title: E6.5_wt_f_6


title: E6.5_wt_f_5

status: Public on Nov 18 2025

type: SRA

city: Paris

first: Laia

last: Richart

address: 13 Rue Pierre et Marie Curie

department: Developmental Biology

country: France

institute: Institut Curie

library_source: transcriptomic

data_processing:
The mm10 fasta file was masked with CAST/EiJ strain-specific SNPs using SNPsplit.
Adapters and low-quality bases were removed with TrimGalore and trimmed reads were mapped against the N-masked reference genome with STAR.
Library size, number of expressed genes, and total amount of RNA were used as criteria to select high-quality samples.
To assess allele-specific expression, reads spanning polymorphic sites were assigned to the maternal or paternal genome with SNPsplit and quantified using SAMtools mpileup.
To assess differential gene expression, exon-overlapping reads were counted using FeatureCounts.
Assembly: mm10
Supplementary files format and content: Tables summarizing raw counts over genes.

molecule: polyA RNA

organism: Mus musculus

source_name: E6.5 extraembryonic ectoderm

extract_protocol:
RNA preparation was done as described in Pérez-Palacios et al. 2021 (PMID: 32944911; DOI: 10.1007/978-1-0716-0958-3_13)
Library construction was performed using the Accel-NGS 2S Unique Dual Indexing DNA library kit (Swift Biosciences), following manufacturer's instructions.
Single embryo RNA-Seq

tag: tissue

value: E6.5 extraembryonic ectoderm

tag: genotype

value: WT

tag: Sex

value: female


title: MEC-1 AID-WT Idelalisib Tazemetostat-3

city: Boston

first: Roberto

last: Chiarle

state: Ma

address: Longwood 333

country: USA

institute: Boston Childrens Hospital

description:
Library name: MEC-1 AID-WT Idelalisib Tazemetostat-3
PE250

library_source: genomic

data_processing:
GEAT_docker(https://github.com/alessandriLuca/HTGTS_alignment) default parameters
Assembly: hg38
Supplementary files format and content: bedfiles tab separated

molecule: genomic DNA

organism: Homo sapiens

source_name: MEC-1 cells

growth_protocol: Cells were cultured at 37 °C with 5% CO2

extract_protocol:
The library preparation was performed as previously described in Zhang, X. et al, Nature 575, 385-389 (2019).
12-16 samples were pooled and sequenced through Illumina MiSeq (PE250) by the Molecular Biology Core Facilities of the Dana-Farber Cancer Institute.

treatment_protocol: LAM-HTGTS libraries were prepared from MEC-1 cells stimulated with EZH2 and/or PI3Kδ inhibitors

tag: cell line

value: MEC-1 cells

tag: cell type

value: Human chronic lymphocytic leukemia (CLL) cell line

tag: treatment

value: Idelalisib + Tazemetostat


title: B017_v_5435B

city: Houston

first: Khandan

last: Keyomarsi

state: Texas

address: 1515 Holcombe Blvd

department: Experimental Radiation Onc

institute: University of Texas - MD Anderson Cancer Center

description:
Library name: B017_v_5435B
Raw_counts_human_n17.csv

data_processing:
Paired-end reads in fastq format were initially checked for read quality using FastQC 0.11.9
Sequence reads were mapped to the combined reference genome (Gencode human GRCh38 and mouse GRCm38 concatenated) using TopHat2 2.1.1 (parameter: --library-type=fr-unstranded)
The BAM file with mapped reads for each sample was sorted and then used as an input for featureCounts (Subread 2.0.6) in order to generate read count data on gene/feature level (parameters: -p --countReadPairs -t exon -g gene_id -s 0)
Genes/features were annotated using the combined GTF file from Gencode human GRCh38 and mouse GRCm38 references
Only the reads that were mapped to the human genome were kept, whereas the reads mapped to the mouse genome were removed
Assembly: Human GRCh38 and mouse GRCm38
Supplementary files format and content: Raw read count data generated by featureCounts (Subread 2.0.6) for each sample

molecule: total RNA

source_name: patient-derived xenograft

extract_protocol:
Total RNA was isolated from cell lysates using Trizol reagent (Ambion Life Technologies) according to manufacturer's protocol
Preparation of RNA library and transcriptome sequencing was conducted by Novogene Corporation Inc (US) following standard Illumina protocols

value: patient-derived xenograft

value: Vehicle:BID, oral


title: MEC-1 AID-WT Idelalisib Tazemetostat-2

description:
Library name: MEC-1 AID-WT Idelalisib Tazemetostat-2
PE250


title: NSC, TF, RNA, rep1

city: Rotterdam

first: Tahsin Stefan

last: Barakat

state: South Holland

address: Dr. Molewaterplein 40

department: Clinical Genetics

country: Netherlands

institute: The Erasmus University Medical Center

data_processing:
The FASTQ files data were trimmed using Trimmomatic (version 0.39) to remove possible adaptor contamination.
Bowtie2 (version 2.4.2) (with --very-sensitive parameter) was used to align both ChIP- and STARR-seq data against the GRCh38/hg38 human genome build. Only properly and uniquely mapped reads, with mapping quality more than 30 (MAPQ >=30), were kept followed by removing possible duplicated reads (only for ChIP-seq data) using Picard's MarkDuplicates (version 4.0.1.1) (http://broadinstitute.github.io/picard/).
The aligned reads were converted to bigwig format using ”bamCoverage” function with --binSize 10 and --normalizeUsing CPM parameters, the read coverage was then computed using “multiBigwigSummary” and pearson correlation between replicates was calculated using “plotCorrelation” via deepTools (version 3.4.3)
Peak calling was performed using MACS2 (version 2.1.2) (with -q 0.05) for each replicate of ESCs and NSCs separately, and took sequencing data of total input as background. Peaks overlapping blacklist regions defined by the ENCODE project (Accession: ENCFF356LFX, Date: 05.05.2020) were removed. The overlapping peaks between replicates were merged as common peaks using intersectBed (version2.30.0).
Assembly: hg38
Supplementary files format and content:
bigwig, narrowPeak
Whole_contri_percentile.txt: bed format file, that additionally gives for each nucleotide in a large number of gene regulatory elements a "contribution score". This score obtained from a convolutional neural network that was trained on massively parallel reporter assay data in which the regulatory elements were tested functionally, and this score predicts for each of the nucleotides how important this nucleotide is for the enhancer activity.

source_name: neural stem cells

extract_protocol:
Briefly, RNA was isolated with Trizol (Sigma), following manufacturer’s instruction and split into two replicates.
The mRNA fraction was captured from each replicate of total RNA using Oligo (dT) 25 beads (61002, Life Technologies), DNaseI treated (18068-015, Life Technologies), and reverse transcribed with a GFP-mRNA specific primer (149 STARRseq rep RNA cDNA synth) following Superscript III protocol (18080-044, Life Technologies). To avoid plasmid DNA contamination, cDNA was PCR amplified in 10 parallel reactions for each replicate using primers spanning a synthetic intron (152 STARR reporter specific primer 2 fw and 153 STARR reporter specific primer 2 rv), as previously described (Arnold et al., 2013). 35 ng of PCR amplified DNA were then used in a second round of PCR to add Illumina index primers (E7335, E7500, NEB). PCR was performed in 5 parallel reactions and using 2 independent index primers for each of the two replicates. In total, we sequenced 4 replicates of STARR-seq RNA for each pooled HIST or TF plasmid library. Corresponding plasmid libraries were similarly amplified using two independent Illumina index primers for each plasmid library. Quantity and quality of generated sequencing libraries was assessed on an Agilent Tapestation. All sequencing occurred on an Illumina HiSeq 2500 platform, using 50bp paired-end sequencing.

value: neural stem cells


title: E6.5_wt_f_4


title: E6.5_wt_m_3

value: male


title: ACC67, dinaciclib, 24 h, biol repl 3

city: Gothenburg

first: Mattias

last: Andersson

address: Medicinaregatan 1F

department: Sahlgrenska Cancer Center

country: Sweden

institute: University of Gothenburg

description: Library name: D_12.bam

data_processing:
Clean reads were obtained by removing reads containing adapter sequences, reads containing poly-N, and low quality reads from raw data.
Processed reads were aligned to the reference genome using HISAT2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the read numbers that mapped to each gene.
Assembly: GRChr38
Supplementary files format and content: tab-limited text file that includes raw counts for each sample and Ensembl gene ids.

source_name: Lacrimal gland ACC

growth_protocol: Cells were maintained in a DMEM-F12 based medium with supplements at 37 C and 5% CO2.

extract_protocol:
Total RNA was extracted using the RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP. cDNAs were then subjected to end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Cells were treated  with 25 nM dinaciclib or equal volumes of vehicle control (DMSO) for 24 h.

value: Lacrimal gland ACC

value: epithelial

value: dinaciclib


title: NSC, histone, RNA, rep4


title: ACC67, dinaciclib, 24 h, biol repl 2

description: Library name: D_11.bam


title: B017_p_5015

description:
Library name: B017_p_5015
Raw_counts_human_n17.csv

value: Palbociclib:50 mg/kg; QD, oral


title: MEC-1 AID-WT Idelalisib-6

description:
Library name: MEC-1 AID-WT Idelalisib-6
PE250

value: Idelalisib


title: E6.5_wt_f_1


title: NSC, histone, RNA, rep2


title: ACC67, dinaciclib, 24 h, biol repl 1

description: Library name: D_10.bam


title: NSC, TF, RNA, rep3


title: ACC67, control, 24 h, biol repl 3

description: Library name: D_9.bam

value: DMSO (control)


title: MEC-1 AID-WT Idelalisib-4

description:
Library name: MEC-1 AID-WT Idelalisib-4
PE250


title: NSC, histone, RNA, rep1


title: blastocyst_matKO_m_6

source_name: blastocysts

value: blastocysts

value: Ezhip matKO


title: blastocyst_matKO_m_7


title: NSC, TF, RNA, rep2


title: ACC67, control, 24 h, biol repl 2

description: Library name: D_8.bam

value: WT


title: B017_v_5014

description:
Library name: B017_v_5014
Raw_counts_human_n17.csv


title: WT_IFM_2

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

institute: igred

data_processing:
Quality score trimming and filtering were performed with Trimmomatic (v0.32).
reads were aligned to the annotated Dm6 genome (Ensembl release 70) using Hisat2 (v2.1.0)
Per gene read counts were calculated from the Hisat2 output using htseq-count (v0.11.2)
RPKM (Reads Per Kilobase of exon per Megabase of library size)  were caclulated using Cufflinks (2.2.1)
Differential gene expression was analyzed using the R package DESeq2 (v1.22.2)
Assembly: BDGP dm6
Supplementary files format and content: tab-delimited text files include FBGN number and RPKM values for each sample.

organism: Drosophila melanogaster

source_name: Flight muscle

growth_protocol: All drosophila lines were cultured at 25°C on standard fly medium (75 g/l organic corn flour, 28 g/l dry yeast, 40 g/l sucrose, 8 g/l agar, 10 ml/l Moldex 20%) with a 12 h dark:light cycle.

extract_protocol:
Wing disc from wandering third instar larvae were dissected on ice cold PBS. Flight muscle fibers were dissected in ice cold PBS on thoraxes of pupae at 96h after puparium formation. Total RNAs were isolated from larval wing discs or pupal flight muscles using TrizolTM extraction. RNA quality and concentration were assessed with Agilent TapeStation and Qubit device.
Libraries were prepared using Ovation® SoLo RNA-Seq Systems for Drosophila from Tecan.

value: Flight muscle

tag: age

value: pupae 96h APF


title: ACC67, control, 24 h, biol repl 1

description: Library name: D_7.bam


title: MEC-1 AID-WT Idelalisib-3

description:
Library name: MEC-1 AID-WT Idelalisib-3
PE250

value: MEC-1 cells

value: Human chronic lymphocytic leukemia (CLL) cell line


title: ACCX11, dinaciclib, 24 h, biol repl 3

description: Library name: D_6.bam

source_name: Minor salivary gland ACC

value: Minor salivary gland ACC


title: MEC-1 AID-WT Idelalisib-2

description:
Library name: MEC-1 AID-WT Idelalisib-2
PE250


title: blastocyst_matKO_m_5


title: E6.5_wt_f_3

value: E6.5 extraembryonic ectoderm

value: female


title: MEC-1 AID-WT Idelalisib Tazemetostat-1

description:
Library name: MEC-1 AID-WT Idelalisib Tazemetostat-1
PE250

value: Idelalisib + Tazemetostat


title: E6.5_wt_f_2


title: GFP_IFM_2

value: TET-GFP


title: MEC-1 AID-WT Idelalisib-1

description:
Library name: MEC-1 AID-WT Idelalisib-1
PE250


title: ACCX11, dinaciclib, 24 h, biol repl 2

description: Library name: D_5.bam

value: epithelial


title: NSC, histone, RNA, rep3

value: neural stem cells


title: blastocyst_matKO_m_3

value: male


title: MEC-1 AID-WT Idelalisib-5

description:
Library name: MEC-1 AID-WT Idelalisib-5
PE250

value: Idelalisib


title: blastocyst_matKO_m_2


title: MEC-1 AID-KO

description: Library name: MEC-1 AID-KO:DMSO-Tazemetostat-Valemetostat

library_source: other

molecule: other

value: Tazemetostat/Valemetostat


title: TET_IFM_CD_2

value: TET catalytic dead


title: ACCX11, dinaciclib, 24 h, biol repl 1

description: Library name: D_4.bam

value: dinaciclib


title: MEC-1 AID-WT Idelalisib

description: Library name: MEC-1 AID-WT-Idelalisib:DMSO-Tazemetostat-Valemetostat


title: blastocyst_matKO_m_4

value: blastocysts

value: Ezhip matKO


title: ACCX11, control, 24 h, biol repl 3

description: Library name: D_3.bam

value: WT

value: DMSO (control)


title: MEC-1 AID-WT

description: Library name: MEC-1 AID-WT:DMSO-Tazemetostat-Valemetostat

value: MEC-1 cells

value: Human chronic lymphocytic leukemia (CLL) cell line


title: TET_IFM_CD_1

value: Flight muscle

value: pupae 96h APF


title: blastocyst_matKO_f_7

value: female


title: TET_IFM_RS_2

value: TET null


title: WT_IFM_1


title: ACCX11, control, 24 h, biol repl 2

description: Library name: D_2.bam

value: Minor salivary gland ACC

value: epithelial


title: HT115 smRNA rep3

city: Basel

first: Geoffrey

last: Fucile

address: Spitalstrasse 41

department: sciCORE

country: Switzerland

institute: University of Basel

data_processing:
For PHIL227, mapping with STAR v2.7.9 and read summarization with FeatureCounts from Subread v2.0.3.
For PHIL246, removal of first three nucleotides and polyA trimming using CutAdapt v3.4, 3` quality trimming using Trimmomatic v0.39, Trinity de novo assembly pipeline v2.11.0, alignment to contigs using Bowtie v1.2.3 (-n 1 -l 10) and read summarization with FeatureCounts from Subread v2.0.3
Assembly: iGenomes Ensembl E. coli K12 DH10B
Supplementary files format and content: tab-delimited raw counts for each sample
Supplementary files format and content: FASTA format of Trinity contigs for PHIL246

organism: Caenorhabditis elegans

source_name: whole organism

extract_protocol:
Total RNA was isolated from the pellets using the Quick-RNA Fungal/Bacterial Kit from Zymo Research.
TruSeq Stranded Total RNA Library Prep Gold Kit was used for PHIL227 samples. The QIAseq FastSelect and Takara Bio SMARTer smRNA-Seq Kit for Illumina was used for PHIL246 samples.

value: whole organism


title: ACCX11, control, 24 h, biol repl 1

description: Library name: D_1.bam


title: blastocyst_matKO_f_6


title: TET_IFM_RS_1

source_name: Wind Disk

value: Wind Disk


title: Donor2206_ADT

first: Pablo

last: Argüeso

state: MA

address: 800 Washington St

department: Ophthalmology

institute: Tufts Medical Cener

description:
Library name: Human3_ADT
lectin-derived oligonucleotide (ADT-like)
Donor2206_filtered_feature_bc_matrix.h5
hCornea.joint.paper.clean.rds

data_processing:
Raw sequencing data were aligned, filtered, and normalized using Cell Ranger (v7.2.0).
Assembly: GRCh38 - human, mm10 - mice
Supplementary files format and content: CellRanger output files: filtered_feature_bc_matrix.h5
Supplementary files format and content: Seurat object with merged and processed samples: hCornea.joint.rds
Supplementary files format and content: Seurat object with merged and processed samples: mCornea.joint.rds
Library strategy: CITE-seq

molecule: protein

source_name: Cornea-conjunctiva

extract_protocol:
Human corneal–limbal and conjunctival tissues were incubated separately at 37 °C for 2 hours in DMEM/F12 containing 2.4 IU/mL Dispase II (Thermo Fisher Scientific, Waltham, MA, USA). The epithelia were scraped, collected, and further digested with Gibco™ TrypLE (Thermo Fisher Scientific) for 5 minutes. The remaining stromal and conjunctival fragments were cut into small pieces, placed each in a MACS C tube (Miltenyi Biotec, Bergisch Gladbach, Germany) containing 4 mg/mL collagenase A (Sigma-Aldrich, St. Louis, MO, USA) in DMEM, and digested for 1 hour at 37 °C using a gentleMACS dissociator (Miltenyi Biotec). After digestion, single cells from all individual compartments were pooled, filtered through a 70 µm cell strainer (Miltenyi Biotec), washed in PBS supplemented with 0.04% bovine serum albumin (BSA; Sigma-Aldrich), and counted. Cells were resuspended in cold 0.04% BSA-PBS, and cold methanol was added dropwise to a final concentration of 80%. Samples were incubated at –20 °C for 30 minutes before storage at –80 °C.  Mouse conjunctival and corneal tissues were digested separately in DMEM containing 2 mg/mL collagenase A and 10 mg/mL Dispase II at 37 °C for 1 hour. During digestion, tissues were gently triturated by passing them through a 20G syringe needle five times every 20 minutes. Following enzymatic digestion, samples were rinsed with DMEM and incubated in TrypLE (Thermo Fisher Scientific) for 10 minutes at 37 °C. Cell suspensions were filtered through a 70 µm cell strainer, washed in 0.04% BSA-PBS, and counted. Cells were resuspended in cold 0.04% BSA–PBS, and cold methanol was added dropwise to a final concentration of 80%. Samples were incubated at –20 °C for 30 minutes before storage at –80 °C.
Single-cell suspensions (1 mL, approx. 106 cells/mL) were thawed and washed in wash-resuspension buffer containing 3× SSC, 1 mM DTT, 0.04% ultrapure BSA, and 0.2 U/μL RNase inhibitor. Cells were incubated on ice for 30 minutes with a mixture of DNA-labeled lectins and biotinylated SNA I, each at 0.5 μg/mL (equivalent to 0.05 μg of lectin per million cells). After three washes in wash-resuspension buffer, cells were incubated with TotalSeq™-B0975 Streptavidin (BioLegend, San Diego, CA) at 0.5 μg/mL (0.05 μg per million cells) for 30 minutes on ice. Cells were then washed three times, counted, and adjusted to a final concentration of ~1,000 cells/μL. Single cells were captured using the Chromium Controller, and single-cell RNA sequencing libraries were prepared with the Chromium Next GEM Single Cell 3′ v3.1 Kit and the 3′ Feature Barcode Kit (10x Genomics, Pleasanton, CA, USA) according to the manufacturer’s instructions to generate both the gene expression and cell surface feature libraries. For sequencing, gene expression and cell surface feature libraries from each sample were pooled at a 4:1 ratio and sequenced using either the Illumina NovaSeq 6000 or NovaSeq X Plus platforms, targeting 20,000 reads per cell.

value: Cornea-conjunctiva

tag: adt

value: Lectin_MPA, Lectin_PNA, Lectin_ECA, Lectin_AAL, Lectin_MAA-I, Lectin_SNA-I, Lectin_ConA, Lectin_DSA, Lectin_WGA

tag: library type

value: ADT


title: blastocyst_matKO_f_5

value: blastocysts


title: GFP_IFM_1

value: TET-GFP


title: WT_WD_3

value: third instar larvae


title: HT115 smRNA rep2


title: HT115 smRNA rep1


title: blastocyst_matKO_m_1

value: Ezhip matKO

value: male


title: OP50_xu363 smRNA rep1


title: blastocyst_matKO_f_2


title: WT_WD_2


title: blastocyst_matKO_f_3


title: blastocyst_matKO_f_4


title: Donor2046_ADT

description:
Library name: Human2_ADT
lectin-derived oligonucleotide (ADT-like)
Donor2046_filtered_feature_bc_matrix.h5
hCornea.joint.paper.clean.rds


title: TET_RS_WD_3


title: Donor2046_mRNA

description:
Library name: Human2_mRNA
polyA RNA
Donor2046_filtered_feature_bc_matrix.h5
hCornea.joint.paper.clean.rds

value: mRNA


title: blastocyst_wt_m_7

value: WT


title: OP50_xu363 smRNA rep2


title: TET_RS_WD_1


title: OP50_xu363 smRNA rep3


title: blastocyst_matKO_f_1


title: OP50 smRNA rep3


title: Donor2206_mRNA

description:
Library name: Human3_mRNA
polyA RNA
Donor2206_filtered_feature_bc_matrix.h5
hCornea.joint.paper.clean.rds


title: Citeseq, P9, ADT

city: Bethesda

first: Niki

last: Moutsopoulos

state: MD

address: 9000 Rockville Pike

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

description:
Library name: Gum_peridontitis_P9_ADT
Antibody-derived oligonucleotide (ADT)

data_processing:
CITE-Seq files were demultiplexed using CellRanger mkfastq
Demultiplexed data was processed using the CellRanger multi pipeline
Assembly: GRCh38-2020-A
Supplementary files format and content: CellRanger output files: raw_mRNA_barcodes.tsv.gz, raw_mRNA_features.tsv.gz, raw_mRNA_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: raw_ADT_barcodes.tsv.gz, raw_ADT_features.tsv.gz, raw_ADT_matrix.mtx.gz
Library strategy: CITE-seq

source_name: Gum

extract_protocol:
Preparation of single cell suspensions for CITE-seq and spectral flow cytometry was carried out as previously described (Greenwell-Wild et al., 2021). Briefly, tissue fragments were minced and digested using collagenase II (Worthington Biochemical Corporation) and DNase (Sigma) and dissociated with the gentleMACS Dissociator (Miltenyi). Cells were then passed through a 70mm filter (Falcon, Corning), washed, and counted (Cellometer Auto 2000 - Nexcelom).
Single cell preparations of between 5x104 and 5x105 single cells from periodontitis samples were stained individually with TotalSeq™-A Human Universal Cocktail, V1.0 (Biolegend, CA) as per the manufacturer’s protocol (Suppl. Table 4). 1.7x104 stained cells were then loaded with the reverse transcription mix on the Chromium chip G and partitioned into single cells in Gel Beads-in-emulsion (GEMs) using the 10X Genomics Chromium Next GEM Single Cell 3’ Kit v3.1 as per manufacturer’s instructions (10X Genomics, CA). cDNA amplification and ADT libraries were prepared as per instructions from Biolegend while gene expression libraries were made as per the 10X Genomics protocol. All amplification steps were performed in an Applied Biosystems Ins (ABI) Veriti 96-well thermal cycler. Quality and quantity of the libraries were assessed using TapeStation (Agilent, CA) and a Qubit fluorometer (ThermoFisher). Libraries were pooled at a concentration of 2nM and sequenced on an Illumina platform (NextSeq 2000, Illumina, San Diego, CA) using the following read lengths: Read 1: 28 base pairs, Index 1: 10 base pairs, Index 2: 10 base pairs, Read 2: 90 base pairs.

value: Gum

value: Single cells


title: TET_RS_WD_2

value: TET null


title: blastocyst_wt_m_8


title: OP50 smRNA rep1


title: blastocyst_wt_m_6


title: HT115 total RNA rep3


title: WT_FLAG_EZHIP_2C_rep1

city: Beijing

first: Feng

last: Kong

address: Qinghuayuan Street

country: China

institute: Tsinghua University

description: Library name: Sample 24

data_processing:
When aligning the paired-end reads to mouse genome (mm9), the following parameters were used: -t -q -N 1 -L 25 -X 700 –no-unal -x by Bowtie2 (version 2.2.2). All unmapped reads, non-uniquely mapped reads, and PCR duplicates were removed. For downstream analysis, we normalized the read counts by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM). To minimize the variation across samples, RPKM values across the whole genome were further normalized by Z-score.
To visualize the CUT&RUN signals in the UCSC genome browser, we generated the RPKM values on a 100-bp-window basis.
Spike-in normalization calculated the relative abundance of mouse genome reads according to yeast genome reads, which equally added to each sample.
Assembly: mm9
Supplementary files format and content: bigWig
Library strategy: CUT&Run

source_name: mouse pre-implantation embryos, late 2 cell

extract_protocol:
The fresh samples were incubated in antibody buffer (containing primary antibody and 2mM EDTA) overnight at 4 ℃. Samples were transferred to pA-MNase buffer after washed once with wash buffer via mouth pipetting. After incubation for 2-3 hours at 4 ℃, samples were bound with concanavalin-coated magnetic beads and equilibrated at room temperature for 10 min. MNase targeted digestion and DNA fragment extraction were performed.
The library was constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Bio- labs, E7645S).

value: wild type

value: FLAG-EZHIP OE


title: Citeseq, P5, GEX

description:
Library name: Gum_peridontitis_P5_mRNA
polyA RNA


title: WT_WD_1


title: Citeseq, P9, GEX

description:
Library name: Gum_peridontitis_P9_mRNA
polyA RNA


title: Citeseq, P8, ADT

description:
Library name: Gum_peridontitis_P8_ADT
Antibody-derived oligonucleotide (ADT)


title: Ezhip_mKO_E425_EED_rep2

description: Library name: Sample 23

source_name: mouse pre-implantation embryos, E3.5

value: mouse pre-implantation embryos, E3.5

value: Ezhip mKO


title: OP50 smRNA rep2

value: whole organism


title: OP50_xu363 total RNA rep3


title: Citeseq, P8, GEX

description:
Library name: Gum_peridontitis_P8_mRNA
polyA RNA


title: Ezhip_mKO_E425_EED_rep1

description: Library name: Sample 22

source_name: mouse pre-implantation embryos, E4.25

value: mouse pre-implantation embryos, E4.25


title: blastocyst_wt_m_4


title: Citeseq, P5, ADT

description:
Library name: Gum_peridontitis_P5_ADT
Antibody-derived oligonucleotide (ADT)


title: blastocyst_wt_m_5


title: WT_FLAG_EZHIP_2C_rep2

description: Library name: Sample 25

value: mouse pre-implantation embryos, late 2 cell


title: OP50 total RNA rep3


title: Ezhip_WT_E425_EED_rep2

description: Library name: Sample 21


title: HT115 total RNA rep2


title: Citeseq, P16, GEX

description:
Library name: Gum_peridontitis_P16_mRNA
polyA RNA


title: blastocyst_wt_m_2

value: blastocysts


title: blastocyst_wt_m_3


title: Ezhip_WT_E425_EED_rep1

description: Library name: Sample 20


title: OP50 total RNA rep2


title: OP50_xu363 total RNA rep2


title: HT115 total RNA rep1


title: blastocyst_wt_f_6

value: female


title: Ezhip_mKO_Bl_H2Aub_rep2

description: Library name: Sample 17


title: blastocyst_wt_m_1


title: Ezhip_mKO_E425_H2Aub_rep2

description: Library name: Sample 19


title: Ezhip_WT_E425_H2Aub_rep2

description: Library name: Sample 18


title: Citeseq, P16, ADT

description:
Library name: Gum_peridontitis_P16_ADT
Antibody-derived oligonucleotide (ADT)


title: blastocyst_wt_f_5


title: UV-C-8d-2.IP

first: Lili

last: Ma

address: 50 Changhua Road, Haidian District

institute: Beijing Academy of Agriculture and Forestry Science

description: Library name: Sample 16

data_processing:
*library strategy: MeRIP-seq
Q30 quality control
matching genome
Use MACS to identify methylation sites in each experimental sample at the transcriptome-wide level
Identification of differentially methylated sites using diffReps software
Functional enrichment analysis
Assembly: SL4.0
Supplementary files format and content: The table contains information on the RNA modification sites identified for each sample.

organism: Solanum lycopersicum

source_name: pericarp

extract_protocol:
Trizol
Add ligation to the 5' end, add adapter to the 3' end, reverse transcription synthesis of cDNA, PCR amplification, library purification

value: pericarp

value: UV-C light at a dose of 4 kJ/m2

tag: time point


title: OP50_xu363 total RNA rep1


title: UV-C-8d-3.Input

description: Library name: Sample 17


title: blastocyst_wt_f_4


title: OP50 total RNA rep1


title: UV-C-8d-1.IP

description: Library name: Sample 14


title: Ezhip_mHet_Bl_H2Aub_rep2

description: Library name: Sample 16

value: Ezhip mHet


title: blastocyst_wt_f_3


title: Ezhip_mKO_2C_Ezh2_rep2

description: Library name: Sample 15


title: UV-C-8d-2.Input

description: Library name: Sample 15


title: Znhit3_Morula_se9

first: Guanghui

last: Yang

state: Maryland

address: 50 South Drive

department: National Institute of Diabetes and Digestive and Kidney Diseases

library_source: transcriptomic single cell

data_processing:
Base calling was finished with RTA2.
Sequenced reads were trimmed using Trimmomatic ver. 0.39 by indicating “NexteraPE-PE.fa” as the adapter sequence file, then mapped to the reference genome using STAR ver. 2.7.6a. The reference genome contains sequences of GRCm38 and ERCC spike-in.
StringTie ver. 2.1.4 was used to generate counts of genes in the GTF reference downloaded from ENSEMBL(release 101) and ERCC spike-in product page.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files include FPKM, TPM values for each sample.

source_name: Embryo

extract_protocol:
To collect embryos, Znhit3+/- females were injected intraperitoneally with eCG (5 IU) followed 46 h to 48 h with hCG (5 IU) and then co-caged with Znhit3+/- males. Fertilized zygotes were flushed from plugged females 16 h post hCG injection and cultured in M2 medium containing hyaluronidase to remove the cumulus mass. Zygotes without cumulus were then washed and cultured in advanced KSOM until sample collection. When collecting samples, embryos were washed in PBS and transferred into acidic Tyrode’s solution to remove zonae pellucidae. Single zona-free embryos were transferred into 8-well PCR strips containing 2.5 µl of RLT plus buffer.
RNAs in each sample were captured by oligo-dT beads and then processed following the G&T-seq protocol to construct the single embryo RNA-Seq library.

tag: strain

tag: developmental stage

value: Morula

value: Embryo


title: blastocyst_wt_f_2

value: WT


title: UV-C-8d-3.IP

description: Library name: Sample 18


title: UV-C-8d-1.Input

description: Library name: Sample 13


title: Ezhip_WT_2C_Ezh2_rep2

description: Library name: Sample 14


title: Znhit3_Morula_se8


title: CK-8d-3.IP

description: Library name: Sample 12

value: control


title: 2C_matKO_m_6

source_name: 2C embryos

value: 2C embryos

value: Ezhip matKO

value: male


title: Ezhip_mKO_E425_K27me3_rep2

description: Library name: Sample 13


title: Znhit3_Morula_se6


title: Ezhip_WT_E425_K27me3_rep2

description: Library name: Sample 12

value: wild type


title: CK-8d-3.Input

description: Library name: Sample 11


title: 2C_matKO_m_5


title: Znhit3_Morula_se7


title: blastocyst_wt_f_1


title: CK-8d-2.Input

description: Library name: Sample 9


title: Ezhip_mHet_8C_K27me3_rep1

description: Library name: Sample 10

source_name: mouse pre-implantation embryos, 8 cell

value: mouse pre-implantation embryos, 8 cell


title: Znhit3_Morula_se4


title: CK-8d-1.IP

description: Library name: Sample 8


title: Znhit3_Morula_se5


title: Ezhip_mKO_8C_K27me3_rep2

description: Library name: Sample 11

value: Ezhip mKO


title: 2C_matKO_m_4


title: 2C_matKO_m_3


title: Znhit3_Morula_se3


title: Ezhip_WT_L2C_K27me3_rep2

description: Library name: Sample 9


title: 2C_matKO_m_2


title: Znhit3_Morula_se22


title: CK-0d-3.IP

description: Library name: Sample 6


title: 2C_matKO_m_1


title: CK-8d-2.IP

description: Library name: Sample 10


title: CK-0d-3.Input

description: Library name: Sample 5


title: Znhit3_Morula_se21


title: WT_PN3_K27me3_rep2

description: Library name: Sample 7

source_name: mouse pre-implantation embryos, 1 cell

value: mouse pre-implantation embryos, 1 cell


title: WT_D14_Ezh2_rep2

description: Library name: Sample 6

source_name: mouse oocytes, D14

value: mouse oocytes, D14


title: 2C_matKO_f_6


title: WT_2C_EED_rep2

description: Library name: Sample 5

value: mouse pre-implantation embryos, late 2 cell


title: 2C_matKO_f_5

value: female


title: 2C_matKO_f_4


title: Znhit3_Morula_se2


title: CK-0d-2.IP

description: Library name: Sample 4

value: pericarp


title: CK-0d-2.Input

description: Library name: Sample 3


title: Znhit3_Morula_se19


title: CK-0d-1.IP

description: Library name: Sample 2


title: WT_FGO_EED_rep1

description: Library name: Sample 3

source_name: mouse oocytes, FGO

value: mouse oocytes, FGO


title: CK-0d-1.Input

description: Library name: Sample 1


title: WT_FGO_EED_rep2

description: Library name: Sample 4


title: 2C_matKO_f_3


title: 2C_matKO_f_2


title: CK-8d-1.Input

description: Library name: Sample 7


title: Ezhip_WT_FGO_K27me3_rep2

description: Library name: Sample 8


title: 2C_matKO_f_1


title: Znhit3_Morula_se20


title: 2C_wt_m_6


title: Znhit3_Morula_se16


title: Znhit3_Morula_se17


title: Znhit3_Morula_se14


title: Znhit3_Morula_se18


title: WT_D14_EED_rep1

description: Library name: Sample 1


title: Ezhip_mHet_E425_H2Aub_rep1

description: Library name: Sample 82

value: mouse pre-implantation embryos, E4.25

value: Ezhip mHet


title: 2C_wt_m_4


title: Tumor B16F10 with ACT, 0021

type: RNA

city: Atlanta

first: Megen

middle: Claire

last: Wittling

state: GA

address: Winship Cancer Institute  Emory University 1365C Clifton Rd. NE Suite C5068, Bays 1-5

department: Surgery

institute: Emory University

description: Tumor was put into RNA later and then stored at 4 degress. Was then given to Emory Genomics Core for processing. RNA isolarion was performed and nucleic acid QC

hyb_protocol: Nanostring's Gene Expression CodeSet RNA Hybridization Protocol was used with the mouse IO360 Panel. Performed by Emory Genomics Core.

scan_protocol: nCounter Digital Analyzer

data_processing:
nSolver software
nSolver software was used to normalize raw RCC files using positive and negative controls.

label: mouse IO 360 CodeSet

source_name: Tumor (mB16F10)

label_protocol: Nanostring's Gene Expression CodeSet RNA Protocol was used with the mouse IO360 Panel. Performed by Emory Genomics Core.

growth_protocol: Both B16F10 and B16KVP tumor cells were grown in complete media before subcutaneous injection into mice. Trypsinization using 0.05% Trysin was used to detach cells when splitting.

extract_protocol: RNeasy Kits from QIAGEN were used for RNA Purification

treatment_protocol: Tumors were subcutaneously injected into the flank of mice, 500,000 cells/mouse. TBI was given 6 days later. Adoptive transfer of 500,00 naïve pmel-1 CD8 T cells was given via tail vein injection 7 days after initial tumor injection OR no treatment was given.

value: Female

value: Tumor

tag: tumor type

tag: therapy

value: naïve pmel-1 CD8 T cells


title: Ezhip_mKO_E425_H2Aub_rep1

description: Library name: Sample 83


title: 2C_wt_m_5

value: 2C embryos

value: WT


title: Ezhip_WT_E425_H2Aub_rep1

description: Library name: Sample 81


title: Tumor B16F10 with ACT, 0022


title: Znhit3_Morula_se13

value: Morula

value: Embryo


title: Tumor B16F10 No Treatment, 0020

value: no treatment


title: Ezhip_mKO_Bl_H2Aub_rep1

description: Library name: Sample 80

value: mouse pre-implantation embryos, E3.5

value: Ezhip mKO


title: 2C_wt_m_3

value: male


title: Znhit3_Morula_se15


title: 2C_wt_m_2


title: WT_D14_EED_rep2

description: Library name: Sample 2

value: mouse oocytes, D14

value: wild type


title: Tumor B16F10 No Treatment, 0018


title: Tumor B16F10 No Treatment, 0019


title: Tumor B16KVP with ACT, 0017

source_name: Tumor (hB16KVP)


title: Ezhip_mHet_Bl_H2Aub_rep1

description: Library name: Sample 79


title: 2C_wt_m_1


title: Tumor B16KVP with ACT, 0016


title: Ezhip_WT_Bl_H2Aub_rep1

description: Library name: Sample 78


title: Znhit3_Morula_se10


title: 2C_wt_f_4

value: female


title: Ezhip_mKO_2C_PRDUBmutOE_K27me3_rep2

description: Library name: Sample 77

source_name: mouse pre-implantation embryos, 2 cell

value: mouse pre-implantation embryos, 2 cell

value: Pr-DUB mutant OE


title: 2C_wt_f_5


title: Znhit3_Morula_se1


title: Znhit3_Morula_se12


title: Ezhip_mKO_2C_PRDUBmutOE_K27me3_rep1

description: Library name: Sample 76


title: Tumor B16KVP with ACT, 0015


title: 2C_wt_f_2


title: Znhit3_EB_se7

value: Early blastocyst


title: Ezhip_mKO_E425_EZH2_rep1

description: Library name: Sample 73

value: mouse pre-implantation embryos, E4.25


title: Znhit3_EB_se6


title: Ezhip_mKO_2C_PRDUBwtOE_K27me3_rep2

description: Library name: Sample 75

value: Pr-DUB wilde type OE


title: 2C_wt_f_1


title: Znhit3_Morula_se11


title: oocyte_matKO_f_4

source_name: oocytes

value: oocytes

value: Ezhip matKO


title: Ezhip_mKO_2C_PRDUBwtOE_K27me3_rep1

description: Library name: Sample 74


title: Tumor B16KVP No Treatment, 0013

value: Female

value: Tumor


title: Tumor B16F10 with ACT, 0009

value: naïve pmel-1 CD8 T cells


title: Tumor B16KVP No Treatment, 0014

value: no treatment


title: Znhit3_EB_se5

value: Embryo


title: Znhit3_EB_se8


title: Tumor B16F10 with ACT, 0010


title: Ezhip_WT_E425_EZH2_rep1

description: Library name: Sample 72


title: Tumor B16F10 with ACT, 0008


title: oocyte_matKO_f_3


title: Ezhip_mKO_2C_Ezh2_rep1

description: Library name: Sample 71

value: mouse pre-implantation embryos, late 2 cell

value: Ezhip mKO


title: Tumor B16F10 No Treatment, 0007


title: Znhit3_EB_se4


title: Znhit3_EB_se9


title: 2C_wt_f_3

value: 2C embryos

value: WT


title: oocyte_matKO_f_2

value: female


title: Znhit3_EB_se3


title: Ezhip_mKO_E65_ExE_K27me3_rep1

description: Library name: Sample 69

source_name: mouse post-implantation embryos, E6.5, Extraembryonic ectoderm


title: Ezhip_mKO_E65_ExE_K27me3_rep2

description: Library name: Sample 70

value: mouse post-implantation embryos, E6.5, Extraembryonic ectoderm


title: Tumor B16KVP with ACT, 0005


title: Tumor B16F10 No Treatment, 0006


title: Znhit3_EB_se22


title: Ezhip_mHet_E65_ExE_K27me3_rep2

description: Library name: Sample 68

value: Ezhip mHet


title: Ezhip_mHet_E65_ExE_K27me3_rep1

description: Library name: Sample 67


title: oocyte_wt_f_1


title: Ezhip_WT_E65_ExE_K27me3_rep2

description: Library name: Sample 66

value: wild type


title: oocyte_wt_f_3


title: oocyte_wt_f_2


title: Tumor B16KVP with ACT, 0004


title: Znhit3_EB_se21

value: Early blastocyst


title: Ezhip_WT_E65_ExE_K27me3_rep1

description: Library name: Sample 65


title: Znhit3_EB_se20


title: Tumor B16KVP No Treatment, 0003


title: synchronized testis, cKO, 4

city: Shenzhen

first: Dongteng

last: Liu

state: Guangdong

address: No. 1, Haiyuan First Road, Futian District

institute: The University of Hong Kong-Shenzhen Hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLCgenomic benchwork (parameter - Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters - mismath cost: 2 insertion cost: 3 deletion cost: 3 length fracton: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: mm10
Supplementary files format and content: Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: testis

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 µg 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 manufcture's protocol.

treatment_protocol: Two tamoxifen injections were administered to the mice on RA7.5 and RA8.5, respectively.

value: testis

value: Tamoxifen injection


title: Znhit3_EB_se2


title: Tumor B16KVP No Treatment, 0002


title: synchronized testis, cKO, 3


title: Znhit3_EB_se18


title: Ezhip_mKO_E65_Epi_K27me3_rep2

description: Library name: Sample 64


title: Tumor B16KVP No Treatment, 0001


title: oocyte_matKO_f_1

value: oocytes

value: Ezhip matKO


title: synchronized testis, cKO, 2


title: LN B16KVP 3

description: Lymph Node was put into RNA later and then stored at 4 degress. Was then given to Emory Genomics Core for processing. RNA isolarion was performed and nucleic acid QC

data_processing: nSolver software

source_name: Lymph Node (hB16KVP)

label_protocol: Nanostring's Gene Expression CodeSet RNA Hybridization Protocol was used with the mouse IO360 Panel. Performed by Emory Genomics Core.

growth_protocol: Both B16F10 and B16KVP tumor cells were grown in complete media before subcutaneous injection into mice. Trysinization using 0.05% Trysin was used to detach cells when splitting.

treatment_protocol: Tumors were subcutaneously injected into the flank of mice, 500,000 cells/mouse. TBI was given 6 days later. Adoptive transfer of 500,00 naïve pmel-1 CD8 T cells was given via tail vein injection 7 days after initial tumor injection.

value: Female

value: Lymph Node


title: Znhit3_EB_se19


title: Znhit3_EB_se17


title: synchronized testis, cKO, 1


title: LN B16KVP 2

value: naïve pmel-1 CD8 T cells


title: Ezhip_mHet_E65_Epi_K27me3_rep2

description: Library name: Sample 62


title: Znhit3_EB_se15

value: Embryo


title: LN B16KVP 1


title: synchronized testis, control, 4

value: Spdyafl/fl


title: synchronized testis, control, 3


title: Znhit3_EB_se14


title: Ezhip_mHet_E65_Epi_K27me3_rep1

description: Library name: Sample 61

source_name: mouse post-implantation embryos, E6.5, Epiblast


title: Ezhip_WT_E65_Epi_K27me3_rep2

description: Library name: Sample 60


title: Znhit3_EB_se13


title: Tumor B16KVP 3

value: Tumor


title: Ezhip_WT_E65_Epi_K27me3_rep1

description: Library name: Sample 59

value: mouse post-implantation embryos, E6.5, Epiblast


title: Znhit3_EB_se12


title: Tumor B16KVP 2


title: Ezhip_mKO_E425_K27me3_rep1

description: Library name: Sample 58

value: mouse pre-implantation embryos, E4.25

value: Ezhip mKO


title: Znhit3_EB_se11


title: LN B16F10 3

source_name: Lymph Node (mB16F10)


title: Cistr KO male mouse hypothalamus animal4

city: Toronto

first: Philipp

last: Maass

state: Ontario

address: 686 Bay St

department: Genetics and Genome Biology

country: Canada

institute: The Hospital for Sick Children

description:
PM_mKO_Cistr_M4_hypothal_S601_L004
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

data_processing:
We aligned reads to hg38 using STAR aligner, version 2.7.0f. We used FeatureCounts to count reads aligning to genes in GENCODE v32 (human), vM33 (mouse).
Assembly: hg38, mm39
Supplementary files format and content: text files include RPKM values for each sample

source_name: hypothalamus

extract_protocol:
RNA was harvested and purified using TRIzol (Invitrogen). 1 ug of total RNA was used for the construction of the sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus following manufacturer's protocols.

value: hypothalamus

value: Cistr-/- male


title: synchronized testis, control, 1


title: Cistr KO male mouse hypothalamus animal3 lane2

description:
PM_mKO_Cistr_M3_hypothal_S45_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Ezhip_mHet_E425_K27me3_rep1

description: Library name: Sample 57

source_name: mouse pre-implantation embryos, E4.25

value: Ezhip mHet


title: Ezhip_WT_E425_K27me3_rep1

description: Library name: Sample 56

value: wild type


title: Znhit3_EB_se10

source_name: Embryo

value: Early blastocyst


title: Znhit3_EB_se1


title: Ezhip_mKO_E65_Epi_K27me3_rep1

description: Library name: Sample 63


title: LN B16F10 1


title: LN B16F10 2


title: Znhit3_8cell_se9


title: Ezhip_mKO_Bl_K27me3_rep2

description: Library name: Sample 55

source_name: mouse pre-implantation embryos, E3.5

value: mouse pre-implantation embryos, E3.5


title: Cistr KO male mouse hypothalamus animal3 lane1

description:
PM_mKO_Cistr_M3_hypothal_S45_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Cistr KO male mouse hypothalamus animal2 lane2

description:
PM_mKO_Cistr_M2_hypothal_S39_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: synchronized testis, control, 2

value: testis

value: Tamoxifen injection


title: Tumor B16F10 2

value: Female


title: Znhit3_8cell_se8


title: Cistr KO male mouse hypothalamus animal2 lane1

description:
PM_mKO_Cistr_M2_hypothal_S39_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Tumor B16F10 3


title: Tumor B16KVP 1


title: Ezhip_mKO_Bl_K27me3_rep1

description: Library name: Sample 54


title: Ezhip_mHet_Bl_K27me3_rep2

description: Library name: Sample 53


title: Znhit3_8cell_se7


title: Tumor B16F10 1


title: Cistr KO male mouse hypothalamus animal1 lane3

description:
PM_mKO_Cistr_M1_hypothal_S4_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Znhit3_8cell_se5


title: Ezhip_mHet_Bl_K27me3_rep1

description: Library name: Sample 52


title: Cistr KO male mouse hypothalamus animal1 lane2

description:
PM_mKO_Cistr_M1_hypothal_S33_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Znhit3_8cell_se4


title: Ezhip_WT_Bl_K27me3_rep2

description: Library name: Sample 51


title: Cistr KO male mouse hypothalamus animal1 lane1

description:
PM_mKO_Cistr_M1_hypothal_S33_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Ezhip_WT_Bl_K27me3_rep1

description: Library name: Sample 50


title: TN-MASH model mouse liver, EVT0185-treated (100mg/kg), biol rep 7

city: Hamilton

first: Russta

last: Fayyazi

state: ON

address: 1280 Main St W

department: Medicine

institute: McMaster University

hyb_protocol: Hybridization of target RNA with the NanoString reporter and capture probe pairs was carried out at 65°C for 16–20 hours following the manufacturer’s instructions. Post-hybridization, excess probes were removed and complexes immobilized using the nCounter Prep Station (NanoString Technologies).

scan_protocol: Digital counts of probe-target complexes were acquired using the NanoString nCounter Digital Analyzer at the McMaster Genomics Facility. Image capture and data extraction were performed using NanoString’s nSolver 4.0 software.

data_processing: Raw counts were processed in NanoString nSolver 4.0. Data were normalized using the global geometric mean of all probes after positive control and background correction. Normalized expression values were used to compute pathway scores as the first principal component of gene expression values within each predefined pathway.

label: nCounter fluorescent barcoded probe pairs (NanoString Technologies)

source_name: liver RNA, treatment group

label_protocol: Hybridization of reporter and capture probe pairs to target RNA molecules was performed according to the NanoString nCounter Fibrosis Panel manufacturer’s protocol.

extract_protocol: Total RNA was isolated from liver tissue using the RNeasy Kit (Qiagen, CA, USA) according to the manufacturer’s instructions. RNA quality and integrity were verified using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano Kit.

value: liver

value: male

tag: housing temperature

value: thermoneutral (29℃)

tag: nash diet

value: 40 kcal% fat (mostly palm oil), 20 kcal% fructose and 0.02% cholesterol (Research Diets, Inc. D19101102)

value: 100 mg/kg of EVT0185 via gavage


title: TN-MASH model mouse liver, EVT0185-treated (100mg/kg), biol rep 6


title: Znhit3_8cell_se32

value: Embryo


title: Ezhip_mKO_8C_K27me3_rep1

description: Library name: Sample 49

source_name: mouse pre-implantation embryos, 8 cell

value: mouse pre-implantation embryos, 8 cell


title: Znhit3_8cell_se30


title: Cistr KO female mouse hypothalamus animal3 lane2

description:
PM_mKO_Cistr_F3_hypothal_S27_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: Cistr-/- female


title: Ezhip_mHet_8C_K27me3_rep2

description: Library name: Sample 48


title: Cistr KO female mouse hypothalamus animal3 lane3

description:
PM_mKO_Cistr_F3_hypothal_S2_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: hypothalamus


title: Znhit3_8cell_se3


title: Cistr KO female mouse hypothalamus animal3 lane1

description:
PM_mKO_Cistr_F3_hypothal_S27_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Cistr KO female mouse hypothalamus animal2 lane2

description:
PM_mKO_Cistr_F2_hypothal_S9_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Ezhip_WT_8C_K27me3_rep1

description: Library name: Sample 45


title: Znhit3_8cell_se29


title: Ezhip_mKO_L2C_K27me3_rep2

description: Library name: Sample 44

source_name: mouse pre-implantation embryos, late 2 cell

value: Ezhip mKO


title: Cistr KO female mouse hypothalamus animal2 lane1

description:
PM_mKO_Cistr_F2_hypothal_S9_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: TN-MASH model mouse liver, EVT0185-treated (100mg/kg), biol rep 2


title: TN-MASH model mouse liver, EVT0185-treated (100mg/kg), biol rep 8


title: Cistr KO female mouse hypothalamus animal1 lane2

description:
PM_mKO_Cistr_F1_hypothal_S3_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: TN-MASH model mouse liver, EVT0185-treated (100mg/kg), biol rep 3


title: Znhit3_8cell_se26


title: Znhit3_8cell_se25


title: TN-MASH model mouse liver, Vehicle, biol rep 8

source_name: liver RNA, vehicle group

value: vehicle (1.5 % CMC and 0.2 % Tween-20)


title: TN-MASH model mouse liver, EVT0185-treated (100mg/kg), biol rep 4


title: TN-MASH model mouse liver, Vehicle, biol rep 7


title: Ezhip_WT_8C_K27me3_rep2

description: Library name: Sample 46

value: wild type


title: Ezhip_mHet_L2C_K27me3_rep1

description: Library name: Sample 41

value: mouse pre-implantation embryos, late 2 cell

value: Ezhip mHet


title: TN-MASH model mouse liver, EVT0185-treated (100mg/kg), biol rep 5


title: TN-MASH model mouse liver, Vehicle, biol rep 6


title: WT male mouse hypothalamus animal2 lane2

description:
PM_mWT_Cistr_M3_hypothal_S69_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: WT male


title: WT male mouse hypothalamus animal2 lane1

description:
PM_mWT_Cistr_M3_hypothal_S69_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Znhit3_8cell_se28


title: Znhit3_8cell_se2


title: Ezhip_WT_L2C_K27me3_rep1

description: Library name: Sample 40


title: Ezhip_mKO_PN5_K27me3_rep2

description: Library name: Sample 39

source_name: mouse pre-implantation embryos, 1 cell

value: mouse pre-implantation embryos, 1 cell


title: Znhit3_8cell_se18


title: TN-MASH model mouse liver, EVT0185-treated (100mg/kg), biol rep 1


title: Znhit3_8cell_se17


title: TN-MASH model mouse liver, Vehicle, biol rep 5


title: TN-MASH model mouse liver, Vehicle, biol rep 4


title: Znhit3_8cell_se27


title: Ezhip_mHet_L2C_K27me3_rep2

description: Library name: Sample 42


title: Znhit3_8cell_se16


title: Ezhip_mKO_L2C_K27me3_rep1

description: Library name: Sample 43


title: WT male mouse hypothalamus animal1 lane1

description:
PM_mWT_Cistr_M2_hypothal_S63_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Cistr KO female mouse hypothalamus animal1 lane1

description:
PM_mKO_Cistr_F1_hypothal_S3_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: WT female mouse hypothalamus animal2 lane2

description:
PM_mWT_Cistr_F5_hypothal_S631_L004
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: WT female


title: Ezhip_mKO_PN5_K27me3_rep1

description: Library name: Sample 38


title: TN-MASH model mouse liver, Vehicle, biol rep 2

value: liver


title: Znhit3_8cell_se14


title: Znhit3_8cell_se12


title: Ezhip_mHet_PN5_K27me3_rep2

description: Library name: Sample 37


title: WT female mouse hypothalamus animal1 lane2

description:
PM_mWT_Cistr_F3_hypothal_S51_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Oocyte, 465_592, control

city: Madison

first: Hasan

last: Khatib

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin Madison

description: Library name: Oocyte_pool_7

data_processing:
Trimming (TrimGalore)
Alignment (Bismark)
Differential methylation analysis (methylKit R package)
Annotation
Assembly: ARS-UI_Ramb_v3.0
Supplementary files format and content: bismark coverage files / methylation counts

organism: Ovis aries

source_name: Oocyte

extract_protocol:
Genomic DNA was extracted from sperm samples using the Quick-DNA Miniprep Plus (Zymo Research).
Oocyte and embryo samples were processed for whole-genome bisulfite sequencing (WGBS) using the EZ DNA Methylation Direct Kit (Zymo Research, Irvine, CA, USA). Following bisulfite conversion, library preparation was performed using the Pico Methyl Kit (Zymo Research).

treatment_protocol: Treatment group dams were supplemented with 3g of methionine per day from weaning to puberty.

value: Oocyte

value: control


title: Ezhip_mHet_PN5_K27me3_rep1

description: Library name: Sample 36


title: Znhit3_8cell_se11


title: Ezhip_WT_PN5_K27me3_rep2

description: Library name: Sample 35


title: Oocyte, 417, control

description: Library name: Oocyte_pool_6


title: WT female mouse hypothalamus animal1 lane1

description:
PM_mWT_Cistr_F3_hypothal_S51_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Ezhip_WT_PN5_K27me3_rep1

description: Library name: Sample 34


title: TN-MASH model mouse liver, Vehicle, biol rep 1

value: male

value: thermoneutral (29℃)

value: 40 kcal% fat (mostly palm oil), 20 kcal% fructose and 0.02% cholesterol (Research Diets, Inc. D19101102)


title: WT male mouse hypothalamus animal1 lane2

description:
PM_mWT_Cistr_M2_hypothal_S63_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Oocyte, 585_514, control

description: Library name: Oocyte_pool_5


title: Znhit3_8cell_se10

value: Embryo


title: Znhit3_8cell_se1


title: Cistr KO male mouse hippocampus animal3 lane3

description:
PM_mKO_Cistr_M3_hcampus_S8_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

source_name: hippocampus

value: hippocampus

value: Cistr-/- male


title: Ezhip_KO_FGO_K27me3_rep2

description: Library name: Sample 33

source_name: mouse oocytes, FGO

value: mouse oocytes, FGO

value: Ezhip KO


title: TN-MASH model mouse liver, Vehicle, biol rep 3

value: vehicle (1.5 % CMC and 0.2 % Tween-20)


title: Cistr KO male mouse hippocampus animal3 lane2

description:
PM_mKO_Cistr_M3_hcampus_S46_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Oocyte, 376_483, control

description: Library name: Oocyte_pool_4


title: Ezhip_KO_FGO_K27me3_rep1

description: Library name: Sample 32


title: Oocyte, 586_377_415, methionine supplemented

description: Library name: Oocyte_pool_3

value: methionine supplemented


title: Znhit3_4cell_se9


title: Ezhip_Het_FGO_K27me3_rep2

description: Library name: Sample 31

value: Ezhip Het


title: Oocyte, 581_590, methionine supplemented

description: Library name: Oocyte_pool_2


title: Znhit3_4cell_se8


title: WT female mouse hypothalamus animal2 lane1

description:
PM_mWT_Cistr_F4_hypothal_S624_L004
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: hypothalamus


title: Cistr KO male mouse hippocampus animal2 lane2

description:
PM_mKO_Cistr_M2_hcampus_S40_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Ezhip_Het_FGO_K27me3_rep1

description: Library name: Sample 30


title: Znhit3_4cell_se6


title: Oocyte, 466_580_512, methionine supplemented

description: Library name: Oocyte_pool_1


title: Cistr KO male mouse hippocampus animal2 lane1

description:
PM_mKO_Cistr_M2_hcampus_S40_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Embryo, 22483, control

description: Library name: Embryo_pool_8


title: Ezhip_WT_FGO_K27me3_rep1

description: Library name: Sample 29

value: wild type


title: Znhit3_4cell_se5


title: Cistr KO male mouse hippocampus animal1 lane2

description:
PM_mKO_Cistr_M1_hcampus_S34_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: GSK343_8C_K27me3_rep1

description: Library name: Sample 28

value: mouse pre-implantation embryos, 8 cell


title: Embryo, 417_483, control

description: Library name: Embryo_pool_7


title: Cistr KO male mouse hippocampus animal1 lane1

description:
PM_mKO_Cistr_M1_hcampus_S34_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Znhit3_4cell_se4


title: Ctrl_DMSO_8C_K27me3_rep1

description: Library name: Sample 27

value: DMSO


title: Embryo, 465_592, control

description: Library name: Embryo_pool_6


title: Znhit3_4cell_se31


title: WT_Bl_K27me3_rep2

description: Library name: Sample 26

value: mouse pre-implantation embryos, E3.5


title: Cistr KO female mouse hippocampus animal3 lane3

description:
PM_mKO_Cistr_F3_hcampus_S3_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: Cistr-/- female


title: Embryo, 376_417, control

description: Library name: Embryo_pool_5

value: control


title: Cistr KO male mouse hippocampus animal 3 lane1

description:
PM_mKO_Cistr_M3_hcampus_S46_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Cistr KO female mouse hippocampus animal3 lane2

description:
PM_mKO_Cistr_F3_hcampus_S28_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: WT_Bl_K27me3_rep1

description: Library name: Sample 25


title: Znhit3_4cell_se29


title: Embryo, 22465, control

description: Library name: Embryo_pool_4


title: WT_PN3_K27me3_rep1

description: Library name: Sample 24

value: mouse pre-implantation embryos, 1 cell


title: Znhit3_4cell_se28


title: Embryo, 22466, methionine supplemented

description: Library name: Embryo_pool_3


title: Cistr KO female mouse hippocampus animal2 lane2

description:
PM_mKO_Cistr_F2_hcampus_S10_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: WT_D21_K27me3_rep1

description: Library name: Sample 23

source_name: mouse oocytes, D21

value: mouse oocytes, D21


title: Cistr KO female mouse hippocampus animal2 lane1

description:
PM_mKO_Cistr_F2_hcampus_S10_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: WT_E6.5Epi_Ezh2_rep2

description: Library name: Sample 22

source_name: mouse pre-implantation embryos, E6.5, Epiblast


title: Embryo, 580_581, methionine supplemented

description: Library name: Embryo_pool_2

value: Embryo


title: Cistr KO female mouse hippocampus animal1 lane3

description:
PM_mKO_Cistr_F1_hcampus_S4_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: hippocampus


title: Znhit3_4cell_se26


title: Znhit3_4cell_se27


title: Embryo, 466_590, methionine supplemented

description: Library name: Embryo_pool_1


title: WT_E6.5Epi_Ezh2_rep1

description: Library name: Sample 21

source_name: mouse pre-implantation embryos, E6.5,  Epiblast


title: Znhit3_4cell_se25


title: Znhit3_4cell_se3


title: Cistr KO female mouse hippocampus animal1 lane2

description:
PM_mKO_Cistr_F1_hcampus_S4_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Znhit3_4cell_se24


title: WT_Bl_Ezh2_rep2

description: Library name: Sample 20


title: Cistr KO female mouse hippocampus animal1 lane1

description:
PM_mKO_Cistr_F1_hcampus_S1_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Cistr KO female mouse hippocampus animal3 lane1

description:
PM_mKO_Cistr_F3_hcampus_S28_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Znhit3_4cell_se23


title: WT_Bl_Ezh2_rep1

description: Library name: Sample 19


title: Znhit3_4cell_se22


title: WT_8C_Ezh2_rep2

description: Library name: Sample 18


title: WT male mouse hippocampus animal2

description:
PM_mWT_Cistr_M5_hcampus_S616_L004
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: WT male


title: Znhit3_4cell_se21


title: WT male mouse hippocampus animal1

description:
PM_mWT_Cistr_M4_hcampus_S595_L004
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: T2DM-3

city: Fuzhou

first: Jinyan

last: Chen

address: No.7 Wusi Road

institute: Fufian Academy of Medical Sciences

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human lncRNA Arrays (4x44K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The lncRNAs that at least 7 out of 14 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed lncRNAs and mRNA with statistical significance between the two groups were identified through Volcano Plot filtering.

source_name: peripheral blood mononuclear cells (PBMCs)

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

extract_protocol: The total RNA from PBMC was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. The concentration of RNA was determined using a NanoDrop ND-1000 spectrophotometer (OD 260 nm, Thermo Scientifc, USA). The integrity of RNA and gDNA contamination were further assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: The anticoagulanted whole blood was collected with BD Vacutainer cell preparation tube (CPT) in the morning after an overnight fast of 10 hours, and PBMC isolated by CPT methods.

tag: subject status

tag: molecule subtype

value: lncRNA and mRNA


title: WT_8C_EZH2_rep1

description: Library name: Sample 17

tag: tissue

tag: genotype


title: WT_2C_Ezh2_rep2

description: Library name: Sample 16

value: mouse pre-implantation embryos, late 2 cell


title: WT female mouse hippocampus animal2

description:
PM_mWT_Cistr_F5_hcampus_S632_L004
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: WT female


title: WT female mouse hippocampus animal1

description:
PM_mWT_Cistr_F4_hcampus_S625_L004
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: T2DM-2

value: peripheral blood mononuclear cells (PBMCs)


title: WT_2C_Ezh2_rep1

description: Library name: Sample 15


title: Znhit3_4cell_se20


title: T2DM-1


title: Cistr KO male mouse cerebral cortex animal3 lane3

description:
PM_mKO_Cistr_M3_ccortex_S9_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

source_name: cerebral cortex

value: cerebral cortex

value: Cistr-/- male


title: Znhit3_4cell_se2


title: Control-3

value: healthy control


title: Control-2


title: Znhit3_4cell_se19


title: Brain, bloom, H1728-FC

city: Miami

first: David

middle: A

last: Davis

state: Florida

address: 1951 NW 7th Avenue

department: Neurology

institute: University of Miami Miller School of Medicine

description: Library name: H1728-FC

data_processing:
Libraries were sequenced on Illumina Novaseq 6000 and ~30M reads were generated per sample.
Primary RNAseq bioinformatics Raw FASTQs were processed through a bioinformatics pipeline including adapter trimming by TrimGalore (v0.6.1) (https://github. com/FelixKrueger/TrimGalore)
Alignment with the STAR aligner 2.5.2a algorithm and
Assembly: Gene counts or reads quantified against the Ensembl v101gene release database for turTru1 using the Gene Counts function in STAR
Supplementary files format and content: raw counts for each sample

organism: Tursiops truncatus

source_name: Dolphin 16

extract_protocol:
Total RNA was extracted from approximately 100 mg of frozen dolphin cerebral cortex using RNeasy Lipid Tissue Mini Kit (Qiagen Inc., USA)
Total dolphin RNAs extracted from the cerebral cortex were submitted for RNA sequencing (n=17, median RIN of 9.1 (CI: 8.9-9.5) were prepared with the Nugen Universal Plus mRNA-Seq (M01442 v2) using 600ng via Qubit and 14 cycles PCR.

treatment_protocol: Frozen Archive Necropsy Brain Tissue

value: Brain-Cerebral Cortex

value: Brain Tissue

value: WT

value: bloom season


title: WT_PN5_Ezh2_rep1

description: Library name: Sample 13

value: wild type


title: Znhit3_4cell_se18


title: Cistr KO male mouse cerebral cortex animal3 lane2

description:
PM_mKO_Cistr_M3_ccortex_S47_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Cistr KO male mouse cerebral cortex animal3 lane1

description:
PM_mKO_Cistr_M3_ccortex_S47_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Cistr KO male mouse cerebral cortex animal2 lane3

description:
PM_mKO_Cistr_M2_ccortex_S6_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: WT_FGO_Ezh2_rep1

description: Library name: Sample 11

value: mouse oocytes, FGO


title: Brain, bloom, H1491-FC

description: Library name: H1491-FC

source_name: Dolphin 13


title: Brain, bloom, H1520-FC

description: Library name: H1520-FC

source_name: Dolphin 14


title: Cistr KO male mouse cerebral cortex animal2 lane2

description:
PM_mKO_Cistr_M2_ccortex_S41_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Znhit3_4cell_se15

source_name: Embryo


title: Brain, bloom, H1830-FC

description: Library name: H1830-FC

source_name: Dolphin 17


title: Control-1


title: Znhit3_4cell_se17


title: WT_FGO_Ezh2_rep2

description: Library name: Sample 12


title: WT_D14_Ezh2_rep1

description: Library name: Sample 10

source_name: mouse oocytes, D14

value: mouse oocytes, D14


title: WT_Bl_EED_rep2

description: Library name: Sample 9

source_name: mouse pre-implantation embryos, E3.5

value: mouse pre-implantation embryos, E3.5


title: Znhit3_4cell_se14

value: Embryo


title: Brain, bloom, H1383-FC

description: Library name: H1383-FC

source_name: Dolphin 12


title: Brain, bloom, H1653-FC

description: Library name: H1653-FC

source_name: Dolphin 15


title: Znhit3_4cell_se13


title: Cistr KO male mouse cerebral cortex animal1 lane2

description:
PM_mKO_Cistr_M1_ccortex_S35_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Znhit3_4cell_se12


title: WT_Bl_EED_rep1

description: Library name: Sample 8


title: Brain, bloom, H1132-FC

description: Library name: H1132-FC

source_name: Dolphin 10


title: Brain, bloom, H1122-FC

description: Library name: H1122-FC

source_name: Dolphin 9


title: WT_2C_EED_rep1

description: Library name: Sample 7

source_name: mouse pre-implantation embryos, late 2 cell


title: Cistr KO female mouse cerebral cortex animal3 lane2

description:
PM_mKO_Cistr_F3_ccortex_S29_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: Cistr-/- female


title: Znhit3_4cell_se16


title: mES_EED_1500_rep1

description: Library name: Sample 6

source_name: mESCs

tag: cell line

value: mESCs


title: Znhit3_4cell_se11

tag: cell type


title: mES_EED_20k_rep1

description: Library name: Sample 5


title: Brain, non-bloom, H1911-FC

description: Library name: H1911-FC

source_name: Dolphin 8

tag: treatment

value: non-bloom season


title: Cistr KO female mouse cerebral cortex animal3 lane1

description:
PM_mKO_Cistr_F3_ccortex_S29_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Znhit3_4cell_se10


title: Cistr KO female mouse cerebral cortex animal2 lane2

description:
PM_mKO_Cistr_F2_ccortex_S11_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Cistr KO male mouse cerebral cortex animal2 lane1

description:
PM_mKO_Cistr_M2_ccortex_S41_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Znhit3_4cell_se1


title: mES_EZH2_500_rep1

description: Library name: Sample 4


title: Brain, bloom, H1235-FC

description: Library name: H1235-FC

source_name: Dolphin 11


title: Cistr KO female mouse cerebral cortex animal2 lane1

description:
PM_mKO_Cistr_F2_ccortex_S11_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: mES_EZH2_20k_rep1

description: Library name: Sample 3


title: scRNAseq_8cell_R50_8

source_name: Blastomere

extract_protocol:
Znhit3+/- female mice were injected intraperitoneally with eCG (5 IU) followed 46 h to 48 h with hCG (5 IU) and then co-caged with Znhit3+/- males. Fertilized zygotes were flushed from plugged females 16 h post hCG injection and cultured in M2 medium containing hyaluronidase to remove the cumulus mass. Zygotes without cumulus were then washed and cultured in advanced KSOM until 8-cell stage. When collecting samples, embryos were first washed in PBS and transferred into acidic Tyrode’s solution to remove zonae pellucidae. Single zona-free embryo was then pipetted into a capillary tube with a diameter of 1.5 to 2 times of the diameter of single blastomeres to physically dissociate single blastomeres. Single blastomeres that remained intact were transferred into PCR strips  containing 2.5 µl of RLT plus buffer.
RNAs in each sample were captured by oligo-dT beads and then processed following the G&T-seq protocol to construct the scRNA-Seq library.

value: Blastomere


title: Brain, non-bloom, H1506-FC

description: Library name: H1506-FC

source_name: Dolphin 5


title: Cistr KO female mouse cerebral cortex animal1 lane2

description:
PM_mKO_Cistr_F1_ccortex_S5_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

source_name: cerebral cortex


title: Brain, non-bloom, H1666-FC

description: Library name: H1666-FC

source_name: Dolphin 6


title: mES_R1_ChIP_Input_rep1

description: Library name: Sample 2

data_processing:
When aligning the paired-end reads to mouse genome (mm9), the following parameters were used: -t -q -N 1 -L 25 -X 700 –no-unal -x by Bowtie2 (version 2.2.2). All unmapped reads, non-uniquely mapped reads, and PCR duplicates were removed. For downstream analysis, we normalized the read counts by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM). To minimize the variation across samples, RPKM values across the whole genome were further normalized by Z-score.
To visualize the CUT&RUN signals in the UCSC genome browser, we generated the RPKM values on a 100-bp-window basis.
Spike-in normalization calculated the relative abundance of mouse genome reads according to yeast genome reads, which equally added to each sample.
Assembly: mm9
Supplementary files format and content: bigWig


title: scRNAseq_8cell_R50_7


title: Cistr KO male mouse cerebral cortex animal1 lane1

description:
PM_mKO_Cistr_M1_ccortex_S35_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Cistr KO female mouse cerebral cortex animal1 lane1

description:
PM_mKO_Cistr_F1_ccortex_S5_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Brain, non-bloom, H1431-FC

description: Library name: H1431-FC

source_name: Dolphin 4


title: mES_R1_ChIP_Ezh2_rep1

description: Library name: Sample 1


title: scRNAseq_8cell_R50_6


title: WT male mouse cerebral cortex animal2

description:
PM_mWT_Cistr_M5_ccortex_S617_L004
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: WT male


title: Brain, non-bloom, H1332-FC

description: Library name: H1332-FC

source_name: Dolphin 3


title: Brain, non-bloom, H1319-FC

description: Library name: H1319-FC

source_name: Dolphin 2


title: Brain, non-bloom, H1904-FC

description: Library name: H1904-FC

source_name: Dolphin 7


title: scRNAseq_8cell_R50_5


title: EZHIP_mKO_Epi_RNAseq_rep2

description:
Library name: Sample 67
EZHIP_KO_Epi_Exe_FPKM.txt

data_processing:
All mRNA-seq data were trimmed by Trim Galore v0.4.2 and subsequently mapped to the mm9 transcriptome using HISAT2 v.2.2.1 (Kim et al., 2019). The gene expression level was calculated by StringTiev2.1.2 (Pertea et al., 2016). based on the annotation of mm9/hg19 refFlat database from UCSC genome browser. HTSeq v.0.6.0 (Anders et al., 2015) was applied to calculate counts per gene with default parameters.
Assembly: mm9
Supplementary files format and content: fpkm

source_name: mouse post-implantation embryos, E6.5, Epiblast

extract_protocol:
Oocytes or embryos were lysed and used directly as input materials for subsequent RNA-seq library preparation
All RNA-seq libraries followed the smart-seq2 protocol as previously describeb (Picelli et al., 2014) and were sequenced by the DNBSEQ-T7 system according to the manufacturer's instructions.

treatment_protocol: GSK343 was dissolved in DMSO as 10uM stock. To block EZH2 activity in embryos, PN3 stage zygotes were collected and cultured in KSOM containing 2.5μM GSK343 or DMSO as control, and then collected at the 8C stage for the following experiments.

value: Ezhip mKO


title: WT_PN5_Ezh2_rep2

description: Library name: Sample 14

source_name: mouse pre-implantation embryos, 1 cell

value: mouse pre-implantation embryos, 1 cell


title: WT male mouse cerebral cortex animal1

description:
PM_mWT_Cistr_M4_ccortex_S596_L004
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: cerebral cortex


title: Brain, non-bloom, H1310-FC

description: Library name: H1310-FC

source_name: Dolphin 1

value: Brain-Cerebral Cortex


title: scRNAseq_8cell_R50_4


title: WT female mouse cerebral cortex animal3 lane1

description:
PM_mWT_Cistr_F5_ccortex_S633_L004
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: WT female


title: scRNAseq_8cell_R50_3


title: EZHIP_mHet_Exe_RNAseq_rep2

description:
Library name: Sample 66
EZHIP_KO_Epi_Exe_FPKM.txt

source_name: mouse post-implantation embryos, E6.5, Extraembryonic ectoderm

value: Ezhip mHet


title: RIBOseq Ba/F3 WT #1

city: Leuven

first: Marino

last: Caruso

address: Herestraat 49

department: Oncology

country: Belgium

institute: KULeuven

description:
Library name: RIBO_WT_024
ColName in RawCounts.xlsx : RIBO_WT_024

data_processing:
For RNA-seq of total RNA, SeqPurge (v2.0.1) was used for trimming sequence adapters
For footprinting, Adaptor sequence ‘TGGAATTCTCGGGTGCC’ was clipped and sequences were trimmed based on sequencing quality in all datasets with the FASTX toolset (0.0.14). Sequences shorter than 20 nucleotides were hereby discarded and the quality threshold was set at 28
All contaminant PhiX, rRNA, snRNA, sn-o-RNA and tRNA sequences were filtered using a reference information for prefiltering purposes including: (i) the PhiX bacteriophage genome from ftp.ncbi.nih.gov, (ii) mouse rRNA nucleotide sequences from ncbi.nlm.nih.gov/nuccore (obtained using the search term ‘biomol_rrna’), (iii) mouse sn-RNA and sn-o-RNA sequences from Biomart (obtained using the gene type filters for ‘sn-RNA’ and ‘sn-o-RNA’) and (iv) mouse tRNA sequences from gtrnadb.ucsc.edu
Pre -processed trimmed reads from total RNA-seq and ribosomes-protected fragments were aligned using the nf-core/rnaseq (v3.0) to the reference genome using STAR aligner (v.2.6.1d)
Quantification was performed by Salmon (v.1.4.0) using the star_salmon option
Differential expression analysis was performed on the triplicates of two groups (WT and mutant) using the package DESeq2 (v.1.30) in the R environment
Assembly: Mus musculus (GRCm38, release 102) reference genome
Supplementary files format and content: RawCounts.csv: Comma separated file containing all raw read counts for each sample, including RNA and RIBO samples (RPFs)
Supplementary files format and content: DifferentialRNA.xlsx: Excel file containing DeSeq2 results analysing differential RNA expression when comparing experimental conditions (one tab per comparison). This was calculated by using RNA samples read counts only.
Supplementary files format and content: DifferentialRIBO.xlsx: Excel file containing DeSeq2 results analysing differential RIBO (RPFs) expression when comparing experimental conditions (one tab per comparison). This was calculated by using RIBO samples read counts only.
Supplementary files format and content: DifferentialTE.xlsx: Excel file containing DeSeq2 results analysing differential Translation Efficiencies (TE) when comparing experimental conditions (one tab per comparison). This was calculated by using both RNA and RIBO samples read counts.
Library strategy: Ribo-Seq

growth_protocol: 10 – 50 million cells cultured in RPMI‐1640 medium (Gibco) supplemented with 10% fetal calf serum (FCS, Gibco) and with 1 ng/mL interleukin‐3 (IL‐3, Miltenyi Biotec)

extract_protocol:
Cell pellets were lysed in 750 μl of ice-cold Lysis buffer supplemented with 100mg/ml cycloheximide. After debris removal, the lysate was divided for total RNA purification and for subsequent footprinting. For RNA-seq of total RNA, RNA was purified from the lysate with the RNA Clean and Concentrator-5 kit (Zymo Research), followed by NEBnext polyA mRNA magnetic isolation. For footprinting, 10 μg of lysate was digested for 45 min with RNase I at 21°C, and the reaction was stopped by adding SuperaseIn RNase Inhibitor (Thermofisher). Digested lysate was purified on a MicroSpin S-400 HR Sephacryl column (GE Healthcare), and flow through was purified with the RNA Clean and Concentrator-5 (ZymoResearch). Ribosome protected fragments (RPFs) corresponding to 28-30 nt were excised after gel electrophoresis on a Novex TBE-Urea gel (15%) (Thermofisher), and excised gel fragments were incubated overnight in molecular grade water supplemented with ammonium acetate at 4°C. The slurry was transferred to CoStar filter tubes and centrifuged, and flow through was incubated at -80°C for 2 hrs with glycogen and isopropanol. Following centrifugation, the pellet was washed with ice-cold 80% EtOH, dried and resuspended in molecular grade water.
For RNA-seq of total RNA, mRNA where processed with the NEBNext Ultra II directional RNA library prep kit (NEB) in combination with NEBNext Multiplex Oligos for Illumina (Dual Index Primer pairs). For Footprinting, RPFs were 3’ dephosphorylated with T4 PNK (New England Biolabs) and purified using the Oligo Clean and Concentrator kit (ZymoResearch). The 3’ adapter was ligated and fragments were purified using the Small RNA Library prep kit (Lexogen). After 5’ phosphorylation of the RPFs and purification with the Oligo Clean and Concentrator kit, 5’ adapter ligation and first strand cDNA synthesis was performed according to the Small RNA Library prep kit manual. Ribosomal RNA (rRNA) was depleted by adding LNA probes from the QIAseq FastSelect rRNA HMR kit (Qiagen) during the cDNA synthesis reaction. In the indexing PCR amplification step (Small RNA Library prep kit), index primers (Lexogen) were added at both ends of the fragments. Library products were purified with AMPure XP beads, and  adapter dimers and excess index primers were removed by running the samples on a Novex TBE gel (8%) (Thermofisher), the gel part corresponding to the correct library products was excised and purified. Quality of the final libraries was determined on the Agilent Bioanalyzer with the High Sensitivity DNA kit.

treatment_protocol: Cells were treated for 1 min with 0.1 mg/ml cycloheximide prior harvesting

value: WT


title: scRNAseq_8cell_R50_2


title: RIBOseq Ba/F3 WT #2

description:
Library name: RIBO_WT_023
ColName in RawCounts.xlsx : RIBO_WT_023


title: EZHIP_mHet_Epi_RNAseq_rep2

description:
Library name: Sample 65
EZHIP_KO_Epi_Exe_FPKM.txt

value: mouse post-implantation embryos, E6.5, Epiblast


title: scRNAseq_8cell_R50_1


title: RIBOseq Ba/F3 WT #3

description:
Library name: RIBO_WT_022
ColName in RawCounts.xlsx : RIBO_WT_022


title: EZHIP_WT_Exe_RNAseq_rep2

description:
Library name: Sample 64
EZHIP_KO_Epi_Exe_FPKM.txt

value: mouse post-implantation embryos, E6.5, Extraembryonic ectoderm

value: wide type


title: EZHIP_mKO_Exe_RNAseq_rep2

description:
Library name: Sample 68
EZHIP_KO_Epi_Exe_FPKM.txt


title: EZHIP_WT_Epi_RNAseq_rep2

description:
Library name: Sample 63
EZHIP_KO_Epi_Exe_FPKM.txt


title: WT female mouse cerebral cortex animal1 lane2

description:
PM_mWT_Cistr_F3_ccortex_S53_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: scRNAseq_8cell_R49_8


title: RIBOseq Ba/F3 Rps15 H137YH137Y #2

description:
Library name: RIBO_Rps15H137Y_021
ColName in RawCounts.xlsx : RIBO_Rps15H137Y_021


title: EZHIP_mKO_Exe_RNAseq_rep1

description:
Library name: Sample 62
EZHIP_KO_Epi_Exe_FPKM.txt


title: WT female mouse cerebral cortex animal1 lane1

description:
PM_mWT_Cistr_F3_ccortex_S10_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: scRNAseq_8cell_R49_7


title: RIBOseq Ba/F3 Rps15 H137YH137Y #6

description:
Library name: RIBO_Rps15H137Y_020
ColName in RawCounts.xlsx : RIBO_Rps15H137Y_020


title: Cistr KO male mouse cerebellum animal3 lane3

description:
PM_mKO_Cistr_M3_cerebellum_S7_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

source_name: cerebellum

value: cerebellum

value: Cistr-/- male


title: EZHIP_mKO_Epi_RNAseq_rep1

description:
Library name: Sample 61
EZHIP_KO_Epi_Exe_FPKM.txt


title: scRNAseq_8cell_R49_6


title: RIBOseq Ba/F3 Rps15 H137YH137Y #16

description:
Library name: RIBO_Rps15H137Y_019
ColName in RawCounts.xlsx : RIBO_Rps15H137Y_019


title: EZHIP_mHet_Exe_RNAseq_rep1

description:
Library name: Sample 60
EZHIP_KO_Epi_Exe_FPKM.txt


title: Cistr KO male mouse cerebellum animal3 lane2

description:
PM_mKO_Cistr_M3_cerebellum_S44_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: WT female mouse cerebral cortex animal2 lane2

description:
PM_mWT_Cistr_F4_ccortex_S626_L004
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: scRNAseq_8cell_R49_5


title: RIBOseq Ba/F3 Rpl10 R98S/R98S #A34

description:
Library name: RIBO_Rpl10_018
ColName in RawCounts.xlsx : RIBO_Rpl10_018

value: Rpl10 R98S/R98S


title: Cistr KO male mouse cerebellum animal3 lane1

description:
PM_mKO_Cistr_M3_cerebellum_S44_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: scRNAseq_8cell_R49_4


title: RIBOseq Ba/F3 Rpl10 R98S/R98S #A29

description:
Library name: RIBO_Rpl10_017
ColName in RawCounts.xlsx : RIBO_Rpl10_017


title: EZHIP_mHet_Epi_RNAseq_rep1

description:
Library name: Sample 59
EZHIP_KO_Epi_Exe_FPKM.txt


title: WT female mouse cerebral cortex animal2 lane1

description:
PM_mWT_Cistr_F3_ccortex_S53_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: RIBOseq Ba/F3 Rpl10 R98S/R98S #A30

description:
Library name: RIBO_Rpl10_016
ColName in RawCounts.xlsx : RIBO_Rpl10_016


title: scRNAseq_8cell_R49_3


title: Cistr KO male mouse cerebellum animal2 lane3

description:
PM_mKO_Cistr_M2_cerebellum_S5_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Cistr KO male mouse cerebellum animal2 lane2

description:
PM_mKO_Cistr_M2_cerebellum_S38_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: scRNAseq_8cell_R49_2


title: EZHIP_WT_Epi_RNAseq_rep1

description:
Library name: Sample 57
EZHIP_KO_Epi_Exe_FPKM.txt


title: RIBOseq Ba/F3 Rpl5 +/- #68

description:
Library name: RIBO_Rpl5_015
ColName in RawCounts.xlsx : RIBO_Rpl5_015


title: Cistr KO male mouse cerebellum animal2 lane1

description:
PM_mKO_Cistr_M2_cerebellum_S38_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: EZHIP_mKO_E425_RNAseq_rep4

description:
Library name: Sample 56
EZHIP_KO_E4.25_FPKM.txt

source_name: mouse pre-implantation embryos, E4.25

value: mouse pre-implantation embryos, E4.25


title: Cistr KO male mouse cerebellum animal1 lane1

description:
PM_mKO_Cistr_M1_cerebellum_S32_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: scRNAseq_8cell_R49_1


title: scRNAseq_8cell_R48_8


title: RIBOseq Ba/F3 Rpl5 +/- #80

description:
Library name: RIBO_Rpl5_013
ColName in RawCounts.xlsx : RIBO_Rpl5_013


title: Cistr KO male mouse cerebellum animal1 lane2

description:
PM_mKO_Cistr_M1_cerebellum_S32_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: RIBOseq Ba/F3 Rpl5 +/- #76

description:
Library name: RIBO_Rpl5_014
ColName in RawCounts.xlsx : RIBO_Rpl5_014


title: EZHIP_mKO_E425_RNAseq_rep3

description:
Library name: Sample 55
EZHIP_KO_E4.25_FPKM.txt


title: scRNAseq_8cell_R48_7


title: RIBOseq Ba/F3 Rpl22 +/- #16

description:
Library name: RIBO_Rpl22het_011
ColName in RawCounts.xlsx : RIBO_Rpl22het_011


title: Cistr KO female mouse cerebellum animal3 lane1

description:
PM_mKO_Cistr_F3_cerebellum_S26_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: Cistr-/- female


title: scRNAseq_8cell_R48_6

value: Blastomere


title: RIBOseq Ba/F3 Rpl22 +/- #60

description:
Library name: RIBO_Rpl22het_012
ColName in RawCounts.xlsx : RIBO_Rpl22het_012


title: EZHIP_mKO_E425_RNAseq_rep2

description:
Library name: Sample 52
EZHIP_KO_E4.25_FPKM.txt


title: RIBOseq Ba/F3 Rpl22 +/- #13

description:
Library name: RIBO_Rpl22het_010
ColName in RawCounts.xlsx : RIBO_Rpl22het_010


title: Cistr KO female mouse cerebellum animal3 lane2

description:
PM_mKO_Cistr_F3_cerebellum_S26_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: EZHIP_WT_E425_RNAseq_rep4

description:
Library name: Sample 54
EZHIP_KO_E4.25_FPKM.txt


title: EZHIP_WT_Exe_RNAseq_rep1

description:
Library name: Sample 58
EZHIP_KO_Epi_Exe_FPKM.txt


title: EZHIP_mKO_E425_RNAseq_rep1

description:
Library name: Sample 51
EZHIP_KO_E4.25_FPKM.txt


title: scRNAseq_8cell_R48_5


title: scRNAseq_8cell_R48_4


title: EZHIP_WT_E425_RNAseq_rep3

description:
Library name: Sample 53
EZHIP_KO_E4.25_FPKM.txt


title: Cistr KO female mouse cerebellum animal2 lane2

description:
PM_mKO_Cistr_F2_cerebellum_S8_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: EZHIP_mHet_E425_RNAseq_rep2

description:
Library name: Sample 50
EZHIP_KO_E4.25_FPKM.txt


title: scRNAseq_8cell_R48_3


title: RIBOseq Ba/F3 Rps15 P131S/P131S #20

description:
Library name: RIBO_Rps15P131S_009
ColName in RawCounts.xlsx : RIBO_Rps15P131S_009


title: RIBOseq Ba/F3 Rps15 P131S/P131S #63

description:
Library name: RIBO_Rps15P131S_008
ColName in RawCounts.xlsx : RIBO_Rps15P131S_008


title: Cistr KO female mouse cerebellum animal1 lane2

description:
PM_mKO_Cistr_F1_cerebellum_S2_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: scRNAseq_8cell_R48_2


title: RIBOseq Ba/F3 Rps15 P131S/P131S #24

description:
Library name: RIBO_Rps15P131S_007
ColName in RawCounts.xlsx : RIBO_Rps15P131S_007


title: Cistr KO female mouse cerebellum animal1 lane1

description:
PM_mKO_Cistr_F1_cerebellum_S2_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: EZHIP_WT_E425_RNAseq_rep2

description:
Library name: Sample 48
EZHIP_KO_E4.25_FPKM.txt


title: scRNAseq_8cell_R48_1


title: EZHIP_WT_E425_RNAseq_rep1

description:
Library name: Sample 47
EZHIP_KO_E4.25_FPKM.txt


title: RIBOseq Ba/F3 Rpl11 +/- #22

description:
Library name: RIBO_Rpl11_006
ColName in RawCounts.xlsx : RIBO_Rpl11_006


title: WT male mouse cerebellum animal2

description:
PM_mWT_Cistr_M5_cerebellum_S614_L004
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: WT male


title: scRNAseq_8cell_R46_8


title: RIBOseq Ba/F3 Rpl11 +/- #414

description:
Library name: RIBO_Rpl11_005
ColName in RawCounts.xlsx : RIBO_Rpl11_005


title: WT male mouse cerebellum animal1

description:
PM_mWT_Cistr_M4_cerebellum_S593_L004
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: scRNAseq_8cell_R46_7


title: EZHIP_mKO_Bl_RNAseq_rep7

description:
Library name: Sample 46
EZHIP_KO_E3.5_2_FPKM.txt

source_name: mouse pre-implantation embryos, E3.5

value: mouse pre-implantation embryos, E3.5

value: Ezhip mKO


title: Cistr KO female mouse cerebellum animal2 lane1

description:
PM_mKO_Cistr_F2_cerebellum_S8_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: scRNAseq_8cell_R46_6


title: EZHIP_mKO_Bl_RNAseq_rep5

description:
Library name: Sample 44
EZHIP_KO_E3.5_2_FPKM.txt


title: RIBOseq Ba/F3 Rpl22 -/- #776

description:
Library name: RIBO_Rpl22hom_003
ColName in RawCounts.xlsx : RIBO_Rpl22hom_003


title: RIBOseq Ba/F3 Rpl11 +/- #406

description:
Library name: RIBO_Rpl11_004
ColName in RawCounts.xlsx : RIBO_Rpl11_004


title: WT female mouse cerebellum animal1

description:
PM_mWT_Cistr_F4_cerebellum_S623_L004
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: EZHIP_mKO_Bl_RNAseq_rep4

description:
Library name: Sample 43
EZHIP_KO_E3.5_2_FPKM.txt


title: scRNAseq_8cell_R46_5


title: scRNAseq_8cell_R46_4


title: RIBOseq Ba/F3 Rpl22 -/- #649

description:
Library name: RIBO_Rpl22hom
ColName in RawCounts.xlsx : RIBO_Rpl22hom_001


title: EZHIP_mHet_E425_RNAseq_rep1

description:
Library name: Sample 49
EZHIP_KO_E4.25_FPKM.txt


title: RIBOseq Ba/F3 Rpl22 -/- #30

description:
Library name: RIBO_Rpl22hom_002
ColName in RawCounts.xlsx : RIBO_Rpl22hom_002


title: Cistr KO male mouse blood animal4

description:
PM_mKO_Cistr_M4_blood_S604_L004
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

source_name: blood

value: blood


title: EZHIP_mKO_Bl_RNAseq_rep3

description:
Library name: Sample 42
EZHIP_KO_E3.5_2_FPKM.txt


title: EZHIP_mHet_Bl_RNAseq_rep7

description:
Library name: Sample 41
EZHIP_KO_E3.5_2_FPKM.txt


title: Cistr KO male mouse blood animal3 lane2

description:
PM_mKO_Cistr_M3_blood_S48_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: scRNAseq_8cell_R46_2


title: KPCA_FSTKO_hFSTL3, omental tumor, scRNAseq

first: Maeva

middle: general

last: Chauvin

address: 55 fruit st

institute: general hosp corp d/b/a mass general hosp

description:
Library name: Sample 2
10X genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
Omental tumors (KPCA_FSTKO, KPCA_FSTKO_hFSTL3) were freshly collected from C57Bl6J mice and dissociated by incubating tumor pieces with a digestion buffer (DMEM 10% supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) at 37 °C for 30 min. The resulting mixture was transferred into a dissociation tube and processed using the MacMachine device to initiate the dissociation process. Cells were then filtered through a 70 µm strainer, washed, and resuspended in PBS. Single-cell RNA sequencing (scRNAseq) was performed on samples with >70% cell viability.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, tumor cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Tumor

value: KPCA

value: Fallopian tube epithelial cells

value: total RNA


title: KPCA_FSTKO, omental tumor, scRNAseq

description:
Library name: Sample 1
10X genomics


title: scRNAseq_8cell_R46_3

source_name: Blastomere


title: EZHIP_mHet_Bl_RNAseq_rep6

description:
Library name: Sample 40
EZHIP_KO_E3.5_2_FPKM.txt

value: Ezhip mHet


title: Cistr KO male mouse blood animal3 lane1

description:
PM_mKO_Cistr_M3_blood_S48_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: scRNAseq_8cell_R46_1


title: EZHIP_mKO_Bl_RNAseq_rep6

description:
Library name: Sample 45
EZHIP_KO_E3.5_2_FPKM.txt


title: Cistr KO male mouse blood animal2 lane2

description:
PM_mKO_Cistr_M2_blood_S42_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Proton, organoids, day 11

city: Groningen

first: Davide

last: Cinat

address: Hanzeplein 1

institute: University Medical Center Groningen

description: 10x Genomics

data_processing:
Processing and filtering was done using the CellRanger software v7.0.1.
Assembly: mm10
Supplementary files format and content: For all conditions filtered features, barcodes sequences and matrix files are provided.

source_name: Submandibular salivary gland

growth_protocol: Organoids derived from 4 different animals were cultured in Matrigel in WRY medium (DMEM/F12, Pen/Strep antibiotics, glutamax 2 mM, EGF 20 ng/ml, FGF2 20 ng/mL, N2 1x, insulin 10 µg/mL, dexamethasone 1  µM, Y27632 10 µM, 10% R-spondin1-conditioned medium and 50% Wnt3a-conditioned medium). All conditions were kept in culture under the same conditions (at 37°C and 5% CO2) until the day of the experiment.

extract_protocol:
Organoids were collected and dissocited into single cells using 0.05% trypsin EDTA for 10 minutes. Cells were then washed with PBS/BSA 0.2% and resuspended with 500 µL PBS/BSA 0.2% and propidium iodide (PI). 45.000 PI negative cells/sample were sorted using a Moflo Astrios sorter and immediately leaded into the 10x Genomics chip.
For the GEM generation and barcoding, immediately after sorting samples were loaded on the Chromium Next GEM Chip G and ran in the Chromium Controller. The preparation of the library was performed by using the 10X Chromoum Next GEM Single Cell 3' kit T Set A following the manufacturer`s protocol step by step.

treatment_protocol: Organoids were irradiated with either 7 Gy photons or 7 Gy protons (plateau) at day 5. Organoid media of control, photon and proton irradiated samples was refreshed after irradiation. Organoids were collected at day 11. All experiments from all the conditions were carried out on the same day.

value: Submandibular salivary gland

tag: age

value: 8-12 weeks old

value: Salivary gland cells derived from organoids

value: Proton irradiated (7 Gy)


title: Photon, organoids, day 11

description: 10x Genomics

value: Photon irradiateed (7 Gy)


title: WT female mouse cerebellum animal2

description:
PM_mWT_Cistr_F5_cerebellum_S630_L004
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: cerebellum

value: WT female


title: EZHIP_mHet_Bl_RNAseq_rep5

description:
Library name: Sample 39
EZHIP_KO_E3.5_2_FPKM.txt


title: EZHIP_mHet_Bl_RNAseq_rep4

description:
Library name: Sample 38
EZHIP_KO_E3.5_2_FPKM.txt


title: Cistr KO male mouse blood animal5

description:
PM_mKO_Cistr_M5_blood_S611_L004
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: Cistr-/- male


title: scRNAseq_8cell_R45_7

value: Blastomere


title: Control, organoids, day 11

description: 10x Genomics

value: Non-irradiated


title: Cistr KO male mouse blood animal2 lane1

description:
PM_mKO_Cistr_M2_blood_S42_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: scRNAseq_8cell_R45_8


title: EZHIP_mHet_Bl_RNAseq_rep3

description:
Library name: Sample 37
EZHIP_KO_E3.5_2_FPKM.txt

value: mouse pre-implantation embryos, E3.5


title: Cistr KO male mouse blood animal1 lane2

description:
PM_mKO_Cistr_M1_blood_S36_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: blood


title: scRNAseq_8cell_R45_6


title: scRNAseq_8cell_R45_5


title: Cistr KO male mouse blood animal1 lane1

description:
PM_mKO_Cistr_M1_blood_S36_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Cistr KO female mouse blood animal3

description:
PM_mKO_Cistr_F5_blood_S649_L004
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: Cistr-/- female


title: 15 Gy, protons, organoids, 6 days, mouse 2

description: Lexogen

data_processing:
For the alignment of the fastq files the mouse genome GRCm39 was used. The gene counts per sample were detected with the QuantSeq 3' mRNA-seq Integrated Data Analysis Pipeline on the BlueBee Genomics Platform provided by Lexogen with default settings. Rstudion v4.1.3 was used for downstream analysis and for the generation of CPM files. The R package edgeR was used for normalization and identification of differentially expressed genes.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files including the raw counts and tab-delimited text files including the CPM for all timepoints, replicates and doses are provided.

growth_protocol: Organoids from all animals and conditions were cultured in Matrigel in WRY medium (DMEM/F12, Pen/Strep antibiotics, glutamax 2 mM, EGF 20 ng/ml, FGF2 20 ng/mL, N2 1x, insulin 10 µg/mL, dexamethasone 1  µM, Y27632 10 µM, 10% R-spondin1-conditioned medium and 50% Wnt3a-conditioned medium). All conditions were kept in culture at 37°C and 5% CO2 until the day of the experiment.

extract_protocol:
For the cDNA library preparation, total RNA was extracted from organoids at 2 and 6 days post irradiation using Rneasy Mini Kit according to the manufacturer`s instructions and its quality was determined using High Sensitivity RNA ScreenTapes on an Agilent 2100 Bioanalyzer. 100 ng of RNA was used as an input for all samples.
100 ng of highly intact RNA (RIN values > 9) was processed for the cDNA library preparation using the Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit following the manufacturers protocol.

treatment_protocol: Organoids were irradiated with either 4, 7 and 15 Gy photons or 4, 7 and 15 Gy (plateau) protons at day 5. Organoid media of all conditions was refreshed after irradiation. Organoids were collected at either day 2 (48 hr) or day 6 post irradiation. Since photon and proton irradiations were performed on different days, each irradiation type and timepoint has its own control (non-irradiated).

value: Proton-irradiated 15 Gy


title: EZHIP_WT_Bl_RNAseq_rep7

description:
Library name: Sample 36
EZHIP_KO_E3.5_2_FPKM.txt

value: wide type


title: Cistr KO female mouse blood animal2

description:
PM_mKO_Cistr_F4_blood_S642_L004
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: EZHIP_WT_Bl_RNAseq_rep6

description:
Library name: Sample 35
EZHIP_KO_E3.5_2_FPKM.txt


title: scRNAseq_8cell_R45_4


title: EZHIP_WT_Bl_RNAseq_rep5

description:
Library name: Sample 34
EZHIP_KO_E3.5_2_FPKM.txt


title: scRNAseq_8cell_R45_3


title: EZHIP_WT_Bl_RNAseq_rep4

description:
Library name: Sample 33
EZHIP_KO_E3.5_2_FPKM.txt


title: 7 Gy, protons, organoids, 6 days, mouse 3

description: Lexogen

value: Proton-irradiated 7 Gy


title: scRNAseq_8cell_R45_2


title: scRNAseq_8cell_R45_1


title: 7 Gy, protons, organoids, 6 days, mouse 2

description: Lexogen


title: 15 Gy, protons, organoids, 6 days, mouse 3

description: Lexogen


title: EZHIP_WT_Bl_RNAseq_rep3

description:
Library name: Sample 32
EZHIP_KO_E3.5_2_FPKM.txt


title: Cistr KO female mouse blood animal1 lane1

description:
PM_mKO_Cistr_F3_blood_S30_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: 7 Gy, protons, organoids, 6 days, mouse 1

description: Lexogen


title: WT male mouse blood animal2 lane2

description:
PM_mWT_Cistr_M3_blood_S72_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: WT male


title: EZHIP_mKO_Bl_RNAseq_rep2

description:
Library name: Sample 31
EZHIP_KO_E3.5_1_FPKM.txt

value: Ezhip mKO


title: scRNAseq_8cell_R43_8


title: 15 Gy, protons, organoids, 6 days, mouse 1

description: Lexogen

value: Submandibular salivary gland

value: 8-12 weeks old


title: 4 Gy, protons, organoids, 6 days, mouse 2

description: Lexogen

value: Salivary gland cells derived from organoids

value: Proton-irradiated 4 Gy


title: WT male mouse blood animal1 lane2

description:
PM_mWT_Cistr_M2_blood_S66_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: EZHIP_mHet_Bl_RNAseq_rep1

description:
Library name: Sample 28
EZHIP_KO_E3.5_1_FPKM.txt

value: Ezhip mHet


title: EZHIP_mKO_Bl_RNAseq_rep1

description:
Library name: Sample 30
EZHIP_KO_E3.5_1_FPKM.txt


title: scRNAseq_8cell_R43_7


title: 4 Gy, protons, organoids, 6 days, mouse 1

description: Lexogen


title: Cistr KO female mouse blood animal1 lane2

description:
PM_mKO_Cistr_F3_blood_S30_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: EZHIP_WT_Bl_RNAseq_rep2

description:
Library name: Sample 27
EZHIP_KO_E3.5_1_FPKM.txt