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title: 202Z_MSCB-068

status: Public on Apr 15 2018

type: SRA

city: Barcelona

first: giovanni

last: iacono

state: Spain

address: Baldiri Reixac, 4

department: single cell sequencing

country: Spain

institute: CNAG,Centro Nacional de Análisis Genómico

description:
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library_source: transcriptomic

data_processing:
Illumina Real-Time Analysis (RTA) 1.18.66.3 software used for basecalling.
Sequenced reads were filtered for low-complexity or low-quality sequence.
Cells with less than 60% of reads mapping on the reference genome were discarded.
MARS-Seq libraries were mapped as single-end reads with the GEMTools 1.7.0 RNA pipeline on the genome reference for human cells.
Gene quantification was performed using UMI corrected transcript information to correct for amplification biases.
Genome_build: Human: Gencode release 24, assembly GRCh38.p5;
Supplementary_files_format_and_content: Excel (.xlsx) file containing gene expression values (rows) as UMI counts (MARS-Seq) for each cell (columns) in condition.
IPSC_Expression.xlsx: gene expression
Table_S1_Linarsson.xlsx: Markers of Zeisel/Linarsson dataset
Table_S2_10xfull.xlsx: Markers 10x genomics developmental pallium (change cluster number)
Table_S3_10x_Reln.xlsx: Markers of Reelin subtypes  (change cluster number)
iCell_10x_brain.h5: Expression data for the iCells, HDF5 format
gene_names_10x.txt: Gene names (rows) for the iCells in HDF5 format
The data of 10x genomics is public in HDF5 format at:
https://support.10xgenomics.com/single-cell-gene-expression/datasets/1.3.0/1M_neurons

molecule: polyA RNA

organism: Homo sapiens

source_name: neuronal progenitors

growth_protocol: Skin fibroblasts from patients with WBS or 7DUP were reprogrammed to induced Pluripotent Stem Cells (iPSC) by retroviral delivery of the pluripotency factors OCT4, SOX2, KLF4 and MYC, at the Centre of Regenerative Medicine in Barcelona (CMR[B]). Individual iPSC were picked to generate single clone colonies that were expanded and fully characterized (Martí et al. 2013). Briefly, genomic stability was confirmed by karyotype; integration and silencing were verified by PCR and quantitative RT-PCR; pluripotency was demonstrated by Alkaline Phosphatase staining and expression of pluripotency markers by immunocytochemistry. Finally, the capacity to differentiate to mesoderm, ectoderm and endoderm germ layers both in vitro and in vivo was verified by embroid bodies and teratoma formation followed by immunostaining. All iPSC were deposited in the Stem Cell Bank repository of the Instituto de Salud Carlos III.  We generated Neural Stem Cells (NSCs) from iPSCs following the Gibco protocol based on PSC Neural Induction Medium (NIM). Briefly, differentiation of iPSC colonies was performed by seven days culture in NIM, followed by several passages of maturation in Complete Neural Expansion Medium (Neurobasal Medium, Advanced DMEM⁄F-12, and Neural Induction Supplement (Gibco)). Confirmation of expression of NSC markers was done by immunocytochemistry (Human Neural Stem Cell Immunocytochemistry Kit, Gibco). After 4-7 passages, NSCs were detached with accutase (gibco) and resuspended. Single-cells were sorted in a BD Influx cell sorter to MARS-seq plates for single cell-RNAseq (Flow Cytometry Core Facility, Univeritat Pompeu Fabra).

extract_protocol: To construct single-cell libraries from polyA-tailed RNA, we applied massively parallel single-cell RNA sequencing (MARS-Seq). Briefly, single cells were FACS-sorted into 384-well plates, containing lysis buffer (0.2% Triton (Sigma-Aldrich); RNase inhibitor (Invitrogen)) and reverse-transcription (RT) primers. The RT primers contained the single-cell barcodes and unique molecular identifiers (UMIs) for subsequent de-multiplexing and correction for amplification biases, respectively. Single-cell lysates were denatured and immediately placed on ice. The RT reaction mix, containing SuperScript III reverse transcriptase (Invitrogen) was added to each sample. In the RT reaction, spike-in artificial transcripts (ERCC, Ambion) were included at a dilution of 1:16x106 per cell. After RT, the cDNA was pooled using an automated pipeline (epMotion, Eppendorf). Unbound primers were eliminated by incubating the cDNA with exonuclease I (NEB). A second pooling was performed through cleanup with SPRI magnetic beads (Beckman Coulter). Subsequently, pooled cDNAs were converted into double-stranded DNA with the Second Strand Synthesis enzyme (NEB), followed by clean up and linear amplification by T7 in vitro transcription overnight. Afterwards, the DNA template was removed by Turbo DNase I (Ambion) and the RNA was purified with SPRI beads. Amplified RNA was chemically fragmented with Zn2+ (Ambion), then purified with SPRI beads. The fragmented RNA was ligated with ligation primers containing a pool barcode and partial Illumina Read1 sequencing adapter using T4 RNA ligase I (NEB). Ligated products were reversed transcribed using the Affinity Script RT enzyme (Agilent Technologies) and a primer complementary to the ligated adapter, partial Read1. The cDNA was purified with SPRI beads. Libraries were completed through a PCR step using the KAPA Hifi Hotstart ReadyMix (Kapa Biosystems); and a forward primer that contains Illumina P5-Read1 sequence and the reverse primer containing the P7-Read2 sequence. The final library was purified with SPRI beads to remove excess primers. Library concentration and molecular size were determined with High Sensitivity DNA Chip (Agilent Technologies). The libraries consisted of 192 single-cell pools. Multiplexed pools (2) were run in one Illumina HiSeq 2500 Rapid two lane flow cell following the manufacturer’s protocol. Primary data analysis was carried out with the standard Illumina pipeline. We produced 52 nt of transcript sequence reads.

tag: cell type

value: neuronal progenitors

tag: patient type


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title: GIST882 Input

city: New York

first: Yu

last: Chen

state: NY

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

country: USA

institute: Memorial Sloan Kettering Cancer Center

library_source: genomic

data_processing:
The sequenced reads from fastq files were mapped to hg19 using Bowtie 1.0
Peaks were called using MACS2. Downstream analysis were performed using Homer and SeqMiner
Genome_build: Hg19
Supplementary_files_format_and_content: ENCODE narrowPeak: Narrow (or Point-Source) Peaks format. See https://genome.ucsc.edu/FAQ/FAQformat.html

molecule: genomic DNA

source_name: GIST882 Human GIST Cells

growth_protocol: Cells were grown in 10% FBS

extract_protocol:
Chromatin was isolated and sheared. For ETV1 IP, chromatin was IP'd using anti-ETV1 antibody (abcam ab81086) and magnetic protein A/G beads.The immunoprecipate was washed and eluted using standing conditions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were harvested in log phase growth

tag: cell line

tag: antibody


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title: Colo800 Input

source_name: Colo800 Human melanoma Cells


title: A375 Input

source_name: A375 Human melanoma Cells


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title: Colo800 ETV1


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title: GIST882 ETV1 IP


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title: GIST-T1 ETV1 IP

source_name: GIST-T1 Human GIST Cells


title: A375 ETV1 IP


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title: GIST-T1 Input


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title: COLO800-ETV1shSCR

data_processing:
The sequenced reads from fastq files were mapped to hg19 using STAR version 2.4
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using  Cufflinks suite v2.2.1 (Trapnell Nature biotechnology). We ran cuffquant on each BAM file and then Cuffnorm using upper quartile normalization. Genes were mapped to Ensembl Hg19 genome
Please note the RPKM of all 6 samples were combined into a single file.

molecule: total RNA

source_name: Colo800 Human Melanoma Cells

extract_protocol:
RNA was purified using Qiagen RNeasy Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected with indicated siRNA for 48 hours and then treated with the indicated drug for 8 hours

tag: hairpin

value: Scrambled

tag: treatment

value: 1uM vemurafinib


title: COLO800-ETV1sh2

value: 5nM trametinib


title: COLO800-ETV1sh1

value: DMSO


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title: A375-ETV1sh1

source_name: A375 Human Melanoma Cells


title: A375-shSCR


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title: A375-ETV1sh2


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title: A375-sgEGFP-Vemurafinib

tag: tissue

value: Human melanoma cell line

tag: crispr guide

value: EGFP


title: A375-sgEGFP-Trametinib


title: A375-sgCOP1-DMSO


title: A375-sgCOP1-Vemurafinib


title: A375-sgCOP1-Trametinib


title: A375-sgEGFP-DMSO


title: GIST882-siSCR-DMSOrep2

data_processing:
The sequenced reads from fastq files were mapped to hg19 using STAR version 2.4
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using  Cufflinks suite v2.2.1 (Trapnell Nature biotechnology). We ran cuffquant on each BAM file and then Cuffnorm using upper quartile normalization. Genes were mapped to Ensembl Hg19 genome
Please note the RPKM of all 12 samples were combined into a single file.

tag: knockdown


title: GIST882-siCOP1-1-PD901rep1


title: GIST882-siCOP1-2-DMSOrep1


title: GIST882-siCOP1-1-DMSOrep1


title: GIST882-siCOP1-1-DMSOrep2


title: GIST882-siCOP1-2-PD901rep1


title: GIST882-siSCR-PD901rep1


title: GIST882-siSCR-PD901rep2


title: GIST882-siCOP1-2-PD901rep2


title: GIST882-siCOP1-1-PD901rep2


title: GIST882-siCOP1-2-DMSOrep2


title: RPC Elute 3

city: IRVINE

first: James

last: Yu

state: ca

address: Med Sci D262

department: Biological Chemistry

institute: University of California Irvine

data_processing:
ChIP-seq reads were mapped to the sacCer3 genome using Bowtie 2 version 2.2.4. Concordant read pairs between 200-900 bases were mapped using the most stringent setting of very-sensitive. Next, Samtools version 0.1.19 was used to filter out read pairs mapped to more than one location. Replicate samples were then merged for peak analysis using MACS2.
Peak analysis was performed with MACS2 version 2.1.0.20150420
Genome_build: sacCer3
Supplementary_files_format_and_content: Bedgraph files generated using MACS2 represent normalized read coverage per base

organism: Saccharomyces cerevisiae

source_name: Cell Pellet

growth_protocol: For ChIP-seq experiments each replicate was grown overnight from a single fresh colony, pelleted, and resuspended to an OD600 of 0.20 in synthetic raffinose media. Culters were grown at room temperature for 24 hours before pelleting and resuspending in synthetic galactose media at an OD600 of 0.20, and grown again for 24 hours. Cultures were then resuspended in YP+glucose grown from a starting OD600 of 0.05 to ~1.0 and harvested for ChIP. Growth protocol was designed to match the process of growing cells during the Ty3 insertion site sequencing experiment.

extract_protocol:
For chromatin preparation, cultures were cross-linked for 15 min by addition of 1/10 culture volume of cross-link solution (50 mM HEPES-KOH pH 7.5, 100mM NaCl, 1 mM EDTA pH 8, 11% formaldehyde) at room temperature with very light shaking. Next cultures were quenched with 300 mM glycine and light shaking for 5 min. Cells were pelleted and washed once with cold 1X PBS, decanted, and frozen in dry ice. Cell pellets were resuspended in Extraction Buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8, 1% Triton-X) plus protease inhibitor cocktail (Sigma-Aldrich). Approximately 0.6 g of glass beads were added and cells were mechanically sheared at 4°C by vortexing for 30 min. Lysates were pelleted at 4°C for 5 min and supernatants cleared. Chromatin pellets were resuspended in 700 µl of Extraction Buffer, divided into two aliquots and sonicated for 7-10 min in a Biorupter Standard (Diagenode). For immunoprecipitations, 20 µl of Anti-FLAG M2 Magnetic Beads (Sigma-Aldrich) were washed once in 1 mL of Extraction Buffer and incubated with 50 µg of chromatin and rotation overnight at 4°C. Following incubation, beads were washed in Extraction Buffer with increasing concentrations of NaCl: 140 mM, 300 mM, 600 mM and final wash with 250 mM LiCl. Each wash was done for 5 minutes at 4°C with rotation. Beads were resuspended in 200 µl of 1X HE (10 mM HEPES-KOH pH 7.5, 1 mM EDTA). For input control samples 5 µgs of chromatin was diluted into 200 µl of 1X HE. IPs and input samples were RNased (20 µg) for 1 h at 37° C followed by Pronase E (40 µgs) treatment for 4-5 hours. DNA was purified using the Zymo DNA Clean and Concentrator kit with 5X ChIP-DNA Binding Buffer (Genesee, Inc.).
ChIP-seq libraries were prepared according to the Illumina Multiplex Sample Preparation Guide. Immunopurified DNA or input control DNA samples were treated with the Fast DNA End Repair kit (Thermo Scientific) to creat blunt DNA ends, then adenylated on their 3’-end using the Klenow Exo- enzyme with 1 mM dATP (Fisher Scientific), and ligated to adapters. Individual IP or input samples were ligated to a unique multiplex barcoded adapter set for sequencing. Following ligation, samples were purified using the Agencourt AMPure XP purification beads (Beckman Coulter, Inc.). Nine replicate PCR reactions with ~ 4-6 ngs of DNA template and Illumina universal primers was done using KOD polymerase with conditions 95°C 5 minutes, 5 cycles of 95°C 30 seconds 65°C 30 seconds 70°C 30 seconds, followed by 10 cycles of 95°C 30 seconds 61°C 30 seconds 70°C 30 seconds, and a final 70°C for 2 minutes. All sequencing libraries were first evaluated by gel electrophoresis, then submitted to the University of California, Irvine Genomics High-throughput Facility for Bioanalyzer 2100 (Agilent) analysis, KAPA quantification for sample mixing and paired-end 100 base sequencing on the Illumina Hi-Seq 2500.

tag: chip antibody

value: FLAG M2 (Sigma-Aldrich, Lot #SLBJ4607V)

tag: strain


title: RPC Input 3


title: GIST882-siSCR-DMSOrep1


title: RPC Elute 4


title: RPC Input 4


title: 4010_Elute_2

growth_protocol: For ChIP-seq experiments each replicate was grown overnight from a single fresh transformation colony, pelleted, and resuspended to an OD600 of 0.20 in synthetic raffinose media lacking uracil to maintain plasmid selection. Culters were grown at room temperature for 24 hours before pelleting and resuspending in synthetic galactose media lacking uracil at an OD600 of 0.20, and grown again for 24 hours. Cultures were then resuspended in YP+glucose plus  antibiotic G418 and grown from a starting OD600 of 0.05 to ~1.0 and harvested for ChIP. Approximately six hours prior to harvesting, cultures were supplemented with 10 µM β-estradiol. Growth protocol was designed to match the process of growing cells during the Ty3 insertion site sequencing experiment.


title: 4010_Input_2


title: 4010_Elute_1


title: 4010_Input_1


title: 3915_Input


title: 3915_Elute


title: WTElute


title: T04

city: Beijing

first: Ke

last: Wang

address: No. 12 Nanfaxinfu Street, Shunyi District, Beijing

country: China

institute: Biomarker institute

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Cufflinks are used for assemble transcripts and remap and quanlity gene-expression level, which is estimate by FPKM value.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Chrysanthemum x morifolium

source_name: leaves

growth_protocol: The buds raised from tissue-cultured seedlings were grown on MS medium (16 h photoperiod, 25 ℃/22℃ day/night temperature) for twenty days. Then twenty-day old chrysanthemum seedlings were transferred to pots filled with a 1:1 mixture of peat and perlite, and acclimated for three days at normal condition.

extract_protocol:
Total RNA was extracted with Trizol Reagent (Invitrogen), following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The four groups of seedlings were respectively subjected to following treatments: (T01) normal condition as control, (T02) 4 ℃ for 24 h, (T03) 4 ℃ for 24 h, followed by -4 ℃ for 4 h, (T04) -4 ℃ for 4 h. The leaves from the mixture of three replicates of each treatment were harvested, then rapidly frozen with liquid nitrogen and stored at -80 ℃. There were four samples in total used for RNA-Seq and differential expression analyses.

value: Jinba

value: leaves

tag: age

value: Twenty day-old

value: -4C freezing treatments for 4 h without prior CA


title: NBRF1Input_2


title: NBRF1Elute_1


title: NBRF1Elute_2


title: NBRF1Input_1


title: SCs proliferating 1

status: Public on Apr 14 2018

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

data_processing:
Basecalls with RTA v2 (Illumina)
Reaper version 13-100 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses.
Mapping: alignment versus the Ensembl mouse genome version mm10 (GRCm38) using STAR 2.4.0a  with the parameter “--outFilterMismatchNoverLmax 0.1"
The number of reads aligning to genes was counted with featureCounts 1.4.5-p1 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers.
Genome_build: mm10
Supplementary_files_format_and_content: library-size normilzed counts per gene

organism: Mus musculus

source_name: skeletal muscle

growth_protocol: MuSCs were isolated from muscles of 12-20 week-old WT animals as described by Guenther et. al (Cell Stem Cell. 2013 Nov 7;13(5):590-601). MuSCs were grown in proliferation medium (40% DMEM, 40% Ham F-10; 20% FCS; Pen/Strep; 2.5 ng/ml human FGF-2, Miltenyi Biotec) for a minimum of 3 days, followed by differentiation medium (DMEM, 2% horse serum, and Pen/Strep) for 6 days.

extract_protocol:
For RNA-seq, RNA was isolated from purified satellite cells using the PureLink RNA Mini Kit (ambion).
100ng of total RNA was used as input for ribosomal depletion with RiboGone-Mammalian (Clontech) followed by library preparation using SMARTer Stranded Total RNA Sample Prep Kit (Clontech).

tag: cell differentiation stage

value: proliferating

value: 12-20 weeks old


title: SCs myotubes 3

value: differentiating


title: I16R031a35

status: Public on Apr 13 2018

city: Saarbrücken

first: Julia

middle: Maria

last: Schulze-Hentrich

address: Campus, Building A2.4

department: Genetics and Epigenetics

institute: Saarland University

data_processing:
Read quality of RNA-seq data in fastq files was assessed using FastQC (v0.11.4) to identify sequencing cycles with low average quality, adaptor contamination, or repetitive sequences from PCR amplification.
Reads were aligned using STAR (v2.5.2b) allowing gapped alignments to account for splicing against the Ensembl Rattus norvegicus genome v87
Raw counts describing gene-level abundances were derived from DESeq2 (v1.16.1)
Genome_build: Ensembl Rattus norvegicus v87
Supplementary_files_format_and_content: comma seperated text file with raw read counts per gene identified by Ensembl gene ID

organism: Rattus norvegicus

source_name: striatum

extract_protocol:
Striatum was removed, flash-frozen on dry ice, and RNA was harvested using the AllPrep DNA/RNA Mini Kit (Qiagen). TruSeq RNA Sample Prep Kit (Illumina) was used with 500 ng of total RNA to construct sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
Poly(A) selected sequencing libraries (68 bp paired-end reads) were generated according to the manufacturer’s instructions. All libraries were sequenced on an Illumina HiSeq 2500 platform at a depth of 12–25 million reads each.

value: Sprague Dawley

value: striatum

tag: genotype

value: WT

tag: environment

value: SE

value: 2 months


title: SCs proliferating 3


title: SCs proliferating 2


title: SCs freshly isolated 2

value: freshly isolated


title: SCs freshly isolated 1


title: SCs myotubes 2


title: I16R031a33

value: ELS


title: SCs freshly isolated 3


title: I16R031a34

value: TG


title: I16R031a36


title: I16R031a31

value: EE


title: I16R031a29


title: I16R031a30


title: I16R031a28


title: WTInput

value: FLAG M2 (Sigma-Aldrich, Lot #SLBJ4607V)


title: T03

value: Jinba

value: -4C freezing treatments for 4 h with prior CA


title: T02

value: leaves

value: Twenty day-old

value: 4C cold acclimation (CA) for 24 h


title: T01

value: control


title: SCs myotubes 1

value: differentiating

value: 12-20 weeks old


title: I16R031a27

value: Sprague Dawley

value: striatum


title: I16R031a26


title: I16R031a24

value: SE


title: I16R031a25

value: WT

value: 2 months


title: I16R031a21


title: I16R031a22


title: I16R031a23


title: I16R031a19

value: ELS


title: I16R031a32

value: TG


title: I16R031a18

value: EE


title: I16R031a17


title: I16R031a11


title: I16R031a12


title: I16R031a08


title: I16R031a09


title: I16R031a14


title: I16R031a13


title: I16R031a10


title: I16R031a16


title: I16R031a05


title: I16R031a07


title: I16R031a04


title: I16R031a02


title: I16R031a03


title: I16R031a01


title: I16R031a20


title: morula siTrim28 input

city: Shanghai

first: Shaorong

last: Gao

state: Shanghai

address: 1239 Siping Road, Yangpu District

department: School of life science and technology

institute: Tongji University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using bwa mem command, reads that have map quality score less than 30 were removed from downstream analysis.
Peaks were called using macs14(v1.4.2) with the parameters "macs14 -g mm --nomodel --nolambda --shiftsize=73" relative to input samples.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files are generated using macs2 callpeak function and normlized to one million reads per sample using --SPMR option. Scores represent normalized tag counts per million reads.

source_name: mouse embryo

extract_protocol:
For MII oocyte and cleavage-stage embryos, the zona pellucida of embryos was removed by 0.5% pronase E (Sigma). Then the embryo was incubated in Ca2+ free CZB for 5 min. Polar bodies were removed by gentle pipetting using an inner diameter of 120 μm fire polished glass needle. For ICM and TE isolation, the zona pellucida of blastocysts was removed by 0.5% pronase E (Sigma). They were then incubated for 20 min in Ca2+ free CZB，the tight junctions TE cells and ICM cells were separated by gently pipetting in a pipette with a diameter of 40-60 μm.For epiblast (Epi) and extraembryonic ectoderm (Exe) isolation, embryos were cuttted at the embryonic/extraembryonic boundary using properly sharpened forceps. A fire-polished glass needle whose inner diameter is silghtly smaller than the width of the embryonic/extraembryonic fragment was used for separating epiblast or extraembryonic ectoderm from the visceral endoderm, and the epiblast or extraembryonic ectoderm were then incubated in Ca2+-free CZB for 10 min. Single cells were separated by gentle pipetting using a fire-polished glass needle with an inner diameter of 15-20 μm.500 cells were washed three times in 0.5% BSA-PBS solution. Lysates were clarified from micrococcal nuclease treated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to KAPA Hyper Prep Kit for illumina platform (kk8504)

treatment_protocol: For gene knockdown，small interference RNAs (siRNAs) against mouse Chaf1a, Sumo2, Setdb1, Ube2i, Trim28 and Zfp809 were diluted in nuclease-free water to 20 μM. The siRNAs for a given gene were mixed for knock-down, with a working concentration of 5 μM. Oocytes were injected with approximately 10 pL of siRNAs using a Piezo-driven micromanipulator. Allow oocytes to recover for at least 1 h in the incubator prior to Intracytoplasmic sperm injection (ICSI). The sperm head was then injected into the oocyte according to the method described previously (Kimura and Yanagimachi, 1995). The injected embryos were observed and summarized from the 2-cell stage to blastocyst stage.

value: morula embryo

value: none (input)


title: morula siTrim28 H3K9me3 rep2_ChIP-seq


title: I16R031a15


title: morula siTrim28 H3K9me3 rep1_ChIP-seq


title: morula siTrim28 1_RNA-seq

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using tophat v1.3.3 with default parameters.
Gene expression for each sample was quantified to RPKM using Cufflinks(v 1.2.0).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each transcript.

source_name: Mouse embryo

extract_protocol:
For MII oocyte and cleavage-stage embryos, the zona pellucida of embryos was removed by 0.5% pronase E (Sigma). Then the embryo was incubated in Ca2+ free CZB for 5 min. Polar bodies were removed by gentle pipetting using an inner diameter of 120 μm fire polished glass needle. For ICM and TE isolation, the zona pellucida of blastocysts was removed by 0.5% pronase E (Sigma). They were then incubated for 20 min in Ca2+ free CZB，the tight junctions TE cells and ICM cells were separated by gently pipetting in a pipette with a diameter of 40-60 μm.For epiblast (Epi) and extraembryonic ectoderm (Exe) isolation, embryos were cuttted at the embryonic/extraembryonic boundary using properly sharpened forceps. A fire-polished glass needle whose inner diameter is silghtly smaller than the width of the embryonic/extraembryonic fragment was used for separating epiblast or extraembryonic ectoderm from the visceral endoderm, and the epiblast or extraembryonic ectoderm were then incubated in Ca2+-free CZB for 10 min. Single cells were separated by gentle pipetting using a fire-polished glass needle with an inner diameter of 15-20 μm.200 cells were washed three times in 0.5% BSA-PBS solution per reaction.
Libraries were prepared according to Ovation® RNA‑Seq System V2 (NuGEN, 7102) following the manufacturer’s instructions.


title: morula siTrim28 H3K9me3 rep3_ChIP-seq


title: morula siZfp809 1_RNA-seq

treatment_protocol: For gene knockdown，small interference RNAs (siRNAs) against mouse Chaf1a, Sumo2, Setdb1, Ube2i and Zfp809 were diluted in nuclease-free water to 20 μM. The siRNAs for a given gene were mixed for knock-down, with a working concentration of 5 μM. Oocytes were injected with approximately 10 pL of siRNAs using a Piezo-driven micromanipulator. Allow oocytes to recover for at least 1 h in the incubator prior to Intracytoplasmic sperm injection (ICSI). The sperm head was then injected into the oocyte according to the method described previously (Kimura and Yanagimachi, 1995). The injected embryos were observed and summarized from the 2-cell stage to blastocyst stage.


title: morula siZfp809 2_RNA-seq


title: morula siTrim28 2_RNA-seq


title: morula siUbe2i 3_RNA-seq


title: morula siSetdb1 1_RNA-seq


title: morula siSetdb1 2_RNA-seq


title: morula siSumo2 2_RNA-seq


title: morula siUbe2i 2_RNA-seq


title: morula siUbe2i 1_RNA-seq


title: I16R031a06


title: morula siChaf1a 1_RNA-seq


title: TE 4_RNA-seq

value: trophoblast


title: morula ctrl 2_RNA-seq


title: E65Exe 2_RNA-seq

value: 6.6 day embyo extraembryonic ectoderm


title: E65Exe 1_RNA-seq

value: 6.5 day embyo extraembryonic ectoderm


title: E65Epi 2_RNA-seq

value: 6.6 day embyo epiblast


title: morula ctrl 1_RNA-seq


title: morula siSumo2 1_RNA-seq


title: TE 3_RNA-seq


title: E65Epi 1_RNA-seq

value: 6.5 day embyo epiblast


title: TE 1_RNA-seq


title: ICM 4_RNA-seq

value: inner cell mass


title: ICM 3_RNA-seq


title: morula 2_RNA-seq


title: ICM 1_RNA-seq


title: morula siChaf1a 2_RNA-seq


title: TE 2_RNA-seq


title: ICM 2_RNA-seq


title: morula 1_RNA-seq


title: 8-cell 2_RNA-seq

value: 8-cell embryo


title: 8-cell 3_RNA-seq


title: Mouse2_scRNAseq

city: Erlangen

first: Soeren

last: Lukassen

address: Schwabachanlage 10

department: Institute of Human Genetics

institute: Friedrich-Alexander Universitaet Erlangen Nuernberg

description:
matrix.mtx
genes.tsv
barcodes.tsv

data_processing:
demultiplexing was performed using the cellranger mkfastq 2.0.0 wrapper for bcl2fastq 2.17.1.14
Reads were aligned and processed by running cellranger count 2.0.0 on multi-flowcell input. The data for the biological replicates was then aggregated using cellranger aggr 2.0.0
Genome_build: Custom version of mm10 - The sequences from RepBase were appended to a repeat-masked mm10.
Supplementary_files_format_and_content: matrix.mtx, barcodes.tsv, genes.tsv. The matrix.mtx matrix market exchange file contains raw expression counts for each gene listed in genes.tsv and cell (barcodes.tsv).

source_name: testis

extract_protocol:
The tunic was removed from the tesetes using forceps. Individual seminiferous tubules were then isolated and cut using McPherson-Vannas microscissors. The tissue was enzymatically disrupted using collagenase, hyaluronidase, dispase, and DNAseI for 30 minutes at 37°C. After passing the cells through a 40 µm cell strainer, barcoded cDNAs for each cell were generated using the Chromium 3' single-cell platform with the v2 chemistry.
Sequencing libraries were constructed according to the protocol provided with the 10X Chromium 3' v2 chemistry.
scRNA-seq (Chromium platform)

value: C57Bl/6J Crl

value: 8 weeks

value: whole testis


title: Mouse1_scRNAseq

description:
matrix.mtx
genes.tsv
barcodes.tsv


title: 4-cell 4_RNA-seq

value: 4-cell embryo


title: 8-cell 1_RNA-seq


title: CC2

city: Chongqing

first: Zhong

last: Jianjun

address: NO.1 Youyi Road, Yuzhong District, Chongqing

department: Neurosurgery Department

institute: The first Affiliated Hospital of Chongqing Medical University

description: Normal

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat2 with parameters read-mismatches=2，read-gap-length=2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10

source_name: brain cortex tissue

extract_protocol:
Total RNA was harvested from cortex around trauma focus and RNA integrity was assessed and judged by A260/A280. Then the total RNA was fragmented into ~200 base pair (bp) units. RNA fragments were used to generate double-stranded cDNA, and then single strand of cDNA labeled by deoxy-UTP, which was enriched by PCR for 12 cycles.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Normal brain cortex

tag: group

value: control

value: wild type


title: TBI3

description: TBI

value: Brain cortex around injury site

value: 24 h after TBI


title: TBI2

description: TBI


title: CC1

description: Normal


title: CC3

description: Normal


title: 4-cell 1_RNA-seq


title: TBI1

description: TBI


title: 4-cell 3_RNA-seq


title: 2-cell 3_RNA-seq

value: 2-cell embryo


title: MII Oocyte 1_RNA-seq

source_name: MII oocyte

value: MII Oocyte


title: 2-cell 1_RNA-seq


title: 2-cell 2_RNA-seq


title: MII Oocyte 2_RNA-seq


title: ICM C57BL/DBA H3K9me3 2_ChIP-seq

value: C57BL/6 x DB/2


title: ICM C57BL/DBA H3K9me3 1_ChIP-seq


title: Late 2-cell C57BL/DBA H3K9me3 3_ChIP-seq

value: late 2-cell embryo


title: ICM C57BL/DBA input


title: Late 2-cell C57BL/DBA input


title: Late 2-cell C57BL/DBA H3K9me3 1_ChIP-seq


title: Late 2-cell C57BL/DBA H3K9me3 2_ChIP-seq


title: Early 2-cell C57BL/DBA input

value: early 2-cell embryo


title: zygote C57BL/DBA H3K9me3 2_ChIP-seq

value: zygote


title: zygote C57BL/DBA H3K9me3 1_ChIP-seq


title: 4-cell 2_RNA-seq


title: morula siZfp809 H3K9me3 rep2_ChIP-seq

value: morula embryo


title: Early 2-cell C57BL/DBA H3K9me3 2_ChIP-seq


title: morula siZfp809 input


title: zygote C57BL/DBA input


title: morula siZfp809 H3K9me3 rep1_ChIP-seq


title: morula siUbe2i input


title: morula siUbe2i H3K9me3 rep2_ChIP-seq


title: morula siUbe2i H3K9me3 rep1_ChIP-seq


title: morula siSumo2 input


title: morula siSumo2 H3K9me3 rep2_ChIP-seq


title: morula siSetdb1 H3K9me3 rep2_ChIP-seq


title: morula siSetdb1 H3K9me3 rep1_ChIP-seq


title: morula siChaf1a input_ChIP-seq


title: morula siSetdb1 input


title: morula siChaf1a H3K9me3 rep2_ChIP-seq


title: morula siChaf1a H3K9me3 rep1_ChIP-seq


title: morula ctrl H3K9me3 rep2_ChIP-seq


title: Early 2-cell C57BL/DBA H3K9me3 1_ChIP-seq


title: morula ctrl input


title: morula ctrl H3K9me3 rep1_ChIP-seq


title: E85Epi H3K9me3 rep2_ChIP-seq

value: 8.5 day embyo epiblast


title: E85Epi H3K27me3 rep3_ChIP-seq

value: H3K27me3(Diagnode, pAb-069-050)


title: E85Epi H3K9me3 rep1_ChIP-seq


title: E85Epi H3K27me3 rep2_ChIP-seq


title: E85Epi H3K27me3 rep1_ChIP-seq


title: E85Epi H3K4me3 rep2_ChIP-seq

value: H3K4me3(Cell signaling Technology, #9727)


title: E85Epi Input_ChIP-seq


title: E75Exe H3K9me3 rep1_ChIP-seq

value: 7.5 day embyo extraembryonic ectoderm


title: E85Epi H3K4me3 rep1_ChIP-seq


title: E75Exe H3K27me3 rep3_ChIP-seq


title: morula siSumo2 H3K9me3 rep1_ChIP-seq


title: E75Exe H3K27me3 rep1_ChIP-seq


title: E75Exe H3K4me3 rep3_ChIP-seq


title: E75Exe H3K4me3 rep2_ChIP-seq


title: E75Epi H3K9me3 rep4_ChIP-seq

value: 7.5 day embyo epiblast


title: E75Exe Input


title: E75Epi H3K9me3 rep1_ChIP-seq


title: E75Epi H3K9me3 rep3_ChIP-seq


title: E75Epi Input


title: E75Epi H3K27me3 rep1_ChIP-seq


title: E75Epi H3K4me3 rep2_ChIP-seq


title: E75Epi H3K4me3 rep3_ChIP-seq


title: E75Epi H3K4me3 rep1_ChIP-seq


title: 2-cell 4_RNA-seq


title: E65Exe H3K9me3 rep2_ChIP-seq

value: 6.5 day embyo extraembryonic ectoderm


title: E65Exe H3K9me3 rep1_ChIP-seq


title: E65Exe H3K27me3 rep2_ChIP-seq


title: E65Exe H3K27me3 rep3_ChIP-seq


title: E75Exe H3K27me3 rep2_ChIP-seq


title: E65Exe H3K4me3 rep1_ChIP-seq


title: E65Exe Input


title: E75Exe H3K4me3 rep1_ChIP-seq


title: E65Epi H3K9me3 rep1_ChIP-seq

value: 6.5 day embyo epiblast


title: E65Epi H3K27me3 rep3_ChIP-seq


title: E65Epi H3K27me3 rep2_ChIP-seq


title: E75Epi H3K9me3 rep2_ChIP-seq


title: E75Epi H3K27me3 rep2_ChIP-seq


title: E65Epi H3K4me3 rep1_ChIP-seq


title: E65Epi H3K27me3 rep1_ChIP-seq


title: E65Epi Input


title: TSC H3K9me3 rep3_ChIP-seq

source_name: mouse trophoblast stem cells

value: mouse trophoblast stem cells

value: mouse TS cell RO-7


title: TSC H3K9me3 rep2_ChIP-seq


title: TSC H3K9me3 rep1_ChIP-seq


title: E75Exe H3K9me3 rep2_ChIP-seq


title: ESC H3K9me3 rep1_ChIP-seq

source_name: mouse embryonic stem cells

value: mouse embryonic stem cells

value: mouse ES cell R1