title: MPNST, PRC2 loss, biological replicate 2 [PECN7_LSN]

city: New York

first: Ping

last: Chi

state: NY

address: 417 East 68th Street

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

description: PNCE7_Left Sciatic Nerve

data_processing:
RNA sequencing reads were 3’ trimmed for base quality 15 and adapter sequences using version 0.4.5 of TrimGalore, and
then aligned to mouse genome assembly mm10 with STAR v2.6 using default parameters to generate BAM alignment files.
Partek Genomics Suite 7.0 was used to quantify gene counts (reads) for each BAM sample followed by quantile normalization, and log2+1 transformation of read counts data.
Assembly: mm10

source_name: malignant peripheral nerve sheath tumor

extract_protocol:
1 mL Trizol reagent was added per tumor followed by homegenization using Tissue Ruptor II(QIAgen). Then phenol/chloroform separation and subsequent steps as outlined by Trizol reagent manufacturer (Thermo Fisher Scientific).
Poly-A mRNA was purified followed by fragmentation, and first and second strand cDNA synthesis with Illumina mRNA TruSeq library preparation protocol. Double stranded cDNAs were processed for TruSeq dual-index Illumina library preparation.

value: malignant peripheral nerve sheath tumor

value: 0.4 mg tamoxifen (day 0-3 post birth)


title: Patient 83

status: Public on Mar 01 2024

type: RNA

city: Bialystok

first: Magdalena

last: Niemira

address: Kilinskiego 1

country: Poland

institute: Medical University of Bialystok

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 83

hyb_protocol: Standard nanostring nCounter miRNA Hybridization Protocol; The final hybridization reaction contained the following components: 10 μL Reporter CodeSet, 10 μL hybridization buffer, a 5 μL aliquot from the miRNA Sample Preparation Protocol, and 5 μL Capture ProbeSet.

scan_protocol: Raw count data were collected and captured by the nCounter Digital Analyzer for image capture (555 fields of view).

data_processing: The miRNA data analysis was performed using nSolver Analysis (version 4·0) software. Each miRNA count data was subtracted from the geometric mean of the negative controls. Profiling data were then normalized by the geometric mean of the positive controls and the geometric mean of the top 100 most highly-expressed microRNAs.

molecule: total RNA

organism: Homo sapiens

source_name: grade 4

label_protocol: Standard nanostring miRNA protocols (nCounter Human v3 miRNA Expression Assays (NanoString Technologies,Seattle, USA))

extract_protocol: Total RNA was extracted from 400 mL of serum sample using miRNeasy Serum/Plasma Kit (Qiagen, Gaithersburg, MD, USA) according to the manufacturer’s protocol.

tag: grade

value: grade 4 (CNS5 WHO)

tag: age

tag: gender

value: female

tag: ihd status

value: MT


title: ICSI_Is_intact_93, blastocyst, scRNA-seq

type: SRA

city: Muenster

first: Wojciech

last: Makalowski

address: Niels Stensen Strasse 14

department: Faculty of Medicine

country: Germany

institute: University of Muenster

description:
Smart-Seq2
plate2-G08-ICSI_Is
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx

library_source: transcriptomic single cell

data_processing:
Reads were trimmed and adapters were removed using Trimmomatic (V.039).
Read quality was checked for each cell using FastQC (v0.12.1).
Reads were mapped to mm10, and expression of genes were quntified using STAR (2.7.10b) pipeline
Assembly: mm10 (GRCm38)
Supplementary files format and content: Tab-seperated values files (features and barcodes) plus matrix files

organism: Mus musculus

source_name: preimplantation embryo Theiler stage 5

growth_protocol: In vitro culture of fertilized oocytes in KSOM medium supplemented with aminoacids, in pool (4-well plate) up to the 2-cell stage, then individually after bisection (one blastomere per well of 96-well plate), at 37 °C under 5% CO2 in air, as described (PMID 28811525).

extract_protocol:
Single blastomeres or single blastocysts were lysed in 10X Lysis Buffer from Takara (cat.no. 635013). Then the RNA was extracted by TaKaRa SMART-Seq Single Cell Kit (cat.no. 634470).
Total RNA was converted to cDNA using the TaKaRa SMART-Seq Single Cell Kit (cat.no. 634470) and sequencing libraries were prepared using the Illumina Nextera XT DNA Library Preparation Kit (cat.no. FC-131-1024). Libraries were sequenced on an Illumina NovaSeq 6000 platform.

treatment_protocol: Sperm deposition by ICSI in three different ooplasmic locations (contralateral, isolateral or equatorial relative to meiotic spindle)

tag: tissue

value: preimplantation embryo Theiler stage 5

tag: cell type

value: blastocyst

tag: genotype


title: ICSI_Is_intact_95, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-G10-ICSI_Is
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: Patient 85

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 85

value: WT


title: Patient 87

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 87

value: male


title: Patient 84

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 84


title: Cre_D3A_2

city: Chongqing

first: taiping

last: Liu

address: Gaotanyan zhengjie 30, Shapingba district, Chongqing

country: China

institute: Department of Pathogenic Biology, Army Medical University (Third Military Medical University)

library_source: transcriptomic

data_processing:
Clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data by Trimmomatic.(parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR.
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene.
We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Splenocytes

growth_protocol: For RNASeq analysis, CD11b+ cells  were isolated from splenocytes of P. yoelii 17XNL-infected mice at Day 0, Day 3 and Day 6 post-infection.

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 SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
P. yoelii 17XNL infection
CD11b+ cells isolated from splenocytes

tag: cell line

value: Splenocytes

value: CD11b+ cells

value: ATG5fl-LysM Cre+

tag: treatment

value: P. yoelii 17XNL infection

tag: time

value: Day 3

tag: agent

value: P. yoelii 17XNL


title: MPNST, PRC2 loss, biological replicate 1 [PECN5]

country: USA

description: PNCE5_Right Paraspinal Nerve


title: ICSI_Is_intact_92, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-G07-ICSI_Is
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: Cre_D3A_1


title: MPNST, PRC2 wildtype, biological replicate 5 [PNC11]

value: Plp-CreERT:Nf1(f/f) Cdkn2a(f/f)


title: Patient 81

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 81


title: ICSI_Is_intact_91, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-G06-ICSI_Is
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: Patient 82

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 82


title: MPNST, PRC2 wildtype, biological replicate 4 [PNC9B]


title: 1_M_Myc

city: Mississauga

first: Iva

last: Zovkic

state: Ontario

address: 3359 Mississauga Rd

department: Department of Psychology

country: Canada

institute: University of Toronto

description: Sample 1

data_processing:
Fastqc (v0.11.9), Rsubread (v2.12.3), R (4.2.3), DESeq2 (v1.38.3)
Sequence reads were quality controlled using fastqc
Sequence reads were aligned to the GRCm39/mm39 genome using Rsubread-align in R (softclipping, paired-end settings)
Read counts were generated using featureCounts in R part of Rsubread. Normalization was performed in R.
Assembly: GRCm39/mm39
Supplementary files format and content: tab-delimited text file containing the raw counts for each sample
Supplementary files format and content: tab-delimited text file containing the rpkm normalized counts for each sample

source_name: Male Myc Overexpression

extract_protocol:
Total RNA was extracted from mouse hippocampal tissue using the RNeasy Mini Kit (Qiagen). 4ug of RNA per sample was sent to CD Genomics.
Samples were sent as total RNA on dry ice to CD Genomics (New York, United States of America)

value: Hippocampus

value: Male

value: Stereotaxic injection into hippocampus


title: Cre_D0B_3

value: ATG5fl-LysM Cre-

value: Day 0


title: ICSI_Is_intact_90, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-G05-ICSI_Is
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: ICSI_Is_intact_97, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-H02-ICSI_Is
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: MPNST, PRC2 loss, biological replicate 3 [PECN7_RSN]

description: PNCE7_Right Sciatic Nerve

value: malignant peripheral nerve sheath tumor

value: 0.4 mg tamoxifen (day 0-3 post birth)


title: MPNST, PRC2 wildtype, biological replicate 3 [PNC9A]


title: Patient 80

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 80

value: grade 4 (CNS5 WHO)

value: female


title: Cre_D3A_3


title: Cre_D3B_1


title: ICSI_Is_intact_89, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-G04-ICSI_Is
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx

value: preimplantation embryo Theiler stage 5

value: blastocyst


title: Patient 79

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 79

value: WT


title: Cre_D3B_2

value: Splenocytes

value: CD11b+ cells


title: Cre_D0B_1

value: P. yoelii 17XNL infection


title: ICSI_Co_intact_88, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-G03-ICSI_Co
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: Cre_D0B_2

value: P. yoelii 17XNL


title: MPNST, PRC2 wildtype, biological replicate 1 [PNC8A]

value: Plp-CreERT:Nf1(f/f) Cdkn2a(f/f)


title: MPNST, PRC2 wildtype, biological replicate 2 [PNC8C]


title: Cre_D0A_5

value: ATG5fl-LysM Cre+


title: Patient 77

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 77


title: Cre_D0A_4


title: mESC_Firre_Rescue_firre_induced_30min_dox_rep3_PROseq

city: Boulder

first: John

last: Rinn

state: CO

address: 3415 Colorado Ave

department: Biochemistry

institute: CU Boulder

data_processing:
Quality control and read mapping was performed using the Dowell Lab's Nascent-Flow Nextflow pipeline (https://github.com/Dowell-Lab/Nascent-Flow, commit: 98a14f74963c34d8002dd78982b9eef8528221b3). In that pipeline, reads were mapped to mm10 using Hisat2 with the flags --very-sensitive and --no-spliced-alignment. Bidirectionals were called with Tfit using the Dowell Lab's Bidirectional-Flow pipeline with the default parameters (https://github.com/Dowell-Lab/Nascent-Flow, commit: 2ef4f86bc4b3b47b8f9956c1ab534eb675c9a5b7).
muMerge v1.1.0 (https://github.com/Dowell-Lab/mumerge) was used to merge bidirectional nascent transcript calls across samples. For quantification, a uniform 600bp region from the center of the muMerge identified bidirectional was used. Counts in each sample were called using Rsubread's (v2.0.1) featureCounts over these regions. To filter to transcripts that produced reads on both transcripts, featureCounts was used to generate counts over the positive and negative strand aligned reads by using separate saf files over these 600bp regions with + and - strand regions. Bidirectionals were then filtered to those that had >=5 reads on each strand and a strand bias ratio of <1.
To identify differentially expressed nascent transcripts over the timecourse, DESeq2 (v1.26.0) was used to calculate a likelihood ratio test between the full model (~timepoint) vs a reduced model (~1). Further, to evaluate the magnitude of expression changes, DESeq2 was run using the Wald test to compare each the 15 and 30 minute time points to the 0 time point. A transcript was considered significant if the LRT test padj < 0.05 and achieved |fold-change| > 1.5 in either time point.
Supplementary files format and content: tfit_mumerge_bidirectionals.bed: Tab-separated text file containing the coordinates of bidirectional transcripts called on each sample using Tfit and merged across samples with muMerge
Supplementary files format and content: tfit_mumerge_bidirectionals_600bp.bed: Tab-separated text file containing the coordinates +/- 300bp from the center of the muMerge bidirectionals. These were the coordinates used with featureCount.
Supplementary files format and content: bidirectional_600bp_counts.csv: Comma-separated text file containing the counts over each 600bp nascent transcript region across each sample.

source_name: mESC

growth_protocol: Cells were maintained on 0.1% gelatin in KnockOut DMEM (Thermo Fisher, 10829018) supplemented with 12.5% FCS (MilliporeSigma, ES-009-B), 1X GlutaMAX supplement (Thermo Fisher, 35050061), 1X non-essential amino acids (Thermo Fisher, 11140050), 100 U/mL penicillin/streptomycin (Thermo Fisher, 15140122), 100 μM 2-mercaptoethanol (Thermo Fisher, 31350010), 1 μM PD0325901 (MilliporeSigma, PZ0162-5MG), 3 μM CHIR99021 (MilliporeSigma, SML1046-5MG), and 100 U/mL LIF (MilliporeSigma, ESG1107) at 37°C and 7.5% CO2. Cells were routinely tested for mycoplasma contamination by PCR.

extract_protocol:
Nuclear RNA was extracted using TRIzol lysis reagent (Thermo Fisher) from purified nuclei described in Miller et al. 2015 and then enriched with biotin  in a nuclear run-on experiments as described in Mahat et al. 2016.
PRO-seq libraries were prepared from 10-20 million mES nuclei and 1% drosophila S2 nuclei and made during the biotin enrichment process as described in Mahat et al. 2016.

treatment_protocol: Cells were treated with 1 ng/μL dox (MilliporeSigma, D9891-5G) the day after they were seeded.

value: mESC

value: embryonic stem cells

value: Firre KO / Firre inducible transgene

value: doxycycline

value: 30 minutes


title: mESC_Firre_Rescue_firre_induced_15min_dox_rep3_PROseq

value: 15 minutes


title: Patient 76

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 76

value: grade 4 (CNS5 WHO)

value: MT


title: ICSI_Co_intact_85, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-F10-ICSI_Co
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx

value: preimplantation embryo Theiler stage 5


title: Patient 75

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 75

value: female


title: Cre_D0A_3

value: Day 0


title: Cre_D0A_2

value: Splenocytes


title: mESC_Firre_Rescue_firre_induced_0min_dox_rep3_PROseq

value: no doxycycline

value: 0 minutes


title: ICSI_Co_intact_84, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-F09-ICSI_Co
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx

value: blastocyst


title: mESC_Firre_Rescue_firre_induced_30min_dox_rep2_PROseq


title: Patient 73

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 73

value: male

value: WT


title: Patient 78

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 78


title: mESC_Firre_Rescue_firre_induced_15min_dox_rep2_PROseq

value: mESC


title: Cre_D0A_1

value: CD11b+ cells

value: ATG5fl-LysM Cre+

value: P. yoelii 17XNL infection

value: P. yoelii 17XNL


title: ICSI_Co_intact_87, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-G02-ICSI_Co
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: ICSI_Co_intact_81, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-F06-ICSI_Co
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: ICSI_Co_intact_83, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-F08-ICSI_Co
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: ICSI_Co_intact_82, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-F07-ICSI_Co
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: Patient 72

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 72


title: VE-IVM

first: MATTHEW

middle: Dae-Young

last: PARK

address: 50 East 98th Street, 6A-1

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Base calling was conducted by the HiSeq Control Software.
Sequence data generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software.
Sequence reads were trimmed to remove possible adaptor sequences and nucleotides with poor quality using Trimmomatic v.0.37.
Trimmed reads were mapped to the Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
BAM files were generated and unique gene hit counts were calculated by using feature counts from the Subread package v.1.5.2.
Assembly: mm10
Supplementary files format and content: Excel files include raw count and TPM values for each Sample

source_name: intravascular macrophages

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Plus Mini kit and quantified using Qubit 2.0 fluorometer and RNA integrity was checked using Agilent TapeStation 4200.
Ultra-low input RNA seq libraries were prepared using the SMART-Seq HT kit for full-length cDNA synthesis and amplification and Illumina Nextera XT library was used for sequencing library preparation.

treatment_protocol:
N/A
N/A

value: intravascular macrophages

value: BRAFV600E mutant


title: mESC_Firre_Rescue_firre_induced_30min_dox_rep1_PROseq

value: embryonic stem cells

value: Firre KO / Firre inducible transgene

value: doxycycline

value: 30 minutes


title: mESC_Firre_Rescue_firre_induced_0min_rep2_PROseq


title: Patient 71

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 71

value: grade 4 (CNS5 WHO)

value: MT


title: VE-monocyte

source_name: monocytes

value: monocytes


title: VE-MG

source_name: microglia

value: microglia


title: ICSI_Co_intact_79, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-F04-ICSI_Co
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx

value: preimplantation embryo Theiler stage 5

value: blastocyst


title: ICSI_Co_intact_86, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-G01-ICSI_Co
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: Patient 74

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 74

value: female


title: WT-MG

value: WT


title: mESC_Firre_Rescue_firre_induced_15min_dox_rep1_PROseq

value: mESC

value: 15 minutes


title: mESC_Firre_Rescue_firre_induced_0min_dox_rep1_PROseq

value: no doxycycline

value: 0 minutes


title: ICSI_Co_intact_77, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-F02-ICSI_Co
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: Patient 69

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 69

value: male


title: Patient 68

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 68


title: WT-monocyte


title: mESC_Firre_Rescue_firre_induced_48h_H3K27me3_ChIPseq

library_source: genomic

data_processing:
Quality control and read mapping were performed using the nf-core/chipseq v1.1.0 pipeline. Using that pipeline, reads were mapped to mm10 with the mm10 ENCODE Blacklist v2 (https://github.com/Boyle-Lab/Blacklist/blob/master/lists/mm10-blacklist.v2.bed.gz) using BWA MEM (v0.7.17-r1188).
Consensus peaks were called with MACS v2.2.71 by using all IP conditions as the treatment and all inputs as controls. This was performed with the flags:--broad --broad-cutoff 0.1 -B.
Counts over peak regions were calculated using Rsubread's (v2.0.1) featureCounts.
To identify differential H3K27me3 peak regions, the DESeq2 (v1.26.0) Wald test was used to compare 48 hour Firre induced samples to controls. Significant peaks were those with Benjamini-Hochberg adjusted p-values < 0.05. Additionally, peak count correlations between 48h and 0h were performed using the normalized counts calculated by DESeq2.
Supplementary files format and content: H3K27me3_chipseq_consensus_peaks.csv: Comma-separated text file containing the coordinates of H3K27me3 ChIP-seq peaks called across all IPs compared to all inputs with MACS. P-value and Q-value are in -log10 format.
Supplementary files format and content: H3K27me3_chipseq_consensus_peak_counts.csv: Comma-separated text file containing the counts over all peak regions across all samples.

molecule: genomic DNA

growth_protocol: Cells were maintained on 0.1% gelatin in KnockOut DMEM supplemented with 12.5% FCS, 1X GlutaMAX supplement, 1X non-essential amino acids, 100 U/mL penicillin/streptomycin, 100 μM 2-mercaptoethanol, 1 μM PD0325901, 3 μM CHIR99021, and 100 U/mL LIF at 37°C and 7.5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Covaris M220 focused-ultrasonicator.
ChIP-seq libraries were prepared using the KAPA HyperPlus Library Preparation Kit. 6.5 ng of DNA was used as starting material for input and IP samples. Libraries were amplified using 13 cycles on the thermocycler. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: embryonic stem cells

tag: chip antibody

value: Firre Firre KO / Firre inducible transgene

value: 48 hours


title: ICSI_Co_intact_76, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-F01-ICSI_Co
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: WT-IVM

value: intravascular macrophages


title: ICSI_Eq_75b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_E10-ICSI_Eq-75b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

source_name: preimplantation embryo Theiler stage 2

value: preimplantation embryo Theiler stage 2

value: blastomere


title: mESC_Firre_Rescue_control_48h_H3K27me3_ChIPseq

value: Firre KO

value: doxycycline


title: ICSI_Eq_75a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_E09-ICSI_Eq-75a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: GM3

city: Fuzhou

first: Fuquan

last: Tu

state: Fujian

address: Xinquan road NO. 29

institute: Fujian Medical University

data_processing:
HISAT2 v2.0.5
DESeq2 R package (1.20.0)
Genes with an adjusted P-value < 0.05 found by DESeq2 were assigned as differentially expressed.
GATK (v4.1.1.0) software was used to perform SNPcalling. Raw vcf files were filtered with GATK standard filter method and other parameters (cluster: 3; WindowSize:35; QD < 2.0; FS>30.0; DP < 10.)
PPI analysis of differentially expressed genes was based on the STRING database, which known and predicted Protein-Protein Interactions.
Supplementary files format and content: mm10
Supplementary files format and content: for transcriptome sequencing, FPKM can be used as gene expression data.

source_name: Periphral blood

growth_protocol: C57BL/6J male mice were purchased from SLAC Laboratory Animal (SCXK 2017-0005, Shanghai, China) between 4 and 5 weeks of age. All mice were maintained at Fujian Medical University and were studied between 6 and 8 weeks of age (body weight, 20-25 g).

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 integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 System (Agilent Technologies, CA, USA). The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer's instructions.

treatment_protocol: Normal group mice were accepted nothing. CLP 5days group mice were accepted CLP and for 5days. The GM group mice were accepted CLP for 5days and then received rmGM-CSF (26.5 ng/g/day, hypodermic injection, 576306, Biolegend, CA, America)  for 5 days

value: Periphral blood

value: PMNs

value: adipogenic differentiation

value: mice accepted CLP for 5days and intervened by GM-CSF for 5days


title: mESC_Firre_OE_firre_induced_48h_H3K27me3_ChIPseq

value: mESC

value: Firre WT / Firre inducible transgene


title: Patient 67

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 67

value: grade 4 (CNS5 WHO)

value: female

value: WT


title: Patient 66

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 66


title: ICSI_Eq_74b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_E08-ICSI_Eq-74b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: Patient 70

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 70

value: male


title: GM2


title: ICSI_Eq_74a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_E07-ICSI_Eq-74a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: Patient 63

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 63

value: MT


title: ICSI_Eq_73b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_E06-ICSI_Eq-73b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_Rescue_control_48h_input_ChIPseq

value: embryonic stem cells

value: 48 hours


title: mESC_Firre_OE_control_48h_H3K27me3_ChIPseq


title: GM1


title: Patient 64

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 64


title: mESC_Firre_Rescue_firre_induced_48h_input_ChIPseq

value: Firre Firre KO / Firre inducible transgene


title: Sep3

value: mice accepted CLP for 5days


title: mESC_Firre_OE_firre_induced_48h_input_ChIPseq


title: Sep2


title: Sep1


title: Patient 62

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 62


title: ICSI_Eq_72b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_E04-ICSI_Eq-72b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

value: preimplantation embryo Theiler stage 2

value: blastomere


title: Nor3

value: Periphral blood

value: Normal mice


title: mESC_Firre_OE_control_48h_input_ChIPseq

value: doxycycline


title: Patient 65

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 65


title: Patient 61

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 61


title: mESC_Firre_Rescue_control_0h_H3K27me3_ChIPseq

value: Firre KO

value: 0 hours


title: mESC_Firre_Rescue_firre_induced_0h_H3K27me3_ChIPseq

value: mESC


title: mESC_Firre_OE_firre_induced_0h_H3K27me3_ChIPseq

value: Firre WT / Firre inducible transgene


title: ICSI_Eq_72a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_E03-ICSI_Eq-72a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: Nor2

value: PMNs

value: adipogenic differentiation


title: Nor1


title: Patient 60

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 60

value: grade 4 (CNS5 WHO)

value: female

value: WT


title: Gs 3

city: Nanjing

first: chen

last: xiang

address: chunhua street

institute: nanjing medical university

data_processing:
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) to be high quality clean data.
Mapping: 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
mm9
Assembly: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: ischemia penumbra

extract_protocol:
ischemia penumbra tissues were removed, flash frozen on dry ice, and RNA was harvested using  mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. TruSeq Stranded mRNA LTSample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: MCAO-Gelsevirine (10 mg/kg)

value: Brain


title: ICSI_Eq_73a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_E05-ICSI_Eq-73a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: ICSI_Eq_71b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_E02-ICSI_Eq-71b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: ICSI_Eq_71a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_E01-ICSI_Eq-71a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: ICSI_Eq_70a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_D09-ICSI_Eq-70a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: Patient 59

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 59

value: male


title: Patient 58

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 58


title: mESC_Firre_Rescue_firre_induced_0h_input_ChIPseq

value: embryonic stem cells

value: Firre Firre KO / Firre inducible transgene


title: mESC_Firre_Rescue_control_0h_input_ChIPseq


title: Patient 55

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 55


title: mESC_Firre_OE_control_0h_H3K27me3_ChIPseq


title: Gs 1


title: Gs 2


title: ICSI_Eq_70b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_D10-ICSI_Eq-70b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

value: preimplantation embryo Theiler stage 2

value: blastomere


title: mESC_Firre_OE_firre_induced_0h_input_ChIPseq

value: doxycycline


title: Vehicle 3

value: MCAO-Vehicle


title: ICSI_Eq_69a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_D07-ICSI_Eq-69a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: Patient 57

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 57


title: Patient 56

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 56


title: ICSI_Eq_68b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_D06-ICSI_Eq-68b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: Vehicle 2


title: Patient 53

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 53


title: ICSI_Eq_69b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_D08-ICSI_Eq-69b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_OE_control_0h_input_ChIPseq

value: 0 hours


title: Patient 52

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 52


title: Vehicle 1


title: ICSI_Eq_67b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_D04-ICSI_Eq-67b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: Patient 51

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 51


title: mESC_Firre_Rescue_firre_induced_330min_dox_short_rep2

data_processing:
Quality control, read mapping, and quantification was performed using nf-core/rnaseq v1.4.2. Reads were mapped to mm10 and quantified with Salmon v1.5.2 using the Gencode M25 annotation.
Assembly: mm10
Supplementary files format and content: comma-separated text file contains TPM values for each Sample
Supplementary files format and content: comma-separated text file contains raw counts values for each Sample

molecule: polyA RNA

extract_protocol:
Total RNA was extracted using TRIzol lysis reagent (Thermo Fisher) and purified using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA concentration was measured with a Qubit fluorometer (Invitrogen), and RNA quality was determined using a Bioanalyzer or TapeStation (Agilent Technologies).
RNA-seq libraries were prepared from 1 μg of total RNA using the TruSeq RNA Library Prep Kit v2 (Illumina) with poly(A) selection according to the manufacturer’s instructions. Multiples of 12 randomized samples were each multiplexed, pooled, and run in one HiSeq lane.

treatment_protocol: Cells were treated with 1 ng/μL dox (MilliporeSigma, D9891-5G) the day after they were seeded and one hour after medium was changed to reduce cell stress.

value: mESC

value: Firre KO / Firre inducible transgene

value: 330 minutes


title: mESC_Firre_Rescue_firre_induced_330min_dox_short_rep1


title: ICSI_Eq_68a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_D05-ICSI_Eq-68a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: ICSI_Eq_67a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_D03-ICSI_Eq-67a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: ONECUT3-OE, ONECUT3-FLAG, rep2

city: Hangzhou

first: Hongyan

last: Tong

state: Zhejiang

address: No. 79 Qingchun Rd., Shangcheng District, Hangzhou, Zhejiang, China

department: Department of Hematology

institute: The First Affiliated Hospital, Zhejiang University School of Medicine

data_processing:
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 ploy-N 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. Paired-end clean reads were aligned to the reference genome using Bowtie v2.2.6.
After mapping reads to the reference genome, we used the MACS2 version 2.1.0 (model-based analysis of ChIP-seq) peak finding algorithm to indentify regions of IP enrichment over background. A p value threshold of enrichment of 0.01 was used for all data sets. Then, the distribute of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed.
Normalized bigWig files were generated by deeptools (version 3.3.2).
Assembly: GRCm38
Supplementary files format and content: bigWig
Supplementary files format and content: tab-delimited peak file include information about identified peaks

source_name: p53 KO MEF

growth_protocol: The primary MEF cells were cultured in DMEM containing 10% fetal bovine serum (FBS), 1% Penicillin/Streptomycin, 1x Sodium Pyruvate (Gibco, USA), 1x MEM Non-Essential Amino Acids Solution (Gibco, USA) and 1x GlutaMAX Supplement (Gibco, USA). And the cells were passaged when the cell confluency reached about 80%-90%. Primary MEF were used for maximum of five passages.

extract_protocol:
MEF cells were crosslinked with 1% formaldehyde at room temperature for 10 minutes. 1.5 M Glycine solution was used to terminate the fixation reaction. After washing with the iced PBS and homogenizing, cells were then lysed with SDS cell-lysis buffer (50 mM Tris pH 8.0, 1 mM EDTA pH 8.0, 0.1% wt/vol SDS and 1 mM PMSF) for 10 min on ice, and the chromatin was sonicated to 100–500bp in a Bioruptor (Diagenode). The size of the sheared chromatin was verified by agarose gel electrophoresis after reverse cross-linking.     For immunoprecipitation, Dynabeads Protein G (Thermo, 10003D) was pre-washed was 0.5% BSA and conjugated to 5 μg of ChIP antibody or normal IgG at 4 °C for 4-6h. After washing with the RIPA/150mM NaCl washing buffer (50 mM Tris pH 8.0, 150 mM NaCl, 1 mM EDTA pH 8.0, 1% wt/vol sodium deoxycholate, 1% vol/vol Triton X-100, 0.1% wt/vol SDS and 1 mM PMSF), the conjugated beads were added to the chromatin slurry and incubated at 4 °C for 12 hours. Afterward, beads were washed twice with RIPA/150mM NaCl washing buffer, twice with RIPA/500mM NaCl washing buffer (50 mM Tris pH 8.0, 500 mM NaCl, 1 mM EDTA pH 8.0, 1% wt/vol sodium deoxycholate, 1% vol/vol Triton X-100, 0.1% wt/vol SDS and 1 mM PMSF), four times LiCl washing buffer (10 mM Tris pH 8.0, 250 mM LiCl, 1 mM EDTA pH 8.0, 0.5% vol/vol NP-40 and 0.5% vol/vol Sodium Deoxycholate) and twice with TE buffer (10 mM Tris pH 8.0, 300 mM NaCl and 0.5 mM EDTA pH 8.0). The precipitated beads were diluted with ChIP elution buffer (10 mM Tris pH 8.0, 250 mM LiCl, 1 mM EDTA pH 8.0, 0.5% vol/vol NP-40 and 0.5% wt/vol SDS). One forth of the solution with beads were added with SDS protein lysis buffer for WB to verify the specificity of ChIP. The rest of the ChIP’d beads and the input were reversed cross-linking with 5 M NaCl solution at 65 °C overnight.     The procedure of the DNA recovery from the immunoprecipitation is as follows. The above reversed cross-linking solution was mixed with 2x SDS lysis buffer (200 mM Tris pH 8.0, 1 M NaCl, 100mM EDTA pH 8.0 and 0.5% wt/vol SDS) with Proteinase K at 200x rpm for 15 minutes and followed by RNase A at 37 °C for 30 minutes. 3 M NaAc (pH 5.2) was used to remove the protein. The clean supernatant was mixed with Isopropanol and Glycogen to precipitate the DNA. After washed twice with pre-cooled 75% ethanol, DNA pellets were dried for 10 minutes, dissolved in 10 mM Tris-HCl (pH 8.0) and then measured by the Qubit dsDNA HS Assay Kit (Thermo Fisher) on the Qubit instrument (ThermoFisher Scientific).
NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645)  was used for library preparation.

treatment_protocol: For control group, no Doxycycline was added, while MEF cells were treated with 100 ng/ml Doxycycline to induce ONECUT3 overexpression.

value: embryo

value: mouse embryonic fibroblast

value: Doxycycline

value: Monoclonal ANTI-FLAG M2 antibody (produced in mouse, Sigma, catalog# F3165)


title: Patient 50

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 50

value: grade 4 (CNS5 WHO)

value: WT


title: Patient 49

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 49

value: male


title: mESC_Firre_Rescue_firre_induced_300min_dox_short_rep1

value: embryonic stem cells

value: 300 minutes


title: ONECUT3-OE, ONECUT3-FLAG, rep3


title: mESC_Firre_Rescue_firre_induced_300min_dox_short_rep2


title: Patient 54

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 54

value: female


title: ICSI_Eq_66b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_D02-ICSI_Eq-66b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

value: preimplantation embryo Theiler stage 2

value: blastomere


title: ONECUT3-OE, ONECUT3-FLAG, rep1


title: ICSI_Eq_66a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_D01-ICSI_Eq-66a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: Patient 48

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 48


title: mESC_Firre_Rescue_firre_induced_270min_dox_short_rep2

value: doxycycline

value: 270 minutes


title: ONECUT3-OE, IgG, rep1

value: Normal Mouse IgG (Millipore, catalog# 12-371, lot# 3543076)


title: mESC_Firre_Rescue_firre_induced_270min_dox_short_rep1

value: mESC

value: Firre KO / Firre inducible transgene


title: ICSI_Is_65a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_C09-ICSI_Is-65a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: ONECUT3-OE, Input, rep1

value: embryo


title: Control, ONECUT3-FLAG, rep1

value: mouse embryonic fibroblast

value: no Doxycycline

value: control


title: Patient 45

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 45

value: grade 4 (CNS5 WHO)


title: ICSI_Is_64b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_C08-ICSI_Is-64b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_Rescue_firre_induced_240min_dox_short_rep1

value: 240 minutes


title: Patient 44

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 44

value: WT


title: Quantseq_T_mesoderm_4

city: London

first: Jernej

last: Ule

address: 10-12 Russell sq

department: Neuromuscular Diseases

country: United Kingdom

institute: UCL Institute of Neurology

description:
T-eGFP Foxa2-tagRFP double reporter mESC line was cultured in different medias to capture ESCs in naïve, rosette, epiblast and mesodermal progenitors state. The following culturing conditions have been applied as listed in doi: https://doi.org/10.1101/2021.03.15.433780.
Sample 20 20170223_miha_mouse_e4.fastq.gz

data_processing:
Reads were quantified using Salmon, with a transcriptome built from GENCODE M22 transcripts, using default settings.
To monitor the expression level of the Lin28a-GFP transgene, the sequence was included with decoy sequences derived from the whole genome sequence.
Differential expression analysis was performed using DESeq2, with effect size shrinkage using the apeglm package.
Genome_build: GENCODE M22

source_name: ESC

growth_protocol: All mouse ESC lines e.g., J1 IDG3.2 and V6.5, were maintained in 1:1 Neurobasal (21103049) DMEM (11320033) medium containing N2 (17502048) and B27 (17504044) supplements, 1% Glutamax (35050), 1% nonessential amino acids (1140050), 0.1 mM 2-mercaptoethanol (31350-010) (all Thermo Fisher Scientific), 1 mM MEK inhibitor PD0325901 (1408, Axon Medchem), 3 mM GSK3 inhibitor CHIR99021 (4953/50 Tocris), and 1,000 U/ml LIF (ESGRO ESG1107, Merck), a condition named 2iLIF. Cells were passaged using Stempro-Accutase (A1110501, Thermo Fisher Scientific). Cells were grown on gelatin coated plates which were prepared by first incubating the wells 0.1% gelatin (EmbryoMax® ES-006-B, Merck) with 1% FBS (EmbryoMax® ES Cell Qualified FBS, ES-009-B, Merck) for 1 h at 37 °C followed by a rinse with PBS. To transit from naive ESC to priming ESC cells, accutased naive ESCs were seeded onto gelatine and FBS-coated plates in N2B27 medium supplemented with recombinant 20 ng ml–1activin A (338-AC-050, R&D Systems) and 12 ng ml–1 bFGF (100-18B, Peprotech) for 12 hours or as indicated in the Figure legends (12, 24, 36 or 48 hours). To determine developmental genes that are downregulated during naive-to-primed transition, the publicly available data were used (Yang et al., 2019a) and analyzed as described in the RNAseq analysis section. Primed epiblast stem cells (EpiSCs) were cultured on gelatine and FCS-coated plates in N2B27 medium supplemented with recombinant 20 ng ml–1activin A (338-AC-050, R&D Systems) and  2 μM IWP2 (3533, Tocris) to suppress spontaneous differentiation. EpiSCs were passaged 1:4–1:10 every 3 days by triturating the colonies into small clumps using 0.5 mg ml–1 collagenase IV (Sigma). MEK/WNT-inhibited RSCs were cultivated with 1,000 U ml–1 LIF, 2 μM IWP2, 1 μM PD (manufacturers as mentioned above) and were passaged as ESCs. To induce primitive streak differentiation we utilized a double reporter mESC line modified to express distinct fluorescent proteins regulated by the promoters of T (Brachyury) and Foxa2 genes, where the expression of T and Foxa2 alone is indicative of mesodermal and endodermal commitment, respectively (Burtscher and Lickert, 2009). First, EpiSCs from these cells were derived by transiting ESCs to primed cells with 1,000 U ml–1 LIF, 2 μM IWP2, 20 ng ml–1 Activin A and 12 ng ml–1 bFGF (manufacturers as mentioned above). After 3 days, LIF has been omitted and derived EpiSCs can be passaged 1:4–1:10 every by triturating the colonies into small clumps using 0.5 mg ml–1 collagenase IV (Sigma). To derive mesodermal progenitors utilizing the T-eGFP FoxA2-tagRFP double knock-in reporter cell lines, the IWP2 that is in EpiSCs used to suppress differentiation was replaced by 250ng/mL of WNT3A (in house produced as described previously (Neagu et al., 2020)) and fresh medium was applied daily. Expression of T-eGFP and FoxA2-tagRFP, indicative of mesodermal and endodermal progenitors, was monitored by Flow cytometry.  All cell lines in culture were tested for mycoplasma contamination every 2–3 months.

extract_protocol:
Total RNA was prepared from cell pellets using miRNeasy Micro Kit (Qiagen, 217084) according to the manufacturer’s instructions
For 3’mRNA-seq, 0.5 μg of totalRNA was used per library prepared using Lexogen QuantSeq-FWD kit (Lexogen GmbH, 0.15).

treatment_protocol: mESCs were co-transfected with 4 μg of transposable vector and 1 μg of the piggyBac transposase using Lipofectamine 3000 (Thermo Fisher Scientific) according to the manufacturer’s instructions. Selection in 5μg/ml blasticidin was initiated 3 days after transfection and maintained until resistant colonies became visible. The LIN28A-GFP overexpression was induced by adding 1μg/ml doxycycline (dox) (ThermoFisher Scientific) in 2iLIF medium.

value: mESC IDG3.2.

tag: developmental stage

value: T-mesodermal prognitors

tag: transgene

value: grown in 250ng/mL of WNT3A, 20 ng ml–1 Activin A and 12 ng ml–1 bFGF and FACS sorted for GFP expressing cells after 3days


title: ICSI_Is_64a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_C07-ICSI_Is-64a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

value: preimplantation embryo Theiler stage 2


title: mESC_Firre_Rescue_firre_induced_210min_dox_short_rep1

value: embryonic stem cells

value: 210 minutes


title: Quantseq_T_mesoderm_5

description:
T-eGFP Foxa2-tagRFP double reporter mESC line
Sample 21 20170223_miha_mouse_e5.fastq.gz


title: Quantseq_T_mesoderm_2

description:
T-eGFP Foxa2-tagRFP double reporter mESC line was cultured in different medias to capture ESCs in naïve, rosette, epiblast and mesodermal progenitors state. The following culturing conditions have been applied as listed in doi: https://doi.org/10.1101/2021.03.15.433780.
Sample 18 20170223_miha_mouse_e2.fastq.gz


title: mESC_Firre_Rescue_firre_induced_210min_dox_short_rep2

value: doxycycline


title: Patient 42

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 42

value: male


title: ICSI_Is_63a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_C05-ICSI_Is-63a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

value: blastomere


title: Patient 43

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 43

value: female

value: MT


title: Quantseq_T_mesoderm_1

description:
T-eGFP Foxa2-tagRFP double reporter mESC line was cultured in different medias to capture ESCs in naïve, rosette, epiblast and mesodermal progenitors state. The following culturing conditions have been applied as listed in doi: https://doi.org/10.1101/2021.03.15.433780.
Sample 17 20170223_miha_mouse_e1.fastq.gz


title: mESC_Firre_Rescue_firre_induced_180min_dox_short_rep2

value: mESC

value: Firre KO / Firre inducible transgene

value: 180 minutes


title: Patient 46

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 46

value: grade 4 (CNS5 WHO)


title: Patient 47

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 47


title: mESC_Firre_Rescue_firre_induced_180min_dox_short_rep1


title: ICSI_Is_65b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_C10-ICSI_Is-65b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_Rescue_firre_induced_240min_dox_short_rep2

value: 240 minutes


title: Quantseq_EpiSCs_6

description:
T-eGFP Foxa2-tagRFP double reporter mESC line was cultured in different medias to capture ESCs in naïve, rosette, epiblast and mesodermal progenitors state. The following culturing conditions have been applied as listed in doi: https://doi.org/10.1101/2021.03.15.433780.
Sample 16 20170223_miha_mouse_e19.fastq.gz

value: epiblas stem cells

value: grown in 2 μM IWP2, 20 ng ml–1 Activin A and 12 ng ml–1 bFGF


title: ICSI_Is_63b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_C06-ICSI_Is-63b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: ICSI_Is_62b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_C04-ICSI_Is-62b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: Patient 40

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 40

value: WT


title: ICSI_Is_61b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_C02-ICSI_Is-61b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: ICSI_Is_62a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_C03-ICSI_Is-62a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_Rescue_firre_induced_150min_dox_short_rep2

value: 150 minutes


title: Patient 39

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 39


title: mESC_Firre_Rescue_firre_induced_150min_dox_short_rep1


title: ICSI_Is_61a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_C01-ICSI_Is-61a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

value: preimplantation embryo Theiler stage 2


title: Patient 38

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 38


title: Quantseq_T_mesoderm_3

description:
T-eGFP Foxa2-tagRFP double reporter mESC line was cultured in different medias to capture ESCs in naïve, rosette, epiblast and mesodermal progenitors state. The following culturing conditions have been applied as listed in doi: https://doi.org/10.1101/2021.03.15.433780.
Sample 19 20170223_miha_mouse_e3.fastq.gz

value: mESC IDG3.2.

value: T-mesodermal prognitors

value: grown in 250ng/mL of WNT3A, 20 ng ml–1 Activin A and 12 ng ml–1 bFGF and FACS sorted for GFP expressing cells after 3days


title: ICSI_Is_60b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_B10-ICSI_Is-60b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_Rescue_firre_induced_120min_dox_short_rep1

value: embryonic stem cells

value: doxycycline

value: 120 minutes


title: Quantseq_EpiSCs_4

description:
T-eGFP Foxa2-tagRFP double reporter mESC line was cultured in different medias to capture ESCs in naïve, rosette, epiblast and mesodermal progenitors state. The following culturing conditions have been applied as listed in doi: https://doi.org/10.1101/2021.03.15.433780.
Sample 14 20170223_miha_mouse_e17.fastq.gz


title: Quantseq_EpiSCs_3

description:
T-eGFP Foxa2-tagRFP double reporter mESC line was cultured in different medias to capture ESCs in naïve, rosette, epiblast and mesodermal progenitors state. The following culturing conditions have been applied as listed in doi: https://doi.org/10.1101/2021.03.15.433780.
Sample 13 20170223_miha_mouse_e16.fastq.gz


title: Quantseq_EpiSCs_2

description:
T-eGFP Foxa2-tagRFP double reporter mESC line was cultured in different medias to capture ESCs in naïve, rosette, epiblast and mesodermal progenitors state. The following culturing conditions have been applied as listed in doi: https://doi.org/10.1101/2021.03.15.433780.
Sample 12 20170223_miha_mouse_e15.fastq.gz


title: Patient 41

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 41

value: female

value: MT


title: mESC_Firre_Rescue_firre_induced_90min_dox_short_rep2

value: mESC

value: Firre KO / Firre inducible transgene

value: 90 minutes


title: ICSI_Is_60a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_B09-ICSI_Is-60a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

value: blastomere


title: Patient 37

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 37

value: grade 4 (CNS5 WHO)

value: male


title: Patient 35

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 35

value: WT


title: Patient 34

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 34


title: Quantseq_EpiSCs_5

description:
T-eGFP Foxa2-tagRFP double reporter mESC line was cultured in different medias to capture ESCs in naïve, rosette, epiblast and mesodermal progenitors state. The following culturing conditions have been applied as listed in doi: https://doi.org/10.1101/2021.03.15.433780.
Sample 15 20170223_miha_mouse_e18.fastq.gz

value: epiblas stem cells

value: grown in 2 μM IWP2, 20 ng ml–1 Activin A and 12 ng ml–1 bFGF


title: mESC_Firre_Rescue_firre_induced_60min_dox_short_rep1

value: 60 minutes


title: ICSI_Is_59b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_B08-ICSI_Is-59b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

value: preimplantation embryo Theiler stage 2


title: Patient 36

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 36


title: Quantseq_RSCs_5

description:
T-eGFP Foxa2-tagRFP double reporter mESC line was cultured in different medias to capture ESCs in naïve, rosette, epiblast and mesodermal progenitors state. The following culturing conditions have been applied as listed in doi: https://doi.org/10.1101/2021.03.15.433780.
Sample 10 20170223_miha_mouse_e13.fastq.gz

value: mESC IDG3.2.

value: rosette stem cells

value: grown in 1,000 U ml–1 LIF, 2 μM IWP2, 1 μM PD


title: ICSI_Is_58b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_B06-ICSI_Is-58b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: Quantseq_EpiSCs_1

description:
T-eGFP Foxa2-tagRFP double reporter mESC line was cultured in different medias to capture ESCs in naïve, rosette, epiblast and mesodermal progenitors state. The following culturing conditions have been applied as listed in doi: https://doi.org/10.1101/2021.03.15.433780.
Sample 11 20170223_miha_mouse_e14.fastq.gz


title: Quantseq_RSCs_3

description:
T-eGFP Foxa2-tagRFP double reporter mESC line was cultured in different medias to capture ESCs in naïve, rosette, epiblast and mesodermal progenitors state. The following culturing conditions have been applied as listed in doi: https://doi.org/10.1101/2021.03.15.433780.
Sample 8 20170223_miha_mouse_e11.fastq.gz


title: Patient 33

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 33


title: mESC_Firre_Rescue_firre_induced_90min_dox_short_rep1

value: embryonic stem cells

value: doxycycline


title: mESC_Firre_Rescue_firre_induced_60min_dox_short_rep2


title: ICSI_Is_59a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_B07-ICSI_Is-59a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: ICSI_Is_58a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_B05-ICSI_Is-58a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: Patient 32

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 32

source_name: grade 2-3

value: grade 2-3 (CNS5 WHO)

value: MT


title: Quantseq_RSCs_2

description:
T-eGFP Foxa2-tagRFP double reporter mESC line was cultured in different medias to capture ESCs in naïve, rosette, epiblast and mesodermal progenitors state. The following culturing conditions have been applied as listed in doi: https://doi.org/10.1101/2021.03.15.433780.
Sample 7 20170223_miha_mouse_e10.fastq.gz


title: mESC_Firre_Rescue_firre_induced_30min_dox_short_rep1

value: mESC

value: Firre KO / Firre inducible transgene

value: 30 minutes


title: mESC_Firre_Rescue_firre_induced_30min_dox_short_rep2


title: ICSI_Is_57b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_B04-ICSI_Is-57b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

value: blastomere


title: mESC_Firre_Rescue_firre_induced_120min_dox_short_rep2

value: 120 minutes


title: Quantseq_RSCs_1

description:
T-eGFP Foxa2-tagRFP double reporter mESC line was cultured in different medias to capture ESCs in naïve, rosette, epiblast and mesodermal progenitors state. The following culturing conditions have been applied as listed in doi: https://doi.org/10.1101/2021.03.15.433780.
Sample 6 20170223_miha_mouse_e9.fastq.gz

value: grown in 1 mM PD0325901, 3 mM CHIR99021 and 1,000 U/ml LIF


title: Quantseq_naïve_ESCs_5

description:
T-eGFP Foxa2-tagRFP double reporter mESC line was cultured in different medias to capture ESCs in naïve, rosette, epiblast and mesodermal progenitors state. The following culturing conditions have been applied as listed in doi: https://doi.org/10.1101/2021.03.15.433780.
Sample 5 20170223_miha_mouse_e22.fastq.gz

value: naive embryonic stem cells


title: Patient 30

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 30

value: male


title: mESC_Firre_Rescue_firre_induced_0min_dox_short_rep2

value: 0 minutes


title: ICSI_Is_56b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_B02-ICSI_Is-56b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

value: preimplantation embryo Theiler stage 2


title: mESC_Firre_Rescue_firre_induced_0min_dox_short_rep1


title: Quantseq_RSCs_4

description:
T-eGFP Foxa2-tagRFP double reporter mESC line was cultured in different medias to capture ESCs in naïve, rosette, epiblast and mesodermal progenitors state. The following culturing conditions have been applied as listed in doi: https://doi.org/10.1101/2021.03.15.433780.
Sample 9 20170223_miha_mouse_e12.fastq.gz

value: mESC IDG3.2.


title: Patient 31

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 31


title: Patient 29

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 29


title: Quantseq_naïve_ESCs_4

description:
T-eGFP Foxa2-tagRFP double reporter mESC line was cultured in different medias to capture ESCs in naïve, rosette, epiblast and mesodermal progenitors state. The following culturing conditions have been applied as listed in doi: https://doi.org/10.1101/2021.03.15.433780.
Sample 4 20170223_miha_mouse_e21.fastq.gz


title: ICSI_Is_56a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_B01-ICSI_Is-56a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: Patient 28

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 28

value: female


title: mESC_Firre_Rescue_control_330min_dox_short_rep2

value: Firre KO

value: 330 minutes


title: ICSI_Co_55b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_A10-ICSI_Co-55b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_Rescue_control_330min_dox_short_rep1

value: embryonic stem cells

value: doxycycline


title: Quantseq_naïve_ESCs_2

description:
T-eGFP Foxa2-tagRFP double reporter mESC line was cultured in different medias to capture ESCs in naïve, rosette, epiblast and mesodermal progenitors state. The following culturing conditions have been applied as listed in doi: https://doi.org/10.1101/2021.03.15.433780.
Sample 2 20170223_miha_mouse_e7.fastq.gz


title: mESC_Firre_Rescue_control_300min_dox_short_rep2

value: 300 minutes


title: Patient 27

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 27

value: grade 2-3 (CNS5 WHO)

value: MT


title: ICSI_Is_57a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_B03-ICSI_Is-57a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: ICSI_Co_55a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_A09-ICSI_Co-55a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: Patient 26

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 26


title: Quantseq_naïve_ESCs_1

description:
T-eGFP Foxa2-tagRFP double reporter mESC line was cultured in different medias to capture ESCs in naïve, rosette, epiblast and mesodermal progenitors state. The following culturing conditions have been applied as listed in doi: https://doi.org/10.1101/2021.03.15.433780.
Sample 1 20170223_miha_mouse_e6.fastq.gz


title: ICSI_Co_54b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_A08-ICSI_Co-54b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: ICSI_Co_54a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_A07-ICSI_Co-54a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_Rescue_control_270min_dox_short_rep2

value: mESC

value: 270 minutes


title: Patient 25

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 25


title: NC-NRF2

first: Xin

last: Yang

address: 1130 Saint Nicholas Ave, ICRC building

department: Institute for Cancer Genetics

institute: Columbia University

data_processing:
*library strategy: CUT&RUN
Raw reads were trimmed to remove sequencing adaptors and low-quality reads using Trim Galore (version 0.6.7) with default parameters.
Sequence reads were mapped back to the human (hg38) reference genome using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis. RNA-Seq reads were aligned to hg38 reference using STAR.
Coverage for each base pair of the human genome was computed using genomeCoverageBed from BEDTools (version 2.29.2) and normalized to library size (reads-per-million; RPM).
Sparse Enrichment Analysis for CUT&RUN (SEACR version 1.3) was used for peak calling (Meers et al., 2019). Overlapped peaks between replicates were retained and then merged to obtain a consensus peak set for each Cut&Run target using BEDTools (version 2.29.2) (Quinlan and Hall, 2010).
Assembly: hg38
Supplementary files format and content: bigwig files were generated using UCSC bedGraphToBigWig (version 359), scores represent the normalization reads density.

growth_protocol: Human lung adenocarcinoma A549 cells were obtained from ATCC. Cells were cultured with DMEM supplemented with 10% (v/v) FBS (Gibco), 100 units/ml penicillin, and 100 μg/ml streptomycin (Gibco) in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
CUT&RUN was performed as previously described (Skene and Henikoff, 2017) with minor modifications.
CUT&RUN libraries were prepared using xGEN ssDNA&Low-Input DNA Library Prep Kit and library PCR was performed using standard Illumina Nextera Dual Indexing primers. Samples were pooled and sequenced using paired-end sequencing on Illumina NextSeq 500 platforms at Columbia University Genome Center.

value: Human lung adenocarcinoma cell line

value: WT

tag: antibody


title: Patient 24

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 24


title: mESC_Firre_Rescue_control_270min_dox_short_rep1


title: Patient 23

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 23


title: MED25-CDK8i

city: Melbourne

first: Charles

middle: C

last: Bell

state: VICTORIA

address: VCCC, Gate 1, 14 Flemington Road

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were trimmed to remove adapter with cutadapt.
K562 ChIP-seq reads were aligned to the GRCh37.73 ensembl genome assembly using BWA.
Sam files were converted into Bam files using samtools. Tdf files were generated using igvtools.
Peak calling was performed using MACS2.
Assembly: hg19
Supplementary files format and content: Bed files

source_name: Haematopoetic

growth_protocol: K562 cells were cultured in RPMI-1640 supplemented with 20% FCS, streptomycin (100ug/ml), penicillin (100 units/ml) and glutamax, under standard culture conditions (5% CO2, 37C).

extract_protocol:
Lysate were isolated from formaldehybe cross-linked cells and sonicated to release the chromatin, then immunoprecipitated with antibody
ThruPLEXTM-FD Prep Kit protocol (Rubicon Genomics)

treatment_protocol: Cells were treated with DMSO, dTAG-v1 (500nM) or CDK8i (Sennexin A, 10uM) for 4hrs prior to crosslinking with 1% formaldehyde for 15mins.

value: Haematopoetic

value: CDK8i 4hrs

value: anti-RNA polymerase II Antibody clone CTD4H8


title: sgGAS41-NRF2

value: GAS41 KO


title: Patient 22

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 22

value: male


title: mESC_Firre_Rescue_control_240min_dox_short_rep2

value: 240 minutes


title: ICSI_Co_53a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_A05-ICSI_Co-53a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

value: preimplantation embryo Theiler stage 2

value: blastomere


title: Quantseq_naïve_ESCs_3

description:
T-eGFP Foxa2-tagRFP double reporter mESC line was cultured in different medias to capture ESCs in naïve, rosette, epiblast and mesodermal progenitors state. The following culturing conditions have been applied as listed in doi: https://doi.org/10.1101/2021.03.15.433780.
Sample 3 20170223_miha_mouse_e8.fastq.gz

value: mESC IDG3.2.

value: naive embryonic stem cells

value: grown in 1 mM PD0325901, 3 mM CHIR99021 and 1,000 U/ml LIF


title: MED25-dTAG

value: dTAG 4hrs


title: Patient 21

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 21

value: grade 2-3 (CNS5 WHO)

value: MT


title: mESC_Firre_Rescue_control_240min_dox_short_rep1

value: mESC

value: embryonic stem cells

value: Firre KO

value: doxycycline


title: ICSI_Co_52a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_A03-ICSI_Co-52a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: MED25-control

value: Haematopoetic

value: DMSO


title: Patient 20

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 20


title: Patient 19

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 19

value: female


title: mESC_Firre_Rescue_control_210min_dox_short_rep1

value: 210 minutes


title: ICSI_Co_51b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_A02-ICSI_Co-51b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_Rescue_control_300min_dox_short_rep1

value: 300 minutes


title: MED12-dTAG

value: anti-RNA polymerase II Antibody clone CTD4H8


title: mESC_Firre_Rescue_control_210min_dox_short_rep2


title: MED12-CDK8i

value: CDK8i 4hrs


title: ICSI_Co_53b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_A06-ICSI_Co-53b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

value: preimplantation embryo Theiler stage 2

value: blastomere


title: ICSI_Co_50b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_J10-ICSI_Co-50b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: ICSI_Co_51a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_A01-ICSI_Co-51a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_Rescue_control_180min_dox_short_rep1

value: 180 minutes


title: Patient 17

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 17


title: Patient 16

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 16

value: male


title: Patient 18

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 18

value: grade 2-3 (CNS5 WHO)


title: ICSI_Co_49b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_J08-ICSI_Co-49b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: MED12-control


title: mESC_Firre_Rescue_control_150min_dox_short_rep1

value: 150 minutes


title: mESC_Firre_Rescue_control_150min_dox_short_rep2

value: mESC


title: ICSI_Co_50a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_J09-ICSI_Co-50a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: MED14-CDK8i


title: ICSI_Co_52b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate2_A04-ICSI_Co-52b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: Patient 15

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 15

value: MT


title: Patient 14

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 14


title: MED14-control


title: ICSI_Co_49a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_J07-ICSI_Co-49a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_Rescue_control_180min_dox_short_rep2

value: embryonic stem cells

value: Firre KO


title: mESC_Firre_Rescue_control_120min_dox_short_rep2

value: doxycycline

value: 120 minutes


title: ICSI_Co_48b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_J06-ICSI_Co-48b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: Patient 13

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 13


title: mESC_Firre_Rescue_control_120min_dox_short_rep1


title: MED14-dTAG-R2

data_processing:
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Quality assessment was performed on sequenced reads using FastQC v0.11.6 and adapters were trimmed using Trim Galore and Cutadapt.
Read alignment to Hg19 reference genome, read filtering, SNP calling and masking, and feature calling were performed with the SlamDunk software v0.2.4. Reads containing at least 2 T>C conversions were retained as nascent transcripts.
edgeR v3.38.187 was used to perform TMM normalisation, before performing differential expression analysis with limma voom v3.52.188.
Genes defined as down-regulated were those with a negative fold change value and an adjusted p-value < 0.05.
Assembly: hg19
Supplementary files format and content: Raw count matrices and sample info sheets

extract_protocol:
RNA extraction was performed using TRIzol (Ambion) following the manufacturer's instructions, with the addition of 1mM DTT to the isopropanol precipitation and ethanol wash steps. Total RNA was eluted in nuclease-free H2O containing 0.1mM DTT. 10ug of total RNA was treated with fresh 10mM iodoacetamide (Pierce) in reaction buffer containing 50mM Tris, pH 8.0 and 50% DMSO at 50oC for 15 minutes, light-protected and shaking at 1000rpm. The alkylation reaction was quenched with 20mM of fresh DTT, followed by adding 1ug of unlabelled Drosophila S2 RNA. Total RNA was cleaned up using the RNeasy MinElute Cleanup Kit (Qiagen) and DNAse treated.
Libraries were prepared using a plate based in-house library prep method based on DRUG-seq (Ye et al., 2018).
Libraries were prepared using 500ng of material using the QuantSeq 3' mRNA-seq Library Prep Kit FWD (Lexogen; V1 kit with single 6nt i7 indexes) according to the standard manufacturer's protocol. Sequencing of cDNA libraries was performed on the Illumina NextSeq with 100bp single-end configuration. SLAM-seq was performed in biological triplicate.

treatment_protocol: Cells were treated with DMSO or dTAG-v1 (500nM) for 4hrs prior to RNA harvest. In the final hour of treatment, cells were labelled with 200uM of 4-thioruidine (4sU; Cayman Chemical) to capture nascent mRNA transcripts.

value: Haematopoetic

value: dTAG (4hrs)


title: mESC_Firre_Rescue_control_90min_dox_short_rep2

value: 90 minutes


title: Patient 12

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 12


title: ICSI_Co_48a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_J05-ICSI_Co-48a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: MED14-dTAG-R3


title: MED14-dTAG

value: dTAG 4hrs

value: anti-RNA polymerase II Antibody clone CTD4H8


title: ICSI_Co_47b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_J04-ICSI_Co-47b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

value: preimplantation embryo Theiler stage 2


title: Patient 11

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 11


title: MED14-dTAG-R1


title: mESC_Firre_Rescue_control_60min_dox_short_rep2

value: 60 minutes


title: mESC_Firre_Rescue_control_90min_dox_short_rep1


title: ICSI_Co_47a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_J03-ICSI_Co-47a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

value: blastomere


title: MED14-DMSO-R3

value: DMSO


title: MED14-DMSO-R2


title: mESC_Firre_Rescue_control_60min_dox_short_rep1


title: Patient 9

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 9

value: grade 2-3 (CNS5 WHO)

value: male


title: ICSI_Co_46a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_J01-ICSI_Co-46a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: Patient 8

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 8

value: female


title: MED14-DMSO-R1


title: ICSI_Eq_45b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_I10-ICSI_Eq-45b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: Patient 7

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 7

value: MT


title: ICSI_Co_46b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_J02-ICSI_Co-46b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_Rescue_control_30min_dox_short_rep1

value: mESC

value: embryonic stem cells

value: 30 minutes


title: Nexus-Pol2-Rpl30-promoter

data_processing:
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
eads that passed the Illumina quality filter were filtered for the presence of a fixed barcode. The fixed barcode was used to demultiplex the samples, before being filtered from the reads by Cutadapt70. The random barcode on each read was retained to enable UMI based quantification. Any remaining adapter sequences were trimmed, and reads were removed if they were less than 22bp in length.
Reads were then aligned using Bowtie271 to a human genome (GRCh38) that was modified to contain an additional chromosome with the relevant reporter construct sequence.
Duplicate reads were removed, and each sample was converted into two bigwig files, one with strand specific information and one that aggregates the reads from both strands. The sequence coverage across the reporter construct was then visualised using IGV.
Assembly: GRCh38
Supplementary files format and content: Bed files

extract_protocol:
Lysate were isolated from formaldehybe cross-linked cells and sonicated to release the chromatin, then immunoprecipitated with antibody. Briefly, the immunoprecipitation and washes were performed using the same conditions as the ChIP protocol. Upon completion of these steps, the DNA was end-repaired, A-tailed, adaptors ligated, exonuclease treated, circularized on Dynabeads as described previously.
Constructed via PCR during ChIP-nexus protocol

treatment_protocol: Cells were treated with DMSO or CDK8i (Sennexin A, 10uM) for 1hrs prior to crosslinking with 1% formaldehyde for 15mins.


title: Nexus-Pol2-Myb-promoter


title: mESC_Firre_Rescue_control_0min_dox_short_rep2

value: Firre KO

value: doxycycline

value: 0 minutes


title: Patient 6

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 6


title: Patient 5

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 5


title: ICSI_Eq_44b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_I08-ICSI_Eq-44b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: ICSI_Eq_45a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_I09-ICSI_Eq-45a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: Nexus-Pol2-SCP-promoter

value: Haematopoetic


title: mESC_Firre_Rescue_control_0min_dox_short_rep1


title: ICSI_Eq_44a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_I07-ICSI_Eq-44a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_Rescue_firre_induced_5760min_dox_long_rep3

value: Firre KO / Firre inducible transgene

value: 5760 minutes


title: Patient 3

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 3


title: mESC_Firre_Rescue_control_30min_dox_short_rep2


title: ICSI_Eq_43b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_I06-ICSI_Eq-43b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

value: preimplantation embryo Theiler stage 2


title: Patient 4

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 4


title: Patient 10

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 10


title: Nexus-Pol2-Myb-TAD CDK8i

value: CDK8i 1hr

value: anti-RNA polymerase II Antibody clone CTD4H8


title: Nexus-Pol2-Myb-TAD DMSO

value: DMSO


title: mESC_Firre_Rescue_firre_induced_2880min_dox_long_rep3

value: 2880 minutes


title: ICSI_Eq_42b, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_I04-ICSI_Eq-42b
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.

value: blastomere


title: Nexus-Pol2-VP64-TAD CDK8i


title: ICSI_Eq_43a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_I05-ICSI_Eq-43a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: mESC_Firre_Rescue_firre_induced_5760min_dox_long_rep1


title: ICSI_Eq_42a, blastomere, scRNA-seq

description:
Smart-Seq2
Plate1_I03-ICSI_Eq-42a
Three output files that originated from analyzing all blastomeres together; barcodes_blastomeres.tsv, features_blastomeres.tsv, umiDedup-Exact_blastomeres.mtx
Initially, sequenced 150 blastomers but 25 did not pass quality control and were not processed further.


title: Nexus-Pol2-CMV-promoter


title: Nexus-Pol2-VP64-TAD DMSO


title: mESC_Firre_Rescue_firre_induced_2880min_dox_long_rep2