: U2OS-CTRL2 ASO-3 days-rep3


title: Antral (MS233_006)

description: Single-cell of oocyte, antral follicle, fresh adult mouse ovary


title: M2_B_lung_rep2

description:
Library name: S12_C299
sample has been sequenced on 3 runs


title: Antral (MS233_046)


title: HFD-fed tirzepatide 4

description: Library name: GC144473


title: U2OS-CTRL1 ASO-3 days-rep3


title: U2OS-CTRL1 ASO-3 days-rep1


title: U2OS-CTRL2 ASO-3 days-rep1


title: M2_B_lung_rep3

description:
Library name: S12_C113
sample has been sequenced on 3 runs


title: HFD-fed tirzepatide 3

description: Library name: GC144472


title: Antral (MS233_044)


title: M1_B_lung_rep2

description:
Library name: S12_C251
sample has been sequenced on 3 runs


title: U2OS-AP1M1 KO-clone B1

data_processing:
Basecalls and sample de-multiplexing performed by bcl2fastq conversion with default parameters
Sequenced reads were quality check with fastqc default parameters and then mapped with STAR using default algorithm parameters against hg38
The resulting BAM files were processed with FeatureCounts (Subreads) to yield count data for RefSeq transcript annotations
Transcripts Per Million (TPM) were calculated.
RefSeq annotations from NCBI Homo sapiens Annotation Release 110
Assembly: hg38
Supplementary files format and content: ap1m1_refseq_count.gct contains raw read counts per RefSeq gene (Entrezgene ID and gene symbol) in gct format
Supplementary files format and content: ap1m1_refseq_tpm.gct contains normalized read counts per RefSeq gene (Entrezgene ID and gene symbol) in gct format

source_name: bone

growth_protocol: AP1M1 KO was performed with CRISPR-Cas9 editing prior to the experiment. HEK293 and U2OS were seeded one day before the experiment, in order to reach 80% confluency.

treatment_protocol: On the day of the experiment, cells were washed with PBS and detached with TripleE. Cell pellets were obtained by centrifugation (300 g for 5 minutes) and kept at -80C. Cell pellets were shipped to GENEWIZ Germany GmbH for subsequent processing.

value: AP1M1 KO


title: M5_A_lung_rep3

description:
Library name: S12_C017
sample has been sequenced on 3 runs

value: Lab


title: U2OS-AP1M1 KO-clone A10


title: HFD-fed tirzepatide 2

description: Library name: GC144471


title: Antral (MS233_042)


title: HFD-fed tirzepatide 1

description: Library name: GC144470


title: Antral (MS233_040)


title: M4_A_lung_rep3

description:
Library name: S12_C351
sample has been sequenced on 3 runs


title: U2OS-WT-clone 2

value: WT


title: HFD-fed semaglutide 8

description: Library name: GC144469

value: HFD-fed semaglutide


title: M3_A_lung_rep3

description:
Library name: S12_C303
sample has been sequenced on 3 runs


title: Antral (MS233_038)


title: HFD-fed semaglutide 7

description: Library name: GC144468


title: M2_A_lung_rep3

description:
Library name: S12_C255
sample has been sequenced on 3 runs


title: U2OS-WT-clone 1


title: Antral (MS233_036)


title: M1_A_lung_rep3

description:
Library name: S12_C207
sample has been sequenced on 3 runs


title: HFD-fed semaglutide 6

description: Library name: GC144467


title: HEK293-WT-clone C11

source_name: embryonic kidney

value: embryonic kidney

value: Griptite HEK293-Cas9


title: HFD-fed semaglutide 5

description: Library name: GC144466


title: HEK293-WT-clone C10


title: HEK293-WT-clone F11


title: M5_A_lung_rep2

description:
Library name: S12_C203
sample has been sequenced on 3 runs


title: HEK293-WT-clone F10


title: Antral (MS233_034)


title: Antral (MS233_032)


title: HFD-fed semaglutide 3

description: Library name: GC144464


title: HFD-fed semaglutide 4

description: Library name: GC144465


title: M4_A_lung_rep2

description:
Library name: S12_C155
sample has been sequenced on 3 runs


title: M2_A_lung_rep2

description:
Library name: S12_C059
sample has been sequenced on 3 runs


title: Antral (MS233_030)


title: HEK293-WT-clone F9


title: Antral (MS233_027)


title: HFD-fed semaglutide 2

description: Library name: GC144463


title: M1_A_lung_rep2

description:
Library name: S12_C011
sample has been sequenced on 3 runs


title: Antral (MS233_025)


title: HFD-fed semaglutide 1

description: Library name: GC144462


title: HEK293-WT-clone F8


title: M3_A_lung_rep1

description:
Library name: S12_C107
sample has been sequenced on 3 runs


title: HEK293-WT-clone D11


title: HEK293-WT-clone D10


title: M5_D_liver_rep3

description:
Library name: S11_C345
sample has been sequenced on 3 runs

source_name: liver

value: liver

value: Wildlings


title: Antral (MS233_017)

value: Adult ovary


title: Antral (MS233_020)


title: HFD-fed 7

description: Library name: GC144460

value: HFD-fed


title: M4_D_liver_rep3

description:
Library name: S11_C297
sample has been sequenced on 3 runs


title: HFD-fed 6

description: Library name: GC144459


title: HEK293-WT-clone D9


title: M3_D_liver_rep3

description:
Library name: S11_C249
sample has been sequenced on 3 runs


title: Antral (MS233_007)

description: Single-cell of oocyte, antral follicle, fresh adult mouse ovary


title: Antral (MS233_022)


title: HFD-fed 5

description: Library name: GC144458


title: M1_D_liver_rep3

description:
Library name: S11_C153
sample has been sequenced on 3 runs


title: Preantral granulosa (MS234_088)

description: Single-cell of 10-20 granulosa cells, preantral follicle, fresh adult mouse ovary ,6wBDF1


title: Preantral granulosa (MS234_027)

description: Single-cell of 10-20 granulosa cells, preantral follicle, fresh adult mouse ovary,7wBDF1


title: HFD-fed 3

description: Library name: GC144456


title: HEK293-WT-clone D7


title: HEK293-AP1M1 KO-clone F3


title: Preantral granulosa (MS234_092)


title: M5_D_liver_rep2

description:
Library name: S11_C149
sample has been sequenced on 3 runs


title: HEK293-AP1M1 KO-clone F2


title: HFD-fed 4

description: Library name: GC144457


title: M4_D_liver_rep2

description:
Library name: S11_C101
sample has been sequenced on 3 runs


title: HEK293-AP1M1 KO-clone E11


title: HEK293-AP1M1 KO-clone E10


title: Preantral granulosa (MS234_025)


title: HFD-fed 2

description: Library name: GC144455


title: HFD-fed 8

description: Library name: GC144461


title: HFD-fed 1

description: Library name: GC144454


title: M2_D_liver_rep2

description:
Library name: S11_C005
sample has been sequenced on 3 runs


title: M3_D_liver_rep2

description:
Library name: S11_C053
sample has been sequenced on 3 runs


title: Preantral granulosa (MS234_090)


title: Preantral granulosa (MS234_016)

description: Single-cell of 10-20 granulosa cells, preantral follicle, fresh adult mouse ovary,6wBDF1


title: HEK293-AP1M1 KO-clone E9


title: M2_D_liver_rep3

description:
Library name: S11_C201
sample has been sequenced on 3 runs


title: ND-fed 8

description: Library name: GC144437

value: ND-fed


title: HEK293-AP1M1 KO-clone E8


title: ND-fed 7

description: Library name: GC144436


title: M1_D_liver_rep2

description:
Library name: S11_C339
sample has been sequenced on 3 runs


title: ND-fed 6

description: Library name: GC144435


title: Preantral (MS234_091)

description: Single-cell of oocyte, preantral follicle, fresh adult mouse ovary ,6wBDF1


title: M4_C_liver_rep3

description:
Library name: S11_C057
sample has been sequenced on 3 runs

value: TXlab


title: HEK293-AP1M1 KO-clone E6


title: M5_C_liver_rep3

description:
Library name: S11_C105
sample has been sequenced on 3 runs


title: Preantral (MS234_093)


title: ND-fed 4

description: Library name: GC144433


title: M3_C_liver_rep3

description:
Library name: S11_C009
sample has been sequenced on 3 runs


title: ND-fed 5

description: Library name: GC144434


title: Preantral (MS234_026)

description: Single-cell of oocyte, preantral follicle, fresh adult mouse ovary,7wBDF1


title: ND-fed 3

description: Library name: GC144432


title: Preantral (MS234_087)


title: HEK293-AP1M1 KO-clone E3


title: HEK293-AP1M1 KO-clone E5


title: HEK293-AP1M1 KO-clone E4


title: ND-fed 2

description: Library name: GC144431


title: Preantral (MS234_024)


title: M1_C_liver_rep3

description:
Library name: S11_C295
sample has been sequenced on 3 runs


title: HEK293-AP1M1 KO-clone E2


title: ND-fed 1

description: Library name: GC144430


title: HEK293-WT-clone B11


title: Preantral (MS234_089)


title: M5_C_liver_rep2

description:
Library name: S11_C291
sample has been sequenced on 3 runs


title: HEK293-AP1M1 KO-clone E7


title: caMKK6_GFP

first: Takuya

last: Yamamoto

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

department: CiRA

institute: Kyoto University

description: 10x Genomics

data_processing:
The 10X Genomics Cell Ranger pipeline (version 4.0.0) was used to perform sample demultiplexing, alignment to the mm10 mouse reference genome and the reporter sequences (mCherry and EGFP), barcode/UMI processing, and gene counting for each cell.
Assembly: mm10
Supplementary files format and content: hdf5 files contain lists of gene names, cell barcodes and UMI counts for each sample

extract_protocol:
Hepatocytes were isolated by a modification of a previously described two-step collagenase perfusion method. Mice were anesthetized, and inferior vena cava was canulated under aseptic conditions. The liver was perfused EGTA solution (calcium-free Hank’s Balanced Salt Solution (HBSS) (Wako) containing 0.5mM EGTA (Sigma) and 10mM HEPES (Nacalai Teque)), followed by a second perfusion with HBSS containing Liberase TM Research Grade (Roche) and 10mM HEPES. After passage through 70µm cell strainer, to enrich hepatocytes, the cells were centrifuged at 50 g for 2 minutes three times. The viability of cells was confirmed by trypan blue staining. Dissociated hepatocytes were passed through 40 µm cell strainer and sorted with FACSAriaⅡ (BD Bioscience) machine using a 130 µm nozzle. Dead cells were gated out by DAPI incorporation (500 ng/mL). To enrich hepatocytes, we used 2 FSC-neutral density (ND) filter and 10-SSC ND filter. Cells were sorted into low glucose DMEM (Nacalai Teque) with 10% fetal bovine serum (Gibco) and 10 mM HEPES and proceeded to the 10X pipeline.
Cells isolated from three mice were loaded into a 10X Genomics Chromium system. scRNA-seq libraries were prepared using Single Cell 3' Reagent Kits (v.3.1, 10X Genomics).

treatment_protocol: Doxycycline (Sigma) was dissolved in drinking water at 0.2 mg/mL for caMEK1 mice and 2 mg/ml for caMKK6 and control mice; the drinking water was also supplemented with 10 mg/mL sucrose (Nacalai Tesque).  Mice were additionally given intraperitoneal injections of Dox-containing PBS twice a day before sample collection to induce uniform transgene expression (0.4 mg/injection for caMEK1 and 1 mg/injection for caMKK6 and control).

tag: strain

tag: Sex

value: male

value: Dox

value: Day 7


title: M4_C_liver_rep2

description:
Library name: S11_C243
sample has been sequenced on 3 runs


title: Preantral (MS234_015)

description: Single-cell of oocyte, preantral follicle, fresh adult mouse ovary,6wBDF1


title: HEK293-WT-clone B10


title: Secondary granulosa (MS234_053)

description: Single-cell of 10-20 granulosa cells, secondary follicle, fresh adult mouse ovary,7wBDF1


title: HEK293-WT-clone B9


title: caMKK6_mCherry

description: 10x Genomics


title: caMEK1_GFP

description: 10x Genomics


title: M2_C_liver_rep3

description:
Library name: S11_C343
sample has been sequenced on 3 runs


title: M2_C_liver_rep2

description:
Library name: S11_C147
sample has been sequenced on 3 runs


title: Secondary granulosa (MS234_049)


title: M3_C_liver_rep2

description:
Library name: S11_C195
sample has been sequenced on 3 runs


title: HEK293-WT-clone B8


title: Secondary granulosa (MS234_021)

description: Single-cell of 10-20 granulosa cells, secondary follicle, fresh adult mouse ovary,6wBDF1


title: M5_B_liver_rep3

description:
Library name: S11_C247
sample has been sequenced on 3 runs

value: TXwildlings


title: M1_C_liver_rep2

description:
Library name: S11_C099
sample has been sequenced on 3 runs


title: HEK293-WT-clone B6


title: HEK293-WT-clone B7


title: Secondary granulosa (MS234_068)


title: M4_B_liver_rep3

description:
Library name: S11_C199
sample has been sequenced on 3 runs


title: PC3 cells, FUT8 KD, 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:
6-KD3-PC3-FUT8
PC3 FUT8 Control-KD.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 knockdown


title: NEC10-margin intestine samples

city: Seoul

first: Murim

last: Choi

address: 103 Daehakro, Jongrogu

country: South Korea

institute: Seoul National University

description: Library name: T18-NE7-N

data_processing:
Read count extraction and normalization were performed using HTSeq
Assembly: RNA reads were aligned to the GRCh38 using STAR
Supplementary files format and content: Normalized count matrix (csv)

source_name: Intestine

extract_protocol:
The tissue samples were obtained as full-thickness sections from specimens collected during surgery, and immediately after collection, the samples were washed with PBS to remove any foreign substances such as feces. The tissue samples were immediately prepared for RNA extraction.
libraries were prepared and sequenced following TruSeq RNA library prep kit protocols

value: Intestine

tag: subject status

value: Necrotizing enterocolitis patients

value: Male


title: Secondary granulosa (MS234_064)


title: Control_mCherry

description: 10x Genomics

value: Control


title: Secondary granulosa (MS234_066)


title: PC3 cells, FUT8 KD, biol rep 2

description:
5-KD2-PC3-FUT8
PC3 FUT8 Control-KD.tabular


title: M2_B_liver_rep3

description:
Library name: S11_C103
sample has been sequenced on 3 runs


title: NEC9-margin intestine samples

description: Library name: T18-NE6-N

value: Female


title: M3_B_liver_rep3

description:
Library name: S11_C151
sample has been sequenced on 3 runs

value: liver


title: Secondary granulosa (MS234_062)


title: PC3 cells, FUT8 KD, biol rep 1

description:
4-KD1-PC3-FUT8
PC3 FUT8 Control-KD.tabular


title: caMEK1_mCherry

description: 10x Genomics


title: Secondary granulosa (MS234_051)


title: NEC7-margin intestine samples

description: Library name: T18-NE4-N


title: PC3 cells, KDControl, biol rep 2

description:
2-C2-PC3
PC3 FUT8 Control-KD.tabular

value: Lenti-shControl


title: M5_B_liver_rep2

description:
Library name: S11_C051
sample has been sequenced on 3 runs


title: Secondary granulosa (MS234_058)

value: Adult ovary


title: PC3 cells, KDControl, biol rep 3

description:
3-C3-PC3
PC3 FUT8 Control-KD.tabular


title: M1_B_liver_rep3

description:
Library name: S11_C055
sample has been sequenced on 3 runs


title: NEC6-margin intestine samples

description: Library name: T18-NE3-N


title: M4_B_liver_rep2

description:
Library name: S11_C003
sample has been sequenced on 3 runs


title: Control_GFP

description: 10x Genomics


title: PC3 cells, KDControl, biol rep 1

description:
1-C1-PC3
PC3 FUT8 Control-KD.tabular


title: NEC5-margin intestine samples

description: Library name: T18-NE2-N


title: M3_B_liver_rep2

description:
Library name: S11_C337
sample has been sequenced on 3 runs


title: Secondary (MS234_052)

description: Single-cell of oocyte, secondary follicle, fresh adult mouse ovary,7wBDF1


title: Secondary (MS234_048)


title: PA#15, PBMC, scRNA-seq

city: shenzhen

first: Minmin

last: Chen

state: GuangDong

address: Gaoke Innovation Center, Guangqiao Road, Guangming District, Shenzhen

country: China

institute: Shenzhen bay lab

description: 10x Genomics

data_processing:
Preprocessing of raw data was initially performed using Cell Ranger software pipeline (version 7.1.0). This step included demultiplexing of raw base call (BCL) files into FASTQ files, reads alignment on human genome assembly GRCh38 using STAR, counting of unique molecular identifier (UMI) and generating a digital gene-cell matrix.
Assembly: GRCh38
Supplementary files format and content: sc_barcodes.tsv.gz: list of cell barcodes
Supplementary files format and content: sc_features.tsv.gz: list of gene IDs
Supplementary files format and content: sc_matrix.mtx.gz: gene expression count data in Matrix Market Exchange format
Supplementary files format and content: sc_metadata.csv:  metadata in csv format

source_name: PBMC

extract_protocol:
Tumors and adjacent normal tissues were cut into approximately 1 mm3 pieces and enzymatically digested with MACS Tumour Dissociation Kit (Miltenyi Biotec,130-095-929) for 40 minutes (for normal tissues) or 1 hour (for tumor tissues) on the gentleMACS™ Octo Dissociator with Heaters, following the manufacturer’s instruction. The dissociated cells were subsequently passed through a 70-μm cell-strainer (BD Bioscience, 352350) to remove debris and centrifuged at 450g for 10 min. Pelleted cells were resuspended in sorting buffer (Miltenyi Biotec, 130-091-221) and stained with FITC Mouse Anti-Human CD45 (BD Bioscience,555482) and APC anti-human CD235a (Biolegend,349114). DAPI (BD Bioscience,564907) was added to the cell suspension immediately before FACS. CD235-DAPI- live cells were FACS-sorted for single-cell RNA-sequencing.
The sorted cells were stained with Typan Blue to count viable cells. Single-cell suspensions with viability >80% were processed to scRNA-seq. Single-cell libraries were generated via the Chromium Controller and the Chromium Next GEM Single Cell 5' Reagent Kits v2 (10xGenomics, 1000244) according to the manufacturer's instructions. Briefly, cells were loaded onto the Single Cell Chip K for encapsulation into droplets, aiming to capture 10,000 cells. cDNA was amplified by 13 PCR cycles and a total of 50ng cDNA was used for library preparation. Qualitative and quantitative assessments of the final libraries were performed on a Bioanalyzer 2200 with the High Sensitivitiy DNA kit (Agilent, 5067-4626), and the Qubit 3.0 Fluorometer with the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854), respectively. Libraries were then normalized, pooled and sequenced on the NovaSeq 6000 (Illumina) with a 150 bp paired-end run.

value: PBMC


title: NEC4-margin intestine samples

description: Library name: T18-NE1-N


title: M2_B_liver_rep2

description:
Library name: S11_C289
sample has been sequenced on 3 runs


title: PA#14, Tumor, scRNA-seq

description: 10x Genomics

source_name: Tumor

value: Tumor


title: M1_B_liver_rep2

description:
Library name: S11_C241
sample has been sequenced on 3 runs


title: Secondary (MS234_063)

description: Single-cell of oocyte, secondary follicle, fresh adult mouse ovary,6wBDF1


title: NEC3-margin intestine samples

description: Library name: T17-NE3-N


title: Secondary (MS234_050)


title: NEC8-margin intestine samples

description: Library name: T18-NE5-N


title: NEC2-margin intestine samples

description: Library name: T17-NE2-N


title: Secondary (MS234_020)


title: PA#13, PBMC, scRNA-seq

description: 10x Genomics


title: M4_A_liver_rep3

description:
Library name: S11_C341
sample has been sequenced on 3 runs

value: Lab


title: Secondary granulosa (MS234_060)

description: Single-cell of 10-20 granulosa cells, secondary follicle, fresh adult mouse ovary,6wBDF1


title: NEC1-margin intestine samples

description: Library name: T17-NE1-N


title: PA#13, Tumor, scRNA-seq

description: 10x Genomics


title: Secondary (MS234_067)


title: PA#12, PBMC, scRNA-seq

description: 10x Genomics


title: NEC10-NEC intestine samples

description: Library name: T18-NE7

tag: molecular subtype


title: M3_A_liver_rep3

description:
Library name: S11_C293
sample has been sequenced on 3 runs


title: Secondary (MS234_065)


title: M2_A_liver_rep3

description:
Library name: S11_C245
sample has been sequenced on 3 runs


title: Secondary (MS234_059)


title: M1_A_liver_rep3

description:
Library name: S11_C197
sample has been sequenced on 3 runs


title: PA#12, Tumor, scRNA-seq

description: 10x Genomics


title: NEC8-NEC intestine samples

description: Library name: T18-NE5


title: PA#14, PBMC, scRNA-seq

description: 10x Genomics


title: Secondary (MS234_061)


title: PA#11, PBMC, scRNA-seq

description: 10x Genomics


title: NEC7-NEC intestine samples

description: Library name: T18-NE4


title: M5_A_liver_rep2

description:
Library name: S11_C193
sample has been sequenced on 3 runs


title: M5_A_liver_rep3

description:
Library name: S11_C007
sample has been sequenced on 3 runs


title: PA#11, Tumor, scRNA-seq

description: 10x Genomics


title: PA#10, PBMC, scRNA-seq

description: 10x Genomics


title: NEC6-NEC intestine samples

description: Library name: T18-NE3


title: Secondary (MS234_057)


title: M4_A_liver_rep2

description:
Library name: S11_C145
sample has been sequenced on 3 runs


title: M3_A_liver_rep2

description:
Library name: S11_C097
sample has been sequenced on 3 runs


title: Primary granulosa (MS234_047)

description: Single-cell of 10-20 granulosa cells, primary follicle, fresh adult mouse ovary,7wBDF1


title: NEC9-NEC intestine samples

description: Library name: T18-NE6


title: PA#10, Normal, scRNA-seq

description: 10x Genomics

source_name: Adjacent normal

value: Adjacent normal


title: PA#10, Tumor, scRNA-seq

description: 10x Genomics


title: M2_A_liver_rep2

description:
Library name: S11_C049
sample has been sequenced on 3 runs


title: NEC4-NEC intestine samples

description: Library name: T18-NE1


title: PA#09, PBMC, scRNA-seq

description: 10x Genomics


title: NEC3-NEC intestine samples

description: Library name: T17-NE3


title: Primary granulosa (MS234_019)

description: Single-cell of 10-20 granulosa cells, primary follicle, fresh adult mouse ovary,6wBDF1


title: Primary granulosa (MS234_010)


title: Primary granulosa (MS234_006)


title: PA#09, Normal, scRNA-seq

description: 10x Genomics


title: Primary granulosa (MS234_012)


title: NEC1-NEC intestine samples

description: Library name: T17-NE1


title: NEC2-NEC intestine samples

description: Library name: T17-NE2


title: M3_D_colon_rep3

description:
Library name: S1_C273
sample has been sequenced on 3 runs

source_name: colon

value: colon

value: Wildlings


title: PA#09, Tumor, scRNA-seq

description: 10x Genomics


title: Primary granulosa (MS234_008)


title: NEC5-NEC intestine samples

description: Library name: T18-NE2


title: M2_D_colon_rep3

description:
Library name: S1_C225
sample has been sequenced on 3 runs


title: PA#08, PBMC, scRNA-seq

description: 10x Genomics


title: Primary granulosa (MS234_041)


title: M1_D_colon_rep3

description:
Library name: S1_C177
sample has been sequenced on 3 runs


title: M1_A_liver_rep2

description:
Library name: S11_C001
sample has been sequenced on 3 runs


title: M5_D_colon_rep3

description:
Library name: S1_C369
sample has been sequenced on 3 runs


title: IGF117149 [AD ]

city: London

first: Paul

middle: M

last: Matthews

address: White City

institute: Imperial College London

description: Library name: IGF117149

data_processing:
Locally generated snRNASeq data were pre-processed using 10X Genomics Cell Ranger. Illumina sequencing files were aligned to the genomic sequence (introns and exons) using GRCh38 annotation in Cell Ranger v3.1. Nuclei were identified above background by the Cell Ranger software.
Assembly: GRCh38
Supplementary files format and content: Count data and associated metadata

molecule: nuclear RNA

source_name: Brain

extract_protocol:
Single nucleus isolation was conducted on frozen tissue blocks. Homologous fresh frozen brain tissue blocks from MTG and SSC were cryosectioned at 80um and 200mg of grey matter was collected in RNAse-free Eppendorf tube. All steps were carried out on ice or at 4°C. Tissue was homogenised in buffer (1% Triton X-100, 0.4 U/μl RNAseIn + 0.2 U/μl SUPERaseIn, 1ul 1mg/ml DAPI) using a 2ml glass douncer. The homogenate was centrifuged at 4°C for 8mins, 500g and supernatant removed. The pellet then was resuspended in homogenisation buffer and filtered through a 70um filter followed by density gradient centrifugation at 13,000g for 40mins. The supernatant was removed and nuclei were washed and filtered in PBS buffer (PBS + 0.5mg/ml BSA + 0.4 U/μl RNAseIn + 0.2 U/μl SUPERaseIn). Nuclei were pelleted, washed twice in PBS buffer and resuspended in 1ml PBS buffer. 100ul of nuclei solution was set aside on ice for single nuclear processing.
Isolated nuclei stained with Acridine Orange dye were counted on a LUNA-FL Dual Fluorescence Cell Counter (Logos Biosystems, L20001). Approximately 7000 nuclei were used for 10x Genomics Chromium Single Cell 3ʹ processing and library generation. All steps were conducted according to the 10x Genomics Chromium Single Cell 3' Reagent Kits v3 User Guide, with 8 cycles of cDNA amplification until fragmentation, where 25ng of amplified cDNA per sample was taken through for fragmentation. The final index PCR was conducted at 14 cycles. cDNA and library prep concentration were measured using Qubit dsDNA HS Assay Kit (ThermoFisher, Q32851) and DNA and library preparations were assessed using the Bioanalyzer High-Sensitivity DNA Kit (Agilent, 5067-4627). Pooled samples at equimolar concentrations were sequenced on an Illumina HiSeq 4000 according to the standard 10X Genomics protocol.

value: Brain

tag: disease state

value: AD

tag: trem2 genotype


title: Primary granulosa (MS234_039)


title: PA#08, Normal, scRNA-seq

description: 10x Genomics


title: IGF113098 [AD ]

description: Library name: IGF113098

value: CV


title: IGF117147 [AD ]

description: Library name: IGF117147


title: PA#08, Tumor, scRNA-seq

description: 10x Genomics


title: Primary granulosa (MS234_045)


title: M3_D_colon_rep2

description:
Library name: S1_C077
sample has been sequenced on 3 runs


title: IGF117142 [AD ]

description: Library name: IGF117142


title: PA#07, Tumor, scRNA-seq

description: 10x Genomics


title: M1_D_colon_rep2

description:
Library name: S1_C363
sample has been sequenced on 3 runs


title: Primary granulosa (MS234_043)


title: IGF117143 [AD ]

description: Library name: IGF117143


title: Primary (MS234_009)

description: Single-cell of oocyte, primary follicle, fresh adult mouse ovary,6wBDF1


title: PA#06, PBMC, scRNA-seq

description: 10x Genomics


title: IGF117144 [AD ]

description: Library name: IGF117144


title: M3_D_colon_rep1

description:
Library name: S1_C125
sample has been sequenced on 3 runs


title: Primary (MS234_005)


title: IGF113090 [AD ]

description: Library name: IGF113090


title: M1_D_colon_rep1

description:
Library name: S1_C029
sample has been sequenced on 3 runs


title: PA#06, Normal, scRNA-seq

description: 10x Genomics


title: IGF113097 [CNTRL ]

description: Library name: IGF113097

value: CNTRL


title: Primary (MS234_018)


title: PA#05, PBMC, scRNA-seq

description: 10x Genomics


title: IGF117141 [AD ]

description: Library name: IGF117141


title: IGF117116 [AD ]

description: Library name: IGF117116


title: M5_C_colon_rep3

description:
Library name: S1_C129
sample has been sequenced on 3 runs

value: TXlab


title: M4_C_colon_rep3

description:
Library name: S1_C081
sample has been sequenced on 3 runs


title: PA#06, Tumor, scRNA-seq

description: 10x Genomics


title: Primary (MS234_011)


title: PA#05, Tumor, scRNA-seq

description: 10x Genomics


title: M5_D_colon_rep2

description:
Library name: S1_C173
sample has been sequenced on 3 runs


title: PA#07, PBMC, scRNA-seq

description: 10x Genomics


title: IGF113099 [CNTRL ]

description: Library name: IGF113099


title: M3_C_colon_rep3

description:
Library name: S1_C033
sample has been sequenced on 3 runs


title: Primary (MS234_040)

description: Single-cell of oocyte, primary follicle, fresh adult mouse ovary,7wBDF1


title: M5_D_colon_rep1

description:
Library name: S1_C321
sample has been sequenced on 3 runs


title: M2_C_colon_rep3

description:
Library name: S1_C367
sample has been sequenced on 3 runs


title: PA#04, Tumor, scRNA-seq

description: 10x Genomics


title: Primary (MS234_046)


title: IGF117125 [AD ]

description: Library name: IGF117125


title: PA#04, Normal, scRNA-seq

description: 10x Genomics


title: IGF117123 [AD ]

description: Library name: IGF117123


title: Primary (MS234_038)


title: M1_C_colon_rep3

description:
Library name: S1_C319
sample has been sequenced on 3 runs


title: Primary (MS234_044)


title: M5_C_colon_rep2

description:
Library name: S1_C315
sample has been sequenced on 3 runs


title: IGF117135 [AD ]

description: Library name: IGF117135


title: IGF117139 [CNTRL ]

description: Library name: IGF117139


title: Primary (MS234_042)


title: PA#24, Tumor, snRNA

description: 10x Genomics

data_processing:
Preprocessing of raw data was initially performed using Cell Ranger software pipeline (version 7.1.0). This step included demultiplexing of raw base call (BCL) files into FASTQ files, reads alignment on human genome assembly GRCh38 using STAR, counting of unique molecular identifier (UMI) and generating a digital gene-cell matrix.
Assembly: GRCh38
Supplementary files format and content: sn_barcodes.tsv.gz: list of cell barcodes
Supplementary files format and content: sn_features.tsv.gz: list of gene IDs
Supplementary files format and content: sn_matrix.mtx.gz: gene expression count data in Matrix Market Exchange format
Supplementary files format and content: sn_metadata.csv:  metadata in csv format

extract_protocol:
Tumors and adjacent normal tissues were cut into approximately 1 mm3 pieces and enzymatically digested with MACS Tumour Dissociation Kit (Miltenyi Biotec,130-095-929) for 40 minutes (for normal tissues) or 1 hour (for tumor tissues) on the gentleMACS™ Octo Dissociator with Heaters, following the manufacturer’s instruction. The dissociated cells were subsequently passed through a 70-μm cell-strainer (BD Bioscience, 352350) to remove debris and centrifuged at 450g for 10 min. Pelleted cells were resuspended in sorting buffer (Miltenyi Biotec, 130-091-221) and stained with FITC Mouse Anti-Human CD45 (BD Bioscience,555482) and APC anti-human CD235a (Biolegend,349114). DAPI (BD Bioscience,564907) was added to the cell suspension immediately before FACS. CD235-DAPI- live cells were FACS-sorted for single-cell RNA-sequencing.
Nuclei library was constructed using the Chromium Fixed RNA Profiling Reagent Kits for multiplex samples (10xGenomics，CG000527). 8,000–10,000 nuclei per sample were loaded for probe hybridization for 20 hours’ incubation. Then the samples were washed as a pool. Single nuclei were obtained using Chromium Next GEM Chip Q running on the Chromium X/iX. GEM recovery, pre-amplification PCR, sample index PCR were performed according to manufacturer’s instructions. The library was sequenced on the NovaSeq 6000 with a 150 bp paired-end run.


title: IGF117136 [AD ]

description: Library name: IGF117136


title: IGF117137 [AD ]

description: Library name: IGF117137


title: PA#29, Tumor, snRNA

description: 10x Genomics


title: Primordial granulosa (MS234_035)

description: Single-cell of 10-20 granulosa cells, primordial follicle, fresh adult mouse ovary,7wBDF1


title: M2_C_colon_rep2

description:
Library name: S1_C171
sample has been sequenced on 3 runs


title: M3_C_colon_rep2

description:
Library name: S1_C219
sample has been sequenced on 3 runs


title: Primordial granulosa (MS234_084)

description: Single-cell of 10-20 granulosa cells, primordial follicle, fresh adult mouse ovary,6wBDF1


title: PA#91, Tumor, snRNA

description: 10x Genomics


title: PA#72, Tumor, snRNA

description: 10x Genomics


title: Primordial granulosa (MS234_030)


title: IGF113086 [AD ]

description: Library name: IGF113086


title: Primordial granulosa (MS234_074)


title: IGF117138 [AD ]

description: Library name: IGF117138


title: Primary (MS234_007)


title: PA#98, Tumor, snRNA

description: 10x Genomics


title: M5_B_colon_rep3

description:
Library name: S1_C271
sample has been sequenced on 3 runs

value: TXwildlings


title: IGF117114 [AD ]

description: Library name: IGF117114


title: M4_B_colon_rep3

description:
Library name: S1_C223
sample has been sequenced on 3 runs


title: PA#02, Tumor, scRNA-seq

description: 10x Genomics


title: PA#01, Tumor, scRNA-seq

description: 10x Genomics


title: Primordial granulosa (MS234_077)


title: M4_C_colon_rep2

description:
Library name: S1_C267
sample has been sequenced on 3 runs


title: IGF113081 [AD ]

description: Library name: IGF113081


title: M3_B_colon_rep3

description:
Library name: S1_C175
sample has been sequenced on 3 runs


title: PA#21, Tumor, snRNA

description: 10x Genomics


title: Primordial (MS234_029)

description: Single-cell of oocyte, primordial follicle, fresh adult mouse ovary,7wBDF1


title: PA#40, Tumor, snRNA

description: 10x Genomics


title: IGF113083 [CNTRL ]

description: Library name: IGF113083


title: M2_B_colon_rep3

description:
Library name: S1_C127
sample has been sequenced on 3 runs


title: Primordial (MS234_073)

description: Single-cell of oocyte, primordial follicle, fresh adult mouse ovary,6wBDF1


title: M1_B_colon_rep3

description:
Library name: S1_C079
sample has been sequenced on 3 runs


title: M1_C_colon_rep2

description:
Library name: S1_C123
sample has been sequenced on 3 runs


title: IGF117109 [AD ]

description: Library name: IGF117109


title: Primordial granulosa (MS234_080)


title: IGF113096 [CNTRL ]

description: Library name: IGF113096


title: M5_B_colon_rep2

description:
Library name: S1_C075
sample has been sequenced on 3 runs


title: IGF117101 [AD ]

description: Library name: IGF117101


title: M2_B_colon_rep2

description:
Library name: S1_C313
sample has been sequenced on 3 runs


title: M1_B_colon_rep2

description:
Library name: S1_C265
sample has been sequenced on 3 runs


title: Primordial (MS234_079)


title: Primordial (MS234_082)


title: Primordial (MS234_081)


title: PA#85, Tumor, snRNA

description: 10x Genomics


title: PA#47, CytAssist, low

description: 10x Genomics

data_processing:
We preprocessed the sequencing outputs for all Visium datasets using Space Ranger and mapped them to the latest human reference genome. The demultiplexed FASTQ files and corresponding H&E images for each sample were processed using the 'count' command in Space Ranger, with default parameters and reoriented images. This step generated an unfiltered feature-barcode matrix using the prebuilt GRCh38 genome reference 2020-A (GRCh38).
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5: filtered feature-barcode matrix in h5 format
Supplementary files format and content: spatial.tar: image and imformation output by Space Ranger
Library strategy: Spatial Transcriptomics

source_name: PDAC

extract_protocol:
For fresh tissue specimen, Optimal cutting temperature (OCT)-embedded tissues were cryo-sectioned at 10-μm and placed on the 6.5 x 6.5 mm capture area of Visium Spatial Gene Expression Slide following Visium Spatial Protocols-Tissue Preparation Guide (10x Genomics, CG00039 Rev D). Sections were fixed in methanol, stained with H&E and imaged at ×20 magnification. For FFPE samples, 4 x 10-μm FFPE sections were collected for RNA extraction by RNeasy FFPE Kit (Qiagen,73504). DV200 of the yielded RNA was evaluated using Agilent RNA 6000 Pico Kit. Samples with DV200＞50% were selected for sectioning, deparafinization and HE staining on the Visium Spatial Slide with 6.5 x 6.5 mm capture area. To capture area of interest, FFPE samples were selected for Visium CytAssist, which facilitates the transfer of transcriptomic probes from standard glass slides to Visium slides, enabling whole transcriptomic spatial profiling. Briefly, archived slides were stained by H&E and imaged at ×20 magnification. Representative regions with at least 2 nerves in a 6.5x 6.5 mm area were selected by appropriate configuration that allows the tissue slide gasket to encompass the region of interest. Then the coverslips were removed and the slides were destained by 0.1N HCl and decrosslinked by Diluted Decrosslinking Buffer at 95°C for 1 h.
For fresh tissue specimen, Tissues were then permeabilized for 12 min and cDNA libraries were constructed following Visium Spatial Gene Expression Reagent Kits User Guide. Libraries were sequenced on the NovaSeq-6000 system. For FFPE samples, Probe hybridization, probe ligation, probe release & extension, and library construction were conducted following the Visium Spatial Gene Expression Reagent Kit for FFPE User Guide (10x Genomics, CG000407 Rev A). FFPE samples for Visium CytAssist, Probe hybridization and probe ligation were processed according to the user guide (10x Genomics, CG000495, RevA). Then the hybridized probes were released and transfer to a Visium CytAssist Spatial Gene Expression Slide. After transfer, probes were extended, eluted, and pre-amplified. Then Sample Index PCR was applied to construct the cDNA library. The libraries were sequenced on the NovaSeq-6000 system.

value: PDAC


title: PA#72, CytAssist, low

description: 10x Genomics


title: M4_B_colon_rep1

description:
Library name: S1_C027
sample has been sequenced on 3 runs


title: PA#40, CytAssist, high

description: 10x Genomics


title: IGF117103 [AD ]

description: Library name: IGF117103


title: IGF113852 [AD ]

description: Library name: IGF113852


title: Primordial (MS234_078)


title: PA#29, CytAssist, high

description: 10x Genomics


title: M3_B_colon_rep1

description:
Library name: S1_C361
sample has been sequenced on 3 runs


title: IGF113854 [AD ]

description: Library name: IGF113854


title: Primordial (MS234_076)


title: PA#98, CytAssist, high

description: 10x Genomics


title: Primordial (MS234_083)


title: Primordial (MS252_215)


title: PA#24, CytAssist, low

description: 10x Genomics


title: PA#85, CytAssist, high

description: 10x Genomics


title: IGF117127 [AD ]

description: Library name: IGF117127


title: IGF117120 [CNTRL ]

description: Library name: IGF117120


title: M4_A_colon_rep3

description:
Library name: S1_C365
sample has been sequenced on 3 runs


title: PA#22, CytAssist, low

description: 10x Genomics


title: intestine_caMKK6_Dox_GFP_3

data_processing:
The sequenced reads were mapped to the mm10 mouse reference genome and reporter sequences (mCherry, EGFP, Xenopus MEK1SDSE and human MKK6EE) using STAR v.2. 6.0.c with the GENCODE vM25 annotation gtf file after trimming adaptor sequences and low-quality bases with cutadapt-1.12. The uniquely mapped reads were summarized at the gene level using HTSeqcount v.0.11.2, with the GENCODE vM25 annotation file.
Expression values were calculated as FPKM.
Assembly: mm10
Supplementary files format and content: tsv file include raw counts or FPKM values

growth_protocol: MEF; Embryos were harvested at E13.5, and MEFs were derived from the eviscerated and decapitated embryos with 0.25% trypsin. MEFs were maintained in high glucose DMEM (Nacalai Tesque) supplemented with 2 mM L-glutamine (Nacalai Tesque), 1× NEAA (Nacalai Tesque), 100 U/mL penicillin, 100 μg/mL streptomycin (Nacalai Tesque), 10% foetal bovine serum (Gibco), and 0.11 mM mercaptoethanol. MEFs were plated into 12-well culture plates at a density of 2 × 104 cells/well. Dox was added at a concentration of 2 μg/mL. Passages were performed every three or four days for MEFs not treated with Dox.

extract_protocol:
Hepatocyte;The liver was perfused with EGTA solution (calcium-free Hank’s balanced salt solution (HBSS) (Wako) containing 0.5 mM EGTA (Sigma) and 10 mM HEPES (Nacalai Tesque)), followed by a second perfusion with HBSS containing collagenase D (SIGMA) for bulk RNA-seq or Liberase TM Research Grade (Roche) for scRNA-seq and 10 mM HEPES. After passage through a 70 µm cell strainer, the cells were centrifuged at 50 g for 2 minutes three times to enrich for hepatocytes.  Colonic epithelial cells; The colon was dissected, cut open longitudinally and rinsed with ice-cold HBSS three times. The total colon without the caecum was used. The tissue was incubated for 30 min at 37 °C in isolation buffer (HBSS containing 10 mM HEPES (Nacalai Tesque), 5 mM EDTA (GIBCO) and 1 mM DTT (Sigma)) and then shaken vigorously for 30 sec to separate the crypt from the stromal tissues. After passage through a 70 µm cell strainer, the crypt suspension was centrifuged at 800 rpm for 3 min. The supernatant was decanted, and the crypt pellet was subsequently resuspended in 0.25% trypsin/1 mM EDTA and incubated for 15 min at 37 °C. The cell suspension was centrifuged at 3000 rpm for 5 min. Dissociated hepatocytes and crypt cells were passed through a 40 µm cell strainer and sorted with a FACSAria II (BD Bioscience) machine using a 130 µm nozzle. Dead cells were gated out by DAPI incorporation (100 ng/mL for crypt cells and 500 ng/mL for hepatocytes). To enrich for hepatocytes, we used 2 FSC-neutral density (ND) filters and 10-SSC ND filters. Ccells were sorted into RNAprotect Cell Reagent (QIAGEN) and stored at -80 °C until RNA extraction.
Total RNA was extracted using the RNeasy plus Mini or Micro Kit (QIAGEN) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop instrument (Thermo Scientific). Total RNA (in vitro sample; 100 ng, FACS-sorted samples; 50 ng) was prepared for library construction. High-quality RNA samples (RNA Integrity Number value > 8, as determined by Bioanalyzer) were used for library construction. RNA-seq libraries were generated using the NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEB). The number of PCR cycles was minimized to avoid skewing the representation of the libraries. RNA-seq libraries were sequenced on a NextSeq 500 (Illumina) as 76-bp single-end reads.

treatment_protocol: Doxycycline (Sigma) was dissolved in drinking water at 0.2 mg/mL for caMEK1 mice and 2 mg/ml for caMKK6 and control mice; the drinking water was also supplemented with 10 mg/mL sucrose (Nacalai Tesque).

value: male

value: Dox

value: Day 7


title: M3_A_colon_rep3

description:
Library name: S1_C317
sample has been sequenced on 3 runs


title: intestine_caMKK6_Dox_GFP_2


title: IGF117100 [AD ]

description: Library name: IGF117100


title: PA#12, CytAssist, low

description: 10x Genomics


title: PA#21, CytAssist, high

description: 10x Genomics


title: IGF113082 [AD ]

description: Library name: IGF113082


title: intestine_caMKK6_Dox_GFP_1


title: M2_A_colon_rep3

description:
Library name: S1_C269
sample has been sequenced on 3 runs


title: IGF117104 [AD ]

description: Library name: IGF117104


title: M1_A_colon_rep3

description:
Library name: S1_C221
sample has been sequenced on 3 runs


title: intestine_caMKK6_Dox_mCherry_2


title: PA#11_2, CytAssist, high

description: 10x Genomics


title: M5_A_colon_rep2

description:
Library name: S1_C217
sample has been sequenced on 3 runs


title: IGF113089 [AD ]

description: Library name: IGF113089


title: intestine_caMKK6_Dox_mCherry_3


title: IGF117128 [CNTRL ]

description: Library name: IGF117128


title: PA#11_1, FF, high

description: 10x Genomics


title: intestine_caMKK6_Dox_mCherry_1


title: M5_A_colon_rep3

description:
Library name: S1_C031
sample has been sequenced on 3 runs


title: M4_A_colon_rep2

description:
Library name: S1_C169
sample has been sequenced on 3 runs


title: PA#08, FF, high

description: 10x Genomics


title: IGF113095 [AD ]

description: Library name: IGF113095


title: M3_A_colon_rep2

description:
Library name: S1_C121
sample has been sequenced on 3 runs


title: intestine_caMKK6_NoDox_GFP_3

value: No Dox


title: IGF117122 [AD ]

description: Library name: IGF117122


title: PA#06, FFPE, high

description: 10x Genomics


title: IGF117112 [CNTRL ]

description: Library name: IGF117112


title: M2_A_colon_rep2

description:
Library name: S1_C073
sample has been sequenced on 3 runs


title: PA#05_2, CytAssist, high

description: 10x Genomics


title: intestine_caMKK6_NoDox_GFP_2


title: M1_A_colon_rep2

description:
Library name: S1_C025
sample has been sequenced on 3 runs


title: intestine_caMKK6_NoDox_GFP_1


title: IGF117117 [AD ]

description: Library name: IGF117117


title: PA#04_2, FF, high

description: 10x Genomics


title: intestine_caMEK1_Dox_GFP_1


title: d6PGCLC, Rep3

description:
Library name: Sample 7
day 6 PGCLC, replicate 3

data_processing:
All reads were processed with Trim_Galore! v0.6.3 with default settings to remove adapter and low-quality sequences.  Processed reads were mapped on the mouse genome, GRCm38.p6, using Bismark v0.22.1 and bowtie2 v2.3.4.1 with the “-X 2000” option.  The resulting BAM files were then processed with the script deduplicate_bismark to remove PCR duplicates, and methylation levels per CpG were calculated using the bismark_methylation_extractor script included in the Bismark package. All four replicates of c0 samples were pooled and plotted as one c0 sample in figures, unless otherwise specified in figure legend.
Assembly: GRCm38.p6
Supplementary files format and content: bismark report text
Library strategy: EM-seq

extract_protocol:
Genomic DNAs were purified from 500 (c34 oocyte-like cells ≥ 60 μm in diameter) to 15,000 cells (c7 oogonia-like cells, c13 fetal oocyte-like cells) by using Nucleospin Tissue XS (Macherey-Nagel, 740901) and eluted in 10 μl elution buffer.  The DNA concentration was quantitated by using a Qubit dsDNA HS Assay Kit (Thermo Fisher, Q32854) and 20–140 ng of genomic DNAs were mixed with 1 pg of pUC19 DNA and 20 pg of unmethylated lambda DNA for a total volume of 50 μl.  The DNAs were then fragmented by sonication using an E220 focused-sonicator from Covaris (peak incident power: 140W; duty factor: 10%; cycles per burst: 200; and treatment time: 130 ms).  The fragmented DNA samples were purified by two rounds of Axygen beadspurification (0.7×volumes and then 0.9×volumes).
All fragments were applied to library construction using a NEBNext Enzymatic Methy-seq Kit (New England Biolabs, E7120) according to the manufacturer’s instructions.  Library concentrations and fragment sizes were evaluated with KAPA Library Quantification Kits (Nippon Genetics, KK4828) and a Labchip GX Touch HT nucleic acid analyzer (Perkin Elmer).  The sequencing was performed using an Illumina Novaseq sequencer (Illumina).

value: PGCLC


title: IGF117121 [AD ]

description: Library name: IGF117121


title: d6PGCLC, Rep2

description:
Library name: Sample 6
day 6 PGCLC, replicate 2


title: intestine_caMEK1_Dox_GFP_2


title: IGF117106 [CNTRL ]

description: Library name: IGF117106


title: PA#04_1, FFPE, high

description: 10x Genomics


title: intestine_caMEK1_Dox_mCherry_2


title: c0, d4 PGCLC, Rep.4

description:
Library name: Sample 4
day 4 PGCLC, replicate 4

value: day 0


title: PA#02, FF, high

description: 10x Genomics


title: IGF113088 [CNTRL ]

description: Library name: IGF113088


title: intestine_caMEK1_Dox_mCherry_1


title: PA#03, FF, high

description: 10x Genomics


title: c0, d4 PGCLC, Rep.3

description:
Library name: Sample 3
day 4 PGCLC, replicate 3


title: intestine_caMEK1_NoDox_GFP_3


title: IGF117124 [AD ]

description: Library name: IGF117124


title: PA#01, FFPE, high

description: 10x Genomics


title: IGF113084 [CNTRL ]

description: Library name: IGF113084


title: c0, d4 PGCLC, Rep.2

description:
Library name: Sample 2
day 4 PGCLC, replicate 2


title: IGF113087 [CNTRL ]

description: Library name: IGF113087


title: intestine_caMEK1_NoDox_GFP_2


title: IGF113855 [AD ]

description: Library name: IGF113855


title: c34 (bulk)

description:
Library name: Sample 1
d4c34 oogonia-like cells, bulk sample

value: day 34


title: intestine_caMEK1_NoDox_GFP_1


title: PA#05_1, FFPE, high

description: 10x Genomics


title: UHRF1-AID/DNMT1-AID_RNAseq_Day8_Rep2

city: Paris

first: Pierre-Antoine

last: Defossez

address: 35 rue Hélène Brion

country: France

institute: Epigenetics and Cell Fate Unit

data_processing:
RNA-Seq reads were processed using STAR. https://github.com/alexdobin/STAR.
read counts from featureCounts.
Assembly: hg38
Supplementary files format and content: read counts

source_name: Colon

growth_protocol: HCT116 cells were maintained in McCoy’s 5A medium with L-glutamine supplemented with 10% FBS and 1% Penicillin/Streptomycin.

extract_protocol:
Total RNA was isolated using the RNAeasy Plus Mini Kit (Qiagen) according to the manufacturer's protocol.
The library preparation for RNA-seq was performed by Novogene company. mRNA-seq libraries were prepared by NEB Next® Ultra™ RNA Library Prep Kit.

treatment_protocol: To facilitate the auxin treatment, HCT116 cells were cultured in a medium supplemented with 2 μg/mL doxycycline and 20 μM auxinole for a duration of one day. Subsequently, the cells were maintained in a medium containing 2 μg/mL doxycycline and 500 μM auxin. During the course of the auxin treatment, the medium was refreshed every two days to ensure a consistent concentration of doxycycline and auxin throughout the experimental period.

value: Colon

value: Colorectal cancer cell

value: Auxin treatment for 8 days


title: UHRF1-AID/DNMT1-AID_RNAseq_Day8_Rep3


title: IGF117107 [AD ]

description: Library name: IGF117107

value: Brain


title: intestine_Control_Dox_GFP_2

value: colon

value: Control


title: NaOH injured AAV-shRNA-Ifitm1-2

city: Chicago

first: Han

last: Peng

state: IL

address: 303 E Chicago Ave, Ward 9-120

country: USA

institute: Feinberg School of Medicine, Northwestern University

data_processing:
follow the protocol from 10X genomics
Assembly: GRCm38.91
Supplementary files format and content: matrix file

source_name: cornea/limbus

extract_protocol:
Whole eyes were harvested. The lens, retina, iris, and trabecular network were removed leaving the entire ocular anterior segment, from which most of the conjunctiva was carefully dissected and discarded. Dissect corneas with ice cold PBS and put corneas into one Eppendorf tube filled with 0.7mg/mL liberase TM (from Roche) in RPMI.  Place tube in 37 degree incubator with 5% CO2 for 1 hour. Then add 500ul 0.25%Trypsin for 15min. Use 40um filter into Eppendorf tube. Cell viability was checked and accepted with at least an 80% viability score. Such cells were processed for scRNA-seq using 10XGenomics pipeline in the Northwestern University NUseq Core.
follow the instructions from 10XGenomics

value: cornea/limbus

value: wt

value: NaOH injured AAV-shRNA-Ifitm1


title: d6PGCLC, Rep1

description:
Library name: Sample 5
day 6 PGCLC, replicate 1


title: UHRF1-AID/DNMT1-AID_RNAseq_Day8_Rep1


title: DNMT1-AID_RNAseq_Day8_Rep3


title: NaOH injured AAV-EV2

value: NaOH injured AAV-EV


title: intestine_Control_Dox_GFP_1

value: male


title: DNMT1-AID_RNAseq_Day8_Rep2


title: IGF113851 [CNTRL ]

description: Library name: IGF113851

value: CNTRL


title: IGF113080 [CNTRL ]

description: Library name: IGF113080

value: CV


title: intestine_Control_Dox_mCherry_2

value: Dox

value: Day 7


title: intestine_Control_Dox_mCherry_1


title: uninjured wild type2

value: uninjured


title: DNMT1-AID_RNAseq_Day8_Rep1


title: uninjured wild type1


title: NaOH injured AAV-shRNA-Ifitm1


title: IGF113856 [CNTRL ]

description: Library name: IGF113856


title: intestine_Control_NoDox_GFP_3

value: No Dox


title: NaOH injured AAV-EV1


title: UHRF1-AID_RNAseq_Day8_Rep2

value: Colon


title: intestine_Control_NoDox_GFP_2


title: IGF113079 [CNTRL ]

description: Library name: IGF113079


title: ABDE3 TSCs, 48h dTAG-13 treatment 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 reads were aligned against the GRCm38/mm10 genome using STAR RNA-seq aligner package, with default parameters and –outSAMtype BAM SortedByCoordinate.
BAM file primary alignments with mapping quality of >254 were treated as RNA-seq data and imported into SeqMonk 1.48.0.
RNA-seq quantitation pipeline using DESeq2 was used to identify significantly differentially expressed genes (P<0.05).
Assembly: GRCm38/mm10
Supplementary files format and content: raw-counts.txt

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

extract_protocol:
Total RNA was harvested using a Quick-RNA MicroPrep kit (Zymo) per the manufacturer’s instructions.
Library preparation was carried out using NEBNext rRNA Depletion Kit (Human/Mouse/Rat) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).

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: intestine_Control_NoDox_GFP_1


title: UHRF1-AID_RNAseq_Day8_Rep1

value: Colorectal cancer cell

value: Auxin treatment for 8 days


title: IGF113853 [AD ]

description: Library name: IGF113853

value: Brain

value: AD


title: IGF113085 [AD ]

description: Library name: IGF113085


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


title: WT_RNAseq_Day8_Rep3

value: WT


title: Entinostat 0.5uM, H3K27ac, rep2

city: Columbus

first: Benjamin

middle: Z.

last: Stanton

state: OH

address: 575 Children's Crossroad

department: Center for Childhood Cancer Research

institute: Nationwide Children's Hospital

description:
H3K27ac-Entinostat_2_no-downsampling.bigWig
H3K27ac-Entinostat_2_PC.bigWig

data_processing:
All fastq files were processed an analyzed using our free, publcly available PerCell ChIP-seq bioinformatic pipeline.
Adapter trimming: Reads were trimmed of their adapter sequences using TrimGalore v.0.6.7
Alignment: Bowtie2 (v2.4.4) was used to align reads separately to hg38 and mm39 genomes, with parameters '-F 2308 -q 30'
Filtering: Reads in blacklisted regions were removed using Samtools (v.1.16.1), and duplicate reads marked and removed using Picard (v.2.27.1)
Scale factor calculation: Primary mapped reads were counted for each sample's alignment to the spike-in mm39 genome using Samtools (v.1.16.1) and used to calculate scaling factors by dividing each sample's number of (properly aligned) spike-in reads by the minimum number of any sample's spike-in reads.
Downsampling: For PerCell normalized files only, reads properly aligned to the experimental hg38 genome were downsampled using the scale factors and Satools (v.1.16.1) with parameters '-f 1 --subsample ${scaling_factor}'
Bigwig generation: Bedgraphs were compiled for inputs and corresponding ChIP samples using a custom MACS2 script (v.2.2.9.1) used to avoid MACS2’s default callpeak command normalizing based on library size from obscuring our own normalization (based on spike-in). Bedgraphs forChIPs were compard for enrichment vs. corresponding inputs using MACS2's bdgcmp command, with the 'ppois' method. Bedgraphs were converted into bigWig files using UCSC's bedGraphToBigWig tool (v445)
Synthetic fastq files with set percentages of aligned spike-in reads were created by subsampling reads properly aligned to the spike-in mm39 genome using Samtools (v.1.16.1) to retain 25%, 50%, and 75% of spike-in reads. These reads were removed from the original fastq input and CTCF ChIP using BBMap (v.39.06) and its FilterByName tool.
Assembly: hg38 and mm39
Supplementary files format and content: bigWigs: Tracks represent ChIP signal for each sample vs. their corresponding inputs using MACS2's ppois method.

growth_protocol: Rh4 and C2C12 were grown in DMEM supplemented with 10% FBS

extract_protocol:
For spike-in normalized PerCell ChIP-seq, human Rh4 and mouse C2C12 cells were fixed in 1% formaldehyde for 10 minutes before quenching with 125 mM glycine. Cells were combined in a ratio of 3 human:1 mouse cells prior to sonication. Sonicated chromatin was immunoprecipitated with antibodies against H3K27ac (Active Motif #39133) or CTCF (CST #2899). Input and ChIP-enriched DNA was decrosslinked and purified using Qiagen MinElute PCR Purification columns prior to library preparation.
ChIP and Input DNA libraries were prepared by blunt end repair using the Lucigen End-It DNA End-Repair Kit, 3’ A-tailing by Klenow fragment (3’-5’ exo-) (NEB), adaptor ligation by T4 DNA ligase(NEB), and size selection on an E-Gel 2% EX agarose gel. Libraries were amplified with barcoded primers for 14 cycles and isolated from unreacted primers by gel purification. Libraries were sequenced on either the HiSeq4000 or NovaSeq6000 platforms, each running in PEx150bp mode.

tag: spike-in cell_line

value: rhabdomyosarcoma tumor

tag: chip antibody

value: H3K27ac (Active Motif #39133)

value: 3:1 Rh4(human):C2C12(mouse) spike-in cell ratio


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


title: liver_caMKK6_Dox_GFP_2

value: liver

value: male


title: liver_caMKK6_Dox_GFP_1

value: Dox


title: ABDE3 TSCs, 48h BRG1 inhibition 3


title: DMSO, H3K27ac, rep2

description:
H3K27ac-DMSO_2_no-downsampling.bigWig
H3K27ac-DMSO_2_PC.bigWig


title: WT_RNAseq_Day8_Rep1


title: UHRF1-AID_RNAseq_Day8_Rep3


title: UHRF1-AID/DNMT1-AID_RNAseq_Day6_Rep3

value: Auxin treatment for 6 days


title: liver_caMKK6_Dox_mCherry_2

value: Day 7


title: liver_caMKK6_NoDox_GFP_3

value: No Dox


title: ABDE3 TSCs, 48h BRG1 inhibition 2


title: WT_RNAseq_Day8_Rep2

value: Colon


title: ABDE3 TSCs, 48h BRG1 inhibition 1

value: Trophoblast stem cell


title: UHRF1-AID/DNMT1-AID_RNAseq_Day6_Rep2


title: A485 0.5uM, Input, rep2

description:
H3K27ac-A485_2_no-downsampling.bigWig
H3K27ac-A485_2_PC.bigWig


title: A485 0.5uM, H3K27ac, rep2


title: liver_caMKK6_Dox_mCherry_1


title: ABDE3 TSCs, 48h DMSO control 3

value: Eomesdeg/deg

value: DMSO control


title: liver_caMKK6_NoDox_GFP_2


title: ABDE3 TSCs, 48h DMSO control 2


title: liver_caMKK6_NoDox_GFP_1


title: DNMT1-AID_RNAseq_Day6_Rep3

value: Colorectal cancer cell


title: Entinostat 0.5uM, Input, rep2


title: UHRF1-AID/DNMT1-AID_RNAseq_Day6_Rep1


title: Entinostat 0.5uM, H3K27ac, rep1

description:
H3K27ac-Entinostat_1_no-downsampling.bigWig
H3K27ac-Entinostat_1_PC.bigWig


title: ABDE3 TSCs, 48h DMSO control 1


title: liver_caMEK1_Dox_GFP_3


title: DNMT1-AID_RNAseq_Day6_Rep2


title: A485 0.5uM, H3K27ac, rep1

description:
H3K27ac-A485_1_no-downsampling.bigWig
H3K27ac-A485_1_PC.bigWig


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


title: UHRF1-AID_RNAseq_Day6_Rep3


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


title: liver_caMEK1_Dox_GFP_1


title: DMSO, H3K27ac, rep1

description:
H3K27ac-DMSO_1_no-downsampling.bigWig
H3K27ac-DMSO_1_PC.bigWig


title: Entinostat 0.5uM, Input, rep1


title: A485 0.5uM, Input, rep1


title: liver_caMEK1_Dox_mCherry_3


title: UHRF1-AID_RNAseq_Day6_Rep2


title: ABDE3 TSCs, 24h BRG1 inhibition 3


title: liver_caMEK1_Dox_mCherry_2


title: ABDE3 TSCs, 24h BRG1 inhibition 2


title: UHRF1-AID_RNAseq_Day6_Rep1


title: liver_caMEK1_NoDox_GFP_3


title: liver_caMEK1_Dox_mCherry_1


title: WT_RNAseq_Day6_Rep2


title: DMSO, Input, rep2


title: WT_RNAseq_Day6_Rep1


title: WT_RNAseq_Day6_Rep3


title: ABDE3 TSCs, 24h DMSO control 3


title: ABDE3 TSCs, 24h BRG1 inhibition 1


title: ABDE3 TSCs, 24h DMSO control 2


title: ATAC-seq_U1AMO3

city: Boston

first: Ana

last: Fiszbein

state: MA

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

department: Biology

institute: Boston University

description: U1 AMO_replicate 3

data_processing:
Raw read pairs were trimmed to a length of 75bp to remove mapping bias towards the longer fragments, and adapter sequences and low-quality 3’ bases were removed using trimmomatic. Trimmed reads were aligned to the reference genome GRCh38.99 using STAR v2.7.9a. The resulting BAM files were merged and converted to bigwig files using a custom script.
Assembly: Ensembl reference genome GRCh38.99
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:
One million HeLa cells after AMO delivery were harvested and washed PBS. Cells were resuspended in 50 µL of lysis buffer (containing 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin in PBS) and incubated for 3 minutes. After incubation, 1 mL of wash buffer was added to the cell lysates. The mixture was then centrifuged at 500 x g for 10 minutes at 4°C. To prepare the transposition master mix, 5 µL of Tn5 transposase and 25 µL of Tagment DNA buffer (Illumina Tagment DNA Enzyme and Buffer Small Kit, 20034197) were combined with PBS containing 0.1% Tween-20 and 0.01% Digitonin. Subsequently, the lysate pellet was gently resuspended in the transposition master mix, and the mixture was incubated at 37°C for 30 minutes with shaking to facilitate DNA fragmentation. Immediately after transposition, DNA was purified using the Monarch PCR & DNA Cleanup Kit (New England Biolabs, #T1030) to eliminate excess transposase and unincorporated adapters.
PCR was performed for 15 cycles with indexing primer sets using Platinum SuperFi II Master Mix (Invitrogen, 12368010). To remove primer dimers and large fragments, a double-sided bead purification step was carried out using AMPure XP beads. Beads were applied at concentrations of 0.5X and 1.3X, as recommended by the manufacturer. The distribution of library fragment size was confirmed using Agilent 2100 Bioanalyzer System using High Sensitivity DNA Chips (Agilent Technologies, cat#5067-4626). Libraries were pooled and treated with Illumina free adapter blocking reagent (Illumina, #20024145).

value: HeLa

value: U1 AMO


title: ATAC-seq_U1AMO1

description: U1 AMO_replicate 1


title: liver_caMEK1_NoDox_GFP_1


title: liver_caMEK1_NoDox_GFP_2


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


title: DNMT1-AID_RNAseq_Day6_Rep1


title: UHRF1-AID/DNMT1-AID_RNAseq_Day2_Rep3

value: Auxin treatment for 2 days


title: liver_Control_Dox_GFP_2

value: Control


title: ATAC-seq_Ctrl2

description: Control AMO_replicate 2

value: Control AMO


title: UHRF1-AID/DNMT1-AID_RNAseq_Day2_Rep1


title: UHRF1-AID/DNMT1-AID_RNAseq_Day2_Rep2


title: ATAC-seq_Ctrl3

description: Control AMO_replicate 3


title: liver_caMEK1_Dox_GFP_2


title: ATAC-seq_Ctrl1

description: Control AMO_replicate 1


title: ABDE3 TSCs, 24h DMSO control 1


title: liver_Control_Dox_GFP_1


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


title: ATAC-seq_U1AMO2

description: U1 AMO_replicate 2


title: liver_Control_Dox_mCherry_2


title: DNMT1-AID_RNAseq_Day2_Rep2


title: ABDE3 TSCs, 12h BRG1 inhibition 3


title: DMSO, Input, rep1

value: rhabdomyosarcoma tumor

value: 3:1 Rh4(human):C2C12(mouse) spike-in cell ratio


title: DNMT1-AID_RNAseq_Day2_Rep1


title: liver_Control_Dox_mCherry_1

value: liver

value: male


title: CES32

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

state: PA

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh

description: Library name: A1795

data_processing:
Quality filtered and trimmed raw fastq files were aligned to the rat genome using STAR aligner (version 2.7.9a) and counted by Feature Counts (v.1.5.0-p3). Differential expression was performed using DESeq2 in R 4.2.0 and the resulting differentially expressed genes (DEGs) were determined using the design matrix of the different factors such as timepoints, condition and sex, at a defined cut-off criteria of |log2 fold-change|≥ 0.25 and p- value <0.1 adjusted using the Benjamini and Hochberg’s approach to control the false discovery rate. DEGs were subjected to REACTOME pathway analyses to determine the significantly enriched pathways. To extract further biological insight from the samples, we implemented gene set enrichment analysis (GSEA)which assesses the statistical enrichment of gene ontologies, and pathways, at a 5% significance, and data were visualized using Cluster profiler v4.8.1.
Assembly: mRatBN7.2
Supplementary files format and content: Count_Data.csv

organism: Rattus norvegicus

source_name: Bone

extract_protocol:
RNA was extracted using miRneasy mini kit (QIAgen) and quantified using Qubit Flurometer
Samples had RNA integrity numbers of 5.5 – 9.6. RNA was shipped to Novogene Co. Ltd. (USA) for library preparation and sequencing. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads and stranded mRNA-seq libraries were generated and individually barcoded using NEBNext® Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations.  Fragmentation was carried out using divalent cations under elevated temperature in NEB Next First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-) ring, the second-strand synthesis in the NEBNext Ultra II Directional RNA Library prep protocol, the reaction uses a buffer containing dUTP, which allows the incorporation of dUTP in place of dTTP. This process is facilitated by the NEBNext Second Strand Synthesis Reaction Buffer with dUTP mix and the NEBNext Second Strand Synthesis Enzyme Mix. The incorporation of dUTP is essential for strand specificity, as it renders the second-strand cDNA uracil-containing, making it susceptible to degradation during subsequent PCR steps. This selective degradation ensures that only the first-strand cDNA is amplified, preserving strand orientation in the final library. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. To select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index Primer and PCR products were purified (AMPure XP system). Library quality was assessed on the Agilent Bioanalyzer 2100 system and sequenced by NovaSeq6000 on an S4 flow cell (PE150 read length).

treatment_protocol:
Rats were housed in 12-hour light/dark conditions with ad libitum access to a standard rodent chow (Lab diets, Prolab RMH1800, St. Louis. MO) and water.  Timed pregnant Sprague-Dawley rats (Charles River, Wilmington, MA) were delivered to the vivarium on gestational day 18.  Dams delivered pups without intervention on PND 0. On PND 2, the dams were randomly transferred to cages containing a standard plexiglass cage with ample sawdust and 3 paper towels to use as nesting material (STD), or an impoverished cage (CES) which had limited sawdust which was inaccessible to the dam by a wire mesh platform which sat 2cm above the cage floor and one half of one paper towel was provided as nesting material (Figure 1). Pups were randomly distributed to dams until each litter contained 12 pups with equal male: female ratio. These cages then remained undisturbed for 7 days. On  PND 10, all litters were transferred to and maintained in standard cages until offspring were weaned on PND 21. On PND 10, 21 and 35, equal numbers of offspring were anesthetized with isoflurane and euthanized by decapitation. The bilateral tibia and lumbar vertebra were collected and stored at -80°C until analyses.
gene expression profiles of the lumbar vertebrae in male and female offspring at PND 10, 21, and 35 and comprehensively evaluated their bone health parameters

value: Bone

value: F

tag: time point

value: Sprague Dawley

value: CES


title: CES31

description: Library name: A1794


title: DNMT1-AID_RNAseq_Day2_Rep3

value: Colon


title: CES30

description: Library name: A1793


title: liver_Control_NoDox_GFP_2

value: No Dox


title: UHRF1-AID_RNAseq_Day2_Rep2


title: CES29

description: Library name: A1788


title: ABDE3 TSCs, 12h BRG1 inhibition 2

value: Trophoblast stem cell

value: Eomesdeg/deg


title: MEF_caMKK6_Dox_d7_3

source_name: MEF

value: MEF

value: Dox

value: Day 7


title: STD30

description: Library name: A1783

value: STD


title: ABDE3 TSCs, 12h DMSO control 2

value: DMSO control


title: MEF_caMKK6_Dox_d7_2


title: UHRF1-AID_RNAseq_Day2_Rep1

value: Colorectal cancer cell

value: Auxin treatment for 2 days


title: UHRF1-AID_RNAseq_Day2_Rep3


title: liver_Control_NoDox_GFP_1

value: liver

value: Control


title: ABDE3 TSCs, 12h BRG1 inhibition 1


title: STD29

description: Library name: A1782

value: Bone


title: STD28

description: Library name: A1781

value: M


title: ABDE3 TSCs, 12h DMSO control 1


title: WT_RNAseq_Day2_Rep3

value: WT


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


title: liver_Control_NoDox_GFP_3

value: male


title: WT_RNAseq_Day2_Rep2

value: Colon


title: MEF_caMKK6_Dox_d7_1


title: ABDE3 TSCs, 6h dTAG-13 treatment 3


title: CES28

description: Library name: A1771

value: F

value: Sprague Dawley

value: CES


title: MEF_caMKK6_Dox_d4_2

value: MEF

value: Day 4


title: CES27

description: Library name: A1770


title: CTCF ChIP, 25% spike-in retained

description:
CTCF_RH4_25_1_no-downsampling.bigWig
CTCF_RH4_25_1_PC.bigWig

value: rhabdomyosarcoma tumor

value: CTCF (CST #2899)

value: 3:1 Rh4(human):C2C12(mouse) spike-in cell ratio


title: WT_RNAseq_Day2_Rep1

value: Colorectal cancer cell


title: ABDE3 TSCs, 12h DMSO control 3

value: Trophoblast stem cell

value: Eomesdeg/deg

value: DMSO control


title: ABDE3 TSCs, 6h dTAG-13 treatment 2


title: CES26

description: Library name: A1769

value: Bone


title: ABDE3 TSCs, 6h dTAG-13 treatment 1


title: MEF_caMKK6_Dox_d4_3

value: Dox


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


title: MEF_caMKK6_Dox_d4_1


title: CTCF Input, 25% spike-in retained


title: STD27

description: Library name: A1759

value: STD


title: CTCF ChIP, 50% spike-in retained

description:
CTCF_RH4_50_1_no-downsampling.bigWig
CTCF_RH4_50_1_PC.bigWig


title: STD26

description: Library name: A1758


title: ABDE3 TSCs, 6h BRG1 inhibition 3


title: ABDE3 TSCs, 6h BRG1 inhibition 2


title: MEF_caMKK6_Dox_d2_2

value: male

value: Day 2


title: STD25

description: Library name: A1757

value: F


title: CTCF Input, 50% spike-in retained


title: MEF_caMKK6_Dox_d2_1


title: CES25

description: Library name: A1747

value: Sprague Dawley


title: CTCF ChIP, 75% spike-in retained

description:
CTCF_RH4_75_1_no-downsampling.bigWig
CTCF_RH4_75_1_PC.bigWig


title: ABDE3 TSCs, 6h DMSO control 3


title: ABDE3 TSCs, 6h BRG1 inhibition 1


title: MEF_caMKK6_NoDox_d2_3

value: No Dox


title: CES24

description: Library name: A1746

value: CES


title: ABDE3 TSCs, 6h DMSO control 2


title: CTCF ChIP, original

description:
CTCF_RH4_100_no-downsampling.bigWig
CTCF_RH4_100_PC.bigWig


title: MEF_caMKK6_NoDox_d2_2

value: MEF


title: ABDE3 TSCs, 6h DMSO control 1


title: CTCF Input, original

value: rhabdomyosarcoma tumor


title: MEF_caMKK6_NoDox_d2_1


title: ABDE3 TSCs, 1h BRG1 inhibition 3


title: STD24

description: Library name: A1735


title: MEF_caMEK1_Dox_d7_3

value: Day 7


title: STD23

description: Library name: A1734


title: ChIP-seq_D2_IgG_rep2

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

description: ChIP-seq

data_processing:
BLIMP-1 ChIP-seq raw reads were processed into BEDPE and bigWig files as described previously (Cao et al., 2023). Replicates were combined for peak calling using cLoops2's callPeaks module (Cao et al., 2022) with parameters -eps 150 and -minPts 10 against the IgG control. Only overlapped peaks from both donors and both BLIMP-1 antibodies are used for the following analysis. Peak targets and distance to nearest gene transcription start sites were obtained with anoPeaks.py script from the cLoops2 package, and target genes Gene Ontology (GO) terms enrichment analysis was performed by findGO.pl in the HOMER package (Heinz et al., 2010), requiring more than ten overlapping genes in the terms, and there are fewer than 1000 genes in the terms as same as previous study (Cao et al., 2023; Cui et al., 2023).  Motif analysis was performed by findMotifsGenome.pl in the HOMER package. Genome-browser like images were presented by the cLoops2 plot module.
Assembly: hg38
Supplementary files format and content: BIGWIG files for ChIP-seq signals.

source_name: Buffy coats

extract_protocol:
For ChIP-seq, genomic DNA was purified with QIAGEN MinElute Reaction Cleanup Kit.
ChIP DNA were end-repaired using an End-It DNA End-Repair kit (Epicentre), universal adaptors were then ligated. The libraries were amplified using indexed primers with the PCR condition: 98°C, 10”; 67°C, 30”; 72°C, 30” for 16 cycles. The fragments between 180bp to 350bp were isolated on E-gel and subjected to sequencing on Illumina HiSeq2500.

value: Buffy coats

value: Tregs

value: Healthy donors

value: Tregs were stimulated with anti-CD3 and anti-CD28 and expanded in the presence of IL-2 for ChIP-seq


title: ABDE3 TSCs, 1h BRG1 inhibition 2

value: Trophoblast stem cell

value: Eomesdeg/deg


title: MEF_caMEK1_Dox_d7_2

value: Dox


title: ABDE3 TSCs, 1h BRG1 inhibition 1


title: MEF_caMKK6_Dox_d2_3


title: ChIP-seq_D2_IgG_rep1

description: ChIP-seq


title: ChIP-seq_D2_Blimp-1_MA5_rep2

description: ChIP-seq


title: MEF_caMEK1_Dox_d4_3

value: Day 4


title: ABDE3 TSCs, 1h DMSO control 3

value: DMSO control


title: STD20

description: Library name: A1722

value: Bone

value: STD


title: ChIP-seq_D2_Blimp-1_MA5_rep1

description: ChIP-seq


title: CTCF Input, 75% spike-in retained

value: 3:1 Rh4(human):C2C12(mouse) spike-in cell ratio


title: MEF_caMEK1_Dox_d4_2

value: male


title: STD22

description: Library name: A1733

value: F

value: Sprague Dawley


title: ABDE3 TSCs, 1h DMSO control 2


title: STD19

description: Library name: A1721

value: M


title: STD21

description: Library name: A1723


title: ChIP-seq_D2_Blimp-1_9115S_rep2

description: ChIP-seq


title: ABDE3 TSCs, 1h DMSO control 1


title: CES23

description: Library name: A1745

value: CES


title: MEF_caMEK1_Dox_d4_1

value: MEF


title: ChIP-seq_D2_Blimp-1_9115S_rep1

description: ChIP-seq

value: Buffy coats

value: Tregs


title: CES22

description: Library name: A1711


title: MEF_caMEK1_Dox_d2_3

value: Day 2


title: ABDE3 TSCs, untreated 3

value: Trophoblast stem cell

value: Untreated


title: CES21

description: Library name: A1710


title: ABDE3 TSCs, untreated 2

value: Eomesdeg/deg


title: ChIP-seq_D1_IgG_rep2

description: ChIP-seq

value: Healthy donors

value: Tregs were stimulated with anti-CD3 and anti-CD28 and expanded in the presence of IL-2 for ChIP-seq


title: MEF_caMEK1_Dox_d2_2

value: Dox


title: MEF_caMEK1_Dox_d7_1

value: Day 7


title: ChIP-seq_D1_IgG_rep1

description: ChIP-seq


title: CES19

description: Library name: A1787

value: Bone


title: ChIP-seq_D1_Blimp-1_MA5_rep2

description: ChIP-seq


title: MEF_caMEK1_NoDox_d2_3

value: male

value: No Dox


title: STD18

description: Library name: A1776

value: F

value: Sprague Dawley

value: STD


title: ChIP-seq_D1_Blimp-1_MA5_rep1

description: ChIP-seq


title: uninjured wild type

data_processing:
follow the protocol from 10X genomics
Assembly: GRCm38.91
Supplementary files format and content: matrix file
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx

extract_protocol:
Whole eyes were harvested . The lens, retina, iris, and trabecular network were removed leaving the entire ocular anterior segment, from which most of the conjunctiva was carefully dissected and discarded. Dissect corneas with ice cold PBS and put corneas into one Eppendorf tube filled with 0.7mg/mL liberase TM (from Roche) in RPMI.  Place tube in 37 degree incubator with 5% CO2 for 1 hour. Then add 500ul 0.25%Trypsin for 15min. Use 40um filter into Eppendorf tube. Cell viability was checked and accepted with at least an 80% viability score. Such cells were processed for scRNA-seq using 10XGenomics pipeline in the Northwestern University NUseq Core.
follow the instructions from 10XGenomics

value: cornea/limbus

value: wt

value: control


title: NaOH injured wild type

value: NaOH injury


title: MEF_caMEK1_NoDox_d2_2

value: MEF

value: Day 2


title: STD17

description: Library name: A1775

value: M


title: ChIP-seq_D1_Blimp-1_9115S_rep2

description: ChIP-seq

value: Buffy coats

value: Tregs

value: Healthy donors


title: c34

description: d4c34 oogonia-like cells

data_processing:
All reads were processed with Trim_Galore! v0.6.3 with default settings to remove adapter and low-quality sequences.  Processed reads were mapped on the mouse genome, GRCm38.p6, using Bismark v0.22.1 and bowtie2 v2.3.4.1 with the “-X 2000” option.  The resulting BAM files were then processed with the script deduplicate_bismark to remove PCR duplicates, and methylation levels per CpG were calculated using the bismark_methylation_extractor script included in the Bismark package.
Assembly: GRCm38.p6
Supplementary files format and content: biskark report text

value: Oocyte-like cell

value: ovarian soma-free culture

value: day 34


title: ChIP-seq_D1_Blimp-1_9115S_rep1

description: ChIP-seq

value: Tregs were stimulated with anti-CD3 and anti-CD28 and expanded in the presence of IL-2 for ChIP-seq


title: c13

description: d4c13 oogonia-like cells

value: day 13