title: mGCcKO_HMD201207003_BA10


title: mGCcKO_HMD201207003_CD01

status: Public on Oct 01 2024

type: SRA

city: Fukuoka

first: Tappei

last: Mishina

address: 744 Motooka Nishi-ku

country: Japan

institute: Kyushu University

library_source: transcriptomic single cell

data_processing:
Adaptor sequences and low quality bases were trimmed using Fastq-mcf v1.1.2 in the ea-utils package.
The RamDA-seq reads were mapped to the mouse genome (GRCm38) using Hisat2 v2.2.0.
The gene count table was obtained using the featureCounts v2.0.1 tool in the Subread package with the option ‘-t exon -g gene_id’ and the annotation gtf file from GENCODE (vM25).
We evaluated the quality control metrics and filtered out low quality samples based on the RNA integrity assessed by coverage profile along the gene body and the number of detected genes ≤ 8,000.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw counts or TPM values for each sample.

molecule: total RNA

organism: Mus musculus

source_name: ovary

growth_protocol: mouse lines used for this study were maintained on a mixed genetic background

extract_protocol:
At postnatal day (PD) 7, ovaries from euthanized control mice (n=3) and from Wls cKO mice (n=8) were collected. Ovaries were treated with a CTK solution (consisting of 0.25% trypsin (Thermo), 0.1% collagenase type IV (Gibco), 20% KSR (Invitrogen) and 1 mM CaCl2 in PBS) for 30 min at 37°C, then further treated with Accutase (Nacalai) at 37°C for 15 min. The reaction was halted by adding L-15 medium with 0.1% penicillin-streptomycin and 5% FBS, and the cells were dissociated by pipetting. The cell suspension was filtered through 70 μm cell strainers, followed by centrifugation at 400 g for 5 min and resuspension in sorting buffer (7.5% BSA (Life Technologies) in PBS). Blocking was performed with rat IgG (5 mg/mL, I8015, Sigma-Aldrich) for 15 min on ice. Subsequently, cell surface staining was conducted using anti-ckit-APC (1:50, 105812, BioLegend) and anti-CD45-Alexa Fluor 488 (1:200, 103122, BioLegend) for 15 min on ice. After centrifugation at 400 g for 5 min, cells were resuspended in sorting buffer. Prior to single-cell sorting by flow cytometry, samples were passed through 40 μm cell strainers, and DAPI (1:10,000) was added. Control and Wls cKO samples were each sorted using MoFlo Astrios EQ with Summit v 6.3.0. software (Beckman Coulter) into 384-well plates containing 286 tdTomato-positive somatic cells and 95 ckit-positive oocytes. DAPI-positive dead cells and CD45-positive leukocytes were excluded.
Library preparation for RamDA-seq was performed according to a previously report. However, to reduce reagent costs and rRNA-derived sequencing reads, the method was modified as follows: To suppress rRNA-derived cDNA synthesis, 0.008 units/µl XRN-1 (NEB) was added to the genomic DNA digestion mix, and the reaction was performed at 30°C for 5 min. To reduce reagent costs, a liquid dispenser Mantis (Formulatrix) was used to perform the reaction up to second strand synthesis at 1/10 the reaction volume. After that, 2.5 μl 0.8 X Tagment DNA Buffer (Illumina) diluted with RNase-free water was added to 0.5 μl of the second strand synthesis products for dilution. Then, 0.5 μl Amplicon Tagment Mix (Illumina) was added to 1.5 μl of the diluted product, and tagmentation was performed at 55°C for 10 min. After that, the library was prepared using 1/10 the reaction volume according to the Nextera XT DNA Library Prep Kit (Illumina) procedure. Twelve PCR cycles were performed. Somatic and oocyte library products were collected separately in equal volumes of 1 μl/well. Subsequently, 50 μl of each sample was fractionated from the equal mixed library, purified with 1.2X AMPureXP (Beckman Coulter), and eluted with 25 μl TE. To prevent large discrepancies in the number of sequencing reads per cell between somatic and oocyte cells, purified libraries were mixed to ensure a constant average molar per cell type using the quantitative results from the Bioanalyzer Agilent High-Sensitivity DNA Kit and the ratio of the number of cells sorted (somatic cells: oocytes = 286:95). The pooled library of 2.3 pM was sequenced in single end read 76 cycles using NextSeq 500 High Output Kit v2.5.

tag: tissue

value: ovary

tag: developmental stage

tag: cell type

value: interstitial cells

tag: subpopulation gc

tag: subpopulation oocyte

tag: genotype

value: Sf1-Cre;Wls flox/del;Ai9 (Wls cKO)

tag: marker expression_tdtomato

tag: marker expression_kit-apc

tag: cell size_(fsc1_area)

tag: intron ratio


title: mGCcKO_HMD201207003_BO02

value: granulosa cells


title: mOCcKO_HMD201207003_DN14

value: altered oocytes


title: mOCcKO_HMD201207003_DJ04

value: excluded by low quality


title: mGCcKO_HMD201207003_CF11

value: ovarian surface epithelial cells


title: mGCcKO_HMD201207003_BI18


title: mGCcKO_HMD201207003_CB03

value: altered granulosa cells


title: mGCcKO_HMD201207003_AK21

value: pre-granulosa cells


title: mGCcKO_HMD201207003_AI17


title: mGCcKO_HMD201207003_BO12


title: mOCcKO_HMD201207003_DN10


title: mGCcKO_HMD201207003_AC23


title: mGCcKO_HMD201207003_AE15


title: mOCcKO_HMD201207003_DD08


title: mGCcKO_HMD201207003_BE22


title: mGCcKO_HMD201207003_AG23


title: mGCcKO_HMD201207003_CL21


title: mOCcKO_HMD201207003_DL02

value: oocytes


title: mGCcKO_HMD201207003_CD03


title: mGCcKO_HMD201207003_CJ13


title: mGCcKO_HMD201207003_BK24


title: mGCcKO_HMD201207003_AC15


title: mGCcKO_HMD201207003_CH23


title: mGCcKO_HMD201207003_AO03


title: mGCcKO_HMD201207003_BK20


title: mGCcKO_HMD201207003_CN17


title: mOCcKO_HMD201207003_DF02


title: mGCcKO_HMD201207003_AI19


title: mGCcKO_HMD201207003_BG22


title: mGCcKO_HMD201207003_AG11


title: mGCcKO_HMD201207003_CN19


title: mGCcKO_HMD201207003_AC21


title: mGCcKO_HMD201207003_CL11


title: mGCcKO_HMD201207003_CP13


title: mOCcKO_HMD201207003_DN02


title: mGCcKO_HMD201207003_AE23


title: mGCcKO_HMD201207003_BO22


title: mGCcKO_HMD201207003_BI16


title: mGCcKO_HMD201207003_CD07


title: mGCcKO_HMD201207003_CN05


title: mGCcKO_HMD201207003_CJ01


title: mGCcKO_HMD201207003_AO15


title: mGCcKO_HMD201207003_CH09


title: mGCcKO_HMD201207003_AK11


title: mGCcKO_HMD201207003_AM13


title: mGCcKO_HMD201207003_AG13


title: mOCcKO_HMD201207003_DH24


title: mGCcKO_HMD201207003_BA20


title: mGCcKO_HMD201207003_CB15


title: mGCcKO_HMD201207003_BC14


title: mGCcKO_HMD201207003_BE24


title: mGCcKO_HMD201207003_BG12


title: mGCcKO_HMD201207003_BM12


title: mGCcKO_HMD201207003_BE14


title: mGCcKO_HMD201207003_BA14


title: mGCcKO_HMD201207003_AG07


title: mGCcKO_HMD201207003_CL19


title: mGCcKO_HMD201207003_BK10


title: mGCcKO_HMD201207003_CD05


title: mGCcKO_HMD201207003_CB11


title: mOCcKO_HMD201207003_DN06


title: mOCcKO_HMD201207003_DB18


title: mGCcKO_HMD201207003_BI12


title: mGCcKO_HMD201207003_BO14


title: mGCcKO_HMD201207003_CB23


title: mGCcKO_HMD201207003_AC11


title: mGCcKO_HMD201207003_BM16


title: mGCcKO_HMD201207003_AK15


title: mOCcKO_HMD201207003_DH10


title: mGCcKO_HMD201207003_BG06


title: mOCcKO_HMD201207003_DJ02


title: mGCcKO_HMD201207003_CP19


title: mOCcKO_HMD201207003_DJ24


title: mOCcKO_HMD201207003_DL08


title: mGCcKO_HMD201207003_AM17


title: mGCcKO_HMD201207003_AI13


title: mGCcKO_HMD201207003_BM08


title: mGCcKO_HMD201207003_CL15


title: mGCcKO_HMD201207003_CN01


title: mGCcKO_HMD201207003_AO23


title: mOCcKO_HMD201207003_DF08


title: mGCcKO_HMD201207003_AM09


title: mOCcKO_HMD201207003_DF22


title: mOCcKO_HMD201207003_DH20


title: mGCcKO_HMD201207003_CN13


title: mGCcKO_HMD201207003_CJ15


title: mGCcKO_HMD201207003_BK14


title: mGCcKO_HMD201207003_CF17


title: mGCcKO_HMD201207003_BG14


title: mGCcKO_HMD201207003_BC20


title: mOCcKO_HMD201207003_DH06


title: mOCcKO_HMD201207003_DJ08


title: mOCcKO_HMD201207003_DF04


title: mOCcKO_HMD201207003_DP06


title: mOCcKO_HMD201207003_DD04


title: mGCcKO_HMD201207003_AE13


title: mOCcKO_HMD201207003_DN20


title: mOCcKO_HMD201207003_DL16


title: mOCcKO_HMD201207003_DJ06


title: mOCcKO_HMD201207003_DH18


title: mGCcKO_HMD201207003_AG15


title: mGCcKO_HMD201207003_BC16


title: mGCcKO_HMD201207003_CH13


title: mGCcKO_HMD201207003_CJ23


title: mGCcKO_HMD201207003_BC22


title: mGCcKO_HMD201207003_BK18


title: mOCcKO_HMD201207003_DB14


title: mGCcKO_HMD201207003_BE12


title: mGCcKO_HMD201207003_AK19


title: mGCcKO_HMD201207003_CB19


title: mGCcKO_HMD201207003_CF13


title: mGCcKO_HMD201207003_CP15


title: mOCcKO_HMD201207003_DB08


title: mOCcKO_HMD201207003_DB22


title: mGCcKO_HMD201207003_BE18


title: mGCcKO_HMD201207003_AA11


title: mGCcKO_HMD201207003_AG21


title: mGCcKO_HMD201207003_AK23


title: mOCcKO_HMD201207003_DB10


title: mOCcKO_HMD201207003_DN08


title: mGCcKO_HMD201207003_AE17


title: mGCcKO_HMD201207003_CP21


title: mGCcKO_HMD201207003_AC13


title: mOCcKO_HMD201207003_DH02


title: mGCcKO_HMD201207003_AI03


title: mGCcKO_HMD201207003_BK22


title: mGCcKO_HMD201207003_BC08


title: mGCcKO_HMD201207003_BE16


title: mOCcKO_HMD201207003_DN24


title: mGCcKO_HMD201207003_CL23


title: mGCcKO_HMD201207003_CL07


title: mGCcKO_HMD201207003_CH17


title: mGCcKO_HMD201207003_CP11


title: mOCcKO_HMD201207003_DL06


title: mGCcKO_HMD201207003_AE19


title: mOCcKO_HMD201207003_DP02


title: mGCcKO_HMD201207003_BC18


title: mOCcKO_HMD201207003_DJ20


title: mGCcKO_HMD201207003_CL05


title: mOCcKO_HMD201207003_DD10


title: mGCcKO_HMD201207003_CB01


title: mGCcKO_HMD201207003_AI01


title: mGCcKO_HMD201207003_AK05


title: mGCcKO_HMD201207003_CH15


title: mOCcKO_HMD201207003_DD12


title: mGCcKO_HMD201207003_BK04


title: mGCcKO_HMD201207003_CP09


title: mGCcKO_HMD201207003_AC03


title: mOCcKO_HMD201207003_DF18


title: mGCcKO_HMD201207003_CB05


title: mGCcKO_HMD201207003_CL13


title: mGCcKO_HMD201207003_AK01


title: mOCcKO_HMD201207003_DD16


title: mGCcKO_HMD201207003_AO05


title: mGCcKO_HMD201207003_CF21


title: mGCcKO_HMD201207003_AG03


title: mGCcKO_HMD201207003_AC01


title: mGCcKO_HMD201207003_AI05


title: mOCcKO_HMD201207003_DH04


title: mGCcKO_HMD201207003_BG02


title: mGCcKO_HMD201207003_CB07


title: mGCcKO_HMD201207003_BA12


title: mGCcKO_HMD201207003_BG20


title: mOCcKO_HMD201207003_DB16


title: mGCcKO_HMD201207003_CF03


title: mGCcKO_HMD201207003_AO11


title: mGCcKO_HMD201207003_BM14


title: mGCcKO_HMD201207003_CB09


title: mOCcKO_HMD201207003_DN22


title: mGCcKO_HMD201207003_BI04


title: mOCcKO_HMD201207003_DD24


title: mGCcKO_HMD201207003_BI02


title: mGCcKO_HMD201207003_CD11


title: mOCcKO_HMD201207003_DN18


title: mGCcKO_HMD201207003_BE08


title: mOCcKO_HMD201207003_DP12


title: mGCcKO_HMD201207003_AE07


title: mGCcKO_HMD201207003_CN03


title: mGCcKO_HMD201207003_BI10


title: mGCcKO_HMD201207003_BE06


title: mOCcKO_HMD201207003_DL10


title: mGCcKO_HMD201207003_AI11


title: mGCcKO_HMD201207003_BO04


title: mGCcKO_HMD201207003_CN11


title: mGCcKO_HMD201207003_AA17


title: mGCcKO_HMD201207003_AA23


title: mGCcKO_HMD201207003_BO10


title: mOCcKO_HMD201207003_DN16


title: mGCcKO_HMD201207003_AM15


title: mOCcKO_HMD201207003_DF10


title: mGCcKO_HMD201207003_CL03


title: mOCcKO_HMD201207003_DJ12


title: mOCcKO_HMD201207003_DH22


title: mOCcKO_HMD201207003_DL20


title: mGCcKO_HMD201207003_CD13


title: mGCcKO_HMD201207003_CP01


title: mGCcKO_HMD201207003_AI09


title: mOCcKO_HMD201207003_DJ18


title: mGCcKO_HMD201207003_AK09


title: mOCcKO_HMD201207003_DP22


title: mGCcKO_HMD201207003_CJ11


title: mGCcKO_HMD201207003_AE03


title: mGCcKO_HMD201207003_AE09


title: mOCcKO_HMD201207003_DB04


title: mGCcKO_HMD201207003_CJ05


title: mOCcKO_HMD201207003_DP16


title: mGCcKO_HMD201207003_BK08


title: mGCcKO_HMD201207003_AI15


title: mGCcKO_HMD201207003_AG17


title: mGCcKO_HMD201207003_BC04


title: mGCcKO_HMD201207003_BC06


title: Ribo mRNA A-SVK-3

city: Shanghai

first: Rao

last: hanyu

address: Huashan Road NO.1954

country: China

institute: Shanghai Jiao Tong University

library_source: other

data_processing:
Adapter sequences were removed from raw sequencing data using cutadapt software. Meanwhile, reads with length between 25 and 35 bp were kept for downstream analysis. Then reads were aligned to rRNA and tRNA sequences so as to remove rRNA and tRNA reads using bowtie software, remaining reads were used to align to reference genome and transcriptome using hisat2 and bowtie software separately. The trinucleotide periodicity of ribosomes and codon usage frequency were estimated using revised riboWaltz package. ORF identification was performed using Price software. Read counts were calculated using featureCounts software. Raw counts were further normalized as RPKM values using fpkm function in DESeq2 package. Translational efficiencies were determined as the ratio of (normalized abundance determined by ribosome profiling)/(normalized abundance determined by RNA-seq) as previously repored. GO and KEGG analysis were performed using clusterProfiler9 package in R software.
Assembly: GRCm38 NCBI
Supplementary files format and content: processed data file includes raw counts for each sample.

molecule: other

source_name: Colon

extract_protocol:
A total of 107 cells were prepared for cell lysis. Then, the cell medium was discarded, and the cells were washed twice with ice-cold PBS containing 100 μg/mL cycloheximide (Adooq, 66-81-9). 100 mg tissue were pulverized manually under liquid nitrogen and treated by ice-cold PBS containing 100 μg/mL cycloheximide. Ribosome profiling was performed using Epi™ Ribosome Profiling Kit (Epibiotek, R1814).
All mRNA and RPFs (ribosome-protected RNA fragments) were extracted using RNA clean&ConcentratorTM-5 kit (ZYMO, R1016). EpiTM RiboRNA Depletion Kit (Human/Mouse/Rat) (Epibiotek, R1805) was used for rRNA depletion. Sequencing libraries were constructed using QIAseq miRNA Library kit (QIAGEN, 1103679).

value: Colon

tag: cell line

value: primary cell

value: intestinal epithelial cells

value: SETD2 knockdown

tag: treatment

value: dextran sulfate sodium treated


title: mGCcKO_HMD201207003_BG16


title: mGCcKO_HMD201207003_CP05


title: mGCcKO_HMD201207003_AA19


title: Ribo mRNA B-SWT-3

value: Wild type


title: mGCcKO_HMD201207003_BG04


title: mGCcKO_HMD201207003_AO01


title: mGCcKO_HMD201207003_BI14


title: mOCcKO_HMD201207003_DB06


title: Ribo mRNA B-SWT-2


title: Ribo mRNA A-SVK-1


title: Total mRNA SVK_2

library_source: transcriptomic


title: mOCcKO_HMD201207003_DJ16


title: mGCcKO_HMD201207003_AE21


title: Total mRNA SVK_3


title: Total mRNA SWT_3


title: Ribo mRNA B-SWT-1


title: mGCcKO_HMD201207003_CF07


title: Total mRNA SVK_1


title: mGCcKO_HMD201207003_AG05


title: mOCcKO_HMD201207003_DF14


title: Ribo mRNA A-SVK-2


title: Total mRNA SWT_1


title: mGCcKO_HMD201207003_BE20


title: 786-O, Mit NAQC, Inp1

city: Paris

first: Marco

last: PONTOGLIO

state: Choisir votre état

address: Inserm U1016, 24 rue du Faubourg Saint-Jacques

department: Growth and Signalling

country: France

institute: Inserm

description:
BamCoverage input control of Mit_Naqc
MitNacq_input_hg19_bamCoverage_CPM_v2.bigwig

library_source: genomic

data_processing:
In order to separate the two genomes (human and the calibrating mouse) ChIP-seq reads were first aligned to the mm10 genome assembly using bowtie2 and the unplaced reads were subsequently aligned to the hg19 genome assembly.
The replicate bams files were respectively pooled with samtools merge
Assembly: hg19
Supplementary files format and content: Bigwig files were generated using bamCoverage with binSize = 1
Supplementary files format and content: Peaks were called using using  GEM version 3.4 http://cgs.csail.mit.edu/gem/, narrowPeak format

molecule: genomic DNA

organism:
Homo sapiens
Mus musculus

growth_protocol: 786-O cells were cultured in Roswell Park Memorial Institute (RPMI) medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37C with 5% CO2. mIMCD3 cells were grown in DMEM, 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol:
Elution and decrosslinking of DNA was performed in Elution Buffer (1% SDS, 0.1M NaHCO3, 100 mM NaCl) with addition of 20 ug/ml RNase A at 65°C overnight. DNA was then extracted with QIAquick PCR Purification Kit (Qiagen) after treatment with 100 ug/ml proteinase K at 55°C for 1–2 h.
Libraries were prepared from 1ng of immunoprecipitated DNA or Inputs with the MicroPlex v2 kit (Diagenode), according to manufacturer's instructions.

treatment_protocol: Mitotic cells were obtained with an RO-3306 treatment (9uM for 20-22h) followed by a nocodazole block (30ng/ml for 2h and 30 minutes). Free cycling mIMCD3 cells were admixed either to interphase or mitotic 786-O cells just before the crosslinking step.

value: Human renal cell carcinoma and Mouse renal cell line as calibration

tag: cell cycle_stage

value: Mitosis

tag: chip antibody


title: 786-O, Mit NAQC, HNF1b, rep2

description:
BamCoverage pool Mit_Nacq of 19ST_12, 19ST_16
pool_Mit_Nacq_THg19_hg19_bamCoverage_CPM_v2.bigwig
Peaks pool of 19ST_12, 19ST_16
gem_pool_Mit_Nacq_THg19.GPS_events.narrowPeak

value: HNF1b (ABclonal custom made rabbit polyclonal)


title: mGCcKO_HMD201207003_CB17

value: ovary

value: Sf1-Cre;Wls flox/del;Ai9 (Wls cKO)


title: 786-O, Mit NAQC, HNF1b, rep1


title: 786-O, Mit AQC, Inp

description:
BamCoverage input control of Mit_Aqc
MitAcq_input_hg19_bamCoverage_CPM_v2.bigwig


title: mGCCtrl_HMD201207001_AO17

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: mGCCtrl_HMD201207001_BG18


title: 786-O, Mit AQC, HNF1b, rep1

description:
BamCoverage pool Mit_Acq of 19ST_20, 19ST_22, 19ST_24
pool_Mit_Acq_THg19_hg19_bamCoverage_CPM_v2.bigwig
Peaks pool of 19ST_20, 19ST_22, 19ST_24
gem_pool_Mit_Acq_THg19.GPS_events.narrowPeak


title: 786-O, Mit AQC, HNF1b, rep3


title: 786-O, Asy NAQC, Inp

description:
BamCoverage input control of Asy_Naqc
AsyNacq_input_hg19_bamCoverage_CPM_v2.bigwig

value: Asynchronous


title: mGCCtrl_HMD201207001_AG11

value: granulosa cells


title: mGCCtrl_HMD201207001_AK13

value: interstitial cells


title: Total mRNA SWT_2


title: 786-O, Mit AQC, HNF1b, rep2


title: 786-O, Asy NAQC, HNF1b, rep1

description:
BamCoverage pool Asy_Nacq of 19ST_11, 19ST_13
pool_Asy_Nacq_THg19_hg19_bamCoverage_CPM_v2.bigwig
Peaks pool of 19ST_11, 19ST_13
gem_pool_Asy_Nacq_THg19.GPS_events.narrowPeak


title: mGCCtrl_HMD201207001_AI23

value: ovarian surface epithelial cells


title: 786-O, Asy NAQC, HNF1b, rep2


title: 786-O, Asy AQC, HNF1b, rep2

description:
BamCoverage pool of 19ST_19, 19ST_21, 19ST_23
pool_Asy_Acq_hg19_bamCoverage_CPM_v2.bigwig
Peaks pool of 19ST_19, 19ST_21, 19ST_23
gem_pool_Asy_Acq.GPS_events.narrowPeak


title: 786-O, Asy AQC, HNF1b, rep3


title: mOCCtrl_HMD201207001_DD04

value: oocytes


title: mGCcKO_HMD201207003_CN15

value: pre-granulosa cells


title: 786-O, Asy AQC, Inp

description:
BamCoverage input control of Asy_Aqc
AsyAcq_input_hg19_bamCoverage_CPM_v2.bigwig


title: 786-O, Asy AQC, HNF1b, rep1

description:
BamCoverage pool Asy_Acq of 19ST_19, 19ST_21, 19ST_23
pool_Asy_Acq_hg19_bamCoverage_CPM_v2.bigwig
Peaks pool of 19ST_19, 19ST_21, 19ST_23
gem_pool_Asy_Acq.GPS_events.narrowPeak


title: mGCcKO_HMD201207003_CD17


title: mOCCtrl_HMD201207001_DB14


title: ASPC-1,pH6.4,rep3

city: hang zhou

first: de yang

last: mu

address: 杭州医学院临安校区

institute: hang zhou medical college

data_processing:
After the library construction was completed, PCR amplification was used for library fragment enrichment, followed by library selection according to the fragment size, which was 450 bp. Then, the library was quality checked by Agilent 2100 Bioanalyzer, and then the total concentration of the library and the effective concentration of the library were detected. Then, according to the effective concentration of the library and the amount of data required for the library, the libraries containing different Index sequences (each sample is added with a different Index, and finally the downstream data of each sample is distinguished according to the Index) are mixed proportionally. The mixed libraries are uniformly diluted to 2nM and denatured by base denaturation to form single-stranded libraries. After RNA extraction, purification and library construction, the libraries were subjected to paired-end (PE) sequencing using Next-Generation Sequencing (NGS) based on the Illumina HiSeq sequencing platform.
Assembly: Ensembl
Supplementary files format and content: The DESeq Excel file is the expression of the differential genes
Supplementary files format and content: The all.heatmap EXCEL file contains the differential gene expression for each sample.

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
In this project, rRNA in total RNA was removed by ribosomal RNA removal kit, and ion interruption was used to break the RNA to a fragment of about 300bp in length. The length of 300bp was chosen because the length of the junction is fixed, if the length of the interrupted fragment is shorter, it will lead to a high proportion of the junction sequence, which will reduce the proportion of valid data; if the length of the interrupted fragment is longer, it will be unfavorable to the generation of clusters in the process of on-line sequencing. The first strand of cDNA was synthesized using RNA as template with 6-base random primer and reverse transcriptase, and the second strand of cDNA was synthesized using the first strand of cDNA as template.
After RNA extraction, purification and library construction, the libraries were subjected to paired-end (PE) sequencing using Next-Generation Sequencing (NGS) based on the Illumina HiSeq sequencing platform.

tag: condition

value: pH differentiation

value: Pancreatic Cancer Cells

value: WT


title: mGCCtrl_HMD201207001_BO18


title: ASPC-1,pH6.4,rep2


title: mGCCtrl_HMD201207001_AE01


title: mGCCtrl_HMD201207001_BK12


title: mOCCtrl_HMD201207001_DL04


title: ASPC-1,pH7.4,rep3


title: ASPC-1,pH6.4,rep1


title: ASPC-1,pH7.4,rep2


title: mGCCtrl_HMD201207001_AO19

value: early theca cells


title: mGCCtrl_HMD201207001_CN23


title: mOCCtrl_HMD201207001_DH14


title: mOCCtrl_HMD201207001_DF24

value: excluded by low quality


title: mGCCtrl_HMD201207001_BA02


title: mGCCtrl_HMD201207001_CH05


title: ASPC-1,pH7.4,rep1


title: mGCCtrl_HMD201207001_BA22


title: mGCCtrl_HMD201207001_BI22


title: mGCCtrl_HMD201207001_BG10


title: mOCCtrl_HMD201207001_DP08


title: P031_9P62_Ontogency

city: Boston

first: Ofer

last: Levy

state: MA

address: 300 Longwood Avenue

department: Infectious Disease

country: USA

institute: Boston Children's Hospital

data_processing:
FastQC v0.11.9 and MultiQC v1.8 1 were used to assess sequence quality
Sequence reads were aligned to the hg38 human reference genome (Ensembl GRCh38v98) using STAR v2.7.3a
Counts of the number of reads mapped per gene were generated using htseq-count (HTSeq v0.11.2 3)
Assembly: Ensembl GRCh38v98
Supplementary files format and content: CSV; Count file containing assigned counts to each gene

source_name: Vaccination: Delayed - Visit 2 collected at day 1

extract_protocol:
Total RNA was extracted from each sample using the Paxgene Blood RNA kit (catalog no.: 762164;Qiagen, Valencia, CA, USA) following the manufacturer’s protocol. RNA quantification and quality assessment was performed using an Agilent 2100 Bioanalyzer (Santa Clara, CA, USA)
The NEBNextPoly(A) mRNA Magnetic Isolation Module (catalog no.: E7490L, NEB; Ipswich, MA, USA) was used to capture poly-adenylated RNA. Strand-specific cDNA libraries were generated using the KAPA RNAHyperPrep Kit (catalog no.: 08098107702, Roche; Basel, Switzerland) on a Freedom EVO 100 (Tecan,Männedorf, Switzerland).

value: blood

value: bulk

tag: Sex

value: Male


title: P040_9H94_Ontogency


title: P030_9M84_Ontogency

source_name: Vaccination: Delayed - Visit 2 collected at day 7

value: Female


title: mGCCtrl_HMD201207001_BM04

value: ovary


title: P011_9P73_Ontogency


title: G760A_9M26_Ontogency


title: G750E_9B64_Ontogency

source_name: Vaccination: Delayed - Visit 2 collected at day 3


title: mGCCtrl_HMD201207001_BA16

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: mGCCtrl_HMD201207001_AM23


title: mGCCtrl_HMD201207001_AA03


title: mGCCtrl_HMD201207001_AG19


title: P004_9A41_Ontogency


title: G764F_9A81_Ontogency


title: P022_9A65_Ontogency


title: G749H_8U65_Ontogency


title: mGCCtrl_HMD201207001_AA01


title: G728D_8S21_Ontogency


title: mGCCtrl_HMD201207001_CF19


title: P001_9P69_Ontogency


title: P012_8R83_Ontogency


title: mGCCtrl_HMD201207001_BO16


title: mGCCtrl_HMD201207001_AO13


title: G735D_8J20_Ontogency


title: mGCCtrl_HMD201207001_BI06


title: mGCCtrl_HMD201207001_AM01


title: mGCCtrl_HMD201207001_BG24


title: mOCCtrl_HMD201207001_DF20


title: G753G_7L77_Ontogency


title: mGCCtrl_HMD201207001_CD21


title: G734E_7U44_Ontogency


title: mGCCtrl_HMD201207001_AC07


title: P024_7K58_Ontogency


title: P037_7J43_Ontogency


title: mGCCtrl_HMD201207001_CB21


title: mGCCtrl_HMD201207001_BO12


title: P027_7H04_Ontogency


title: G726A_7D26_Ontogency


title: mGCCtrl_HMD201207001_BK16


title: mOCCtrl_HMD201207001_DB10


title: P044_7B79_Ontogency


title: P042_7B77_Ontogency


title: mGCCtrl_HMD201207001_AC05


title: mGCCtrl_HMD201207001_CD23


title: G755H_8G29_Ontogency


title: P023_8C32_Ontogency


title: mGCCtrl_HMD201207001_AM05


title: P038_6T47_Ontogency


title: mOCCtrl_HMD201207001_DB22


title: P028_6T84_Ontogency


title: G727B_7A35_Ontogency


title: G752A_6T71_Ontogency


title: mGCCtrl_HMD201207001_CB13


title: mGCCtrl_HMD201207001_BM22


title: P017_7R58_Ontogency


title: mGCCtrl_HMD201207001_AK17


title: G762B_6R37_Ontogency


title: mGCCtrl_HMD201207001_CH01


title: P045_6M43_Ontogency


title: G724H_7J31_Ontogency


title: mOCCtrl_HMD201207001_DF02


title: G737H_6M04_Ontogency


title: P032_6L53_Ontogency


title: G725C_6C45_Ontogency


title: mOCCtrl_HMD201207001_DB08


title: P007_6A05_Ontogency


title: mGCCtrl_HMD201207001_BE02


title: mGCCtrl_HMD201207001_AI07


title: mGCCtrl_HMD201207001_CF15


title: mGCCtrl_HMD201207001_CJ17


title: G765K_5S64_Ontogency


title: G741K_5M78_Ontogency


title: mOCCtrl_HMD201207001_DN10


title: G751C_5L24_Ontogency


title: mOCCtrl_HMD201207001_DN02


title: P009_5K23_Ontogency


title: P005_5L09_Ontogency


title: mGCCtrl_HMD201207001_AC19


title: mGCCtrl_HMD201207001_CJ19


title: G763H_5K04_Ontogency


title: mGCCtrl_HMD201207001_BK24


title: mGCCtrl_HMD201207001_CP17


title: G744D_5J25_Ontogency


title: mOCCtrl_HMD201207001_DL02


title: P006_5D85_Ontogency


title: mGCCtrl_HMD201207001_BA04


title: mGCCtrl_HMD201207001_BC02


title: G745G_5F07_Ontogency


title: mGCCtrl_HMD201207001_CN17


title: mGCCtrl_HMD201207001_CD15


title: P016_4S27_Ontogency


title: mGCCtrl_HMD201207001_AI17


title: G739A_4S28_Ontogency


title: P014_5D17_Ontogency


title: mGCCtrl_HMD201207001_BI18


title: mOCCtrl_HMD201207001_DJ04


title: G748B_5H51_Ontogency


title: mGCCtrl_HMD201207001_AA05


title: P019_4Q92_Ontogency


title: G743F_5C28_Ontogency


title: mOCCtrl_HMD201207001_DF06


title: mGCCtrl_HMD201207001_CF11


title: G740J_4L50_Ontogency


title: G758F_4L55_Ontogency


title: mGCCtrl_HMD201207001_AK21


title: mGCCtrl_HMD201207001_BA06


title: P035_3T12_Ontogency


title: P036_3S83_Ontogency


title: G732J_5A87_Ontogency


title: mGCCtrl_HMD201207001_CJ13


title: P003_3L80_Ontogency


title: P025_3K97_Ontogency


title: mGCCtrl_HMD201207001_AE15


title: G729E_3H53_Ontogency


title: mGCCtrl_HMD201207001_CL21


title: G747A_2T10_Ontogency


title: mGCCtrl_HMD201207001_AG23


title: G759K_2U76_Ontogency


title: G731F_2S69_Ontogency


title: G723K_2S59_Ontogency


title: mGCCtrl_HMD201207001_AE23


title: mGCCtrl_HMD201207001_CH23


title: mGCCtrl_HMD201207001_AO03


title: mGCCtrl_HMD201207001_BE14


title: mOCCtrl_HMD201207001_DN14


title: mGCCtrl_HMD201207001_BE22


title: G736G_2M00_Ontogency


title: P026_4K83_Ontogency


title: mGCCtrl_HMD201207001_BK20


title: G754J_4D36_Ontogency


title: mGCCtrl_HMD201207001_BG22


title: G756B_2Q31_Ontogency


title: A. niger VG8.27 (Tet-On luciferase) + 5 Dox , biol rep 2

city: Berlin

first: Stephan

last: Starke

address: Gustav Meyer Allee 25

department: Microbiology

country: Germany

institute: TU Berlin

data_processing:
Quality control via multiQC
Mapping against A. niger N402 genome using STAR at default settings
Normalization and Differential gene expression using DESeq2 at default settings
Assembly: GCA_900248155.1
Supplementary files format and content: Mapping generated RawCounts as a comma delimited text file
Supplementary files format and content: DESeq2 generated differentially expressed genes 5 Dox ref to 0 Dox (STS4.10) as comma delimited txt file
Supplementary files format and content: DESeq2 generated differentially expressed genes 5 Dox ref to 0 Dox (VG8.27) as comma delimited txt file

organism: Aspergillus niger

source_name: Aspergillus niger N402 (ATCC 64974)

growth_protocol: Strain STS4.10 and VG8.27 were cultivated in a 5L bioreactor at 30°C. Complete medium was used (MM + 1% yeast extract and 0.5% casamino acids, without doxycycline). Hyphae were harvested in the mid exponential growth phase by filtration of 7 ml through a nitrocellulose membrane. The biomass on the filter was transferred to agar plates containing minimal medium without glucose, in presence or absence of 5 µg/ml doxycycline. A second nitrocellulose membrane was placed on top to repress sporulation. Cultures were subsequently starved for 35 hours at 30°C and ~300 mg were used for RNA extraction.

extract_protocol:
Biomass was shock-frozen in liquid nitrogen and stored at -80°C until RNA extraction. Approximately 300 mg of thawed wet weight biomass was homogenized using glass beads and 1ml of TRIzol solution in a bead mill. The lysis procedure was performed in three 30s steps at maximum speed. Total RNA was extracted using a commercially available kit (Zymo Research, Direct-zol RNA Miniprep R2050). To eliminate possible genomic DNA contamination, a DNA-free Kit from Thermo Fischer was used (AM1906).
Done by Azenta (Sequencing copany): RNA samples were quantified using Qubit 4.0 Fluorometer (Life Technologies, Carlsbad,CA, USA) and RNA integrity was checked with RNA Kit on Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA). The sequencing libraries were multiplexed and loaded on the flowcell on the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration v1.5. Image analysis and base calling were conducted by the NovaSeq Control Software v1.7 on the NovaSeq instrument. Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.

value: mycelium

tag: strain

tag: phenotype

value: luciferase overexpression

value: Tet-On luciferase

value: 5 Doxycycline


title: P033_2L13_Ontogency

tag: tissue


title: A. niger VG8.27 (Tet-On luciferase) + 5 Dox , biol rep 1


title: mOCCtrl_HMD201207001_DP04

tag: developmental stage

tag: cell type

value: oocytes


title: mGCCtrl_HMD201207001_BO02

value: granulosa cells

tag: subpopulation gc

tag: subpopulation oocyte


title: A. niger VG8.27 (Tet-On luciferase) + 0 Dox , biol rep 2

value: luciferase knockout

tag: genotype

value: 0 Doxycycline


title: G761D_2K90_Ontogency


title: A. niger VG8.27 (Tet-On luciferase) + 0 Dox , biol rep 1


title: A. niger STS4.10 (Tet-On anafp) + 5 Dox , biol rep 2

value: anafp overexpression

value: Tet-On anafp


title: A. niger STS4.10 (Tet-On anafp) + 5 Dox , biol rep 1


title: mGCCtrl_HMD201207001_AI19

value: early theca cells

tag: marker expression_tdtomato

tag: marker expression_kit-apc


title: mGCCtrl_HMD201207001_AA13

value: excluded by low quality

tag: cell size_(fsc1_area)

tag: intron ratio


title: A. niger STS4.10 (Tet-On anafp) + 0 Dox , biol rep 2

value: anafp knockout

tag: treatment


title: A. niger STS4.10 (Tet-On anafp) + 0 Dox , biol rep 1


title: Xylose as carbon source

type: RNA

city: Cuernavaca

first: Alfredo

last: Martínez

state: Morelos

address: Av. Universidad 2001, Col. Chamilpa

department: Departamento de Ingeniería Celular y Biocatálisis

country: Mexico

institute: Instituto de Biotecnología, Universidad Nacional Autónoma de México

description: Analysis was performed using wild-type BL21(DE3) RNA as control samples to compare with the experimental samples of the xylose-selective strain BL21(DE3) Δglk, ΔmanZ, ΔptsG, xylR::Kmr, lacZ::xylRC91A-Gmr. Both strains were cultured using xylose as a carbon source.

hyb_protocol: Incorporation of fluorophore was analyzed by using the absorbance at 555 nm and 647 respectively. Equal quantities of labeled cDNA were hybridized using hybridization solution HybIT2 (TeleChem International INC). The arrays were incubated for 14 h at 42 °C, and then washed tree times with 1X SCC, 0.05 % SDS at room temperature.

scan_protocol: Acquisition and quantification of array images were performed in GenePix 4100-A reader with its accompanying software. For each spot, the mean density, mean background, and mean normalized signal values were calculated with the Array-Pro Analyzer software from Media Cybernetics.

data_processing:
Microarray data analysis was performed as follows. The data obtained from the quantification of the images were analyzed with Genarise in SWAP mode. The free software genArise, was developed in the Computing Unit of Cellular Physiology Institute of UNAM (http://www.ifc.unam.mx/genarise/). GenArise carry out a number of transformations: background correction, lowess normalization, intensity filter, replicates analysis and selecting differentially expressed genes. The goal of genArise is to identify which of the genes show good evidence of being differentially expressed. The software identifies differential expressed genes by calculating an intensity-dependent z-score. Using a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point, and define a z-score where z measures the number of standard deviations a data point is from the mean.
zi = (Ri – mean(R)) / sd(R) Where zi is the z-score for each element, Ri is the log-ratio for each element, and sd(R) is the standard deviation of the log-ratio. With this criterion, the elements with a z-score > 2 standard deviations would be the significantly differentially expressed genes.

label: Alexa555, Alexa647

organism: Escherichia coli BL21(DE3)

source_name: Control samples of the exponential growth phase of the wild-type BL21(DE3)in cultures with xylose as a carbon source as control

label_protocol: 10 ug of total RNA were used for cDNA synthesis, incorporating dUTP-Alexa555 or dUTP-Alexa647, employing the SuperScript Plus direct labeling kit (Invitrogen).

growth_protocol: The strains wild-type (BL21DE3)) and the xylose-selective strain (BL21(DE3) Δglk, ΔmanZ, ΔptsG, xylR::Kmr, lacZ::xylRC91A-Gmr) were grown on minimal medium M9 (pH 7) supplemented with 20 mM MOPS and 33 mM xylose or 28 mM glucose. The cultures were carried out in a 250 mL flask with 50 mL medium at 300 rpm and 37 °C until strains reached the middle exponential phase (~ 0.3-0.4 gDCW L-1)

extract_protocol: 10 mL of middle exponential phase culture were mixed with 500 µL of RNAlaterTM (Thermo Fisher Scientific, Baltics, UAB), then gently mixed by inversion. The samples were centrifugated at 5,000 rpm for 5 minutes, the supernatant was discarded, and the pellet was frozen at -70 °C until further analysis. Total RNA was isolated using an RNAeasy Midi kit (cat. no. 75142, Qiagen, Hilden, Germany). Chromosomal DNA was removed with the turbo-DNA free kit (cat no. AM1907, Thermo Fisher Scientific, Baltics, UAB).

treatment_protocol: The strains were grown on mineral medium with glucose or xylose as carbon source

source_name: Experimental samples of the exponential growth phase of the  xylose-selective strain derived from BL21(DE3) in cultures with xylose as a carbon source

value: ES04 (BL21(DE3) Δglk, ΔmanZ, ΔptsG, xylR::Kmr, lacZ::xylRC91A-Gmr)


title: G757D_2C93_Ontogency

value: blood

value: bulk

value: Male


title: mGCCtrl_HMD201207001_CL11

value: ovary

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: mGCCtrl_HMD201207001_CD19

value: interstitial cells


title: P010_2L55_Ontogency

value: Female


title: Glucose as carbon source

description: Analysis was performed using the experimental samples of the xylose-selective ES04 (BL21(DE3) Δglk, ΔmanZ, ΔptsG, xylR::Kmr, lacZ::xylRC91A-Gmr) strain compared with the control samples of wild-type BL21(DE3). Both strains were cultured using glucose as a carbon source.

source_name: Control samples of the exponential growth phase of wild-type BL21(DE3)in cultures with glucose as a carbon source as control

source_name: Experimental samples of the exponential growth phase of xylose-selective strain derived from BL21(DE3) in cultures with glucose as a carbon source


title: P021_1T26_Ontogency


title: G722G_1S88_Ontogency


title: mGCCtrl_HMD201207001_CP13


title: G721J_1S27_Ontogency


title: Testis, D180-2

city: Nanning

first: Zhiqiang

last: Wang

address: No. 6 TaoYuan Rd.

institute: Guangxi Academy of Medical Sciences and the People’s Hospital of Guangxi Zhuang Autonomous Region

data_processing:
HISAT2 version 2.1.0 for alignment
StringTie v2.1.1 for transcripts assemble and FPKM counts generation
Assembly: GCF_001704415.2
Supplementary files format and content: csv files with FPKM value

organism: Capra hircus

source_name: Testis

extract_protocol:
The total RNA was extracted from the testes using TRIzol reagent (Invitrogen Life Technologies Inc., Carlsbad, CA, USA), 1 μg of total RNA was used for the construction of sequencing libraries.
RNA  libraries for  RNA-seq were prepared using the lncRNA Sample Preparation Kit (Illumina, NEB) according to the manufacturer’s instructions.

value: Testis

tag: age

value: postpuberty

value: WT


title: mGCCtrl_HMD201207001_AA07

value: ovarian surface epithelial cells


title: Testis, D180-1


title: Testis, D90-2

value: puberty


title: Testis, D90-3


title: Testis, D90-1


title: P018_1Q40_Ontogency


title: mGCCtrl_HMD201207001_BI16


title: G733B_1M96_Ontogency


title: Testis, D30-3

value: prepuberty


title: G746C_1U49_Ontogency


title: mOCCtrl_HMD201207001_DJ10


title: Testis, D30-2


title: Testis, D3-3

value: neonatal


title: Testis, D30-1


title: mGCCtrl_HMD201207001_CN19

value: granulosa cells


title: Testis, D180-3


title: Testis, D3-1


title: P039_1M41_Ontogency


title: P013_1M00_Ontogency


title: Testis, D3-2


title: HFD+MGIG 3

first: Wenjiao

last: Jiang

address: No. 1, Zhongke Road

institute: Chinese Academy of Sciences

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: mm10
Supplementary files format and content: The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method.

source_name: white adipose tissue

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’ s instructions. Then RNA quality was determined by 5300 Bioanalyser(Agilent) and quantified using the ND-2000 (NanoDrop Technologies).
The RNA-seq transcriptome librariy was prepared following SMART-Seq_V4 Ultra Low Input RNA Kit for Sequencing from Clontech (San Diego, CA) using 10ng of total RNA.

value: white adipose tissue

tag: cell line

value: adipose tissue macrophages

value: macrophages

value: HFD+MGIG


title: mOCCtrl_HMD201207001_DH08

value: oocytes


title: P029_1L96_Ontogency

value: blood

value: bulk


title: HFD+MGIG 1


title: mGCCtrl_HMD201207001_AC23

value: ovary

value: pre-granulosa cells

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: mGCCtrl_HMD201207001_CF09


title: HFD 2

value: HFD


title: HFD+MGIG 2

value: WT


title: HFD 1


title: HFD 3


title: P002_1L76_Ontogency

value: Female


title: mGCCtrl_HMD201207001_CH19


title: MCD+EMPA, replicate 2, scRNAseq

city: Guangzhou

first: Huijie

last: Zhang

address: No. 1838, North Guangzhou Avenue, Baiyun District, Guangzhou

institute: Nanfang Hospital, Southern Medical University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using in Cell Ranger software 10X.
Assembly: mm10
Supplementary files format and content: Tar archives include tab-separated values files and matrix files (barcodes.tsv, features.tsv/genes.tsv, matrix.mtx).

source_name: liver

extract_protocol:
Mouse liver tissue was digested, passed through a 100 mm cell strainer, and subjected to red blood cell lysis. Cells were incubated with CD45 antibody at 4°C for 30 minutes, followed by incubation with DAPI (Thermo Scientific, 62248, 1:1000) for 5 minutes. Cells were resuspended in 1640 medium and filtered through a 40 mm cell strainer. Pre-prepared collection tubes containing 1640 medium with 10% FBS were sent to the sorting room. The sample tubes were loaded into the sample chamber for target cell sorting. Sorted cells were mixed, and a portion was reanalyzed to record flow cytometry data. Cells were quality controlled to ensure >80% viability, washed, and resuspended to 700-1200 cells/µL.
Libraries were constructed for 3’ gene expression by fragmentation, end repair, adapter ligation, and indexing. Sequencing was performed on the Illumina Novaseq 6000 platform with PE150 mode, achieving a depth of 50,000 read pairs per cell.

tag: model

value: NASH

value: liver

value: hepatic CD45+ cells

value: EMPA


title: P020_1L60_Ontogency

tag: Sex


title: MCD+EMPA, replicate 1, scRNAseq


title: G742E_1M84_Ontogency


title: mOCCtrl_HMD201207001_DN04

value: excluded by low quality


title: G738K_1K73_Ontogency


title: MCD, replicate 2, scRNAseq

value: control


title: ZJDC3

city: Shenyang

first: Zhichao

last: Chen

address: 103 Wenhua Road

institute: Shenyang Pharmaceutical University

data_processing:
The quality information of raw data in FASTQ format was calculated and then the raw data was filtered using fastp(0.22.0) software.
Reference genome index was built by HISAT2 (v2.1.0) and the filtered reads were mapping to the reference genome using HISAT2.
The gene read count value was counted using HTSeq(v0.9.1) as the original expression level of the gene.
FPKM(fragments per kilobaseof exon per million fragments mapped) is used to normalize the expression.
Assembly: http://www.ensembl.org/Mus_musculus/Info/Annotation
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: cell

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cell

value: dendritic cells


title: MCD, replicate 1, scRNAseq


title: P034_1K67_Ontogency


title: ZJDC2


title: ZJDC1


title: PBSDC2


title: mGCCtrl_HMD201207001_AO21

value: interstitial cells


title: P043_1K57_Ontogency

value: blood


title: PBSDC3


title: P041_1H02_Ontogency

value: bulk

value: Male


title: mGCCtrl_HMD201207001_BO20

value: ovary

value: early theca cells


title: OMVSSDC2


title: OMVSSDC3


title: P008_1G80_Ontogency


title: mGCCtrl_HMD201207001_AK07

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: PBSDC1


title: P015_1B60_Ontogency


title: male, LKO, rep2

city: Lincoln

first: Xinghui

last: Sun

state: NE

address: 1901 Vine Street

department: Biochemistry

institute: University of Nebraska - Lincoln

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house (Novogene) perl scripts
The paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2Rpackage (1.20.0)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: Mice were housed on a normal 12/12 light-dark cycle. Mice had ad libitum access to a chow diet (Envigo, cat# 2016) and water.

extract_protocol:
About 50 to 100 mg of liver tissues from two mice were used for total RNA extraction using TRIzol Reagent.
A total RNA sample from two livers tissues was used to contruct one library. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library. This was done by Novogene.
Stranded bulk RNA-seq

treatment_protocol: Matrin-3 floxed mice were bred with Albumin-Cre mice (The Jackson Laboratory, #003574) to produce liver-specific matrin-3 knockout mice (LKO).

tag: gender

value: male

value: liver-specific KO


title: OMVSSDC1


title: male, LKO, rep1


title: mGCCtrl_HMD201207001_CD07

value: pre-granulosa cells


title: male, floxed, rep2

value: liver

value: floxed


title: mGCCtrl_HMD201207001_CB03

value: ovarian surface epithelial cells


title: male, floxed, rep1


title: P020_9T54_Ontogency

value: Female


title: mOCCtrl_HMD201207001_DB18

value: oocytes


title: mGCCtrl_HMD201207001_CH21


title: P003_9R58_Ontogency


title: female, LKO, rep2

value: female


title: mGCCtrl_HMD201207001_AC21


title: female, LKO, rep1


title: G740J_9L60_Ontogency


title: mGCCtrl_HMD201207001_BA18

value: excluded by low quality


title: female, floxed, rep2


title: P011_9K68_Ontogency


title: female, floxed, rep1


title: G728D_9H62_Ontogency


title: mGCCtrl_HMD201207001_BK06


title: P041_9H27_Ontogency


title: mGCCtrl_HMD201207001_CN07

value: granulosa cells


title: Skin Biopsy, unwounded skin, Day0, rep3

city: Farmington

first: Junyu

last: Zhu

state: CT

address: 263 Farmington Avenue

institute: UConn Health

data_processing:
Raw reads were trimmed with Trimmomatic with a quality threshold of 30 and length threshold of 45. Following that, trimmed reads were mapped to the GRCm39 reference genome with HISAT2 (version 2.1.0). The resulting SAM files were converted into BAM format using samtools (version 1.9), and gene expression estimated by generating a count matrix with htseq-count.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Skin

extract_protocol:
Wound samples were freshly harvested and snap frozen in liquid nitrogen from mice at day 2, 4 and 12 post injury, or unwounded animals as indicated. Total RNA was extracted using TRIzol reagent (Invitrogen, Thermo Fisher Scientific), purified with chloroform, isopropanol and 75% ice cold ethanol, dissolved in RNase free water.
500 ng total RNA per sample submitted to the Center for Genomic Innovation at the University of Connecticut for library preparation (TruSeq Stranded mRNA) and sequencing on the Illumina NovaSeq 6000 platform.

value: Skin

value: unwounded skin, Day0


title: Treg, HTO-derived cDNA

city: La Jolla

first: Stanislav

last: Dikiy

state: CA

address: 10550 North Torrey Pines Road

department: Immunology

institute: Scripps Research

description: Cell Hashing library; R1 -10X barcode and UMI, R2-Insert, I1-sample index, I2-sample index

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where HTO sequences were concatenated and treated as Custom library with default settings (v7.0.1) and aligning to the custom mm10 genome build that contained Foxp3thy1.1, Il10tdTomato-CreER, and Gt(ROSA)26SorLSL-YFP targeted mutations and ncBI RefSeq annotations.
Assembly: custom mm10 genome build that contained Foxp3thy1.1, Il10tdTomato-CreER, and Gt(ROSA)26SorLSL-YFP targeted mutations
Supplementary files format and content: 10x Genomics output files (filtered): barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz,  airr_rearrangement.tsv, filtered_contig_annotations.csv
Supplementary files format and content: HTO feature reference and h5ad files: feature_reference.csv, Treg_hto.h5ad
Library strategy: CITE-seq

molecule: protein

source_name: Large Intestine, Small Intestine

extract_protocol:
Cells were sorted into 0.04% BSA/PBS, pelleted, and then resuspended at 1000-1500 cells/ul
Library was prepared using Chromium Single Cell 5ʹ v3 protocol with V(D)J enrichment for immune profiling (10x Genomics). For T-cell receptor (TCR) library construction, TCR transcripts were enriched from amplified cDNA by PCR. Subsequently, enriched PCR product was fragmented and end-repaired, size-selected, PCR-amplified with sample-indexing primers, and size-selected. For antibody-derived tagged library, we followed the protocol provided by BioLegend (HTO, TotalSeq-A)

value: Large Intestine, Small Intestine

value: Regulatory T cell


title: Skin Biopsy, unwounded skin, Day0, rep2


title: Skin Biopsy, unwounded skin, Day0, rep1


title: G751C_9D51_Ontogency

value: blood

value: bulk


title: Treg, mRNA-derived cDNA

description: 5' mRNA library; R1 -10X barcode and UMI, R2-Insert, I1-sample index, I2-sample index

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where HTO sequences were concatenated and treated as Custom library with default settings (v7.0.1) and aligning to the custom mm10 genome build that contained Foxp3thy1.1, Il10tdTomato-CreER, and Gt(ROSA)26SorLSL-YFP targeted mutations and ncBI RefSeq annotations.
Assembly: custom mm10 genome build that contained Foxp3thy1.1, Il10tdTomato-CreER, and Gt(ROSA)26SorLSL-YFP targeted mutations
Supplementary files format and content: 10x Genomics output files (filtered): barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz,  airr_rearrangement.tsv, filtered_contig_annotations.csv
Supplementary files format and content: HTO feature reference and h5ad files: feature_reference.csv, Treg_hto.h5ad


title: mOCCtrl_HMD201207001_DL18

value: ovary

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: mOCCtrl_HMD201207001_DD24


title: Skin Biopsy, PD, Day2, rep5

value: PD, Day2


title: mGCCtrl_HMD201207001_CJ03

value: interstitial cells


title: Skin Biopsy, PD, Day2, rep3


title: Skin Biopsy, PD, Day2, rep2


title: P023_9D05_Ontogency

value: Male


title: Skin Biopsy, PD, Day2, rep1


title: G727B_8U11_Ontogency


title: Treg, VDJ-seq, mRNA-derived cDNA

description: 5' VDJ-seq mRNA library; R1 -10X barcode and UMI, R2-Insert, I1-sample index, I2-sample index

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where HTO sequences were concatenated and treated as Custom library with default settings (v7.0.1) and aligning to the custom mm10 genome build that contained Foxp3thy1.1, Il10tdTomato-CreER, and Gt(ROSA)26SorLSL-YFP targeted mutations and ncBI RefSeq annotations.
Assembly: custom mm10 genome build that contained Foxp3thy1.1, Il10tdTomato-CreER, and Gt(ROSA)26SorLSL-YFP targeted mutations
Supplementary files format and content: 10x Genomics output files (filtered): barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz,  airr_rearrangement.tsv, filtered_contig_annotations.csv
Supplementary files format and content: HTO feature reference and h5ad files: feature_reference.csv, Treg_hto.h5ad
Library strategy: scVDJ-seq


title: mOCCtrl_HMD201207001_DB06


title: Skin Biopsy, P, Day2, rep4

value: P, Day2


title: mGCCtrl_HMD201207001_CL09

value: pre-granulosa cells


title: Skin Biopsy, P, Day2, rep5


title: Skin Biopsy, P, Day2, rep3


title: G755H_8P00_Ontogency


title: mGCCtrl_HMD201207001_CD03


title: Skin Biopsy, P, Day2, rep2


title: G760A_8L78_Ontogency


title: Skin Biopsy, P, Day2, rep1


title: Skin Biopsy, PD, Day4, rep6

value: PD, Day4


title: mOCCtrl_HMD201207001_DL14

value: oocytes


title: Skin Biopsy, PD, Day2, rep4


title: mGCCtrl_HMD201207001_CH11


title: P005_8H68_Ontogency


title: Skin Biopsy, PD, Day4, rep5


title: Skin Biopsy, PD, Day4, rep4


title: Skin Biopsy, PD, Day4, rep3


title: Skin Biopsy, PD, Day4, rep2


title: P027_8H46_Ontogency

value: Female


title: G753G_8H20_Ontogency


title: G745G_9A88_Ontogency


title: mGCCtrl_HMD201207001_AK03

value: granulosa cells


title: Skin Biopsy, P, Day4, rep5

value: Skin

value: P, Day4


title: Skin Biopsy, P, Day4, rep3


title: Skin Biopsy, P, Day4, rep4


title: Skin Biopsy, PD, Day4, rep1


title: mGCCtrl_HMD201207001_AG01


title: mGCCtrl_HMD201207001_AO07

value: ovarian surface epithelial cells


title: P032_8G93_Ontogency


title: Skin Biopsy, P, Day4, rep1


title: mGCCtrl_HMD201207001_BO08

value: early theca cells


title: Skin Biopsy, PD, Day12, rep5

value: PD, Day12


title: P004_8G07_Ontogency

value: blood

value: bulk


title: Skin Biopsy, P, Day4, rep2


title: Skin Biopsy, PD, Day12, rep4


title: P036_8D77_Ontogency


title: Skin Biopsy, PD, Day12, rep3


title: mGCCtrl_HMD201207001_CF23

value: ovary

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: Skin Biopsy, PD, Day12, rep1


title: Skin Biopsy, PD, Day12, rep2


title: P021_8C34_Ontogency


title: mGCCtrl_HMD201207001_BM10


title: G729E_8C71_Ontogency


title: Skin Biopsy, P, Day12, rep6

value: P, Day12


title: mOCCtrl_HMD201207001_DL24


title: mGCCtrl_HMD201207001_AO09


title: Skin Biopsy, P, Day12, rep2


title: P028_8F58_Ontogency

value: Male


title: Skin Biopsy, PD, Day12, rep6


title: mGCCtrl_HMD201207001_BA24


title: P010_8B24_Ontogency


title: G742E_8C18_Ontogency


title: mGCCtrl_HMD201207001_BC12


title: ES-E14TG2a, HDAC1-E63R, OHT treated, Rep 3

city: Leicester

first: Shaun

last: Cowley

address: Henry Wellcome Building, Lancaster Road

department: Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

data_processing:
Reads were mapped to mm10 using HISAT2 version 2.1.0 with default parameters
SAM files were then sorted and converted to BAM files using SAMtools version 1.9 with default parameters, SAMtools was also used to index BAM files
Read counts were generated using LiBiNorm version 2.4, run in htseq-count compatible mode using the Mus musculusGRCm38.92 genome annotation from Ensembl with parameters as follows: count -z -r pos -i gene_name -s reverse
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

growth_protocol: ESCs were grown on tissue culture plates pre-treated with 0.1% gelatine in KO DMEM supplemented with 15% FBS, pen-strep glutamine, 2-Mercaptoethanol and leukemia inhibitory factor in humidified atmosphere at 37 C with 5% CO2.

extract_protocol:
Total RNA was extracted using the TRI Reagent (Zymo Research, R2050-1-200) based Direct-Zol RNA MiniPrep Kit (Zymo Research, R2052) following the manufacturers instructions and quality checked using an Agilent Bioanalyzer by the NUCLEUS facility at the University of Leicester.
Library construction was performed by Novogene Cambridge using the NEB Next Ultra RNA Library Prep kit.

treatment_protocol: ESCs were  treated with 1uM 4-hydroxytamoxifen for 5 days to remove endogenous HDAC1/2.

value: Embryonic stem cells

value: OHT treated 5 days


title: ES-E14TG2a, HDAC1-E63R, OHT treated, Rep 2


title: P031_7R04_Ontogency


title: ES-E14TG2a, HDAC1-E63R, OHT treated, Rep 1


title: Skin Biopsy, P, Day12, rep1


title: ES-E14TG2a, HDAC1-E63R, untreated, Rep 3

value: Untreated 5 days


title: Skin Biopsy, P, Day12, rep4


title: mGCCtrl_HMD201207001_AC09

data_processing:
Adaptor sequences and low quality bases were trimmed using Fastq-mcf v1.1.2 in the ea-utils package.
The RamDA-seq reads were mapped to the mouse genome (GRCm38) using Hisat2 v2.2.0.
The gene count table was obtained using the featureCounts v2.0.1 tool in the Subread package with the option ‘-t exon -g gene_id’ and the annotation gtf file from GENCODE (vM25).
We evaluated the quality control metrics and filtered out low quality samples based on the RNA integrity assessed by coverage profile along the gene body and the number of detected genes ≤ 8,000.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw counts or TPM values for each sample.

value: interstitial cells


title: ES-E14TG2a, HDAC1-E63R, untreated, Rep 2


title: mOCCtrl_HMD201207001_DB04

value: oocytes


title: G752A_7P70_Ontogency

value: Female


title: Skin Biopsy, P, Day12, rep5

value: Skin


title: mOCCtrl_HMD201207001_DP18


title: ES-E14TG2a, HDAC1-Y48E, OHT treated, Rep 3


title: G746C_7P56_Ontogency


title: mGCCtrl_HMD201207001_CD01

value: granulosa cells


title: Skin Biopsy, P, Day12, rep3


title: ES-E14TG2a, HDAC1-Y48E, OHT treated, Rep 2


title: G734E_8C16_Ontogency


title: P042_7J91_Ontogency


title: ES-E14TG2a, HDAC1-Y48E, untreated, Rep 3


title: mGCCtrl_HMD201207001_AM11


title: mOCCtrl_HMD201207001_DN12


title: ES-E14TG2a, HDAC1-Y48E, untreated, Rep 1


title: ES-E14TG2a, HDAC1-Y48E, untreated, Rep 2


title: P002_7B96_Ontogency


title: ES-E14TG2a, HDAC1-WT, OHT treated, Rep 1


title: ES-E14TG2a, HDAC1-WT, OHT treated, Rep 2


title: ES-E14TG2a, HDAC1-WT, OHT treated, Rep 3


title: ES-E14TG2a, HDAC1-WT, untreated, Rep 3


title: G725C_7B42_Ontogency


title: P001_7A59_Ontogency


title: mGCCtrl_HMD201207001_BO06

value: pre-granulosa cells


title: ES-E14TG2a, HDAC1-E63R, untreated, Rep 1


title: G733B_6U56_Ontogency


title: ES-E14TG2a, HDAC1-WT, untreated, Rep 2


title: mGCCtrl_HMD201207001_CF01


title: P025_6T92_Ontogency


title: ES-E14TG2a, HDAC1-Y48E, OHT treated, Rep 1


title: ES-E14TG2a, HDAC1-WT, untreated, Rep 1


title: ES-E14TG2a, dTAG, 24 hour, ATAC-seq, Rep 2

description: 24 hour dTAG Rep2

data_processing:
Adapters were trimmed from the raw paired-end reads using trimmomatic, using the Nextera adapter sequence ‘CTGTCTCTTATACACATCT’
Trimmed reads were aligned to GRCm38 (mm10) using Bowtie 2, creating SAM files.
SAM files were converted to BAM files using SAMtools, duplicates were removed using the 'MarkDuplicates' function in Picard tools.
Reads were downsampled using the -view functiion in SAMtools based on the equation Subsampling ratio = Target coverage / Average genome coverage
Unpaired reads which became apparent after downsampling were re-paired using SAMtools -fixmate.
The Tn5 shift was corrected using deepTools alignmentSieve -ATACshift to correct by +4bp on the positive strand and -5bp on the negative strand, producing shifted BAM files.
Deeptools bamCoverage was used to generate bigWig files with a bin size of 10, blacklisted mm10 regions were removed using ENCODEs blacklist.
Assembly: mm10
Supplementary files format and content: BigWig files containing dense, continuous data to view on a genome browser.

extract_protocol:
DNA was extracted as part of the ATAC-seq protocol using the Active Motif ATAC-seq kit (Cat no:53150), following the manufacturers protocol.
Library was constructed as part of the Active Motif ATAC-seq kit (Cat no:53150) protocol.

treatment_protocol: ESCs were first treated with 1uM 4-hydroxytamoxifen for 5 days to remove endogenous HDAC1/2, these cells were then treated with 100 nM dTAGV-1 for 2/6/24 hours or with an equivlaent volume of DMSO.

value: dTAGV-1 100 nM 24 hour


title: mGCCtrl_HMD201207001_BI08


title: G747A_6R89_Ontogency


title: ES-E14TG2a, dTAG, 6 hour, ATAC-seq, Rep 2

description: 6 hour dTAG Rep2

value: dTAGV-1 100 nM 6 hour


title: ES-E14TG2a, dTAG, 24 hour, ATAC-seq, Rep 1

description: 24 hour dTAG Rep1


title: ES-E14TG2a, dTAG, 6 hour, ATAC-seq, Rep 1

description: 6 hour dTAG Rep1


title: ES-E14TG2a, dTAG, 2 hour, ATAC-seq, Rep 2

description: 2 hour dTAG Rep2

value: dTAGV-1 100 nM 2 hour


title: G765K_6J07_Ontogency

value: blood

value: bulk


title: ES-E14TG2a, dTAG, 2 hour, ATAC-seq, Rep 1

description: 2 hour dTAG Rep1


title: mGCCtrl_HMD201207001_AC17

value: ovary

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: ES-E14TG2a, DMSO, 24 hour, ATAC-seq, Rep 1

value: DMSO 24 hour


title: G754J_6H62_Ontogency

value: Male


title: mGCCtrl_HMD201207001_AE05


title: ES-E14TG2a, DMSO, 24 hour, ATAC-seq, Rep 2

value: Embryonic stem cells


title: mOCCtrl_HMD201207001_DJ14


title: wile-type mice, rep3

city: Kunming

first: Ming

last: Li

state: Yunnan

address: NO 32 Jiao-Chang Donglu

institute: Kunming Institute of Zoology, Chinese Academy of Sciences

data_processing:
Illumina NovaSeq 6000 reads were trimmed and clipped for quality control in Trimmomatic v0.39. (parameter: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 HEADCROP:15)
High-quality reads were then imported into STAR 2.7.10 for alignment into BAM files. (parameter: --genomeDir /path/to/ensembl_mm10/ --outSAMtype BAM SortedByCoordinate)
Gene read counts were calculated by featureCounts v2.0.3. (parameter: -T 24 -s 0 --primary -p -t exon -Q 10 -g gene_id -a /path/to/Mus_musculus.GRCm38.94.chr.gtf)
Assembly: ensembl_mm10
Supplementary files format and content: whitespace-delimited text file including raw counts for each sample

source_name: medial prefrontal cortex

extract_protocol:
Total RNA was extracted by Trizol.
RNA library for Strand-specific RNA-seq was prepared as fllows: mRNA was purified  from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA was synthesised using DNA polymerase I and dNTPs (dATP, dUTP, dCTP and dGTP). Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template without U was enriched by PCR, and the PCR product was purified to obtain the final library.

value: medial prefrontal cortex


title: mGCCtrl_HMD201207001_BE10

source_name: ovary

extract_protocol:
At postnatal day (PD) 7, ovaries from euthanized control mice (n=3) and from Wls cKO mice (n=8) were collected. Ovaries were treated with a CTK solution (consisting of 0.25% trypsin (Thermo), 0.1% collagenase type IV (Gibco), 20% KSR (Invitrogen) and 1 mM CaCl2 in PBS) for 30 min at 37°C, then further treated with Accutase (Nacalai) at 37°C for 15 min. The reaction was halted by adding L-15 medium with 0.1% penicillin-streptomycin and 5% FBS, and the cells were dissociated by pipetting. The cell suspension was filtered through 70 μm cell strainers, followed by centrifugation at 400 g for 5 min and resuspension in sorting buffer (7.5% BSA (Life Technologies) in PBS). Blocking was performed with rat IgG (5 mg/mL, I8015, Sigma-Aldrich) for 15 min on ice. Subsequently, cell surface staining was conducted using anti-ckit-APC (1:50, 105812, BioLegend) and anti-CD45-Alexa Fluor 488 (1:200, 103122, BioLegend) for 15 min on ice. After centrifugation at 400 g for 5 min, cells were resuspended in sorting buffer. Prior to single-cell sorting by flow cytometry, samples were passed through 40 μm cell strainers, and DAPI (1:10,000) was added. Control and Wls cKO samples were each sorted using MoFlo Astrios EQ with Summit v 6.3.0. software (Beckman Coulter) into 384-well plates containing 286 tdTomato-positive somatic cells and 95 ckit-positive oocytes. DAPI-positive dead cells and CD45-positive leukocytes were excluded.
Library preparation for RamDA-seq was performed according to a previously report. However, to reduce reagent costs and rRNA-derived sequencing reads, the method was modified as follows: To suppress rRNA-derived cDNA synthesis, 0.008 units/µl XRN-1 (NEB) was added to the genomic DNA digestion mix, and the reaction was performed at 30°C for 5 min. To reduce reagent costs, a liquid dispenser Mantis (Formulatrix) was used to perform the reaction up to second strand synthesis at 1/10 the reaction volume. After that, 2.5 μl 0.8 X Tagment DNA Buffer (Illumina) diluted with RNase-free water was added to 0.5 μl of the second strand synthesis products for dilution. Then, 0.5 μl Amplicon Tagment Mix (Illumina) was added to 1.5 μl of the diluted product, and tagmentation was performed at 55°C for 10 min. After that, the library was prepared using 1/10 the reaction volume according to the Nextera XT DNA Library Prep Kit (Illumina) procedure. Twelve PCR cycles were performed. Somatic and oocyte library products were collected separately in equal volumes of 1 μl/well. Subsequently, 50 μl of each sample was fractionated from the equal mixed library, purified with 1.2X AMPureXP (Beckman Coulter), and eluted with 25 μl TE. To prevent large discrepancies in the number of sequencing reads per cell between somatic and oocyte cells, purified libraries were mixed to ensure a constant average molar per cell type using the quantitative results from the Bioanalyzer Agilent High-Sensitivity DNA Kit and the ratio of the number of cells sorted (somatic cells: oocytes = 286:95). The pooled library of 2.3 pM was sequenced in single end read 76 cycles using NextSeq 500 High Output Kit v2.5.


title: wile-type mice, rep1


title: P009_6F91_Ontogency


title: wile-type mice, rep2


title: P006_6C43_Ontogency


title: Ino80e overexpression mice, rep3


title: mGCCtrl_HMD201207001_BK02


title: mGCCtrl_HMD201207001_CD09

value: interstitial cells


title: Ino80e overexpression mice, rep1


title: Ino80e overexpression mice, rep2


title: G764F_6B97_Ontogency


title: SKEL-4

city: Iowa City

first: Michael

middle: S

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

data_processing:
Barcoded samples were pooled and sequenced using an Illumina NovaSeq 6000 in the Iowa Institute of Human Genetics (IIHG) Genomics Core Facility. Paired-end reads were demultiplexed and converted from the native Illumina BCL format to FASTQ format using a custom python workflow wrapper to Illumina’s ‘bcl2fastq’ conversion utility. FASTQ data were processed with nf-core/rnaseq (v3.12), a best-practices pipeline available at the open-source ‘nf-core’ project (https://nf-co.re/, Nextflow version 22.10). Reads from the samples were aligned against the mouse reference genome ‘GRCm38’ using the STAR aligner and quantified with ‘salmon’. Samtools was used in conjunction with Qualimap and MultiQC to inspect alignment results. Length-normalized gene-level counts from the STAR/salmon pipeline were used for differential gene expression analysis with DESeq2.
nextflow run nf-core/rnaseq -r 3.10 -profile argon --igenomes_base /Users/mchiment/igenomes/references --input samplesheet_NOSKEL4.csv --outdir nf_NOSKEL4 --genome GRCm38 --email michael-chimenti@uiowa.edu --save_merged_fastq FALSE --skip_markduplicates TRUE --skip_preseq TRUE --skip_dupradar TRUE --skip_stringtie TRUE
Assembly: GRCm38
Supplementary files format and content: counts data

source_name: Quadricep

extract_protocol:
Tumor was homogenized using the mortar and pestal. Then RNA was isolated using Invitrogen purelink RNA mini kit.
Illumina TruSeq Stranded Total RNA w/ RiboZero was used following manufacture's protocol to make RNA library for RNA-seq .

value: Quadricep

value: Skeletal Muscle


title: mOCCtrl_HMD201207001_DD12

first: Tappei

last: Mishina

address: 744 Motooka Nishi-ku

institute: Kyushu University

value: oocytes


title: mGCCtrl_HMD201207001_AM19

value: granulosa cells


title: G731F_6B58_Ontogency

data_processing:
FastQC v0.11.9 and MultiQC v1.8 1 were used to assess sequence quality
Sequence reads were aligned to the hg38 human reference genome (Ensembl GRCh38v98) using STAR v2.7.3a
Counts of the number of reads mapped per gene were generated using htseq-count (HTSeq v0.11.2 3)
Assembly: Ensembl GRCh38v98
Supplementary files format and content: CSV; Count file containing assigned counts to each gene

value: Female


title: mGCCtrl_HMD201207001_AC15


title: wile-type mice, rep4


title: G757D_5U94_Ontogency

source_name: Vaccination: Delayed - Visit 2 collected at day 1


title: mGCCtrl_HMD201207001_CJ21

value: pre-granulosa cells


title: G739A_5U83_Ontogency


title: G741K_6G70_Ontogency


title: SKEL-1


title: QUAD-3

value: Tumor


title: SKEL-2


title: Ino80e overexpression mice, rep4


title: mGCCtrl_HMD201207001_AA15

value: excluded by low quality


title: mOCCtrl_HMD201207001_DF16


title: QUAD-2


title: P007_5S17_Ontogency

value: blood


title: P013_6C30_Ontogency

value: bulk


title: SKEL-3


title: QUAD-1


title: QUAD-5


title: mGCCtrl_HMD201207001_AE11

value: ovary


title: QUAD-6


title: SKEL-5


title: P017_5L07_Ontogency


title: TAZ-5


title: mGCCtrl_HMD201207001_AA21

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: TAZ-9


title: G758F_5J63_Ontogency


title: TAZ-2


title: mGCCtrl_HMD201207001_BE04


title: TAZ-1


title: YAP-5


title: mOCCtrl_HMD201207001_DD10


title: YAP-4


title: YAP-3


title: YAP-2


title: G744D_5B98_Ontogency


title: P034_5F69_Ontogency


title: mGCCtrl_HMD201207001_BM18

value: ovarian surface epithelial cells


title: YAP-1


title: PTEN-4


title: PTEN-5


title: mOCCtrl_HMD201207001_DP14


title: PTEN-3


title: TAZ-4


title: PTEN-1


title: PTEN-2


title: mOCCtrl_HMD201207001_DJ22


title: mGCCtrl_HMD201207001_AM07


title: mGCCtrl_HMD201207001_AI09


title: corticosterone group, scRNAseq

city: Beijing

first: Yingying

last: Huang

address: Yanyuan Street

institute: Peking University

description: GWXSCOPE single cell RNA library

data_processing:
Basecalls performed using bcl2fastq V2.19.
Assembly: GRCm38
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: microglia

extract_protocol:
The prefrontal cortical tissues of mice were freshly dissected and minced into small pieces on ice. The tissues were digested in RPMI 1640 (Thermo Fisher Scientific) / 0.1mg/ml Liberase TL (Roche) / 20g/ml DNase I (Sigma-Aldrich) / 10mM HEPES / 3% heat-inactivated fetal bovine serum (HI-FBS; Sigma-Aldrich) at 37oC for 15 min. The tissues were mashed through a 70-m cell strainer and centrifuged at 500 g for 5 min. The cells were re-suspended in PBS / 2% HI-FBS / 10mM EDTA-Na (pH 8.0) and stained with PE/Cyanine7 anti-mouse CD45 (BioLegend, #103114, RRID:AB_312979) and FITC anti-mouse/human CD11b (BioLegend, #101206, RRID:AB_312788). FACS-stained cells were processed on the Beckman MoFlo Astrios EQ, and microglia were sorted as CD45low CD11b+ by the common standard.
The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron) . Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

value: microglia


title: vehicle group, scRNAseq

description: GWXSCOPE single cell RNA library


title: P040_5B97_Ontogency

value: Male


title: mGCCtrl_HMD201207001_CL01

city: Fukuoka


title: G756B_5G90_Ontogency

source_name: Vaccination: Delayed - Visit 2 collected at day 7


title: Smo-Cre 3

city: Durham

first: KUO

last: DU

state: NC

address: 905 SOUTH LASALLE STREET, Room 1063

department: Medicine

institute: Duke Universty

data_processing:
RNA-seq data were processed using the fastp toolkit to trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads. Only reads that were ≥20nt after trimming were kept for further analysis. Reads were mapped to mice genome reference combining the GRCm38. STAR v2.7.5 was used to align reads to reference genome. Gene count was quantified by featureCounts v2.0.1.
Assembly: GRCm38
Supplementary files format and content: count.txt

source_name: Liver

extract_protocol:
RNA was harvested using Trizol (Invitrogen)
RNA samples were sequenced by Novogene Corporation following standard construction protocol.
In brief, RNA degradation and contamination were monitored on 1% agarose gels. RNA purity was checked using a NanoPhotometer Spectrophotometer (IMPLEN). RNA integrity and quantity were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies). Sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Clustering of index-coded samples was performed on an Illumina NovaSeq sequencer

value: Liver

value: SMO KO

value: AAV8-TBG-Cre Recombinase


title: G723K_4L48_Ontogency

source_name: Vaccination: Delayed - Visit 2 collected at day 3

extract_protocol:
Total RNA was extracted from each sample using the Paxgene Blood RNA kit (catalog no.: 762164;Qiagen, Valencia, CA, USA) following the manufacturer’s protocol. RNA quantification and quality assessment was performed using an Agilent 2100 Bioanalyzer (Santa Clara, CA, USA)
The NEBNextPoly(A) mRNA Magnetic Isolation Module (catalog no.: E7490L, NEB; Ipswich, MA, USA) was used to capture poly-adenylated RNA. Strand-specific cDNA libraries were generated using the KAPA RNAHyperPrep Kit (catalog no.: 08098107702, Roche; Basel, Switzerland) on a Freedom EVO 100 (Tecan,Männedorf, Switzerland).


title: mOCCtrl_HMD201207001_DH12


title: P008_4R46_Ontogency


title: Smo-Cre 2


title: G721J_4K65_Ontogency


title: Smo-Luc 4

value: WT


title: P045_4G54_Ontogency


title: Smo-Luc 3


title: Smo-Luc 2


title: mGCCtrl_HMD201207001_CP03


title: Smo-Luc 1


title: P030_4B83_Ontogency


title: Lcmr1 KO RNA poll III ChIP-seq

city: Nanjing

first: Kai

address: #818, East Tianyuan Road

institute: Nanjing Medical University

data_processing:
Alignment by BWA
Filtering by Samtools
Narrow peaks by Macs2
BigWig files by Deeptools bamCoverage
Deseq2 for differential analysis
Assembly: Assembly: mm10
Supplementary files format and content: Supplementary files format and content:BigWig files

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using sonication.
The DNA libraries were amplified for 15 cycles and sequenced using Illumina NovaSeq 6000 with paired-end 150 as the sequencing mode

treatment_protocol: Primary hepatocyte were isolated with two step-digestion method (Charni-Natan, M. et al, STAR Protocol 2020). Primary hepatocytes were stimulated with 100 nM glucagon for 12 h at 37°C.

value: liver

value: primary hepatocyte

value: hepatocyte

value: ko (Lcmr1f/f * albumin-cre)

value: primary hepatocyte were seperated and cultured in vitro for 24h


title: G749H_4M44_Ontogency

first: Ofer

address: 300 Longwood Avenue

institute: Boston Children's Hospital

value: Female


title: mGCCtrl_HMD201207001_BM20

value: interstitial cells


title: Con RNA poll III ChIP-seq

value: control (Lcmr1f/f)


title: Smo-Cre 4


title: G732J_4A74_Ontogency

value: blood

value: bulk


title: P043_3S86_Ontogency


title: Lcmr1 KO3 RNA-seq

description: KO3 (colum in kovsctl.txt)

data_processing:
Perl script was used to filter the original data (Raw Data)
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated
DEGseq v1.18.0 was used for differential gene expression analysis
Assembly: Assembly: mm10
Supplementary files format and content: Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA from 10^6 primary hepatocytes were extracted using the RNeasy Plus Micro Kit (Qiagen).
Libraries were prepared using a TruSeq RNA Sample Prep Kit (Illumina, 20020594)


title: Lcmr1 KO1 RNA-seq

description: KO1 (colum in kovsctl.txt)


title: P024_4Q69_Ontogency


title: mGCCtrl_HMD201207001_CN09

value: ovary

value: ovarian surface epithelial cells

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: mGCCtrl_HMD201207001_BI24


title: Ctl3 RNA-seq

description: Ctl3 (colum in kovsctl.txt)


title: P019_3S38_Ontogency


title: mGCCtrl_HMD201207001_AM21

value: granulosa cells


title: Ctl2 RNA-seq

description: Ctl2 (colum in kovsctl.txt)


title: P022_3Q99_Ontogency

value: Male


title: Ctl1 RNA-seq

description: Ctl1 (colum in kovsctl.txt)


title: M2 macrophage Ets1 ChIP-seq

data_processing:
Alignment by BWA
Filtering by Samtools
Narrow peaks by Macs2
BigWig files by Deeptools bamCoverage
Deseq2 for differential analysis
Assembly: mm10
Supplementary files format and content: BigWig files

source_name: Bone Marrow-derived Macrophage (BMDM)

treatment_protocol: Bone marrow cells were isolated from 8-week-old male mice. The cells were then cultured for 7 days to retain only the bone marrow-derived macrophages (BMDMs), using the medium containing 10% FBS, 10ng/ml M-CSF, and antibiotics.

value: Bone Marrow-derived Macrophage (BMDM)

value: primary macrophage

value: macrophage

value: wild type C57

value: primary BMDM were seperated and cultured in vitro for 7d, followed by induced M2 polarization.


title: Smo-Cre 1

value: Liver

value: SMO KO

value: AAV8-TBG-Cre Recombinase


title: mGCCtrl_HMD201207001_CH03


title: mGCCtrl_HMD201207001_CL17

value: pre-granulosa cells


title: ko3 RNA-seq

description: K3 (column in ConvsKo.xlsx)

data_processing:
Perl script was used to filter the original data (Raw Data)
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated
DEGseq v1.18.0 was used for differential gene expression analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA from 10^6 primary BMDM were extracted using the RNeasy Plus Micro Kit (Qiagen).
Libraries were prepared using a TruSeq RNA Sample Prep Kit (Illumina, 20020594)

value: ko (Ets1 f/f * Lyz2-cre)

value: primary BMDM were seperated and cultured in vitro for 7d


title: P014_3G56_Ontogency

value: blood

value: bulk

value: Female


title: ko2 RNA-seq

description: K2 (column in ConvsKo.xlsx)


title: mGCCtrl_HMD201207001_CJ07

value: ovary

value: early theca cells

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: ko1 RNA-seq

description: K1 (column in ConvsKo.xlsx)

value: Bone Marrow-derived Macrophage (BMDM)


title: Lcmr1 KO2 RNA-seq

description: KO2 (colum in kovsctl.txt)

value: liver

value: primary hepatocyte

value: hepatocyte

value: ko (Lcmr1f/f * albumin-cre)

value: primary hepatocyte were seperated and cultured in vitro for 24h


title: con2 RNA-seq

description: C2 (column in ConvsKo.xlsx)

value: primary macrophage

value: macrophage

value: control (Ets1 f/f)


title: P029_3F41_Ontogency


title: con3 RNA-seq

description: C3 (column in ConvsKo.xlsx)


title: mGCCtrl_HMD201207001_BC24

value: pre-granulosa cells


title: mOCCtrl_HMD201207001_DF12

value: oocytes


title: con1 RNA-seq

description: C1 (column in ConvsKo.xlsx)

value: primary BMDM were seperated and cultured in vitro for 7d


title: G730C_3F20_Ontogency

value: blood

value: bulk


title: G763H_3F05_Ontogency

value: Female


title: scATAC_Multiome of liver nuclei from LKO mice

description: 10 x Genomics

library_source: genomic single cell

data_processing:
Demultiplexed snRNA- and snATAC-seq fastq files were processed using the Cell Ranger ARC pipeline (2.0.2) from 10x Genomics to perform alignment, filtering, and generate barcoded count matrices of gene expression and ATAC data. Quality control was performed to include nuclei with TSS enrichment > 3, more than 2,500 ATAC fragments, 200 - 50,000 RNA transcripts, < 1% mitochondrial reads, and < 5% ribosomal reads. Doublets were removed using the filterDoublets function in ArchR (1.0.2). For snRNA-seq data analysis, Seurat (4.3.0) was used to analyze snRNA-seq data after quality control filtering [363 (5%) < nCount_RNA < 8568 (95%), 240 (5%) < nFeature_RNA < 3138 (95%), and < 13% (95%) mitochondrial reads] and removal of doublets.  The total number of cells is 1,543.
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

source_name: liver single nuclei

growth_protocol: Mice were housed on a normal 12/12 light-dark cycle. Mice had ad libitum access to a normal chow diet (Envigo, cat# 2016) and water, or a HFD with 60 kcal% fat (Research Diets, D12492) and water

extract_protocol:
Nuclei were isolated from the pooled liver tissues of six mice (20 mg per liver) using 10 x genomics nuclei isolation kit
Single nucleus multiome libraries were prepared using the 10x Genomics Single Cell Multiome ATAC + Gene Expression kit following the manufacturer’s instructions

treatment_protocol: Female mice were fed a high-fat diet (D12492) for 16 weeks

value: female

value: liver-specific knockout

value: high-fat diet


title: mGCCtrl_HMD201207001_CN21

value: ovary

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: scRNA_Multiome of liver nuclei from LKO mice

description: 10 x Genomics

molecule: nuclear RNA

value: liver


title: mOCCtrl_HMD201207001_DL06


title: G738K_3D80_Ontogency


title: M1 macrophage Ets1 ChIP-seq

value: Bone Marrow-derived Macrophage (BMDM)

value: wild type C57

value: primary BMDM were seperated and cultured in vitro for 7d, followed by induced M1 polarization.


title: scRNA_Multiome of liver nuclei from floxed mice

description: 10 x Genomics

value: floxed


title: G743F_3B31_Ontogency

value: Male


title: mGCCtrl_HMD201207001_CF05

value: early theca cells


title: P016_3L70_Ontogency


title: Brain macrophages, APP-KI, Fit2-Mut, scRNAseq, Biol Rep 1

city: Singapore

first: James

middle: Alastair

last: Miller

address: 11 Mandalay Road

department: Lee Kong Chian School of Medicine

country: Singapore

institute: Nanyang Technological University

description: 10X Genomics

data_processing:
Sample was mapped to transcriptome mm10-2020-A via cellranger pipeline version 7.0.0 using chemistry Single Cell 3' v3
Assembly: mm10
Supplementary files format and content: Tab-separated barcode, features, and matrix files

source_name: Whole brain

extract_protocol:
Macrophages were isolated from mouse brain. In brief, mice were decapitated, and their brains were harvested and digested in 2% FBS Iscove's Modified Dulbecco's Medium (IMDM) containing DNase Ⅰ (Roche), Collagenase D (Roche), and Dispase Ⅱ (Gibco). Afterwards, tissues were crushed and homogenized using a syringe, and then filtered through a cell strainer. Myelin debris and red blood cell contamination were removed via Percoll® gradient and 0.89 % NH4CL lysis buffer. Finally, the cell suspension was collected for further antibody staining. CD45(int) microglia and CD206+border-associated macrophages were sorted for further steps.
The library was performed according to the manufacturer's instructions (10x Genomics Single Cell Gene Expression 3’ v3.1).

value: Whole brain

value: macrophages


title: P038_3B01_Ontogency

city: Boston

last: Levy

value: blood


title: Brain macrophages, APP-KI, Fit2-Mut, scRNAseq, Biol Rep 2

description: 10X Genomics


title: mGCCtrl_HMD201207001_BM02

value: interstitial cells


title: mGCCtrl_HMD201207001_AI21


title: Brain macrophages, APP-KI, Fit2-Mut, scRNAseq, Biol Rep 4

description: 10X Genomics


title: P026_2U83_Ontogency

value: bulk

value: Female


title: Brain macrophages, APP-KI, Fit2-WT, scRNAseq, Biol Rep 2

description: 10X Genomics


title: Brain macrophages, APP-KI, Fit2-WT, scRNAseq, Biol Rep 4

description: 10X Genomics


title: Brain macrophages, APP-KI, Fit2-WT, scRNAseq, Biol Rep 3

description: 10X Genomics


title: mGCCtrl_HMD201207001_AA09


title: P012_2U19_Ontogency


title: Brain macrophages, APP-KI, Fit2-Mut, scRNAseq, Biol Rep 3

description: 10X Genomics


title: scATAC_Multiome of liver nuclei from floxed mice

description: 10 x Genomics

value: female


title: Brain macrophages, Fit2-Mut, scRNAseq, Biol Rep 3

description: 10X Genomics


title: Brain macrophages, Fit2-Mut, scRNAseq, Biol Rep 4

description: 10X Genomics


title: Brain macrophages, APP-KI, Fit2-WT, scRNAseq, Biol Rep 1

description: 10X Genomics


title: G724H_2S11_Ontogency


title: Brain macrophages, Fit2-Mut, scRNAseq, Biol Rep 2

description: 10X Genomics


title: Brain macrophages, Fit2-Mut, scRNAseq, Biol Rep 1

description: 10X Genomics


title: G735D_2P55_Ontogency


title: mOCCtrl_HMD201207001_DP20

value: oocytes


title: Brain macrophages, Fit2-WT, scRNAseq, Biol Rep 4

description: 10X Genomics


title: mGCCtrl_HMD201207001_AG09

value: ovary


title: Brain macrophages, Fit2-WT, scRNAseq, Biol Rep 3

description: 10X Genomics


title: P039_2M12_Ontogency


title: Brain macrophages, Fit2-WT, scRNAseq, Biol Rep 2

description: 10X Genomics


title: Brain macrophages, Fit2-WT, scRNAseq, Biol Rep 1

description: 10X Genomics


title: G722G_2L45_Ontogency


title: mOCCtrl_HMD201207001_DL22

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: CC+Cortex, P15, Mu, rep2

first: 敏溪

last: 方

address: 杭师大仓前

institute: 浙江大学

data_processing:
To identify DEGs (differential expressed genes) upon Smoothened overexpression, the expression level of each gene was calculated according to the transcripts per million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundance. Differential expression analysis was performed using DESeq2, and DEGs with log2-fold ≥1 and p-adjust ≤0.05 were considered to be significantly differentially expressed genes.
Assembly: GRCm38.p6
Supplementary files format and content: Differentially expressed genes text files include TPM values for each Sample

source_name: CC+Cortex

extract_protocol:
Segments of cc and cortex tissues were dissected from wild type and Pdgfra-creER;SmoM2 at P15
The transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1 μg of total RNA.

value: CC+Cortex

value: P5-P7 injected tamoxifen


title: G748B_2J51_Ontogency


title: CC+Cortex, P15, Mu, rep1


title: CC+Cortex, P15, WT, rep2

value: WT


title: mGCCtrl_HMD201207001_BG08

value: ovarian surface epithelial cells


title: CC+Cortex, P15, WT, rep1


title: G736G_2G73_Ontogency


title: ChAT-IRES-cre Control HFD

city: Bronx

first: Jeffrey

middle: E

last: Pessin

state: NY

address: 1301 Morris Park Avenue

department: Medicine and Molecular Pharmacology

institute: Albert Einstein College of Medicine

description:
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

data_processing:
FASTQ files were analyzed and aggregated with Space Ranger Pipeline with default settings (10x Genomics https://www.10xgenomics.com/support/software/space-ranger/latest)
Expression violin plots were generated using Loupe Browser
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: aggregated cloupe file
Library strategy: Spatial transcriptomics

extract_protocol:
Liver tissue was flash-frozen in liquid nitrogen, sectioned at 10um thickiness, and mounted on the gene expression slide provided in the 10X Visium kit
Tissue sections were fixed, stained (H&E) and imaged according to 10x Genomics protocol CG000160 • Rev B.  An NGS library was produced from each section accoding to User Guide CG000239 Rev D

treatment_protocol: All mice were fed HFD (research diets #D12492) for 10 weeks

value: Liver

tag: strain

value: ChAT-IRES-cre+GFP

tag: diet

value: HFD:research diets #D12492


title: mGCCtrl_HMD201207001_BC10

tag: tissue

tag: developmental stage


title: mGCCtrl_HMD201207001_CP07

tag: cell type

value: pre-granulosa cells

tag: subpopulation gc


title: P044_2A10_Ontogency


title: ChAT-IRES-cre dTA HFD

value: Male

tag: genotype

value: ChAT-IRES-cre+dTA


title: mOCCtrl_HMD201207001_DB16

value: excluded by low quality

tag: subpopulation oocyte

tag: marker expression_tdtomato


title: spinal cord, P0, WT

data_processing:
Pair-end sequencing was performed on Illumina platform (San Diego, CA)
Data were processed further with MACS version 2.1.0 peak calling software to identify regions enriched in IP over Input samples.
HOMER was used to detect the de novo motif and the matched known motifs of Myt1 peaks.
Assembly: mm39
Supplementary files format and content: Differentially expressed genes text files include RPKM values for each Sample
Supplementary files format and content: bigwig

source_name: spinal cord

extract_protocol:
Segments of spinal cord tissues at the thoracic region were dissected from wild type and Myt1-/- embryos at P0
Library construction and sequencing of ATAC-seq were performed by Novogene Co., Ltd. (Beijing, China).go, CA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: spinal cord


title: G762B_1U79_Ontogency

value: blood

value: bulk


title: mGCCtrl_HMD201207001_BM24

tag: marker expression_kit-apc

tag: cell size_(fsc1_area)


title: spinal cord, P0, Myt1-/-, rep2

data_processing:
To identify DEGs (differential expressed genes) upon Myt1 deletion, the expression level of each gene was calculated according to the transcripts per million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundance. Differential expression analysis was performed using DESeq2, and DEGs with log2-fold ≥1 and p-adjust ≤0.05 were considered to be significantly differentially expressed genes.
Assembly: GRCm38.p6
Supplementary files format and content: Differentially expressed genes text files include RPKM values for each Sample

extract_protocol:
Segments of spinal cord tissues at the thoracic region were dissected from wild type and Myt1-/- embryos at P0
The transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1 μg of total RNA.


title: G761D_1U56_Ontogency

tag: treatment


title: mGCCtrl_HMD201207001_BI20

data_processing:
Adaptor sequences and low quality bases were trimmed using Fastq-mcf v1.1.2 in the ea-utils package.
The RamDA-seq reads were mapped to the mouse genome (GRCm38) using Hisat2 v2.2.0.
The gene count table was obtained using the featureCounts v2.0.1 tool in the Subread package with the option ‘-t exon -g gene_id’ and the annotation gtf file from GENCODE (vM25).
We evaluated the quality control metrics and filtered out low quality samples based on the RNA integrity assessed by coverage profile along the gene body and the number of detected genes ≤ 8,000.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw counts or TPM values for each sample.

value: interstitial cells

tag: intron ratio


title: mGCCtrl_HMD201207001_CJ09

value: ovary


title: spinal cord, P0, WT, rep3

tag: age


title: spinal cord, P0, Myt1-/-, rep3


title: spinal cord, P0, Myt1-/-, rep1


title: spinal cord, P0, Myt1-/-


title: spinal cord, P0, WT, rep2


title: P035_1T97_Ontogency

value: Female


title: P018_1T23_Ontogency


title: spinal cord, P0, WT, rep1


title: mOCCtrl_HMD201207001_DL12

value: oocytes

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: mGCCtrl_HMD201207001_CH07


title: E135_H3K27ac_Hdac1&2_cKO_rep2

city: Shanghai

first: Yunli

last: Xie

state: Shanghai

address: 131 Dong'an Road, Shanghai

department: Institutes of Brain Science

institute: Fudan University

data_processing:
Raw data were aligned to the GRCm38/mm10 genome by Bowtie2 v2.2.5 using parameters: -end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Bam files were converted to paired end BED files using BEDTools v2.30.0 bamtobed with the -bedpe flag, then the read pairs that are on the same chromosome and fragment length less than 1000bp were selected to generate a new BED file, and finally we converted bed file to a bedgraph file using genomecov from BEDTools.
Peaks were called using SEACR v.1.3.0 with the parameters: -0.01 -norm -stringent.
Normalized bigwig files were generated by BamCoverage from Deeptools v3.5.1, which were then visualized on IGV v2.16.2.
Diffbind v3.2.7 was used to differential peaks binding affinity analysis.
Assembly: mm10
Library strategy: CUT&Tag

source_name: brain

extract_protocol:
Histone modifications in this study were identified using the Cleavage Under Targets and Tagmentation (CUT&Tag) technique, following the protocol published by the Henikoff lab. For both wild-type (WT) and HDAC1/2 conditional knockout (cKO) cerebral cortices, three biological replicates were prepared.
We employed the Rabbit anti-H3K27ac antibody (Active Motif 39136) for specific targeting. The Tn5-tagmented DNA fragments were then amplified using the 2x CAM Mix, a uniquely barcoded i5 primer, and a uniquely barcoded i7 primer, undergoing 12 amplification cycles. Libraries were quantified on a Qubit 4 fluorometer (Thermo Fisher Scientific Q33226). We performed size-selection on the libraries, isolating DNA fragments exceeding 300 base pairs using VAHTS DNA Clean Beads (Vazyme N411). Finally, the pooled libraries were sequenced in a paired-end mode using the Illumina NovaSeq 6000 platform.

value: brain

tag: cell line

value: mouse brain cells

value: embryonic day 13.5


title: mOCCtrl_HMD201207001_DD16


title: E135_H3K27ac_Hdac1&2_cKO_rep1


title: E135_CTX_H3K27ac_Control_rep2

value: wild type


title: mOCCtrl_HMD201207001_DP10


title: E135_CTX_H3K27ac_Control_rep3


title: P033_1F51_Ontogency

tag: Sex


title: mGCCtrl_HMD201207001_BA08


title: E165_Wnt9a_IUE_rep3

data_processing:
raw data were first trimmed using Trim Galore v.0.6.7 then mapped to the mm10 genome by HISAT2 v2.2.1 with default parameters.
The number of reads mapping to each gene were counted by featureCounts v2.0.1 with parameters: -a gencode.vM20.annotation.gtf. And transcripts per million (TPM) were calculated.
Assembly: mm10

extract_protocol:
Total RNA was isolated from cerebral cortices at E13.5, E14.5, E15.5 and E16.5 using TRIzol reagent (ThermoScientific) according to the manufacturer’s instructions.
Total RNA was isRNA-seq was performed at Novogene Biotech Co., Ltd in Beijing, China.

value: Wnt9a OE

value: embryonic day 16.5


title: G750E_1M07_Ontogency

value: Male


title: E135_CTX_H3K27ac_Control_rep1


title: E165_Wnt9a_IUE_rep1


title: G759K_1D89_Ontogency


title: E165_Wnt9a_IUE_Control_rep2


title: G726A_1F08_Ontogency


title: E165_Wnt9a_IUE_rep2


title: mOCCtrl_HMD201207001_DD18


title: G737H_1D87_Ontogency


title: E165_Wnt9a_IUE_Control_rep3


title: E12.5_control_scRNAseq

value: embryonic day 12.5


title: E135_H3K27ac_Hdac1&2_cKO_rep3


title: mOCCtrl_HMD201207001_DH16


title: P037_1P35_Ontogency


title: E165_Wnt9a_IUE_Control_rep1


title: mGCCtrl_HMD201207001_AC13


title: EHF_H3K4me1

first: fu

last: Ai

state: Guangdong

address: Jingxijiedao

institute: Southern Medical University

data_processing:
Reads containing barcodes were de-multiplexed to generate single cell profiles by custom scripts.
Trimmed paired-end reads were mapped to a mouse mm10 genome reference genome with bowtie2.
Duplicate reads were removed using picard. Only uniquely reads>1500 cells will be remained.
Peaks were called uing macs2 with nolambda、nomedel and broad.
Bigwig files were generated using the Deeptools BamCoverage，reads were normalized to 1000000.
Assembly: mm10
Supplementary files format and content: broadPeak
Supplementary files format and content: Tab-separated values files and matrix files

source_name: embryos

growth_protocol: Mouse embryos were dissected at time points of E6.0, E6.5, E7.0, E7.25 and E7.5, and the individual embryo was micro-dissected and staged as pre-streak (Pre_Ps), Early Streak (ES), Mid-Streak (MS), Late Streak (LS), No Allantoic Bud (OB), and Early Headfold (EHF) stages according to their morphology. Pre-PS, ES, MS and LS embryos were dissected to remove extra-embryo tissues.

extract_protocol:
The embryos were microdissected and digested with Collagenase I dissociation buffer at 37°C for 15-60 min to generate single-cell suspension. The dissociated single cells were collected by centrifugation at 600 g for 3 min. After incubation with Con-A beads, the cell-bead mixture was fixed with methyl alcohol and incubate on ice for 5 min.
Custom library preparation was performed by two steps of PCR amplification. The first step was performed by addition of 0.5 μL 25 μM Truseq connector primer (Connector primer F:5′-ACACTCTTTCCCTACACGACGCTCTTCCGATCTTCGTCGGCAGCGTCTCCACGC-3′.Connector primer R:5′-GACTGGAGTTCAGACGTGTGCTCTTCCGATCTGTCTCGTGGGCTCGGCTGTCCCTGT-3′), 25 μL 2X Taq master mix and 16.5 μL 1mM MgCI2 to the 3 μL CoBATCH cell lysis in each tube and the reaction was set up by incubation at 72°C for 5 min, 95°C for 5 min, 13-16 cycles of amplification (95°C for 30 s, 63°C for 30 s, 72°C for 1 min), and final 72°C extension for 5 min. The PCR enrichment was directly performed in the same tube as described above. Then 0.4 μL Exo1 was added and incubated at 37°C for 1 h followed by inactivation at 72°C for 20 min. The second PCR enrichment was performed by adding 0.7 μL 10 μM Truseq i5 primer (5′- AATGATACGGCGACCACCGAGATCTACAC[i5]TCGTCGGCAGCGTC-3′), 0.7 μL 25 μM i7 index primer (5′-CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGG-3′), 20 μL 2X Taq master mix and 8.6 μL 1 mM MgCI2 followed by incubation at 95°C for 5 min, 5-7 cycles of  95°C for 30 s, 63°C for 30 s, 72°C for 1 min, and final 72°C extension for 5 min. Finally, the PCR products were purified and selected by SPRI beads for 200-1000 bp.

value: embryos

tag: time point

tag: Stage

value: gastrulation

tag: gastrulation stage

value: EHF

tag: chip antibody