title: C-39_B_control_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq22
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 170 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: DKO_Olig2_Rep1

status: Public on Mar 23 2024

type: SRA

city: Toronto

first: Chi-chung

last: Hui

state: Ontario

address: 686 Bay Street. Room 16-9712

department: Developmental & Stem Cell Biology

country: Canada

institute: The Hospital for Sick Children

library_source: genomic

data_processing:
Adaptor sequences were trimmed using Trimmomatic 0.36 with adaptor sequence file TruSeq3-PE-2.fa
Reads were aligned to the mm9 reference genome using default parameters of BWA MEM
Aligned reads were filtered using bamtools to exclude unmappped reads, mapping quality < 5, and not proper pairs.
ENCODE blacklist regions in mm9 were filtered out using bedtools
Peaks were called using MACS2 with q = 0.05
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated from bam files using bamCoverage tool from DeepTools. They represent sequencing-depth-normalized continuous profile of read coverages.

molecule: genomic DNA

organism: Mus musculus

source_name: DKO_Olig2_P13 medulloblastoma

extract_protocol:
Tumours were dissected, cut into small pieces, and crosslinked in solution A (1% formaldehyde, 50mM Hepes-KOH, 100 mM NaCl, 1mM EDTA, 0.5 mM EGTA) for 20 minutes at room temperature. 1/20 volume of 2.5 M glycine was added to quench formaldehyde. Tissues were rinsed in ice-cold PBS and dounced in Wheaton tissue grinder. Cell suspensions were passed through a 100μm cell strainer to remove connective tissues, then centrifuged at 4 °C at 2500 × rcf for 3 min, followed by a wash in PBS. Olig2 antibody (EMD Millipore, ab15328) was incubated with pre-blocked magnetic beads in 250μL total volume for 8 hours at 4 °C, then washed and resuspended in 100μL 0.5% BSA (w/v) solution. Cell pellets were lysed by sequentially resuspending and centrifuging in LB1 (50 mM Hepes-KOH, pH 7.5; 140 mM NaCl; 1mM EDTA; 10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100), and LB2 (10 mM Tris-HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA). Pellet was resuspended in LB3 (10 mM Tris-HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na-Deoxycholate; 0.5% N-lauroylsarcosine) and sonicated into 200-400bp fragments. Sonicated lysates were diluted with LB3. After saving 50μL for input control, they were split into tubes containing 10% v/v Triton X-100 with Olig2 antibody, and incubated overnight. Beads were washed 6 times in RIPA buffer (50 mM Hepes-KOH, pH 7.5; 500 mM LiCl; 1mM EDTA; 1% NP-40 or Igepal CA-630; 0.7% Na-Deoxycholate), and once in TBS (20 mM Tris-HCl, pH 7.6; 150 mM NaCl). Protein-DNA complexes were eluted and crosslink reversed with 200 μL of elution buffer (50 mM Tris-HCl, pH 8; 10 mM EDTA; 1% SDS). The 50μL input lysate was also included in this step. Eluted DNA was diluted with 200 μL of TE, and treated with RNaseA for 30 min at 37°C, and subsequently with proteinase K for 2 hours at 55°C. Phenol:chloroform:isoamyl alcohol was used to extract DNA.
Libraries were prepared according to manfacturer's instructions for the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® kit.

tag: developmental stage

tag: tissue

value: medulloblastoma

tag: genotype/variation

value: Sufu;Spop double knockout

tag: chip antibody

value: Olig2 (EMD Millipore, catalog# ab15328, lot# 2898266)


title: DKO_input_Rep2

source_name: DKO_input_P13 medulloblastoma


title: GM2_Olig2_Rep2

source_name: GM2_Olig2_P13 medulloblastoma

value: SmoM2 overexpression


title: C-32_B_control_primary_single_oocyte_RNA

city: Beijing

first: Bofeng

last: Liu

address: Haidian District

department: School of Life Science

country: China

institute: Tsinghua University

library_source: transcriptomic

data_processing:
library strategy: Smart-seq15
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

molecule: total RNA

source_name: Oocyte

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 163 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).

tag: genotype

value: wild-type

tag: cell type

value: oocyte


title: DKO_input_Rep1


title: DKO_Olig2_Rep2


title: Motor Neuron, Empty Vector Unpreturbed, Day 12, Bio Rep 1  [EV1]

city: Cambridge

first: Kristina

middle: M

last: Holton

state: MA

address: 7 Divinity Ave

department: HSCRB

country: USA

institute: Harvard University

description:
EV1
Day 12 11a Motor Neuron Empty Vector Rep 1

data_processing:
bcl2fastq v2.20
fastqc 0.11.9
multiqc 1.13.0
STAR aligner 2.7.1a, sjdb 100 (read length-1) ; --outSAMtype BAM SortedByCoordinate \--outSAMunmapped Within \--outSAMattributes NH HI NM MD AS \--outReadsUnmapped Fastx \--quantMode GeneCounts; MultiQC post-alignment:>80% uniquely mapped reads, low duplication levels
Assembly: Ensemble GRCh38 r109, with YFP chromosome added; Gene Symbol from org.Hs.eg.db
Supplementary files format and content: counts_unnorm.txt ; Tab Delimited file of read counts by gene symbol in all 32 samples

molecule: polyA RNA

organism: Homo sapiens

source_name: Spinal Cord

growth_protocol: Motor neurons were produced by differentiation from 11a iPSCs previously transduced with Neurogenin 2 Doxycycline inducible overexpression construct. Cells were differentiated using an accelerated motor neuron differentiation protocol that couples NGN2 overexpression with exposure to patterning factors to direct differentiation to spinal cord motor neurons. The full protocol and characterization of the method can be located in Limone, et. al 2023. Neurons were cultured without a mouse glia baselayer. The 11a iPSC line was derived from a biopsy from a 37-year-old healthy male patient as previously described in Boulting et al. 2011. Neurons were maintained for 5 days following completion of the differentiation protocol before harvesting RNA, for a total of 12 days in culture.

extract_protocol:
Homogenization of samples prior to column extraction was performed using Qiagen Qiashredder columns. RNA extraction was performed using Qiagen Mini RNEasy Plus Kits accoding to manufacturer's instructions.
Kapa mRNA Hyperprep

treatment_protocol: ATXN2 knockout was conferred to 11a iPSCs using CRISPR and single-cell cloning before transduction with inducible TDP-43 perturbations. TDP-43 perturbations were conferred in ATXN2 intact and knockout via recombination at the AAVS1 safe harbor locus with a plasmid harboring a doxycycline inducible expression cassette.

value: Spinal Cord

tag: cell line

value: Motor Neuron

value: Wild Type


title: C-31_B_control_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq14
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 162 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: GM2_input_Rep2

source_name: GM2_input_P13 medulloblastoma


title: Motor Neuron, Empty Vector Unpreturbed, Day 12, Bio Rep 2 [EV2]

description:
EV2
Day 12 11a Motor Neuron Empty Vector Rep 2


title: C-36_B_control_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq19
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 167 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: Glc-3

city: Rochester

first: Alexander

middle: Quinn

last: Wixom

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

description:
Glc-3
normalized_counts_Glc.txt

data_processing:
Fastq reads were trimmed using fastx_trimmer (v0.0.14).
Trimmed sequence reads were mapped to hg38 using STAR (v2.7.9a), and counts were obtained using --quantMode GeneCount.
Stranded read counts from STAR were imported into R and normalized using DESeq2.
Assembly: hg38
Supplementary files format and content: normalized count files include DESeq2 normalized counts for each sample

source_name: hepatic stellate cells

growth_protocol: Hepatic stellate cells (HSCs) were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Primary human HSCs were transfected with either Control or HK2 shRNAs for 48 hours and then cultured in the presence or absence of 1 g/L glucose for 8 hours (samples 1 through 12).
Primary human HSCs were cultured in the presence of 1 g/L glucose and treated with vehicle or 2-deoxyglucose for 8 hours (samples 13 through 18).

value: hepatic stellate cells

value: stromal cells (liver)

value: WT

tag: treatment

tag: time

value: 8 hours


title: Glc+2DG-3

description:
Glc_plus_2DG-3
normalized_counts_Glc.txt


title: GM2_input_Rep1


title: GM2_Olig2_Rep1


title: C-30_B_control_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq13
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 161 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: Motor Neuron, Empty Vector Unpreturbed, Day 12, Bio Rep 4 [EV4]

description:
EV4
Day 12 11a Motor Neuron Empty Vector Rep 4


title: PLC/PRF/5, IFRD1_KO_2 ATAC_seq

city: hefei

first: sun

last: xuedan

address: daoxiangcun

institute: ustc

data_processing:
(RNASeq)Quality Control:  In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or   fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by   Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N:   0.1) to be high quality clean data.   Alignment:   Firstly, reference genome sequences and gene model annotation files of relative species were downloaded   from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index  reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2   (v2.0.1).   Expression analysis   In the beginning transcripts in fasta format are converted from known gff annotation file and indexed   properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform   expression levels from the pair-end clean data.   Differential expression analysis   Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative   binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven   prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
(ATACSeq)The data analysis workflow first involved adapter trimming and removing low-quality reads using Trim_Galore software in paired-end mode. Clean reads were then mapped to the hg38 reference genome with Bowtie2 followed by removing PCR duplicates using Picard. The genome browser tracks in bigwig format were produced from merged replicates using samtools and peaks called using MACS2 using parameters ‘-f BAMPE --nomodel --shift -100 --extsize 200 -nomodel’. The bigwig data were visualized using the IGV software (Broad Institute). Peak visualizations were prepared using Deeptools.
Assembly: hg38
Supplementary files format and content: text files include FPKM values for each Sample
Supplementary files format and content: bigwig

extract_protocol:
phenol/chloroform
RNA libraries for RNA-seq were prepared using AZENTA mRNA-Seq Library Prep Kit following manufacturer's protocols.And ATAC-Seq libraries were generated following manufacturer’s protocol (NOVOPROTEIN, N248)

value: Hepatocellular carcinoma cells

value: glutamine starvation


title: Glc+2DG-2

description:
Glc_plus_2DG-2
normalized_counts_Glc.txt


title: PLC/PRF/5,  IFRD1_KO_1 ATAC_seq


title: C-29_B_control_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq12
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 160 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: PLC/PRF/5, WT-1 ATAC_seq


title: PLC/PRF/5, WT-2 ATAC_seq


title: C-28_B_control_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq11
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 159 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: HepG2, CB839_2


title: HepG2, CB839_1


title: Glc+2DG-1

description:
Glc_plus_2DG-1
normalized_counts_Glc.txt


title: HepG2, Ctrl_2

value: Ctrl


title: Glc-1

description:
Glc-1
normalized_counts_Glc.txt


title: HepG2, Ctrl_1


title: shHK2+Glucose-3

description:
shHK2_plus_Glucose-3
normalized_counts_shKD.txt


title: C-23_A_control_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq10
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 158 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: C-20_A_control_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq8
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 156 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: C-22_A_control_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq9
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 157 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: Het_HFD_10

city: New York

first: Nneka

last: Southwell

state: New York

address: 407 E 64th St Fl 5

department: Brain and Mind Research Institute

institute: Weill Cornell Graduate School

data_processing:
Raw sequence reads were processed using the BBDuk program in the BBMap package.
Trimmed reads were aligned to the mouse genome assembly GRCm38.p6 using the STAR aligner (version 2.5.0a).
SAM files were converted to BAM to read overlapping reads per gene using HTSeq-count (version 0.6.1)
Assembly: GRCm38.p6
Supplementary files format and content: Tab-delimited text files contain raw counts for each sample

source_name: Heart

extract_protocol:
Hearts were removed and flash frozen in liquid nitrogen. RNA was harvested using Trizol and the SV Total RNA Isolation Kit (Promega). 500 ng of RNA were used to construct the sequencing libraries.
Libraries were sequenced on the Illumina NextSeq500 sequencer.

value: Heart

tag: strain

tag: age (d)

tag: Sex

value: M

value: CHCHD10 S55L Het

value: High Fat Diet


title: C-1_A_control_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq7
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 155 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: Het_HFD_6


title: shControl+Glucose-3

description:
shControl_plus_Glucose-3
normalized_counts_shKD.txt


title: Het_HFD_5

value: F


title: C-19_A_control_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq6
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 154 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).

value: wild-type


title: Het_HFD_7


title: Het_HFD_4


title: Glc-2

description:
Glc-2
normalized_counts_Glc.txt


title: Het_HFD_3


title: Het_HFD_2


title: C-18_A_control_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq5
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 153 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).

value: oocyte


title: shHK2+Glucose-2

description:
shHK2_plus_Glucose-2
normalized_counts_shKD.txt


title: Het_HFD_1


title: Het_HFD_9


title: shHK2-2

description:
shHK2-2
normalized_counts_shKD.txt


title: Het_HFD_8


title: C-16_A_control_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq3
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 151 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: C-17_A_control_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq4
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 152 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: shControl+Glucose-2

description:
shControl_plus_Glucose-2
normalized_counts_shKD.txt


title: WT_HFD_9


title: C-10_A_control_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq2
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 150 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: WT_HFD_10


title: WT_HFD_7


title: shControl-3

description:
shControl-3
normalized_counts_shKD.txt


title: WT_HFD_8


title: WT_HFD_6


title: shControl-2

description:
shControl-2
normalized_counts_shKD.txt


title: WT_HFD_3


title: p10_Lamin_4

data_processing:
library strategy: DamID
Basecalls performed using CASAVA version 1.8
DamID was processed as previously described (Borsos et al., 2019). Briefly, DamID was mapped to mm10 genome, and the computation of OE value per bin was carried out as previously described (Kind et al., 2015). Reads that precisely flanked an annotated GATC site were associated with GATC fragments and kept for downstream analysis.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The DamID procedure was performed as previously described (Borsos et al., 2019). Briefly, an mRNA mixture containing 100 ng/μl membrane-eGFP, and AID–Dam–lamin B1 or AID–Dam were injected into the cytoplasm of oocytes. Oocytes were isolated and injected with 5 ng/μl AID–Dam–lamin B1 or 20 ng/μl AID–Dam and kept in auxin-free M2 medium for 6–8 h to methylate LADs or accessible regions, respectively. Following oocyte collection, library preparation and sequencing were performed as previously described (Borsos et al., 2019).

value: Growing oocyte P10


title: WT_HFD_4


title: WT_HFD_5


title: p10_Lamin_3


title: shHK2-1

description:
shHK2-1
normalized_counts_shKD.txt


title: WT_HFD_2


title: shHK2+Glucose-1

description:
shHK2_plus_Glucose-1
normalized_counts_shKD.txt


title: T-4_a_Tcf3_12_dKO_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq89
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 237 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).

value: Tcf3/12 KO


title: WT_HFD_1


title: Het_CD_10

value: Control Diet


title: Het_CD_9


title: shHK2-3

description:
shHK2-3
normalized_counts_shKD.txt

data_processing:
Fastq reads were trimmed using fastx_trimmer (v0.0.14).
Trimmed sequence reads were mapped to hg38 using STAR (v2.7.9a), and counts were obtained using --quantMode GeneCount.
Stranded read counts from STAR were imported into R and normalized using DESeq2.
Assembly: hg38
Supplementary files format and content: normalized count files include DESeq2 normalized counts for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: hepatic stellate cells


title: Het_CD_7


title: Regorafenib-treated sorafenib-resistant huh7 (SR+Rego)-3

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

country: South Korea

institute: Hanyang Univ.

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
To avoid low-quality data, we clipped and trimmed the reads using Trimmomatic (v0.33)
For the analysis of differentially expressed genes, the data of quality-checked reads for each condition were processed with the STAR (version 2.7.1) software based on reference genome sequence (The GENCODE Homo sapiens reference sequence GRCh38 (Release 27) and the differential gene expressed values of each sample were calculated by the DESeq2 Bioconductor package.
The number of reads mapped to gene ID features were counted using STAR.
Assembly: The GENCODE Homo sapiens reference sequence GRCh38 (Release 27)
Supplementary files format and content: tab-delimited text files including normalized read counts for each sample

source_name: Huh7 cells

growth_protocol: The HCC cell line Huh7 (https://cellbank.snu.ac.kr/eng/tmpl/sub_main.php?m_cd=46&m_id=0201&sp=2&c_id=769) was purchased from the Korean Cell Line Bank (Seoul, Korea) and cultured in MEM supplemented with 10 % heat-inactivated FBS, penicillin, and streptomycin (Thermo Fisher Scientific, Waltham, MA, USA) at 37 °C in a humidified atmosphere with 95 % air / 5 % CO2.

extract_protocol:
Total RNA was extracted using RNAiso Plus (Takara, Shiga, Japan) and QIAGEN RNeasy® Mini kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions.
RNA libraries were created using the NEBNext Ultra Directional RNA Library Preparation Kit for Illumina (New England BioLabs, Ipswich, MA, USA), and transcriptome sequencing was performed using the Illumina HiSeq2500 platform (Macrogen, Seoul, Korea).

treatment_protocol: To establish sorafenib-resistant (SR) HCC cells, the cells were treated with increasing concentrations of sorafenib from 1 to 10 µM over a period of 6 months. Con and SR Cells were treated with DMSO (Con), Regorafenib (5 uM).

value: Hepatocellular carcinoma

value: Sorafenib-resistant (SR) cells were treated with regorafenib


title: BULK-TCRb_COH4_56

city: PARIS

first: Anne-laure

last: Le gac

address: 26 rue d'ulm

country: France

institute: Institut Curie

data_processing:
For the single cells, the demultiplexing, barcoded processing, gene counting  were made using the Cell Ranger software version 7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
For the bulk TCR seq, Mixcr (version 4.4.2) was used to perform the alignment and assemble the reads with the following parameters: milab-human-rna-tcr-umi-multiplex.
Assembly: GRCh38-2020-A for the scRNA-seq and vdj_GRCh38_alts_ensembl-3.1.0-3.1.0 for sc V(D)J-seq.

source_name: blood

extract_protocol:
Trizol for bulk TCR
Human TCR RNA Multiplex-Thrm-001 Kit (MiLaboratories)  for bulk TCR,
10X
Other : CITE-seq, bulk TCRseq

treatment_protocol: FACS sorting for scRNAseq

value: blood

value: T cells


title: p10_Lamin_1


title: Het_CD_8


title: shControl-1

description:
shControl-1
normalized_counts_shKD.txt

value: stromal cells (liver)

value: WT

value: 8 hours


title: p10_Dam_4


title: Regorafenib-treated sorafenib-resistant huh7 (SR+Rego)-2


title: p10_Dam_3


title: Regorafenib-treated sorafenib-resistant huh7 (SR+Rego)-1


title: BULK-TCRa_COH4_56


title: p10_Dam_1


title: Het_CD_5

value: Heart


title: p10_Dam_2


title: SCRNAseq_COH4_56

description: 10x Genomics

library_source: transcriptomic single cell

source_name: tumor

value: tumor


title: Het_CD_4

value: CHCHD10 S55L Het


title: Het_CD_6

value: M


title: STARR_lib_DNA_input

data_processing:
library strategy: STARR-seq
Basecalls performed using CASAVA version 1.8
STARR-seq was processed as previously described (Neumayr et al., 2019). Briefly, STARR-seq was mapped to mm9 genome by Bowtie with similar parameters as ChIP-seq data. All unmapped reads and non-uniquely mapped reads were removed. For downstream analysis, we calculated the read counts by computing RPKM on the genome 100-bp bin for input controls and RNA. STARR-seq signals were then calculated as RNA / input. The background level of STARR-seq was estimated using all negative controls (n = 64; 16 negative controls x 2 replicates x both strands). After excluding outliers (n = 4), the cut-off was determined as the values that correspond to mean + 3 standard deviation (FC = 0.29, 99.7% confidence level). Enhancer candidates with STARR-seq RNA/input higher than the cut-off in both replicates from at least one strand of enhancers were identified as STARR-seq positive enhancers. The rest were classified as STARR-seq negative enhancers.
Assembly: mm9

source_name: genomic DNA

extract_protocol: The candidate enhancer sequences were obtained from PCR of genome DNA (primer sequences in Supplementary Table 3) and cloned between the ORF, a truncated form of GFP, and the polyA site in the hSTARR-seq_ORI vector (Addgene, #99296), which makes each candidate sequence serving as its own barcode. Briefly, the PCR products of each candidate enhancer were purified, pooled together, and ligated with Illumina adaptors in NEBNext Ultr II DNA Library Prep Kit (NEB, E7645S). Subsequently, adaptor-ligated PCR products were cleaned up with AMPure XP beads and amplificated by PCR with library cloning primers (forward: 5`-TAGAGCATGCACCGGACACTCTTTCCCTACACGACGCTCTTCCGATCT, reverse: 5`-GGCCGAATTCGTCGAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT) (1 μl adaptor-ligated PCR products, 2.5 μl 10 μM library cloning forward primer, 2.5 μl 10 μM library cloning reverse primer, 25 μl KAPA 2X HiFi HotStart Ready Mix (Roche, KK2602), and 19 μl H2O) with the program of 98 °C for 45 s, (98°C for 15 s, 65°C for 30 s, and 72°C for 45 s) with 5 cycles, and 72 °C for 2 min, which results in that candidate sequences were flanked by overlap sequences with vector around insertion site. The hSTARR-seq_ORI vector was restriction digested by AgeI-HF and SalI-HF and purified for Gibson assembly with ClonExpress II One Step Cloning Kit (Vazyme, C112). The STARR-seq plasmid library was amplified using Illumina i5 and i7 index primers and its quality and complexity were assessed by deep sequencing.

value: wild-type


title: BULK-TCRa_COH4_76


title: Sorafenib-resistant huh7 (SR)-1

value: Huh7 cells were treated with chronic sorafenib, resulting in sorafenib resistance


title: shControl+Glucose-1

description:
shControl_plus_Glucose-1
normalized_counts_shKD.txt


title: p10_Lamin_2

value: Growing oocyte P10

value: oocyte


title: Het_CD_3

value: F

value: Control Diet


title: Sorafenib-resistant huh7 (SR)-2

value: Hepatocellular carcinoma


title: FGO_STARR_seq_rep2

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The STARR-seq plasmid library was purified and injected into the pronucleus of FGOs cultured with milrinone. After 24 hrs, the FGOs were lysed in hypotonic lysis buffer (Vazyme, N712), and the polyadenylated mRNAs were captured by the Oligo (dT) primers. After 3 min at 72 °C, the Smart-seq2 reverse transcription reactions were performed. After pre-amplification and AMPure XP beads purification, cDNAs were amplified with junction PCR primers (forward: 5`-TCGTGAGGCACTGGGCAG*G*T*G*T*C, reverse: 5`-CTTATCATGTCTGCTCGA*A*G*C, *:phosphorothioate bond), which specifically enriches reporter transcripts and excludes STARR-seq plasmids, as the junction forward primer only binds to the spliced intron of the reporter transcripts. Then the PCR products were cleaned up with AMPure XP beads, and we performed sequencing-ready PCR to add Illumina i5 and i7 indexes for deep sequencing. All libraries were sequenced on Illumina HiSeq 2500 according to the manufacturer’s instruction.

value: Full grown oocyte


title: SCRNAseq_COH4_76

description: 10x Genomics


title: Regorafenib-treated huh7 (Rego)-3

value: Huh7 cells were treated with regorafenib


title: FGO_STARR_seq_rep1


title: BULK-TCRb_COH4_84

value: blood

value: T cells


title: Het_CD_1


title: Regorafenib-treated huh7 (Rego)-2


title: Sorafenib-resistant huh7 (SR)-3


title: BULK-TCRa_COH4_84


title: GO_P7_ATAC_rep2

data_processing:
Basecalls performed using CASAVA version 1.8.
ATAC-seq reads were aligned to the mm9 genome using bowtie 2.2.2. Replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome.
Assembly: mm9
Supplementary files format and content: bigWig files

extract_protocol:
P7 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ATAC-seq procedure was performed as previously described (Wu et al. 2018). Briefly, cells were transferred into 6 μl of lysis buffer [10 mM tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, and 0.02% digitonin) in ice for 10 min. The ATAC reaction was performed by adding 4 μl of ddH2O, 4 μl of 5× TTBL, and 5 μl TTE mix V5 (Vazyme Biotech Co.,Ltd, catalog no. TD502) at 37°C for 30 min and then stopped by adding 5 μl of 5× TS stop buffer at room temperature for 5 min. DNA was extracted by phenol chloroform and ethanol purification after adding 40 ng of carrier RNA and 103 μl of tris-EDTA. Then, DNA was PCR-amplified with 10 μl of index (Vazyme Biotech Co.,Ltd, catalog no. TD202), 10 μl of 5× TAB and 1 μl tris-acetate-EDTA (Vazyme Biotech Co.,Ltd, catalog no. TD502) with the program of 72°C for 3 min, 98°C for 30 s, (98°C for 15 s, 60°C for 30 s, and 72°C for 3 min) with 18 cycles, and 72°C for 5 min.

value: Oocyte

value: Growing oocyte P7


title: BULK-TCRb_COH4_76


title: WT_CD_9

value: Heart

value: WT


title: Regorafenib-treated huh7 (Rego)-1


title: Control Huh7 (Con)-3

value: Huh7 cells were treated with DMSO


title: SCRNAseq_COH4_84

description: 10x Genomics

value: tumor


title: PC9-BrM3

city: Dalian

first: Mengyi

last: Tang

address: 467 Zhongshan Road

institute: the Second Affiliated Hospital of Dalian Medical University

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
(For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . padj<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression.
Assembly: Hisat2 (v2.0.5).
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: lung cancer

growth_protocol: PC9-BrM3 were routinely cultured in Roswell Park Memorial Institute medium-1640 (RPMI1640) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin and streptomycin (all these reagents were obtained from Gibco, Invitrogen, Inc, California, USA). Human HA1800 astrocytes were purchased from ScienCell (USA) and cultured in the medium recommended by the manufacturer. All cells maintained in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using Trizol (Transgen, China) and RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

treatment_protocol: Astrocytes and tumor cells were planted in the upper or lower layers of the transwell, respectively. Co-culture experiments were performed when cell fusion was 90% for astrocytes and 60% for cancer cells. The duration of co-culture was 12 h, and used a polyethylene terephthalate (PET)membrane (pore size: 0.4 µm) Tissue Culture Plate Insert.

value: lung cancer

value: lung cancer cell line

value: routine culture


title: WT_CD_8

value: M


title: mESC_WT_H3K4me3_rep2

description: STAR ChIP-seq

data_processing:
Basecalls performed using CASAVA version 1.8.
STAR ChIP-seq reads were aligned to the mm9 genome using bowtie 2.2.2. Replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome.
Assembly: mm9
Supplementary files format and content: bigWig files

source_name: Embryonic stem cell

extract_protocol: STAR ChIP-seq was performed as previously described (Zhang et al., 2016). Briefly, samples were lysed followed by fragmented by micrococcal nuclease (MNase, Sigma, N3755-200UN) at 37 °C for 5 min. After being terminated, the supernatant containing chromatin was incubated with the primary antibody at 4 °C overnight with rotation. The next day, 100 μg of Protein A/G dynabeads (mixed at 1:1, Thermo Fisher Scientific) was added to each sample and incubated at 4 °C for 2–3 h with rotation. The beads were then washed five times with 150 μl RIPA buffer and once with 150 μl LiCl buffer. For each sample, beads were resuspended with 28 μl H2O, 1 μl 10× Ex-Taq buffer (Takara, RR006B) and 1 μl proteinase K (NEB, P8107S) and incubated at 55 °C for 90 min, followed by incubation at 72 °C for 40 min to inactivate the proteinase K. Samples were then subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). STAR ChIP-seq libraries were sequenced using the HiSeq X Ten system or NovaSeq (Illumina) according to the manufacturer’s protocol.

value: Embryonic stem cell

value: wild-type

tag: antibody

value: H3K27ac (Active Motif 39133)


title: Control Huh7 (Con)-2

value: Hepatocellular carcinoma


title: PC9-BrM3+Astro

value: cultured with astrocytes for 12 h


title: WT_CD_7

extract_protocol:
Hearts were removed and flash frozen in liquid nitrogen. RNA was harvested using Trizol and the SV Total RNA Isolation Kit (Promega). 500 ng of RNA were used to construct the sequencing libraries.
Libraries were sequenced on the Illumina NextSeq500 sequencer.

value: Control Diet


title: Het_CD_2

value: F

value: CHCHD10 S55L Het


title: WT_CD_6


title: mESC_Dnmt3ab_dKO_H3K4me3_rep2

description: STAR ChIP-seq

value: Dnmt3a/b KO


title: Astro

source_name: astrocyte cell line

value: astrocyte cell line


title: Control Huh7 (Con)-1


title: Setdb1-KO bio rep1 and rep 2[ATAC-seq]

city: Lyon

first: Pauline

last: GARCIA

address: 8 avenue Rockefeller

institute: INMG

data_processing:
nf-core/atacseq v1.2.1
Nf-core/atacseq v1.2.1 was used on a docker container and in standard parameters to compute a rds archive readable in R and different files in multiple formats (bigwig, bed, bam). Data were filtered to conserve only features in canonical chromosomes (1 to 19, X, Y and mitochondrial).
To determine chromatin occupancy, bam files were parsed and only reads paired were conserved, properly paired and MAPQ score = 60 with Rsamtools package (v2.10.0).
Differential analysis was performed on count reads over regions from peak calling with DEseq2 package (v1.34.0).
Assembly: GRCm38
Supplementary files format and content: bigwig

source_name: primary cell line

extract_protocol:
Cells were trypsinized and frozen in F10 medium+20%FBS+10%DMSO
Library construction was done following the Diagenode kit instruction by the Diagenode services: Library amplification, library purification, QC on the ATAC-seq library, library pooling       Library purification      QC on the ATAC-seq library (DNA concentration, analysis of library profile)      Library pooling
Gain insight into gene regulation and understand open chromatin signature

value: primary cell line

value: Muscle stem cells

value: KO

value: Tamoxifen

value: 3 days


title: mESC_Dnmt3ab_dKO_H3K4me3_rep1

description: STAR ChIP-seq


title: mESC_WT_H3K4me3_rep1

description: STAR ChIP-seq


title: WT_CD_5

data_processing:
Raw sequence reads were processed using the BBDuk program in the BBMap package.
Trimmed reads were aligned to the mouse genome assembly GRCm38.p6 using the STAR aligner (version 2.5.0a).
SAM files were converted to BAM to read overlapping reads per gene using HTSeq-count (version 0.6.1)
Assembly: GRCm38.p6
Supplementary files format and content: Tab-delimited text files contain raw counts for each sample

value: Heart

value: WT


title: Astro+PC9-BrM3

value: cultured with PC9-BrM3 for 12 h


title: GO_P7_ATAC_rep1

value: Oocyte

value: wild-type

value: Growing oocyte P7


title: Control bio rep1 and rep 2  [ATAC-seq]

value: Oil


title: WT_CD_10

value: M

value: Control Diet


title: WT_CD_3

value: F


title: GO_P7_H3K27ac_rep1

description: STAR ChIP-seq

data_processing:
Basecalls performed using CASAVA version 1.8.
STAR ChIP-seq reads were aligned to the mm9 genome using bowtie 2.2.2. Replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome.
Assembly: mm9
Supplementary files format and content: bed file

extract_protocol:
P7 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
STAR ChIP-seq was performed as previously described (Zhang et al., 2016). Briefly, samples were lysed followed by fragmented by micrococcal nuclease (MNase, Sigma, N3755-200UN) at 37 °C for 5 min. After being terminated, the supernatant containing chromatin was incubated with the primary antibody at 4 °C overnight with rotation. The next day, 100 μg of Protein A/G dynabeads (mixed at 1:1, Thermo Fisher Scientific) was added to each sample and incubated at 4 °C for 2–3 h with rotation. The beads were then washed five times with 150 μl RIPA buffer and once with 150 μl LiCl buffer. For each sample, beads were resuspended with 28 μl H2O, 1 μl 10× Ex-Taq buffer (Takara, RR006B) and 1 μl proteinase K (NEB, P8107S) and incubated at 55 °C for 90 min, followed by incubation at 72 °C for 40 min to inactivate the proteinase K. Samples were then subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). STAR ChIP-seq libraries were sequenced using the HiSeq X Ten system or NovaSeq (Illumina) according to the manufacturer’s protocol.

value: H3K27ac (Active Motif 39133)


title: Liver tissue, Tspo fl/fl , 3

city: Ithaca

first: Vimal

last: Selvaraj

state: NY

address: 204 Morrison Hall

department: Animal Sciences

institute: Cornell University

data_processing:
After adaptor trimming and low-quality sequence removal the reads were mapped to mouse genome using STAR to obtain raw reads
The counts per million (CPM) for each gene was obtained using EdgeR
The differential gene expression analysis was performed using EdgeR
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read values for each Sample

source_name: Liver

extract_protocol:
Total RNA was isolated using Trizol.
mRNA was captured using poly (A) and cDNA libraries were prepared using TruSeq stranded total RNA sample preparation kit (Illumina)

value: Liver

value: Tspo fl/fl

value: 8-12 weeks


title: SampleJ, Spatial transcriptome sequencing

city: Bei jing

first: Xiaojian

last: Lu

state: Bei jing

address: No.3, Datusi Road, Chaoyang District, Beijing

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology，Chinese Academy of Sciences

description: 10x Genomics

data_processing:
The Visium spatial transcriptomics array was processed using the Spaceranger software (version 1.0.0) provided by 10X Genomics, which enabled the alignment and summarization of unique molecular identifier (UMI) counts against the hg38 human reference genome for every spot.
Supplementary files format and content: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: testis tumor

extract_protocol:
Before sequencing, we assessed RNA quality using DV200, DV200≥50% be used. We then conducted a tissue adhesion test, followed by deparaffinization and H&E staining. After staining, we captured images of the area using brightfield settings and released the RNA through decrosslinking. We then added an integrative transcriptome probe panel, which consisted of a pair of specific probes for each target gene, to the previously stained tissue. Probe pairs hybridized to their complementary target RNA and formed a stable ligation product with the addition of a ligase. After processing the ligation structure, we released the single-stranded ligation products from the tissue. RT Master Mix containing reverse transcription reagents was then added for amplification, followed by the addition of UMI, barcode and partial Read1. The library with barcoded ligation products was released to qPCR to determine cycle amplification number, added with index, and finally constructed the library containing P5 and P7 primers used for Illumina amplification. The library molecules were cleaned up by SPRIselect and assessed, quantified, and sequenced on a bioanalyzer or similar instrument using PE150 mode sequencing on the Illumina NovaSeq600 platform
Spatial transcriptome sequencing

value: testis tumor


title: SampleZ, Spatial transcriptome sequencing

description: 10x Genomics


title: 8cell_H3K27ac_rep2

description: STAR ChIP-seq

source_name: Preimplantation embryo

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG. Embryos were harvested in M2 medium 65 h after hCG.
STAR ChIP-seq was performed as previously described (Zhang et al., 2016). Briefly, samples were lysed followed by fragmented by micrococcal nuclease (MNase, Sigma, N3755-200UN) at 37 °C for 5 min. After being terminated, the supernatant containing chromatin was incubated with the primary antibody at 4 °C overnight with rotation. The next day, 100 μg of Protein A/G dynabeads (mixed at 1:1, Thermo Fisher Scientific) was added to each sample and incubated at 4 °C for 2–3 h with rotation. The beads were then washed five times with 150 μl RIPA buffer and once with 150 μl LiCl buffer. For each sample, beads were resuspended with 28 μl H2O, 1 μl 10× Ex-Taq buffer (Takara, RR006B) and 1 μl proteinase K (NEB, P8107S) and incubated at 55 °C for 90 min, followed by incubation at 72 °C for 40 min to inactivate the proteinase K. Samples were then subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). STAR ChIP-seq libraries were sequenced using the HiSeq X Ten system or NovaSeq (Illumina) according to the manufacturer’s protocol.

value: Preimplantation embryo


title: Liver tissue, Tspo fl/fl , 1


title: WT_CD_1


title: 19355X4, scRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: testis

extract_protocol:
For each single-cell RNA sequencing experiment, a single cryovial of tissue was swiftly thawed. The tissues were rinsed twice with PBS and transformed into a single-cell suspension using the previously described protocol. First, the tissues were scraped with razor blades and then enzymatically digested using 1mg/mL collagenase type IV (Sigma Aldrich)/1mg/mL DNase I (Sigma Aldrich) followed by the digestion with trypsin-EDTA (Invitrogen)/1mg/mL DNase I at 37℃ for 5 minutes. Afterward, single cells were filtered through 40 µm strainers (Thermo Fisher Scientific) and washed with D-PBS (Thermo Fisher Scientific). At last, the cells were resuspended in D-PBS +0.4% BSA (Thermo Fisher Scientific) at a concentration of ~1,000 cells/mL, rendering them ready for single-cell sequencing
The protocol used for the experiment was based on the user guide provided by 10X Genomics for Chromium Next GEM Single Cell 3ʹReagent Kits v3.1. To generate and barcode the GEMs, cells were diluted to achieve approximately 5000 cells per lane and were loaded with the master mix onto the Chromium Next GEM Chip G. Following post-GEM-RT cleanup, cDNA Amplification was conducted using 12 cycles. The resulting libraries were then sequenced on an Illumina Novaseq instrument using the following settings: 28 cycles for Read 1, 10 cycles for i5 index, 10 cycles for i7 index, and 90 cycles for Read 2

value: testis

tag: disease state

value: tumor stage

tag: age

value: 38 years old


title: 2cell_late_Parthenogenetic_Eed_KO_H3K27ac_rep1

description: STAR ChIP-seq

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG. MII oocytes were harvested in M2 medium 13 h after hCG.
STAR ChIP-seq was performed as previously described (Zhang et al., 2016). Briefly, samples were lysed followed by fragmented by micrococcal nuclease (MNase, Sigma, N3755-200UN) at 37 °C for 5 min. After being terminated, the supernatant containing chromatin was incubated with the primary antibody at 4 °C overnight with rotation. The next day, 100 μg of Protein A/G dynabeads (mixed at 1:1, Thermo Fisher Scientific) was added to each sample and incubated at 4 °C for 2–3 h with rotation. The beads were then washed five times with 150 μl RIPA buffer and once with 150 μl LiCl buffer. For each sample, beads were resuspended with 28 μl H2O, 1 μl 10× Ex-Taq buffer (Takara, RR006B) and 1 μl proteinase K (NEB, P8107S) and incubated at 55 °C for 90 min, followed by incubation at 72 °C for 40 min to inactivate the proteinase K. Samples were then subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). STAR ChIP-seq libraries were sequenced using the HiSeq X Ten system or NovaSeq (Illumina) according to the manufacturer’s protocol.

treatment_protocol: Without specific statement, all reagents were purchased from Sigma Aldrich. Calcium ion free CZB with few modifications: 81.62 mM NaCl, 4.83 mM KCl, 1.18 mM KH2PO4, 1.18mM MgSO4, 25.12 mM NaHCO3, 0.27mM sodium pyruvate (11360070, Gibco), 1x GlutaMAX (35050061, Gibco) 5 mg/ml bovine serum albumin (BSA). For parthenogenetic activation, unfertilized MII oocyte from 6-8 weeks B6D2F1/J or C57BL/6J mice were treated with Calcium ion free Chatot-Ziomek-Bavister (CZB) medium supplement with 2.5 mM SrCl2 6H2O and 2.5 μg/ml cytochalasin B for 6hr in 37℃ under 5% CO2 in air. Then we collect PA zygote with two distinct pronuclei and transfer the zygote in to KSOM culture medium with a mouth pipette. Further culture, for 6hr, late zygotes (PN5) was collected base on the morphology. Zona pellucida were gently removed by the treatment with tyrode solution. Polar body was gently removed with a sharp glass.

value: Eed KO

value: late 2-cell


title: MuSCs, total KO, input rep1

data_processing:
Nf-core/chipseq v2.0.0 was used on a singularity container, in standard and custom parameters to compute a rds archive readable in R and different files in multiple formats (bigwig, bed, bam, broadpeak). BWA aligner v0.7.17-r1188 was used, the read length used to calculate MACS2 genome size for peak calling was 50bp and the broad cutoff was 0.1.
Broadpeak output files were used to identify broad regions specific to one condition or both. Regions were annotated with ChIPseeker (v1.30.3) from TxDB.Mmusculus.UCSC.mm10.knownGene : the region range of TSS was [-2500;2500].
To determine the nearest repeat element to regions, distances were calculated by distanceToNearest function from GenomicRanges, references used from UCSC rmsk database. Visualization of regions with broadpeak in control-condition and absent broadpeak in KO-condition were managed by Gviz package (v1.38.4).
Assembly: Mus Musculus
Supplementary files format and content: H3K9me3_KO_REP2_peaks.broadPeak
Supplementary files format and content: H3K9me3_WT_REP2_peaks.broadPeak

source_name: Muscle

growth_protocol: Cells were maintained in growth medium before the experiment.

extract_protocol:
Around 1 × 10^7 cells were col- lected, washed with PBS and resuspended in 250ul of ice- cold Douncing buffer (10 mM Tris-HCl (pH 7.5), 4 mM MgCl2 , 1 mM CaCl2 , 0.2% Triton X100), followed by ho- mogenization with syringe with 26 gauge X1/2 needles (BD Microlance; Cat#: BD 303800). To obtain mononu- cleosomes, cells were digested with 1.25 ul of micrococ- cal nuclease (Mnase) (0.5 U/ul; Sigma-Aldrich; Cat#: N3755-500UN) for 5 min at 37C with 600 rpm. The reaction was stopped with 10 mM EDTA, pH 8. Nu- clei were swollen to release chromatin after addition of Hypotonization buffer (0.2 mM EDTA (pH 8), FPIC (Fast Protease Inhibitors cocktail; Sigma-Aldrich; Cat#: S8830-20TAB), DTT). Chromatin corresponding to 8 ug of DNA was incubated with anti-H3K9me3 (Diagenode; Cat#: C15410193), anti-H3K27me3 (Diagenode; Cat#: C15410069), anti-H3K27ac (Diagenode; Cat#: C15410196) or anti-H3K4me3 (Diagenode; Cat#: C15410003) antibod- ies overnight at 4C. The DNA protein antibody com-plexes were captured by DiaMag protein A-coated mag- netic beads (Diagenode; Cat#: C03010020) by incubating at 4C for 2 h. Magnetic beads were then washed with Low- Salt buffer (20 mM Tris?HCl (pH 8), 0.1% SDS, 1% Tri- ton X100, 2 mM EDTA (pH 8), 150 mM NaCI and FPIC) and High-Salt buffer (20 mM Tris?HCl (pH 8), 0.1% SDS, 1% Triton X100, 2 mM EDTA (pH 8), 500 mM NaCI and FPIC). DNA was eluted with TE buffer (100 mM Tris-HCl (pH 8), 1% SDS, 1 mM EDTA (pH 8)) from the beads overnight, inputs corresponding to 1% of IP were treated as well, followed by incubation with 1 _x0002_l of RNase A (10 ug/ml; Sigma-Aldrich; Cat#: R4642) for 1 h. DNA was pu- rified using MinElute PCR Purification Kit (Qiagen; Cat#: 28004).
Libraries were prepared using the MicroPlex V2 library preparation Kit (Diagenode; Cat#: C05010012), following the manufacturer's instructions, 10ul of DNA was used as starting material. After end repair of the double-stranded DNA templates, cleavable stem-loop adaptors were ligated, and then adaptor enriched DNA was amplified with 10 PCR cycles to add Illumina compatible indexes. The li- braries were then purified with the Agencourt AMPure XP bead-based purification system. Final libraries were quan- tified with Qubit dsDNA HS assay (Thermo Fisher; Cat#: Q32851), and size distribution was monitored by capillary electrophoresis on Agilent 2100 Bioanalyzer using DNA High Sensitivity HS Kit. Libraries were then normalized to 10 pM and pooled before sequencing. Libraries were sequenced on an Illumina Nextseq 500 in a paired-end mode in two independent biological replicates at Platform GENOM IC Institute Cochin.

treatment_protocol: Cells were treated with either Ethanol or 4-Hydroxytamoxifen in order to induce Setdb1 deletion.

value: Muscle

value: primary cell line

value: Muscle stem cells


title: Liver tissue, Tspo -/-, 4

value: Tspo -/-


title: Liver tissue, Tspo -/-, 3


title: Liver tissue, Tspo fl/fl , 2


title: 2cell_late_Parthenogenetic_Eed_KO_H3K27ac_rep2

description: STAR ChIP-seq


title: 19355X3, scRNAseq

description: 10x Genomics

value: 63 years old


title: 2cell_late_Parthenogenetic_Eed_control_H3K27ac_rep2

description: STAR ChIP-seq

value: wild-type


title: MuSCs, total control, input rep1

value: Ethanol


title: ICM_H3K27ac_rep2

description: STAR ChIP-seq

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG. Embryos were harvested in M2 medium 98 h after hCG.
STAR ChIP-seq was performed as previously described (Zhang et al., 2016). Briefly, samples were lysed followed by fragmented by micrococcal nuclease (MNase, Sigma, N3755-200UN) at 37 °C for 5 min. After being terminated, the supernatant containing chromatin was incubated with the primary antibody at 4 °C overnight with rotation. The next day, 100 μg of Protein A/G dynabeads (mixed at 1:1, Thermo Fisher Scientific) was added to each sample and incubated at 4 °C for 2–3 h with rotation. The beads were then washed five times with 150 μl RIPA buffer and once with 150 μl LiCl buffer. For each sample, beads were resuspended with 28 μl H2O, 1 μl 10× Ex-Taq buffer (Takara, RR006B) and 1 μl proteinase K (NEB, P8107S) and incubated at 55 °C for 90 min, followed by incubation at 72 °C for 40 min to inactivate the proteinase K. Samples were then subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). STAR ChIP-seq libraries were sequenced using the HiSeq X Ten system or NovaSeq (Illumina) according to the manufacturer’s protocol.

value: ICM

value: H3K27ac (Active Motif 39133)


title: 19355X2, scRNAseq

description: 10x Genomics

value: 34 years old


title: WT_CD_4

value: Heart

value: F

value: WT

value: Control Diet


title: 2cell_late_Parthenogenetic_Eed_control_H3K27ac_rep1

description: STAR ChIP-seq

value: Preimplantation embryo


title: 2cell_early_H3K27ac_rep2

description: STAR ChIP-seq

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG. Embryos were harvested in M2 medium 36 h after hCG.
STAR ChIP-seq was performed as previously described (Zhang et al., 2016). Briefly, samples were lysed followed by fragmented by micrococcal nuclease (MNase, Sigma, N3755-200UN) at 37 °C for 5 min. After being terminated, the supernatant containing chromatin was incubated with the primary antibody at 4 °C overnight with rotation. The next day, 100 μg of Protein A/G dynabeads (mixed at 1:1, Thermo Fisher Scientific) was added to each sample and incubated at 4 °C for 2–3 h with rotation. The beads were then washed five times with 150 μl RIPA buffer and once with 150 μl LiCl buffer. For each sample, beads were resuspended with 28 μl H2O, 1 μl 10× Ex-Taq buffer (Takara, RR006B) and 1 μl proteinase K (NEB, P8107S) and incubated at 55 °C for 90 min, followed by incubation at 72 °C for 40 min to inactivate the proteinase K. Samples were then subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). STAR ChIP-seq libraries were sequenced using the HiSeq X Ten system or NovaSeq (Illumina) according to the manufacturer’s protocol.

value: early 2-cell


title: 19355X1, scRNAseq

description: 10x Genomics

value: testis

value: tumor stage

value: 28 years old


title: Liver tissue, Tspo -/-, 1

value: Liver

value: 8-12 weeks


title: Liver tissue, Tspo -/-, 2

value: Tspo -/-


title: MuSCs, control, H3K9Me3, rep1

value: Muscle

value: primary cell line

value: Muscle stem cells


title: WT_CD_2


title: thigh; ASC; F73a

status: Public on Mar 22 2024

type: RNA

city: Stanford

first: Heather

last: Clemons

state: CA

address: Beckman Center

department: Dept of Biochemistry

institute: Stanford School of Medicine

hyb_protocol: HEEBO oligonucleotide microarrays, containing ~45,000 70-mer oligonucleotide probes, representing ~30,000 unique genes, were printed on epoxysilane-coated glass (Schott Nexterion E) by the Stanford Functional Genomics Facility. Prior to hybridization, slides were first incubated in a humidity chamber (Sigma Cat# H6644) containing 0.5× SSC (1× SSC = 150 mM NaCl, 15 mM sodium citrate [pH 7.0]) for 30 min at room temperature. Slides were snap-dried at 70–80°C on an inverted heat block. The free epoxysilane groups were blocked by incubation with 1M Tris-HCl (pH 9.0), 100 mM ethanolamine, and 0.1% SDS for 20 min at 50 °C. Slides were washed for 1 min in each of 2 wash chambers containing 400 ml of water, and then dried by centrifugation. Slides were used the same day. The sample was incubated at 90 °C for 5 min, spun at 14,000 rpm for 10 min in a microcentrifuge, then hybridized at 65 °C using the MAUI hybridization system (BioMicro) for 12–16 hours.

scan_protocol: Following hybridization, microarrays were washed in a series of four solutions containing 400 ml of 2× SSC with 0.05% SDS, 2x SSC, 1× SSC, and 0.2× SSC, respectively. The first wash was performed for 5 min at 65 °C. The subsequent washes were performed at room temperature for 2 min each. Following the last wash, the microarrays were dried by centrifugation in a low-ozone environment (<5 ppb) to prevent destruction of Cy dyes. Once dry, the microarrays were kept in a low-ozone environment during storage and scanning. Microarrays were scanned using AxonScanner 4000B (Molecular Devices). PMT levels were adjusted manually to achieve minimal saturation. Each element was located and analyzed using SpotReader (Niles Scientific) or GenePix Pro 6.0 (Molecular Devices).

data_processing:
The microarrays were submitted to the Stanford Microarray Database for further analysis. Data were filtered to exclude elements that did not have: a regression correlation of ≥ 0.6 between Cy5 and Cy3 signal over the pixels comprising the array element, and an intensity/background ratio of ≥ 2.5 in at least one channel.
Cy5/Cy3 log2 ratio

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

label_protocol: 1 μg of each total RNA sample was amplified using Ambion Amino Allyl MessageAmp II-96 Kit (Cat# 1821) according to the manufacturer's protocol.  Poly-adenylated RNAs were amplified in the presence of aminoallyl-UTP with Ambion Amino Allyl MessageAmp II-96 Kit (Cat# 1821). For mRNA expression experiments, Universal Reference RNA was used as an internal standard to enable reliable comparison of relative mRNA levels in multiple samples (Stratagene Cat# 740000). 10 μg each of amplified sample and reference RNA was fluorescently labeled with NHS-monoester Cy5 or Cy3 respectively (GE HealthSciences Cat# RPN5661). Differentially dye-labeled sample and reference RNA samples were combined, fragmented (Ambion Cat# 8740), then diluted into in a 50-μl solution containing 3× SSC, 25 mM Hepes-NaOH (pH 7.0), 20 μg of human Cot-1 DNA (Invitrogen Cat# 15279011), 20 μg of poly(A) RNA (Sigma Cat# P9403), 25 μg of yeast tRNA (Invitrogen Cat# 15401029), and 0.3% SDS.

growth_protocol: One-half of each stromal-vascular pellet fraction from the “Tissue Fractionation” procedure was reserved to culture adipose stem cells. The cell suspension was centrifuged at 400g for 7 minutes and the buffer was carefully aspirated with a pipette to avoid losing pelleted cells. Cells originating from the pericolonic or omental depots were additionally treated for 10 min with RBC lysis buffer*, again centrifuged, and the lysis buffer aspirated. Cells were resuspended in 10 ml DMEM + 10% FBS + 2.5 μg/ml Fungizone (Invitrogen Cat# 15290-018) + Pen/Strep/Glutamine (Invitrogen 10378-016). Cells were transferred to the appropriate size culture flask (10-20 g starting tissue in 1 x T25, 20-50g in 1x T75). Additional DMEM (~1ml/5cm2) was added to cells and mixed by pipetting. Cells were incubated overnight or up to 24 hours to allow time for adipose stem cells to adhere. Cells were rinsed with warm PBS and given fresh medium. Presence of adherent stromal cells was assessed visually at 10x magnification. Successful cultures were continually grown in DMEM + 10%FBS + Pen/Strep/Glutamine. Fungizone was no longer added after 2 passages. Cells were split 1 to 3 at 70-90% confluence. When enough cells were obtained (at least 1 confluent T225 flask), cells were rinsed with PBS and trypsinized, pelleted by centrifugation and resuspended in fresh medium. Each of 2, 10 cm dishes were plated, one for pre- and one for post-differentiation RNA collection. For the latter see “Adipocyte Differentiation”. Cells for pre-differentiation RNA collection were plated at 100% confluence in fresh DMEM and incubated overnight. Cells were photographed at 10x magnification to document confluence and morphology of cells.

extract_protocol: Cells were rinsed with warm PBS. PBS was replaced with 6 ml Trizol. Plates were gently scraped and Trizol/cell lysate was transferred to a 15 ml conical tube and stored at -80°C until RNA isolation. Samples in Trizol were removed from the -80°C storage freezer and thawed at room temperature. Chloroform was added to each sample (10 ml to adipocyte, 5 ml to stromal-vascular pellet, 1 ml to cell culture), and tubes were recapped and vigorously shaken. Samples were then centrifuged at 12,000g for 15 minutes at 4°C. Following centrifugation, the aqueous phase was removed and transferred to a fresh conical tube and an equivalent volume of 70% ethanol was added. Tubes were recapped and shaken. Samples were loaded onto RNeasy Maxi Kit (Qiagen Cat# 75152) columns and the RNeasy protocol for RNA washes and elution was followed (RNeasy Midi/Maxi Handbook, “Animal Tissues” Protocol beginning at step 7). RNA was eluted with 1.6 ml water. RNA was precipitated as follows: one-tenth volume 3M sodium acetate and 2.5x volume 100% ethanol were added to the 1.6 ml RNA sample. Tubes were capped, shaken to mix and stored overnight at -80°C. Tubes were removed from -80°C, thawed at room temperature and centrifuged at 16,000g for 20 minutes, 4°C. Tubes were gently removed from the centrifuge, uncapped and quickly inverted to pour off liquid. These were left upside-down on paper towels to dry. Remaining ethanol droplets were aspirated and the RNA pellet was resuspended in 200 μl RNase-free water. RNA concentration was measured (Nanodrop ND-1000 spectrophotometer) and samples were stored at -80°C.

treatment_protocol: Adipose stem cells were grown to confluence as described in “Cell Culture”. Cells were rinsed with warm PBS and trypsinized. Trypsinized cells were transferred to a 15 ml conical tube, pelleted by centrifugation and resuspended in 5 ml DMEM + 10% FBS + Pen/Strep/Glutamine (Invitrogen Cat# 10378-016). Cells were plated to achieve the greatest density possible depending on the number of cells available, as higher confluence yielded a greater percentage of differentiating cells. In general, cells were plated at 100-300% confluence. Cells were incubated overnight and photographed the following day at 10x magnification to document confluence and record the morphology of cells. Cells were rinsed with warm PBS. PBS was replaced with Zen-Bio differentiation medium (Cat# DM-2) and the differentiation procedure was followed as described in Zen-Bio instruction manual ZBM-1. At 16 days following induction of differentiation, cells were photographed at 10x magnification to document the number and morphology of differentiating cells.

tag: tag

value: reference:Stratagene Human Universal Reference

source_name: thigh; ASC; F73a, 10 ug labeled aRNA

tag: organism part

value: thigh

tag: sample fraction

value: ASC


title: SampleC, Spatial transcriptome sequencing

description: 10x Genomics

tag: tissue

value: testis tumor


title: thigh; ASC; F52e

source_name: thigh; ASC; F52e, 10 ug labeled aRNA

value: F


title: thigh; ASC; F43a

source_name: thigh; ASC; F43a, 10 ug labeled aRNA


title: BN1053, Rep3, GFP::Dam

city: Seville

first: Peter

last: Askjaer

address: UPO Carretera de Utrera km 1

country: Spain

institute: Centro Andaluz de Biología del Desarrollo

data_processing:
FASTQ files from the NextSeq500 platform were processed in R Studio using the pipelines RDamIDSeq (https://github.com/damidseq/RDamIDSeq) and RGeneDamIDSeq (https://github.com/damidseq/-RGeneDamIDSeq-) (Sharma et al. 2016) for mapping of reads to bins of fixed size (e.g. 2 kb, 10 kb or 100 kb) and to genes, respectively. The pipelines include a quality check where only reads that contain the DamID adapter (“CGCGGCCGAG”) and map to GATC sites in the C. elegans genome are retained for further analysis. The number of reads fulfilling these criteria ranged from 0.5 to 9 million (see Supplementary Table S7). Both pipelines also provide mapped read numbers per individual GATC fragment. For mapping to genes, the script was modified to include 500 bp distal to transcriptional start and termination sites. UCSC genome version ce11 (BSgenome.Celegans.UCSC.ce11) was used for alignment.
The DESeq2 package (Love et al. 2014) was used to identify bins with significantly more reads with either Dam::BAF-1  or Dam::BAF-1(G12T) compared to GFP::Dam across the 3 replicas. A false discovery rate (FDR) of 0.05 was used as threshold. Next, for each sample a pseudocount of 1 was added to each bin and the relative number of reads per bin was calculated followed by averaging across the replicas. The ratio of Dam::BAF-1  or Dam::BAF-1(G12T) to GFP::Dam was calculated for each bin and log2-transformed. Finally, normalization was done by subtracting the genome-wide average log2 ratio from the log2 ratio of each bin (Brueckner et al. 2020).
Assembly: ce11
Supplementary files format and content: Files contain columns for gene names (except in 2 kb bin files), coordinates, log2 values (Dam::BAF-1/GFP::Dam or Dam::BAF-1(G12T)/GFP::Dam)(average and individual replicas), bin (or gene) number and padj value.

organism: Caenorhabditis elegans

source_name: Intestine

growth_protocol: Worms were grown asynchronically at 20C on NGM plates seeded with E. coli GM119 for at least two generations before egg-prepping with hypochlorite. Hatched L1s were counted the day after and 1000 L1s were aliquoted onto 10 cm NGM plates seeded with E. coli GM119 as described above. Worms were grown at 20C for 48 h before collecting 4000 L4 stage nematodes per strain and washed 8 times with 15 ml of M9 with 0.01% Tween-20. Worms were transferred to 1.5 ml tubes with M9 with 0.01% Tween-20 using Pasteur pipettes followed by two additional washes. Supernatants were aspirated and aliquots of 30 µl were snap frozen in liquid nitrogen and maintained at -80C until DNA extraction.

extract_protocol:
To purify genomic DNA, samples were lysed in 5 freeze/thaw cycles (1min in liquid nitrogen; 3min in 37C shaker) and processed with DNeasy Blood and Tissue Kit (QIAGEN #69504).
DamID was performed on 400 ng genomic DNA  extracted from 4000 L4 animals cultured and collected as indicated above. Three replicates were performed as described (de la Cruz Ruiz et al. 2022), using primer AdR (5'-NNNNGTGGTCGCGGCCGAGGATC) and 22 PCR cycles. Successful amplification of Dam-methylated genomic DNA yielded a smear of ~400-~1500 bp fragments when analyzed on Agilent Bioanalyzer. 400 ng of PCR amplified fragments were used for library preparation as described (de la Cruz Ruiz et al. 2022), using E7370 NEBNext® Ultra™ DNA Library Prep Kit for Illumina. Library amplicons’ size distribution was checked to be maintained as for PCR fragments indicated above followed by pooling, repurification and sequencing on a Illumina NextSeq500 platform at EMBL GeneCore.

value: Intestine


title: BN561, Rep3, GFP::Dam

source_name: Hypodermis

value: Hypodermis

value: WT


title: BN1054, Rep3, Dam::BAF-1(G12T)


title: BN1050, Rep3, Dam::BAF-1(G12T)


title: BN1054, Rep2, Dam::BAF-1(G12T)


title: BN1048, Rep3, GFP::Dam


title: BN1047, Rep3, Dam::BAF-1


title: BN1051, Rep3, GFP::Dam


title: BN1052, Rep3, Dam::BAF-1


title: BN1052, Rep2, Dam::BAF-1


title: BN1051, Rep2, GFP::Dam


title: thigh; ASC; F58b

source_name: thigh; ASC; F58b, 10 ug labeled aRNA


title: thigh; ASC; F29

source_name: thigh; ASC; F29, 10 ug labeled aRNA


title: BN1050, Rep2, Dam::BAF-1(G12T)


title: thigh; ASC; F83

source_name: thigh; ASC; F83, 10 ug labeled aRNA


title: BN1047, Rep2, Dam::BAF-1


title: BN1048, Rep2, GFP::Dam


title: shin; ASC; M51

source_name: shin; ASC; M51, 10 ug labeled aRNA

value: shin

value: M


title: shin; ASC; F12

source_name: shin; ASC; F12, 10 ug labeled aRNA


title: BN1054, Rep1, Dam::BAF-1(G12T)


title: shin; ASC; UUh

source_name: shin; ASC; UUh, 10 ug labeled aRNA

value: UUh


title: BN1051, Rep1, GFP::Dam


title: BN1052, Rep1, Dam::BAF-1


title: BN1050, Rep1, Dam::BAF-1(G12T)


title: BN561, Rep1, GFP::Dam


title: shin; ASC; F81

source_name: shin; ASC; F81, 10 ug labeled aRNA


title: shin; ASC; F81a

source_name: shin; ASC; F81a, 10 ug labeled aRNA


title: omentum; ASC; F58c

source_name: omentum; ASC; F58c, 10 ug labeled aRNA

value: omentum


title: thigh; ASC; F58a

source_name: thigh; ASC; F58a, 10 ug labeled aRNA


title: shin; ASC; F71

source_name: shin; ASC; F71, 10 ug labeled aRNA


title: shin; ASC; F83

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

source_name: shin; ASC; F83, 10 ug labeled aRNA


title: BN1048, Rep1, GFP::Dam


title: BN1047, Rep1, Dam::BAF-1


title: omentum; ASC; M17

source_name: omentum; ASC; M17, 10 ug labeled aRNA


title: thigh; ASC; F62

source_name: thigh; ASC; F62, 10 ug labeled aRNA


title: Input_Arid1aWt_R2

city: New York City

first: Christopher

middle: Russell

last: Chin

address: 413 E 69th Street, Belfer Building, BB-1462

institute: Weill Cornell

data_processing:
Processed through nfcore ChIPseq analysis pipeline.
Trimmed by TrimGalore, aligned with BWA, sequences filtered and duplicates marked.
Peak calling by macs2
Assembly: hg38
Supplementary files format and content: bed files for peak calls

source_name: cell line

growth_protocol: 20% IMDM with P/S, GlutaMax

extract_protocol:
AMPure XP Beads
NEB Ultra II

value: cell line

value: RIVA

value: B-cell lymphoma ABC-DLBCL

value: Arid1a WT

value: Input


title: BN1053, Rep2, GFP::Dam

source_name: Intestine


title: BN561, Rep2, GFP::Dam

source_name: Hypodermis


title: LMNA-KD NT 2

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

hyb_protocol: One-color mixes of labelled cRNA pairs were hybridized to 4×44K whole human genome oligonucleotide microarray (Agilent G4112F, 41000 unique probes), at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit. The hybridized microarrays were disassembled at room temperature in Agilent Gene Expression Wash Buffer 1. After the disassembly, the microarrays were washed in Gene Expression Buffer 1 for one minute at room temperature, followed by washing with Gene Expression Wash Buffer 2 for one minute at 37°C. The microarrays were then treated with acetonitrile for one minute at room temperature.

scan_protocol: Post-hybridization image acquisition was accomplished using the Agilent Scanner G2564B. Data extraction from the 20 bits TIFF images was accomplished by Agilent Feature Extraction ver 10.1 software using the standard Agilent one-color gene expression extraction protocol (GE1_107_Sep09).

data_processing: The gProcessedSignal data column of the Feature Extraction *.txt output file was used, containing the median signals corrected by spatial and multiplicative detrend. Data quality filtering was performed using Agilent GeneSpring GX 11.0, discarding features with the Feature Extraction flag gIsWellAboveBG=0 in any sample, wich is a statistical method approximately equivalent to discarding features with a Signal/Noise ratio smaller than 2.0-3.0, where Signal = (median of the spot - median spot background level) and Noise is the Standard Deviation of the median spot background. Differential gene lists were obtained from filtered data using Microsoft Excel. A threshold of 350.0 in the absolute expression level was chosen to obtain a higher stringency and a smaller relative error of the signal. Differentially expressed genes were identified as those showing an average fold change ratio >1.5 or <1/1.5 in the linear scale.

source_name: American Type Culture Collection (ATCC, Manassas, VA, USA)

label_protocol: The cyanine 3-CTP labeled cRNA was prepared using the Agilent Low Input Linear Amplification Kit, following the standard one-color Agilent protocol

growth_protocol: SHSY5Y cells were grown in a 1:1 mixture of Eagle's Minimum Essential Medium and F12 Medium (Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (FBS, Hyclone), 2 mM L-glutamine, 0.5% non-essential amino acids, 0.5% sodium pyruvate and 1% penicillin and streptomycin in a fully-humidified incubator containing 5% CO2 at 37˚C.

extract_protocol: Cells were seeded in complete medium, harvested after the different treatments and total RNA was isolated from each sample using NucleoSpin RNA II silica columns (Macherey-Nagel).

treatment_protocol: For differentiation experiments cells were seeded at a density of 5×103 cells/cm2. The following day cells were induced to differentiate by 10 µM retinoic acid (RA) in a “differentiation medium” (DM) composed by 50% fresh and 50% conditioned culture medium. Cells were fed after 3 days with DM containing fresh RA. Untreated cells (NT) were harvested after 3 days of growth. RA-treated cells were harvested after 5 days of RA treatment (corresponding to 6 days after seeding).

tag: disease

value: Human malignant neuroblastoma (NB)


title: omentum; ASC; M49a

value: reference:Stratagene Human Universal Reference

source_name: omentum; ASC; M49a, 10 ug labeled aRNA