title: Suv39h1, Suv39h2 double knock-out, RNA-Seq replicate 2

data_processing:
Base calling and quality scoring was performed by Illumina Real-Time Analysis (v2) software. FASTQ file generation and de-multiplexing was performed by bcl2fastq conversion software (v2.15.0.4).
Reads were aligned to the mouse genome by Rsubread version 1.24.0
Read counts were summarized by Ensembl Gene ID using the Rsubread's featureCounts function and Gencode annotation vM22.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files (tsv). Columns represent Ensembl Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene. The supplementary file `Counts_all_samples.txt` provides genewise counts for all samples in one file.

extract_protocol:
Single cell suspensions were generated from mouse thymus by mechanical homogenization following by red blood cell lysis (156mM NH4Cl, 11.9mM NaHCO3, 97μM EDTA). DP thymocyte cells were then flow-cytometrically sorted as CD45.2+CD19-CD4+CD8+ cells on a BD FACSAria™ cell sorter.
RNA was extracted using a Qiagen Rneasy Plus Kit.
Illumina TruSeq RNA Library Prep

tag: background strain

tag: gender

value: Male

value: CD4+CD8+ double positive thymocytes


title: NK_atRA_7days_rep2

status: Public on Mar 27 2024

type: RNA

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

description: Gene expression data after treatment

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 15, from SAS. Gene expression profiling was performed using arrays of Mouse Clariom D from Thermo Fischer Scientific. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: splenic NK cells, atRA and IL-2, 7days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: NK cells sorted as CD45+CD3-NK1.1+NKp46+TRAIL-CD200R- were cultured in RPMI-1640 medium supplemented with 10% FCS, 2 mM glutamine, 1% non-essential amino acids, 1 mM sodium pyruvate, 100 U/ml Penicillin/Streptomycin, 50 µM β-mercaptoethanol and 1700 U/ml recombinant human IL-2.

extract_protocol: RNA extraction was performed using RNeasy® Mini Kit (Qiagen). DNA was removed using TURBO DNA‐free™ kit (ThermoFisher)

treatment_protocol: NK cells were treated with 1uM all-trans retinoic acid or DMSO 0.01% v/v (as solvent control) for 7 days

tag: age

value: adult

tag: Sex

value: female+male

tag: genotype

value: Rag 2 ko

tag: strain

tag: tissue

value: spleen

tag: cell type

value: sorted NK cells


title: PT-00267366_NT_AA

type: genomic

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

country: USA

institute: ROSWELL PARK CANCER INSTITUTE

hyb_protocol: Illumina Infinium HD Methylation

scan_protocol: Illumina iScan Control Software

data_processing:
Illumina GenomeStudio V1
m450K_Proc_Funnorm.tsv (Normalized Beta values from minfi’s preprocessFunnorm)
m450K_MatrixSignal.tsv (Unmethylated and methylated signal intensities)

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Adjacent Tumor

label_protocol: Illumina Infinium HD Methylation

extract_protocol: QIAamp DNA mini Kit

value: prostate

tag: tissue region

value: Adjacent Tumor

tag: race

value: AA


title: Suv39h1, Suv39h2 double knock-out, RNA-Seq replicate 1

type: SRA

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

library_source: transcriptomic

molecule: polyA RNA

source_name: Thymus


title: P1_OSVZ_LS, rep1

city: Sant Joan d’Alacant

first: Lucia

last: Del-Valle-Anton

address: Av. Santiago Ramón y Cajal s/n

country: Spain

institute: Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández

description: 10x Genomics Single Cell 3’ Reagent Kit v3

library_source: transcriptomic single cell

data_processing:
Genome alignment: Ferret gene annotation from Johnson et al., 2018, comprising Ensembl Mustela putorius furo annotation expanded using bulk RNAseq data, was further enriched with NCBI’s RefSeq mitochondrial genes from Mustela putorius furo annotation release 101 (Accession No. NC_020638.1), and transformed from a general feature format (GFF3) into gene transfer format (GTF) using Cufflinks-2.2.1. Johnson’s GenBank accessions were matched to RefSeq accessions through cthreepo-0.1.1 and gene_name and transcript_name attibutes were added to GTF rows where they were missing by appending gene_id and transcript_id entries. scRNA-seq reads were mapped to NCBI ferret reference genome (MusPutFur1.0/GCF_000215625.1) and Unique Molecular Identifiers (UMIs) were collapsed by STAR-2.7.3a adapting the parameters to v2 or v3 10x chemistry, depending on the sample.
Cell barcode filtering: Count matrices from each sample were loaded and cell-containing droplets were identified and distinguished from empty droplets retaining ambient RNA by DropletsUtils-1.6.1. Increased niters argument to 100,000 and decreased false discovery rate (FDR) to 0.1% were applied to all samples. A lower bound of 80 was implemented for replicates P1_VZ_LS_rep1 and E34_VZ_SG_rep1. Mitochondrial genes were removed before cell calling for replicates E34_VZ_LS_rep2, P1_VZ_SG_rep2, P1_VZ_LS_rep3, P1_OSVZ_SG_rep1 and P1_OSVZ_LS_rep1 to promote potential unhealthy cell removal. The automatic retention of droplets with large total UMI counts (determined by the knee point) was disabled for replicate P1_VZ_LS_rep3.
Assembly: MusPutFur1.0/GCF_000215625.1
Supplementary files format and content: Tab-separated values files from cell barcodes and genes (barcodes.tsv, genes.tsv) and matrix file (matrix.mtx) for each sample after genome alignment and cell barcode filtering.

organism: Mustela putorius

source_name: cerebral cortex

extract_protocol:
After microdissecting individual germinal zones from living cortical slices, tissue pieces were enzymatically dissociated for 20-30’ at 37ºC using MACS Neural Tissue Dissociation Kit P (Miltenyi Biotec) according to the manufacturer’s instructions. Cells were mechanically suspended using wide-tipped, fire-polished Pasteur pipettes (Fisher Scientific) followed by P1000 pipettes (Gilson). Cell suspensions were filtered to 2ml DNA LoBind tubes (Eppendorf) through 40 μm PluriStrainer Mini (PluriSelect) pre-wet with Hank’s Balanced Salt Solution (1X) without CaCl2/MgCl2/pH indicator (HBSS, Gibco). Cells were centrifuged (Spectrafuge 24D, Labnet) twice for 5min at 1000 rpm, and cell pellets were resuspended in 40μl of Phosphate Buffered Saline ph7.4 (1X) without CaCl2/MgCl2 (PBS, Gibco) containing 0.04% Bovine Serum Albumin (BSA, Sigma-Aldrich). Cell concentration from homogeneous suspensions was measured, and cell death was estimated twice using trypan blue 0.4% stain (Thermo Fisher Scientific): first on an automatic cell counter (Countess II FL, Thermo Fisher Scientific) and second using a hemocytometer (BLAUBRAND Neubauer, BRAND) on an inverted microscope (Leica DM IL). Debris-free suspensions with cell viability over 90% were used immediately for single-cell isolation.
Cell suspensions from 400 to 1200 cells/μl were loaded into the Chromium Single Cell Controller (10x Genomics) to target a recovery of 7k to 10k cells/sample. Single-cell Gel bead-in-EMulsions (GEMs) were generated, cells were lysed, and the released RNAs were retrotranscribed (RT) and barcoded inside the GEMs according to Single Cell 3’ Reagent Kits v2 and v3 (10x Genomics) protocols. Following GEMs break, barcoded cDNAs were pooled and cleaned from leftover RT reagents using DynaBeads MyOne Silane Beads (Invitrogen) and amplified (8 to 14 cDNA amplification cycles) following the Single Cell 3’ Reagent Kits v2 and v3 (10x Genomics) protocols. Enzymatic fragmentation, size selection and cleanup with SPRIselect Reagent kit (Beckman Coulter) were followed by library construction (total sample index cycles from 12 to 16 cycles), consistent with standard Illumina sequencing constructs and performed in line with Single Cell 3’ Reagent Kits v2 and v3 (10x Genomics) protocols. cDNA and library concentration and quality check were assessed using Bioanalyzer High Sensitivity DNA Kit (Agilent) and 2100 Expert Software (Agilent).

value: cerebral cortex

tag: litter

tag: region

value: lateral sulcus

tag: germinal zone

value: outer subventricular zone

tag: developmental stage

value: postnatal day 1

tag: sequencing flowcell


title: P1_OSVZ_LS, rep2

description: 10x Genomics Single Cell 3’ Reagent Kit v2


title: Control, RNA-Seq replicate 3


title: Ovarian granulosa cells-DOR_rep2

city: Jinan

first: li

last: dong

address: No. 42 Wen Hua Xi Road

country: China

institute: shandong university of traditional Chinese medcine

data_processing:
Illumina Casava1.7 software used for basecalling.
Cutadapt (v1.9) was used to remove the reads that contained adapter contamination, low quality bases and undetermined bases.
The sequence quality was verified using FastQC (v0.10.1).
The valid reads were mapped to the human reference genome (GRCh38) using HISAT software (v2.0.4).
The mapped reads of each sample were assembled using StringTie (v1.3.0) with default parameters. Then, all transcriptomes from samples were merged to reconstruct a comprehensive transcriptome using gffcompare.
After the final transcriptome was generated, StringTie was used to perform expression level for mRNAs by calculating fragments per kilobase of exon model per million mapped reads (FPKM).
Genome_build: Human reference genome (GRCh38)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Ovarian granulosa cells

extract_protocol:
Total RNA was isolated and purified using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity of each sample were analysis of Agilent Bioanalyzer 2100 and RNA Nano1000 Assay Kit with RIN number >7.0. Approximately 5 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ rRNA Removal Kit (Illumina, San Diego, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ovarian

tag: treatment

value: untreated


title: Ovarian granulosa cells-DOR_rep3


title: P1_OSVZ_SG, rep3

value: splenial gyrus


title: Ovarian granulosa cells-DOR_rep4


title: NK_atRA_7days_rep1

description: Gene expression data after treatment


title: NK_DMSO_7days_rep1

description: Gene expression data after treatment

source_name: splenic NK cells, DMSO and IL-2, 7days


title: PT-00282384_NT_AA


title: Control, RNA-Seq replicate 2

value: Male


title: Ovarian granulosa cells-NOR_rep1


title: P1_OSVZ_SG, rep2


title: PT-00267366_T_AA

source_name: Tumor

value: Tumor


title: Ovarian granulosa cells-DOR_rep1


title: Suv39h1, Suv39h2 double knock-out, RNA-Seq replicate 3

value: CD4+CD8+ double positive thymocytes


title: PT-00282384_T_AA


title: Control, RNA-Seq replicate 1


title: siRPL24_Input_01

city: New Haven

first: Karla

last: Neugebauer

state: Connecticut

address: 333 Cedar St

institute: Yale

library_source: genomic

data_processing:
FASTQC quality check
Reads trimmed with cutadapt
Reads aligned to reference genome hg38 using Bowtie2
Peaks called with MACS2, using input as a noIP control
Assembly: hg_38
Supplementary files format and content: pileup tracks in .bigWig format
Supplementary files format and content: peaks .narrowPeak

source_name: HeLa Kyoto

growth_protocol: Cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum and pennicilin/streptomycin antibiotics at 37˚C with 5% CO2.

extract_protocol: Cells were crosslinked with 1% formaldehyde for 10 min at room temperature. After cell lysis, DNA was sheared to fragments of ~200bp and lysate was cleared by centrifugation. 25% of the supernatant was used as input and the remaiining part was used to precipitate coilin with Dynabeads Protein G coupled to goat anti-EGFP antibody. After stringent washing, the DNA was eluted and de-crosslinked by Proteinase K treatment. DNA fragments were purified by phenol-chlorophorm extraction.

treatment_protocol: HeLa cells were reverse transfected with ON-Target Plus siRNA mix in SMARTPool format and incubated for 72h before experimental assays.

tag: chip antibody

value: RPL24 siRNA, 72 hours

tag: sirna

value: L-011144-02, Horizon Discovery, ONTarget Plus


title: T24-ko2-IP

city: Nanning

first: Zengnan

last: Mo

state: Guangxi

address: Zhongshan Street

department: Center for Genomics and Personalized Medicine

institute: Guangxi Medical University

data_processing:
150 bp paired-end reads were mapped to the reference human genome build GRCh38/hg38 by using Bowtie2.
Only unique mapping paired reads were sorted using SAMtools and kept for subsequent analysis.
Peaks of each samples and differential methylation peak were called  using the exomePeak R-package.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: peak files

extract_protocol:
RNA fragments were incubated with anti-N6-methyladenosine (m6A) antibodies (Sigma-Aldrich, Burlington, USA) inimmunoprecipitation (IP) buffer for 2 h at 4℃. The samples were then washed with low-salt precipitation buffer and high-salt buffer thrice continuously. RNA was extracted using a phenol-chloroform lysate to obtain a purified product.
The purified RNA was collected for the generation of an RNA-seq library with NEBNext R Ultra™ RNA Library Prep Kit (New England Biolabs, MA, USA). The quality of the library was done using Bioptic Qsep100 analyzer and sequencing was done using NovaSeq's high-throughput sequencing platform

tag: cell line

value: IGF2BP3 knockout

tag: rip antibody


title: Ovarian granulosa cells-DOR_rep5

tag: age


title: P1_OSVZ_SG, rep1


title: Suv39h1, Suv39h2 double knock-out, replicate 2

data_processing:
Reads pairs from each sample were aligned to the mouse genome and counted into 50 kB bin pairs using the R package diffHic v1.9.1.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files give the number of reads supporting each interaction, where an interaction corresponds to a pair of 50 kB bins. The .mtx files are space-delimited text files in Matrix Market Exchange format with integer entries. The first two columns give the indices of the two interacting genomic bins and the third column gives the read count. Bin pairs with no reads are omitted. The indices correspond to rows of the BED format supplementary file GenomicRegions.bed.gz. The processed data files can be read into R using the readMTX2IntSet function of the diffHic package or the readMM function of the Matrix package.

extract_protocol:
Cells were fixed with formaldehyde as described by Rao et al (Cell 2014; PMID: 25497547).
In situ Hi-C was performed as described by Rao et al (Cell 2014; PMID: 25497547). In situ Hi-C libraries were sequenced on an Illumina NextSeq 500 to produce paired-end 81bp reads.

tag: genotype

tag: gender

tag: background strain


title: Input-wt

city: Harbin

first: Changzhu

last: Li

address: Department of Pharmacology (State Key Laboratory of Frigid Zone Cardiovascular Disease, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy

institute: Harbin Medical University

data_processing:
Illumina Casava software used for basecalling.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score >30, using Trimmomatic v0.36, discarding reads left with <20 bp.
ChIP-seq reads were aligned to the UCSC GRCm38 genome using Bowtie version 2.1.0. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million,  rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value<=0.01.
Assembly: GRCm38
Supplementary files format and content: bigWig,norrowPeak

source_name: heart

extract_protocol:
Cell Signaling SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads) #9005 kit was used. Cardiac tissue was cross-linked with paraformaldehyde, and DNA was digested enzymatically to a length of approximately 150 to 900 bp. 1μg of antibody was used for chromatin immunoprecipitation, and purified DNA was obtained by centrifugal column after enzymatic hydrolysis.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: heart

value: Wild-type

value: 2-week-old,hearts from at least 3 mice


title: P1_VZ_LS, rep3

value: ventricular zone


title: T24-ko1-IP

value: anti-N6-methyladenosine (m6A) antibodies (Sigma-Aldrich, Burlington, USA)


title: Suv39h1, Suv39h2 double knock-out, replicate 1

tag: cell type


title: T24-2-IP

value: control


title: Control, replicate 2


title: Input-cko

value: CXXC1 null


title: P1_VZ_LS, rep2

value: cerebral cortex

value: lateral sulcus

value: postnatal day 1


title: P1_VZ_LS, rep1


title: T24-1-IP


title: Suv39h1, Suv39h2 double knock-out LaminB1 ChIP replicate 2

data_processing:
The replicates FASTQ files were merged, then reads were aligned to the mouse genome (mm10) with Rsubread.
Bam files were sorted with Rsamtools and duplicate reads were removed with MarkDuplicates from Picard tools.
WCE samples were down sampled to the size of the ChIP libraries (~53 million reads) using DownsampleSam from Picard tools.
The Enriched Domain Detector (EDD) tool (https://github.com/CollasLab/edd) was used to call LADs on the bam files using the WCE to the corresponding ChIP (WT: gap penalty 4.79 and bin size 6 kbp, KO: gap penalty 9.1 and bin size 8 kbp). This produced two BED files of peaks, one or control mice and one the DKO mice.
Genome_build: mm10
Supplementary_files_format_and_content: Bed format file containing LADs called by EDD (a tab-delimited text file specifying genomic regions by chromosome name, start position, end position).

extract_protocol:
Flow cytometrically sorted DP thymocyte cells (CD45.2+CD19-CD4+CD8+) were fixed in 1% formaldehyde. Chromatin was Mnase digested then immunoprecipitated using anti-LaminB1 antibody. Chromatin was reverse cross-linked and purified using Zymo ChIP clean and concentrator kit.
Libraries were prepared using Illumina TruSeq DNA kit. Libraries were sequenced on an Illumina NextSeq 500 to produce paired-end 81bp reads.


title: H3k4me3-wt


title: P1_VZ_SG, rep2

value: splenial gyrus


title: Control, replicate 1

value: Male


title: H3K4me3-cko


title: T24-ko1-input


title: Suv39h1, Suv39h2 double knock-out LaminB1 ChIP replicate 1


title: P1_VZ_SG, rep3


title: T24-2-input


title: Suv39h1, Suv39h2 double knock-out whole cell extract replicate 2


title: heart, WT2

description:
fpkm.anno.txt
total_fpkm.txt

data_processing:
Illumina Casava software used for basecalling.
（1）Remove adapter polluted reads (remove reads contain adapter more than 5bp. For paired-end sequencing, both reads will be filtered if either end is polluted )
（2）Remove low-quality reads (low-quality reads refer to reads in which more than 15% bases with base calling quality Q≤19. For paired-end sequencing, both reads will be filtered if either end is low-quality).
（3）Remove reads which contain N higher than 5% (For paired-end sequencing, both reads will be filtered if either end has N beyond the offset 5%).
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
DESeq2 was designed for differential gene expression analysis between two samples with biological replicates. Genes with P<0.05 and |log2_ratio|>0.5 are identified as differentially expressed genes.
Assembly: GRCm38
Supplementary files format and content: fpkm.anno.txt
Supplementary files format and content: total_fpkm.txt

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the  construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: heart, WT1

description:
fpkm.anno.txt
total_fpkm.txt


title: E34_VZ_LS, rep3

value: embryonic day 34

value: BCDPYRANXX


title: Suv39h1, Suv39h2 double knock-out whole cell extract replicate 1

value: CD4+CD8+ double positive thymocytes


title: T24-1-input


title: heart, CKO3

description:
fpkm.anno.txt
total_fpkm.txt


title: E34_VZ_LS, rep2


title: T24-ko2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human genome (hg38) using the CLC Biomedical Genomics Workbench 4 (QIAGEN Bioinformatics).
The read numbers mapped of each gene was counted and Reads Per Kilobase of exon model per Million mapped reads,(RPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene by using the CLC Biomedical Genomics Workbench 4 (QIAGEN Bioinformatics).
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample.

extract_protocol:
Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions.
The construction of RNA-seq library was based on the protocol of the IlluminaTruSeq RNA Sample Preparation Kit (illumina)


title: Control LaminB1 ChIP replicate 2


title: heart, CKO2

description:
fpkm.anno.txt
total_fpkm.txt


title: T24-ko1


title: Control LaminB1 ChIP replicate 1


title: T24-ko2-input


title: E34_VZ_LS, rep1


title: heart, WT3

description:
fpkm.anno.txt
total_fpkm.txt


title: heart, CKO1

description:
fpkm.anno.txt
total_fpkm.txt


title: E34_VZ_SG, rep3


title: E34_VZ_SG, rep2


title: T24-2


title: Control whole cell extract replicate 1


title: Control whole cell extract replicate 2


title: T24-1


title: E34_VZ_SG, rep1


title: P1_VZ_SG, rep1


title: RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia 12

status: Public on Mar 26 2024

city: Göttingen

first: Lalit

last: Kaurani

address: Von-Siebold-Straße 3A

institute: DZNE-Göttingen

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia.txt
PNCPMNC6_mm_rna_sr_kauranil_B_6_S31_L005_R1_001.fastq

data_processing:
The sequencing data were processed using a customized in-house software pipeline. Illumina’s conversion software bcl2fastq (v2.20.2) was employed for adapter trimming and converting the base calls in the per-cycle BCL files to the per-read FASTQ format from raw images. Quality control of raw sequencing data was carried out using FastQC (v0.11.5)(http://www.bioinformatics.babraham. ac.uk/projects/fastqc/). Reads were aligned using the STAR aligner (v2.5.2b) and read counts were generated using featureCounts (v1.5.1). The mouse genome version mm10 was utilized.
Assembly: mm10
Supplementary files format and content: RNA-sequencing from mouse mPFC region.txt; This file contains raw counts of treatment group and scramble treated group from adult mouse PFC brain region.
Supplementary files format and content: RNA-Sequencing from mouse primary microglia.txt; This file contains raw counts of treatment group and scramble treated group from primary microglia.
Supplementary files format and content: RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia.txt; This file contains raw counts of treatment group and scramble treated group from primary cortical neurons co-cultured with primary microglia.

source_name: Mouse cortical neuron + primary microglia co-culture

growth_protocol:
primary neurons were derived from mouse embryos at embryonic day 17.5 according to Animal Welfare regulations. Neurons were seeded onto poly-D-lysine-coated cell culture dishes in plating medium (DMEM media, 100U/ml Penicillin and 0,1mg/ml Streptomycin). Plating medium was replaced with maintenance medium (MEM supplemented, 2% B27 supplement (Gibco), 2mM Glutamax, 100U/ml Penicillin and 0,1mg/ml Streptomycin) 2-3 hours later and kept in a humidified incubator, 37C, 5% CO2.
primary microglia were derived from P1 mouse according to Animal Welfare regulations. In brief, newborn mice (P1 pups) were used to prepare mixed glia cultures. Cells were grown in DMEM (Thermo Fisher Scientific) with 10% FBS, 20% L929 conditioned medium and 100 U ml–1 penicillin–streptomycin (Thermo Fisher Scientific). Microglia were collected 10-12 days after cultivation by shake off, counted and plated in DMEM supplemented with 10% FBS, 20% L929 conditioned medium and 100 U ml–1 penicillin–streptomycin. The microglia were shaken off up to two times. Microglia were seeded onto poly-D-lysine-coated cell culture dishes in plating medium and kept in a humidified incubator, 37C, 5% CO2.

extract_protocol:
RNA was isolated using trizol and with Zymo RNA isolation kit.
Total RNA was used for the library preparation using the TrueSeq RNA library prep kit v2 (Illumina, USA) according to the manufacturer's protocol. 500 ng RNA was used as starting material. The quality of the libraries was assessed using the Bioanalyzer (Agilent Technologies). Library concentration was measured by Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific, USA). Multiplexed libraries were directly loaded onto a Hiseq2000 (Ilumina) with 50 bp single read setup.

treatment_protocol:
Adult mice (3-months old) PFC brain region were treated with miR-99b-5p inhibitor or scramble sequence.
Primary microglia were treated with miR-99b-5p inhibitor or scramble sequence.

value: Primary cortical neuron and Primary microglia co-culture

tag: strain

value: Microglia treated with scramble sequence and co-cultured with primary cortical neurons

tag: batch

value: Primary neurons from E17.5 and Primary microglia from P1


title: RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia 15

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia.txt
PNCPMNC12_mm_rna_sr_kauranil_B_12_S43_L007_R1_001.fastq

value: Mouse cortical neuron + primary microglia co-culture


title: RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia 14

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia.txt
PNCPMNC11_mm_rna_sr_kauranil_B_11_S42_L007_R1_001.fastq


title: RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia 13

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia.txt
PNCPMNC8_mm_rna_sr_kauranil_B_8_S36_L006_R1_001.fastq


title: RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia 10

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia.txt
PNCPMNC4_mm_rna_sr_kauranil_B_4_S27_L005_R1_001.fastq


title: RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia 7

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia.txt
PNCPM99b12_mm_rna_sr_kauranil_A_12_S44_L007_R1_001.fastq

value: Microglia treated with miR-99b-5p inhibitor and co-cultured with primary cortical neurons


title: RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia 8

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia.txt
PNCPMNC1_mm_rna_sr_kauranil_B_1_S22_L004_R1_001.fastq


title: RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia 6

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia.txt
PNCPM99b11_mm_rna_sr_kauranil_A_11_S41_L007_R1_001.fastq


title: RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia 9

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia.txt
PNCPMNC2_mm_rna_sr_kauranil_B_2_S23_L004_R1_001.fastq


title: RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia 11

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia.txt
PNCPMNC5_mm_rna_sr_kauranil_B_5_S30_L005_R1_001.fastq


title: RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia 4

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia.txt
PNCPM99b7_mm_rna_sr_kauranil_A_7_S34_L006_R1_001.fastq


title: RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia 3

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia.txt
PNCPM99b5_mm_rna_sr_kauranil_A_5_S29_L005_R1_001.fastq


title: RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia 5

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia.txt
PNCPM99b10_mm_rna_sr_kauranil_A_10_S40_L007_R1_001.fastq


title: RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia 2

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia.txt
PNCPM99b3_mm_rna_sr_kauranil_A_3_S25_L004_R1_001.fastq


title: RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia 1

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-sequencing from mouse primary cortical neurons co-culture with mouse primary microglia.txt
PNCPM99b2_mm_rna_sr_kauranil_A_2_S24_L004_R1_001.fastq


title: RNA-Sequencing from mouse primary microglia 7

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-Sequencing from mouse primary microglia.txt
PM99b4_mm_rna_sr_kauranil_T_4_S35_L006_R1_001.fastq

source_name: Mouse primary microglia culture

value: Mouse primary microglia culture

value: Primary microglia

value: miR-99b-5p inhibitor treated


title: RNA-Sequencing from mouse primary microglia 8

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-Sequencing from mouse primary microglia.txt
PM99b5_mm_rna_sr_kauranil_T_5_S38_L006_R1_001.fastq


title: RNA-Sequencing from mouse primary microglia 5

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-Sequencing from mouse primary microglia.txt
PM99b1_mm_rna_sr_kauranil_T_1_S29_L005_R1_001.fastq


title: RNA-Sequencing from mouse primary microglia 4

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-Sequencing from mouse primary microglia.txt
PMNC6_mm_rna_sr_kauranil_C_6_S40_L006_R1_001.fastq

value: Scramble treated


title: exomiRNA1

city: Seoul

first: IN HWA

last: BAE

state: --- Select One ---

address: 75 Nowon-ro, Nowon-gu

country: South Korea

institute: Korea Institute of Radiological  & Medical Sciences

description: miRNA expression

hyb_protocol: biotin-labeled sample were hybridized using GeneChip® Hybridization Oven to the Affymetrix miRNA microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the GeneChip® Scanner

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

label_protocol: 1 ug total RNA using the FlashTag™ Biotin HSR RNA Labeling Kit

growth_protocol: U251 vector and Bcl-w overexpressing cells were cultured in DMEM medium in an incubator.

extract_protocol: RNA was extracted from exosomes using the SeraMir Exosome RNA Purification Column Kit (System biosciences), following the manufacturer's instructions.

treatment_protocol: Exosomes were isolated from the conditioned media of cells using ExoQuick-TC (System biosciences), following the manufacturer's instructions.

tag: sample type

value: Exosome


title: exomiRNA2

description: miRNA expression


title: RNA-Sequencing from mouse primary microglia 3

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-Sequencing from mouse primary microglia.txt
PMNC4_mm_rna_sr_kauranil_C_4_S36_L006_R1_001.fastq


title: RNA-Sequencing from mouse primary microglia 6

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-Sequencing from mouse primary microglia.txt
PM99b3_mm_rna_sr_kauranil_T_3_S33_L005_R1_001.fastq


title: RNA-Sequencing from mouse primary microglia 2

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-Sequencing from mouse primary microglia.txt
PMNC3_mm_rna_sr_kauranil_C_3_S34_L005_R1_001.fastq


title: RNA-sequencing from mouse mPFC region 5

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-sequencing from mouse mPFC region.txt
PFCNC3_mm_rna_sr_kauranil_W_3_S30_L006_R1_001.fastq

source_name: Mouse mPFC tissue

value: Mouse mPFC tissue

value: Pre frontal cortex (PFC) tissue

value: 3 month


title: RNA-sequencing from mouse mPFC region 6

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-sequencing from mouse mPFC region.txt
PFCNC4_mm_rna_sr_kauranil_W_4_S32_L007_R1_001.fastq


title: RNA-sequencing from mouse mPFC region 4

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-sequencing from mouse mPFC region.txt
PFCNC2_mm_rna_sr_kauranil_W_2_S29_L006_R1_001.fastq


title: RNA-sequencing from mouse mPFC region 2

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-sequencing from mouse mPFC region.txt
PFCIN2_mm_rna_sr_kauranil_T_2_S28_L006_R1_001.fastq


title: RNA-sequencing from mouse mPFC region 1

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-sequencing from mouse mPFC region.txt
PFCIN1_mm_rna_sr_kauranil_T_1_S27_L006_R1_001.fastq


title: RNA-sequencing from mouse mPFC region 3

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-sequencing from mouse mPFC region.txt
PFCIN3_mm_rna_sr_kauranil_T_3_S31_L007_R1_001.fastq


title: mESC Wt1 KO, RA

city: Berhampur

first: Ruthrothaselvi

last: Bharathavikru

state: Odisha

address: IISER Berhampur, Transit Campus

department: Biological Sciences

country: India

institute: Indian Institute of Science Education and Research

description: Small RNA

data_processing:
The abundance of mature mouse miRNA from miRBase (http://www.mirbase.org) was quantified using mirna_soft (http://seidman.med.harvard.edu/fgs/software/mirna_soft/mirna_soft.tar.gz) PMCID: PMC4138881.
Supplementary_files_format_and_content: tab separated file with counts per miRNA

source_name: Embryonic stem cells

growth_protocol: Embryonic stem cells were maintained on 0.1% gelatin coated dishes, maintained in GMEM reconstituted with NEAA, sodium pyruvate, 10% FCS, LIF and β-mercaptoethanol.

extract_protocol:
Total RNA was extracted from the cells using the Qiagen miRNeasy column as per the manufacturers protocol
Total RNA equivalent to 1µg was ligated with the 3’ RNA adapter with the help of the T4 RNA ligase 2 (deletion mutant) followed by ligation of the 5’ RNA adapter using T4 RNA ligase. The adapter ligated RNA was then subjected to reverse transcription with Superscript II RT followed by PCR amplification. The amplified cDNA was electrophoresed on a 6% PAGE gel. Mature microRNA, which is approximately 22 bp, gives an adapter ligated fragment of approximately 147 bp. A second band of 157 bp corresponding to piRNAs, other small noncoding RNA arising from 30 bp small RNAs was also excised together to give rise to the pool of small RNA.

treatment_protocol: ES cells were treated with 1µm retinoic acid or 1µg/ml doxycycline as per the conditions mentioned.

value: Wt1 KO

value: embryonic stem cells

value: treated with retinoic acid


title: mESC wildtype, RA

description: Small RNA

value: wild type


title: mESC wild type

description: Small RNA

value: untreated


title: mESC Wt1 KO, Dox24

description: Small RNA

value: induced with dox for 24 hours


title: mESC Wt1 KO, Dox12

description: Small RNA

value: induced with dox for 12 hours


title: CspE CLIP-seq, UV-crosslinked, biol rep 3 (Sample 11)

city: Würzburg

first: Laura

last: Jenniches

address: Josef-Schneider-Straße 2/D15

institute: Helmholtz Institute for RNA-based Infection Research

description:
ID-003809
cspE_CLIP_peaks.gff
CspE_counts.csv

data_processing:
PCR duplicates were removed using FastUniq v1.1 (Xu et al. 2012)
Adapters were removed with Cutadapt v4.1, read length 12-25
Alignment: segemehl 0.3.4
Peak Calling: blockbuster 0.0.1.1
Adapters were removed with Cutadapt v4.1, no upper limit on read length, min. read length 12
Alignment: STAR 2.6.0a (Dobin et al., 2013)
Quantification of peaks: htseq-count 2.0.2
Assembly: FQ312003.1, HE654724.1, HE654725.1 and HE654726.1
Supplementary files format and content: Quantification of peaks

organism: Salmonella enterica subsp. enterica serovar Typhimurium

growth_protocol: Overnight growth from single colonies at 37 °C in LB medium

extract_protocol:
Phase-lock tubes (5PRIME) were used to mix 450 µl of Phenol:Chloroform:Isoamyl alcohol 25:24:1 (PCI; Roth) with the supernatant from proteinase K treated samples (around 450 µl).
cDNA libraries were prepared using the NEBnext Multiplex Small RNA library kit (#E7300) according to the manufacturer’s recommendation.

treatment_protocol: One half of the culture was irradiated with UV-C light at 800 mJ to induce RBP crosslinking. Bacteria were lysed and the FLAG-tagged protein was immunoprecipitated using a monoclonal anti-FLAG antibody.

value: UV-crosslinked

value: anti-FLAG


title: CspE CLIP-seq, not UV-crosslinked, biol rep 2 (Sample 10)

description:
ID-003808
cspE_CLIP_peaks.gff
CspE_counts.csv

value: Not UV-crosslinked


title: mESC Wt1 KO

description: Small RNA


title: CspC CLIP-seq, not UV-crosslinked, biol rep 3 (Sample 6)

description:
ID-003804
cspC_CLIP_peaks.gff
CspC_counts.csv


title: CspE CLIP-seq, UV-crosslinked, biol rep 1 (Sample 7)

description:
ID-003805
cspE_CLIP_peaks.gff
CspE_counts.csv


title: CspE CLIP-seq, not UV-crosslinked, biol rep 1 (Sample 8)

description:
ID-003806
cspE_CLIP_peaks.gff
CspE_counts.csv


title: RNA-Sequencing from mouse primary microglia 1

description:
Illumina TrueSeq library preparation kit. Oligo-dT beads capture polyA tails.
RNA-Sequencing from mouse primary microglia.txt
PMNC2_mm_rna_sr_kauranil_C_2_S32_L005_R1_001.fastq

value: Mouse primary microglia culture

value: Primary microglia


title: CspC CLIP-seq, UV-crosslinked, biol rep 3 (Sample 5)

description:
ID-003803
cspC_CLIP_peaks.gff
CspC_counts.csv


title: Control_Med1_6h and Med15_6h

city: Umea

first: ALEXANDER

last: VERGARA

address: Historiegrand 9, 1002

department: Physics

country: Sweden

institute: Umea University

description: Control for Med1_6h and Med15_6h

data_processing:
Reads were mapped using Bowtie2 to the sacCer3 reference genome. After mapping of reads, we called narrow peaks at an average fragment size of 300 bp and an FDR value < 0.05
ChIP-seq using an untagged wild type strain was used as control for peak calling and enrichment analyses
Assembly: sacCer3
Supplementary files format and content: bigwig files (narrow peaks)

organism: Saccharomyces cerevisiae

growth_protocol: For experiments using cells at different growth phases, single colonies of Saccharomyces cerevisiae BY4742 cells were inoculated into 10 ml of YPD medium (1% yeast extract, 2% bacto-peptone and 2% glucose), precultivated in YPD at 30 ◦C, diluted in fresh YPD to an OD600nm of 0.1 to 0.15 and cultivated for 2 h at 30 ºC after which the first samples (labelled 0 h in the figures) were harvested. Subsequent samples were harvested at 2 h, 4 h and 6 h after the 0 h point

extract_protocol:
Cell lysis and separation of chromatin fractions were performed using the standard protocol Svejstrup et al., (2003), except that we used ammonium sulfate to 0.5 M final concentration instead of 1 M to release chromatin-associated proteins, as we have described previously
DNA fragments were then cleaned using the ChIP DNA clean & concentratorTM kit (ZYMO RESEARCH). Aliquots of 1 to 2 ng of DNA from each sample were tested for proper shearing using a fragment analyzer (Agilent 2100 Bioanalyzer G2938C), and then sent for library preparation using the SMARTer ThruPLEX kit and subsequent pair-ended sequencing using Illumina NovaSeq S4-200 cycle flow cells in individual lanes.

value: Wt

value: IgG

tag: time (hrs)


title: CspC CLIP-seq, UV-crosslinked, biol rep 2 (Sample 3)

description:
ID-003801
cspC_CLIP_peaks.gff
CspC_counts.csv


title: CspC CLIP-seq, UV-crosslinked, biol rep 1 (Sample 1)

description:
ID-003799
cspC_CLIP_peaks.gff
CspC_counts.csv


title: CspC CLIP-seq, not UV-crosslinked, biol rep 1 (Sample 2)

description:
ID-003800
cspC_CLIP_peaks.gff
CspC_counts.csv


title: Med1_6h

description: Wt Med1-Ab ChIP 6 hours


title: Control Lsm3-TAP R3_2h

description: Control for Lsm3 2 h Rep3


title: Lsm3-TAP R3_2h

description: Lsm3-TAP IgG-Ab 2h Rep3

value: Lsm3-TAP R3


title: Med15_2h

description: Wt Med15-Ab ChIP 2 hours


title: CspC CLIP-seq, not UV-crosslinked, biol rep 2 (Sample 4)

description:
ID-003802
cspC_CLIP_peaks.gff
CspC_counts.csv


title: Med1_2h

description: Wt Med1-Ab ChIP 2 hours


title: Med15_6h

description: Wt Med15-Ab ChIP 6 hours


title: CspE CLIP-seq, not UV-crosslinked, biol rep 3 (Sample 12)

description:
ID-003810
cspE_CLIP_peaks.gff
CspE_counts.csv


title: 12_SARS1-3

city: Daejeon

first: Dongbin

last: Park

address: 55, Expo-ro

institute: Institute for Basic Science

data_processing:
Seurat package (version 4.2.1).
CellRanger (version 7.1.0)
Assembly: not provided
Supplementary files format and content: Tab-delimited text files including feature-cell matrix.

source_name: Human bronchial epithelial (HBE) organoid

extract_protocol:
RNA was extracted from both uninfected and virus-infected ALI cells using the Trizol reagent.
Single-cell RNA libraries were prepared using the 10x Genomics Chromium™ Single Cell 3′ Gel Bead and Library kit (10X Genomics).

value: SARS-CoV infection


title: 13_SARS2-1

value: Human bronchial epithelial (HBE) organoid

value: SARS-CoV-2 infection


title: 14_SARS2-2


title: 4_MERS-1

value: MERS-CoV infection


title: 6_MERS-3


title: 5_MERS-2


title: 15_SARS2-3


title: 11_SARS1-2


title: 21_OC43-3

value: HCoV-OC43 infection


title: 20_OC43-2


title: CspE CLIP-seq, UV-crosslinked, biol rep 2 (Sample 9)

description:
ID-003807
cspE_CLIP_peaks.gff
CspE_counts.csv


title: 24_Control-3

value: Mock infection


title: 22_Control-1


title: 19_OC43-1


title: 23_Control-2


title: PERFFseq_IL3RAplus

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

library_source: other

data_processing:
Fastqs were generated using CellRanger v7.2 mkfastq
Reads were aligned to the Flex probeset v1.0.1 reference
Assembly: N/A (probe set v.1.0.1)
Supplementary files format and content: For development libraries, a summary of the metrics from the CellRanger count call
Supplementary files format and content: For the PERFF-seq libraries, h5 files representing probe gene expression counts
Library strategy: 10x Genomics Flex

molecule: other

source_name: peripherial blood mononculear cells

extract_protocol:
cDNA was extracted according to the 10x Genomics Flex scRNA-seq workflow
Libraries were constructed according to 10x Genomics Flex workflow; R1 is technical barcode sequence; R2 is the probe barcode sequences

value: peripherial blood mononculear cells

tag: flowfish probes

value: immune


title: PERFFseq_CD3Pool


title: PERFFseq_TFPool


title: PERFFseq_GBMPool

source_name: GBM tumor FFPE block

value: GBM tumor FFPE block

value: brain


title: PERFFseq_LogicPool


title: 10_SARS1-1


title: PERFFseq_IL3RAminus


title: T_13_V2

city: Marseille

first: Jonatane

last: Andrieu

address: 14 rue de chanterac

department: Recherche

country: France

institute: ADES EFS CNRS

data_processing:
Nextflow, FastQC, Trimgalore, Fastp, MultiQC
Assembly: NCBI
Supplementary files format and content: Raw data, annotations of RNA-seq

source_name: T = Control patient with normal pregnancy; V2 = Blood sample between 30-60 days after birth

growth_protocol: Total blood sample (PAXgene tube, PreAnalytiX) was taken at the time of preeclampsia diagnosis (and matched on gestational age at inclusion for controls) and was repeated 4 to 6 weeks postpartum. PAXgene tubes were stored at 4°C for 24 hours, before freezing for 24 hours at -20°C and then permanently stored at -80°C. At-term placental biopsy was also performed at the time of delivery for each of the included women. Placental biopsy was defined as a macroscopically placental area of 2x2 cm including both chorionic and basal membranes. Biopsies were immediately preserved in RNAlater (Thermo Fisher Scientific) for 24 hours at 4°C, before freezing for 24 hours at -20°C, then permanently at -80°C.

extract_protocol:
RNAs from total blood samples were extracted using the PAXgene Blood RNA kit according to the procedure recommended by the manufacturer (Qiagen). Briefly, total blood was lyzed using proteinase K and the nucleic acids were precipitated by the addition of ethanol. DNA was digested with DNase I RNase-free for 15 minutes at room temperature. Total RNAs were eluted and then incubated at 65°C for 5 minutes before being placed at -80°C.  Total RNAs from placenta biopsies were extracted using the RNeasy Mini Kit according to the procedure recommended by the manufacturer (Qiagen). After dissolution of placental tissue with RLT-β-mercapto-ethanol, nucleic acids were precipitated with the addition of ethanol. DNA was digested with DNase I RNase-free for 15 minutes at room temperature. Total RNAs were eluted before being placed at -80°C.  The quality and quantity of the extracted RNAs were evaluated using the Bioanalyzer 2100 (Agilent Technologies) and by NanoDrop Spectrophotometer (Nanodrop Technologies).
None

value: Whole blood + serum

tag: experimental group


title: T_27bis_V2

value: T = Control patient with normal pregnancy; V2 = Blood sample between 30-60 days after birth


title: T_10_V2


title: T_11_V2


title: T_22_V2


title: T_14_V2


title: PE_28_V2

source_name: PE = Preeclampsia event during pregnancy; V2 = Blood sample between 30-60 days after birth


title: PE_09_V2

value: PE = Preeclampsia event during pregnancy; V2 = Blood sample between 30-60 days after birth


title: PE_06_V2


title: PE_07_V2


title: PE_08_V2


title: T_20_V2


title: PE_25_V2


title: PE_24_V2


title: T_16_V2


title: EFO27_CTCF_25_Input

city: Los Angeles

first: Michelle

middle: Renee

last: Jones

state: CA

address: 8720 Alden Dv

department: Biomedical Sciences

institute: Cedars-Sinai Medical Center

description:
ChIP-Seq for CTCF with Replicate 1 (R1) and Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1), Replicate 2 (R2) and Input.
EFO27-A-CTCF_5Jan2018_GRCh38_CGC_BWAmem.nodup_pooled.tagAlign_x_EFO27-25-Input_14Dec2017_GRCh38_CGC_BWAmem.nodup.tagAlign.naive_overlap.filt.regionPeak.narrowpeak.gz

data_processing:
ChIP sequencing data was processed based on ENCODE phase 3 histone ChIP-Seq pipeline with modifications on the peak calling algorithm to retain peaks with p-value < 10e-9.
Reads were aligned to the reference human genome (hg38), filtered by read quality and duplicate reads removed. Peak calling was performed with MACS2 within the AQUOS pipeline, with pooled replicate peaks that overlap 50% or more of each individual replicate selected for the final peak set. When replicates were not available pseudo replicates were formed and pooled peaks selected in the same manner from these pseudo replicates. Narrowpeaks were retained for downstream analysis.
Assembly: hg38
Supplementary files format and content: narrowpeak

growth_protocol: FT33, FT246 and FT282 lines were maintained in DMEM-F12 medium (Gibco, Invitrogen, Carlsbad) supplemented with 10% fetal bovine serum (Gibco). The HGSOC cell line UWB 1.289 was cultured in a mixture (1:1) of 50% RPMI and  50% MEGM medium with 3% FBS and Kuramochi was cultured in RPMI-1640 media supplemented with 10% FBS. The remaining cell lines were maintained according to the recommended conditions (ATCC).   All cell lines were thawed and allowed to recover for 1 day before expansion. All cell lines were passaged and plated onto 150mm plates. Cells were harvested at 80% confluency to be fixed, pelleted and snap frozen.

extract_protocol:
Four 15-cm dishes of confluent cells were fixed in formaldehyde for 10 min, before quenching the fixation with glycine. Cells were collected, lysed in a sarkosyl-containing lysis buffer and sonicated  to yield 100- to 300-bp genomic DNA fragments. Five micrograms of an antibody raised against H3K4me1 was incubated with blocked magnetic Dynabeads (Life Technologies) at 4 °C for 4 h. Antibody–bead conjugates were incubated with 100 μg of chromatin at 4 °C overnight, with constant agitation. Beads were washed extensively with RIPA buffer and then treated with RNase and proteinase K (both Qiagen). DNA was then eluted from the beads in TE buffer and cleaned up using the QIAquick PCR Purification kit (Qiagen).
Sequencing libraries were prepared using a ThruPlex DNA-seq kit (Rubicon R400407), pooled and sequenced on an Illumina HiSeq 5000 for 2 x 150 bp paired-end for an average of 40 million reads (Fulgent Genetics; Temple City, CA).

value: Mucinous serous ovarian cancer


title: EFO27_CTCF_A

value: CTCF (Active Motif 61311)


title: MCAS_CTCF-Input

description:
ChIP-Seq for CTCF with Replicate 1 (R1) and Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1), Replicate 2 (R2) and Input.
MCAS_CTCF_hg38.rep1-rep2.idr0.05.bfilt.regionPeak.narrowpeak.gz

source_name: MCAS

value: MCAS


title: T_27_BP

source_name: T_BP = Placental biopsy of a control patient during delivery

value: Placental biopsy taken from the umbilical cord axis


title: EFO27_CTCF_B


title: T_16_BP

value: T_BP = Placental biopsy of a control patient during delivery


title: PE_04_V2


title: PE_23_V2


title: PE_02_V2


title: MCAS_CTCF-B


title: MCAS_CTCF-A


title: T_26_BP


title: T_14_BP


title: GFTR230_CTCF-25_Input

description:
ChIP-Seq for CTCF with Replicate 1 (R1) and Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1), Replicate 2 (R2) and Input.
GTFR230_CTCF_hg38.rep1-rep2.idr0.05.bfilt.regionPeak.narrowpeak.gz


title: T_12_BP


title: GFTR230_CTCF-B


title: GFTR230_CTCF-A


title: VOA1056_CTCF_25_Input

description:
ChIP-Seq for CTCF with Replicate 1 (R1) and Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1), Replicate 2 (R2) and Input.
VOA1056_CTCF_hg38.rep1-rep2.idr0.05.bfilt.regionPeak.narrowpeak.gz

value: Low grade serous ovarian cancer


title: PE_25_BP

source_name: PE_BP = Placental biopsy of a preeclampsia patient during delivery


title: T_11_BP


title: PE_24_BP

value: PE_BP = Placental biopsy of a preeclampsia patient during delivery


title: VOA1056_CTCF_B


title: FT-SA11838

description:
ChIP-Seq for CTCF with Replicate 1 (R1) and Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1), Replicate 2 (R2) and Input.
OAW42_CTCF_hg38.rep1-rep2.idr0.05.bfilt.regionPeak.narrowpeak.gz


title: VOA1056_CTCF_A


title: PE_28_BP


title: FT-SA11845


title: PE_09_BP


title: PE_23bis_BP


title: PE_08_BP


title: PE_02_BP


title: OAW42_CTCF


title: UWB1.289_CTCF

description:
ChIP-Seq for CTCF with Replicate 1 (R1) and Input available. Fastq provided for Replicate 1 (R1) and Input.
UWB1.289-CTCF_5Jan2018_GRCh38_CGC_BWAmem.nodup.tagAlign_x_UWB1.289-25-Input_5Jan2018_GRCh38_CGC_BWAmem.nodup.tagAlign.naive_overlap.filt.regionPeak.narrowpeak.gz

value: High grade serous ovarian cancer


title: T_26_V1

source_name: T = Control patient with normal pregnancy; V1 = Blood sample at detection of preeclampsia


title: T_27_V1

value: T = Control patient with normal pregnancy; V1 = Blood sample at detection of preeclampsia


title: Kuramochi_CTCF_2

description:
ChIP-Seq for CTCF with Replicate 1 (R1) and Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1), Replicate 2 (R2) and Input.
Kura_CTCF_hg38.rep1-rep2.idr0.05.bfilt.regionPeak.narrowpeak.gz

source_name: Kuramochi

value: Kuramochi


title: Kuramochi_CTCF_5_Input


title: PE_04bis_BP


title: Kuramochi_CTCF_6


title: T_22_V1


title: Hey_CTCF_25_Input

description:
ChIP-Seq for CTCF with Replicate 1 (R1) and Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1), Replicate 2 (R2) and Input.
HeyA8_CTCF_hg38.rep1-rep2.idr0.05.bfilt.regionPeak.narrowpeak.gz

source_name: Hey

value: Hey


title: T_20_V1


title: T_14_V1


title: Hey_CTCF_B


title: T_16_V1


title: PE_06_BP


title: CaOV3_CTCF_25_Input

description:
ChIP-Seq for CTCF with Replicate 1 (R1) and Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1), Replicate 2 (R2) and Input.
CaOV3-A-CTCF_5Jan2018_GRCh38_CGC_BWAmem.nodup_pooled.tagAlign_x_CaOV3-25-Input_5Jan2018_GRCh38_CGC_BWAmem.nodup.tagAlign.naive_overlap.filt.regionPeak.narrowpeak.gz


title: Hey_CTCF_A


title: UWB1.289_CTCF_25_Input


title: T_13_V1


title: T_12_V1


title: CaOV3_CTCF_A


title: CaOV3_CTCF_B


title: T_11_V1


title: FT-SA11849

description:
ChIP-Seq for CTCF with Replicate 1 (R1) and Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1), Replicate 2 (R2) and Input.
RMGII_2D_CTCF_hg38.rep1-rep2.idr0.05.bfilt.regionPeak.narrowpeak.gz

source_name: RMG-II

value: RMG-II

value: Clear cell ovarian cancer


title: T_10_V1

source_name: PE = Preeclampsia event during pregnancy; V1 = Blood sample at detection of preeclampsia


title: PE_28_V1

value: PE = Preeclampsia event during pregnancy; V1 = Blood sample at detection of preeclampsia


title: RMG-II_CTCF


title: 22Rv1-FOXA1-C258A, Input

city: La Jolla

first: Yuxiang

last: Zhang

address: 10550 N. Torrey Pines Rd.

department: Chemistry

institute: The Scripps Research Institute

data_processing:
Raw basecall (or BCL) files from the NextSeq2000 sequencer were converted to sample fastqs with single-end reads using an in-house custom built wrapper around Illumina’s bcl2fastq conversion software v2.19.0.
The sequencing reads were aligned to human genome build hg19 and RefSeq genes by Bowtie2.
The signal-enriched regions were identified by Model-based Analysis of ChIP-seq (MACS) peak-finding algorithm (v1.4.1) with the P value threshold of 1e-9 using the input sample as background. Bed files and wiggle files were created by MACS.
Assembly: hg19
Supplementary files format and content: wiggle file, bed file (except for Input sample)

source_name: Prostate

growth_protocol: All 22Rv1 cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum (FBS), 2 mM L-alanyl-L-glutamine (GlutaMAX), penicillin (100 U/ml), and streptomycin (100 μg/ml) and maintained at 37 °C with 5% CO2.

extract_protocol:
Cells were fixed with 1.1 % formaldehyde and lysed for genomic DNA extraction. Genomic DNA was fragmented by sonication, enriched by corresponding antibody, and extracted with phenol:chloroform:isoamyl alcocol for NGS library preparation.
ChIP-seq libraries were prepared with Takara ThruPLEX DNA-Seq Kit and barcoded with Takara DNA Unique Dual Index Kit following manufacturer's instructions, purified with AMPure XP beads, and validated on Agilent TapeStation.

treatment_protocol: Cells were treated with DMSO (0.1%), stereoprobes (WX-02-23, WX-02-43, 20 uM), PladB (10 nM for parental 22Rv1, 100 nM for engineered 22Rv1) for 3 h.

value: Prostate

tag: group

value: engineered

value: Overexpression of Y36C-PHF5A, dox-inducible-C258A-FOXA1

tag: treatment

value: Dox + DMSO


title: 22Rv1-FOXA1-WT, Input

value: Overexpression of Y36C-PHF5A, dox-inducible-WT-FOXA1

tag: chip antibody


title: 22Rv1-parental, WX-02-23, FOXA1

tag: cell line

value: parental

value: Parental


title: 22Rv1-FOXA1-C258A, WX23, rep2

data_processing:
Reads were were aligned to the human genome build hg19 with Bowtie2. Blacklist regions were excluded using data file wgEncodeDacMapabilityConsensusExcludable.bed.gz. Unmapped/low quality and duplicated reads were filtered with sambamba.
Peaks were called by MACS2 with pareameters: -q 0.01 --nomodel --shift -100 --extsize 150.
Assembly: hg19
Supplementary files format and content: narrowPeak

extract_protocol:
ATAC-seq fragmentes were extracted with ATAC-Seq Kit (Active Motif, Cat#: 53150) following manufacturer's instruction.
ATAC-seq libraries were prepared with ATAC-Seq Kit (Active Motif, Cat#: 53150) following manufacturer's instruction.

treatment_protocol: Cells were treated with DMSO (0.1%), stereoprobes (WX-02-23, WX-02-43, 20 uM), PladB (10 nM and 100 nM for parental 22Rv1, 100 nM for engineered 22Rv1) for 3 h.


title: 22Rv1-FOXA1-C258A, PladB, rep2

value: Dox + PladB, 100 nM


title: 22Rv1-parental, PladB, FOXA1

value: PladB, 100 nM


title: 22Rv1-parental, siFOXA1, FOXA1


title: 22Rv1-FOXA1-C258A, noDox, FOXA1

value: DMSO


title: 22Rv1-FOXA1-C258A, WX-02-23, FOXA1


title: 22Rv1-FOXA1-WT, WX-02-23, FOXA1


title: 22Rv1-FOXA1-WT, DMSO, FOXA1


title: 22Rv1-parental, WX-02-43, FOXA1


title: 22Rv1-FOXA1-C258A, DMSO, rep2


title: 22Rv1-FOXA1-C258A, PladB, rep1


title: 22Rv1-FOXA1-WT, noDox, FOXA1


title: 22Rv1-parental, DMSO, FOXA1


title: 22Rv1-FOXA1-C258A, DMSO, FOXA1


title: 22Rv1-parental, Input


title: 22Rv1-parental, si-control, FOXA1

value: siControl


title: ES2_25_Input

description:
ChIP-Seq for CTCF with Replicate 1 (R1) and Input available. Fastq provided for Replicate 1 (R1) and Input.
ES2_CTCF_hg38.rep1-rep2.idr0.05.bfilt.regionPeak.narrowpeak.gz


title: 22Rv1-FOXA1-C258A, DMSO, rep1


title: PE_25_V1

value: Whole blood + serum


title: 22Rv1-FOXA1-WT, no Dox, rep2


title: 22Rv1-FOXA1-WT, no Dox, rep1


title: FT-SA11850

value: CTCF (Active Motif 61311)


title: 22Rv1-FOXA1-C258A, WX23, rep1


title: PE_24_V1


title: ES2_CTCF


title: 22Rv1-FOXA1-WT, PladB, rep1


title: FT-SA11848

description:
ChIP-Seq for CTCF with Replicate 1 (R1) and Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1), Replicate 2 (R2) and Input.
JHOC5_CTCF_hg38.rep1-rep2.idr0.05.bfilt.regionPeak.narrowpeak.gz


title: PE_23_V1


title: 22Rv1-FOXA1-WT, WX23, rep1


title: 22Rv1-FOXA1-WT, DMSO, rep2


title: 22Rv1-parental, PladB, 10nM, rep3

value: PladB, 10 nM


title: EEC16_CTCF_25_Input

description:
ChIP-Seq for CTCF with Replicate 1 (R1) and Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1), Replicate 2 (R2) and Input.
EEC16_CTCF_hg38.rep1-rep2.idr0.05.bfilt.regionPeak.narrowpeak.gz

value: Endometriosis


title: PE_09_V1


title: EEC16_CTCF_B


title: 22Rv1-FOXA1-WT, WX23, rep2


title: PE_06bis_V1


title: 22Rv1-parental, PladB, 100nM, rep3


title: 22Rv1-parental, PladB, 100nM, rep1


title: 22Rv1-parental, WX43, rep3


title: FT-SA11847

value: Clear cell ovarian cancer


title: 22Rv1-FOXA1-WT, DMSO, rep1


title: PE_04_V1

value: PE = Preeclampsia event during pregnancy; V1 = Blood sample at detection of preeclampsia


title: PE_08_V1


title: 22Rv1-parental, PladB, 100nM, rep2

value: Prostate


title: PE_07_V1


title: PE_02_V1


title: JHOC5_CTCF


title: 22Rv1-FOXA1-WT, PladB, rep2

value: engineered


title: FT-SA11855

description:
ChIP-Seq for CTCF with Replicate 1 (R1) and Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1), Replicate 2 (R2) and Input.
IOSE11-A-CTCF_5Jan2018_GRCh38_CGC_BWAmem.nodup_pooled.tagAlign_x_IOSE11-25-Input_5Jan2018_GRCh38_CGC_BWAmem.nodup.tagAlign.naive_overlap.filt.regionPeak.narrowpeak.gz

value: Ovarian surface epithelial cell


title: 22Rv1-parental, WX43, rep1


title: MCF7, Nutlin treated, rep2

city: Nagoya

first: Mai

last: Nagasaka

address: 3-1 Tanabe-dori, Mizuhoku

country: Japan

institute: Nagoya City University

data_processing:
Read count estimation/normalization and analysis of differentially expressed genes were carried out by RaNA-seq (https://ranaseq.eu/).
Reference genome assembly = Human, Homo sapiens (GRCh38), Method = DESeq2, Test = Wald, Fit Type = parametric.
Assembly: Homo sapiens (GRCh38)
Supplementary files format and content: Excel files include TPM values for each samples.

growth_protocol: MCF7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using FastGene RNA Premium Kit (Nippon Genetics Co., Ltd.).
Total RNA was used for the construction of sequencing libraries. Paired-end Illumina sequencing were performed by Novogene. Bioinformatics Technology Co., Ltd. (Beijing, China)

treatment_protocol: Cells were treated with DMSO (as vehicle control) or 10 μM Nutlin-3 for 8h.

value: epithelial cell


title: 22Rv1-parental, WX43, rep2


title: 22Rv1-parental, PladB, 10nM, rep1


title: 22Rv1-parental, PladB, 10nM, rep2


title: EEC16_CTCF_A


title: 22Rv1-parental, WX23, rep2


title: FT-SA11854


title: 22Rv1-parental, WX23, rep1


title: IOSE11_CTCF


title: 22Rv1-parental, WX23, rep3


title: MCF7, Nutlin treated, rep1


title: 22Rv1-parental, DMSO, rep3


title: 22Rv1-parental, DMSO, rep2


title: 22Rv1-parental, DMSO, rep1


title: MCF7, DMSO treated, rep2


title: FT-SA11852

description:
ChIP-Seq for CTCF with Replicate 1 (R1) and Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1), Replicate 2 (R2) and Input.
IOSE4-A-CTCF_5Jan2018_GRCh38_CGC_BWAmem.nodup_pooled.tagAlign_x_IOSE4-25-Input_5Jan2018_GRCh38_CGC_BWAmem.nodup.tagAlign.naive_overlap.filt.regionPeak.narrowpeak.gz


title: S11, healthy donor, GEX, source: BM, donor: E, sorting: CD34p

city: Milano

first: Guido

last: Pacini

address: Via Olgettina 60

department: Pathogenesis and therapy of primary immunodeficiencies

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

description:
polyA RNA
GEX (3' mRNA) library: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains transcript
S11_mRNA

data_processing:
Sequenced libraries were processed and de-multiplexed by Cell Ranger Single-Cell Software Suite (version 4.0.0, 10X Genomics) by “cellranger mkfastq” function. We generated a genes-barcode matrix of UMI counts for each of the samples separately and aligned the reads to the GRCh38 human reference genome using STAR v.2.5.1b. We used the “cellranger count” function to generate a UMI count matrix for both GEX and ADT libraries.
After importing UMI counts matrix, gene and cell barcode lists, we generated a Seurat object (Seurat R package v.3.0) including every sequenced cell. Cells with a percentage of mitochondrial reads higher than 20%, as well as those with <200 or >8,000 expressed genes, were removed from the dataset. The filtered UMI count matrix was then log-normalized with the “NormalizeData” function in Seurat, and the top 20% most variable genes were selected for downstream analysis through the “FindVariableFeatures” function in Seurat, which relies on the “vst” method. The cell cycle phase of each cell was inferred by the expression levels of specific cell cycle marker genes (Regev list) with the “CellCycleScore” function in Seurat. Following this we computed the difference between the S and G2M scores, which indicates if the cell is actively cycling (G2M/S) or rather in a quiescent state (G1). Each single-cell UMI count was regressed for the following covariates: cell cycle difference, total number of UMIs and percentage of mitochondrial UMI counts. Where the above scaling procedure was performed through the “ScaleData” function in Seurat. Furthermore, between-donor variability was accounted for using the Harmony data integration procedure (harmony R package v.0.1), with the “RunHarmony” function in harmony.
UMAP dimensionality reduction and cell clustering were performed with default parameters using the first 80 Harmony components and setting the cluster’s resolution parameter to 0.6, respectively using the “RunUMAP” and “FindClusters” functions in Seurat. Differentially expressed genes across clusters were identified with the “FindAllMarkers” function in Seurat. The above test was performed separately for each cluster, restricting the analysis to the subset of genes expressed by at least 10% of cells in either of the two groups being compared (min.pct = 0.1). Cluster-specific marker genes were identified as the most significant genes (Bonferroni’s adjusted p < 0.05) whose expression was enriched in the cluster of interest (logFC > 0). Cell type annotation was inferred (SingleR R package v.1.8.1) based on the expression of specific lineage marker genes and published HSPC gene signatures. Each cluster was classified by inspecting the expression of curated marker genes and published gene signatures, respectively using the “FeaturePlot” and “AddModuleScore” functions in Seurat. A custom gating strategy was defined by first converting sequencing data into “.fcs” files to be explored manually with FlowJo software v.10.5.3 (BD Biosciences) through the flowcore R package v.2.8.0. Gates were manually set based on comparison with conventional flow cytometry analysis performed on the same sample prior to single-cell library preparation. For samples enriched for primitive CD38- HSPC fraction, the proportions of ADT-detected HSPC subsets were normalized according to FACS immunophenotyping performed prior to single-cell library preparation.
For each cluster under investigation, the “FindMarkers” function in Seurat was used to identify differentially expressed genes between PB and BM cells. Where the above function performs, gene-wise Wilcoxon signed-rank tests between cells isolated by PB and BM samples, separately for each cell cluster. Notably the above tests were performed setting the logFC threshold parameter (logfc.threshold) to 0, in order to obtain unfiltered gene lists for all tested conditions. Furthermore, only intra-cluster comparisons between groups with at least 5 cells were considered for differential gene expression analysis. We then performed Gene Set Enrichment Analysis using the “GSEA” function of ClusterProfiler R package v.3.16 17 aiming to identify enriched Gene Ontology (GO) sets, focusing mainly on the Biological Process (GO-BP) terms. This procedure results in a list of statistically significant (adjusted p < 0.05) GO-BP terms. These can be further divided into enriched and depleted terms based on their normalized enrichment score (NES) value, NES>0 (NESpos) and NES<0 (NESneg) respectively. Where positive NES values indicate gene sets with higher expression in the PB samples, conversely negative NES values indicate gene sets whose expression is enriched in the BM samples. To perform transcriptional analyses on lymphoid cells, we investigated the expression of TSP1 gene signature19 on lymphoid clusters (namely, clusters 4 and 15). Cells were first clustered into K=3 groups by K-means clustering algorithm based on the percentage of expressed (UMI > 0) TSP1-associated genes. Specifically, TSP-high cells express more than 75% of the TSP1 genes, while TSP-low genes express less than 45% of these genes. Similarly to the previous section, a putative set of genes regulating the TSP1 signature was identified performing gene-wise differential expression analyses through Wilcoxon signed-rank tests. This procedure was used to identify the genes which significantly (adjusted p < 0.05) drive the expression of the TSP1 signature (PB-TSPhigh vs PB-TSPlow, BM-TSPhigh vs BM-TSPlow), and the ones which differentially modulate its expression across RNA sources (BM-TSPhigh vs PB-TSPhigh).
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: {SampleID}_features.tsv.gz, {SampleID}_barcodes.tsv.gz, {SampleID}_matrix.mtx.gz
Supplementary files format and content: scRNA-Seq UMI count matrices (scRNA_CountMatrix.rds): matrix of counts quantifying the expression of each GRCh38 annotated gene (rows) across all single cells (columns)
Supplementary files format and content: ADT count matrix (ADT_CountMatrix.rds): matrix of counts quantifying the expression of each ADT under investigation (rows) across all single cells (columns)
Supplementary files format and content: Seurat metadata object (Metadata.rds): matrix storing the features (columns) associated to each single cell (rows)
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

source_name: Bone Marrow

extract_protocol:
PB and BM mononuclear cells (MNC) from healthy donors (HD) were isolated using Lympholyte human cell separation medium (Euroclone). PB CD34+ cells were purified from PBMC using positive selection with immunomagnetic beads according to the manufacturer’s specifications (Miltenyi Biotec). HD-derived BM CD34+ cells were purchased from Stem Cell Technologies or purified from BM MNC using positive selection with immunomagnetic beads according to the manufacturer’s specifications (Miltenyi Biotec). Both mononuclear cells and purified PB and BM CD34+ cell fractions were frozen in liquid nitrogen until use. Upon thawing, adult HD-derived BM or PB purified CD34+ or PBMC samples were labeled with a mix composed by both fluorescent antibodies against lineage markers (LIN, anti-CD3/CD14/ CD16/CD19/CD20/CD56), CD15, CD38, CD34 (Biolegend) for FACS immunophenotyping, and  TotalSeq-A antibodies against CD90, CD45RA, CD7, CD10, CD71, CD41 (Biolegend) for ADT barcoding through scRNAseq. Staining for ADT barcoding was applied only on the following HD-derived samples: BM C, BM D, BM E, PB D, PB H, PB I. Staining with TotalSeq-A antibodies and reagents was performed according to the manufacturer’s specifications, and TotalSeq-A antibodies were used at concentrations defined by titration of corresponding fluorescent antibodies. After surface marking, cells were incubated with PI (Biolegend) to label dead cells. We applied three different FACS sorting strategies for sample preparation prior to scRNAseq processing: 1) isolation of both bulk HSPC (live LIN- CD34+) and primitive HSPC (live LIN- CD34+ CD38-) fractions starting from purified CD34+ cells (BM A, BM B, PB F, PB G); 2) isolation of both primitive (live LIN- CD34+ CD38-) and progenitor (live LIN- CD34+ CD38+) HSPC fractions starting from purified CD34+ cells (BM C, BM D, PB H) or PBMC (PB D); 3) isolation of bulk HSPC (live LIN- CD34+) starting from purified CD34+ cells (BME, PB I).  Sorted BM and PB samples were counted with trypan blue for vitality when FACS cell recovery was >10,000 cells.
3’ gene expression (GEX) libraries and ADT libraries constructions were performed following Chromium 10x 3’ Gene Expression protocol v2 or v3 chemistry and TotalSeq™-A Antibodies and Cell Hashing with 10x Single Cell 3' Reagent Kit v3 Protocol. Chromium 10x 3’ GEX libraries were sequenced on Illumina NovaSeq S1 platform, while ADT libraries were sequenced together with GEX libraries or independently on Illumina NextSeq platform following manufacturer’s indications.

tag: facs sorting

value: HSPCs

value: Bone Marrow

tag: donor

value: E

tag: Sex

value: Male

tag: library type

value: mRNA


title: FT-SA11844


title: sinegative control, CENPA, rep3

city: Bethesda

first: Vinutha

last: Balachandra

state: MD

address: 10 Center Drive

department: National Cancer Institute, Genetics Branch

institute: National Institute for Health

data_processing:
Basecalls were performed using bcl2fastq for NextSeq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using cudadapt v4.0, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the NCBI T2T genome using Bowtie version 2-2.4.5.
Peaks were called uing GoPeaks v2.1.0 with the significance cut-off q-value <=0.05. broadPeaks settings were used.
Assembly: T2T-CHM13v2.0
Supplementary files format and content: bed, broadPeak (except for Input sample)
Supplementary files format and content: bigWig, broadPeak (except for Input sample)

growth_protocol: RPE1-Tet-GFP-CENPA cells were grown in DMEM/F-12 (11320033) supplemented with 10% FCS (Sigma-F6178), penicillin/streptomycin (15140122, ThermoFisher Scientific), fungizone (15290018, ThermoFisher Scientific), at 37oC with 5% CO2.

extract_protocol:
The CUT&RUN kit by EpiCypher (14-1048) was utilized according to EpiCypher’s protocol.
Libraries were constructed according to Accel-NGS® 2S Plus DNA Library Kit (cat# 21024/21096).

treatment_protocol: Cells were transfected with negative control and DNAJC9 siRNAs. After 48 hrs of transfection, cells were induced with 1 ug/ml DOX for another 48 hrs before processing for CUT&RUN.

value: anti-CENP-A antibody, Invitrogen, MA1-20832


title: IOSE4_CTCF


title: sinegative control, IgG, rep2

value: IgG negative control, SCBT, sc-2025


title: S12, healthy donor, GEX, source: PB, donor: I, sorting: CD34p

description:
polyA RNA
GEX (3' mRNA) library: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains transcript
S12_mRNA

source_name: Peripheral Blood

value: Peripheral Blood

value: I


title: FT282CTCF-25_Input

description:
ChIP-Seq for CTCF with Replicate 1 (R1) and Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1), Replicate 2 (R2) and Input.
FT282_CTCF_hg38.rep1-rep2.idr0.05.bfilt.regionPeak.narrowpeak.gz

value: Fallopian tube derived epithelial cell


title: sinegative control, CENPA, rep1


title: siDNAJC9, CENPA, rep3


title: S10, healthy donor, GEX, source: PB, donor: H, sorting: CD34pCD38p

description:
polyA RNA
GEX (3' mRNA) library: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains transcript
S10_mRNA

value: Progenitor HSPCs

value: H

value: Female


title: S9, healthy donor, GEX, source: PB, donor: H, sorting: CD34pCD38n

description:
polyA RNA
GEX (3' mRNA) library: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains transcript
S9_mRNA

value: Primitive HSPCs


title: CRISPRi human, cyno (gRNAs)

city: Planegg

first: Ines

last: Hellmann

address: Großhaderner Straße 2

institute: Ludwig-Maximilians-Universität München

description: 10x Genomics 5' CRISPR

data_processing:
Reads were processed using the 10x CellRanger software (Version 7.0.0)
The CRISPR library was mapped to a custom reference
The GEX library was mapped to both the extended hg38 and the extended macFas6 genomes
Assembly: hg38, macFas6 (both extended by the KRAB-dCas9-coding donor plasmid)
Supplementary files format and content: Hierarchical data format 5 files and comma-separated values file

organism:
Macaca fascicularis
Homo sapiens

source_name: iPSC

extract_protocol:
Generate single cell suspension with Accumax, wash cells with PBS+0.04 % Bsa and also store in that buffer until use
According to the manufaterer's instructions (Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index); CG000510 Rev B)
5' scRNA-seq based on polyA priming and CRISPR libraries from the gRNA based on capture of constant gRNA region

treatment_protocol: Cells were transduced with lentivirus, selected with pyromicing and then grown in doxycycline-containing medium for another 5 days

value: iPSC

tag: genotype


title: 7day-adECM+ASC

city: Beijing

first: Guan

email: umemaro@163.com, zzmbysy@sina.com

state: Beijing

address: 49 North Garden Road

institute: Peking University Third Hospital

description: muscle regeneration snNRA-seq data

data_processing:
The FASTQ files were processed and aligned to mm10 mouse reference genome through MobiVision (version 2.1) with unique molecular identifier (UMI) counts for each barcode. The UMI count matrix was then analyzed through Seurat R package. Cells with less than 200 genes, more than 4000genes, top 1% UMI or more than 20% mitochondrial gene ratio were considered abnormal and filtered out. Further analysis, including data normalization, highly variable gene identification, data scaling, and dimension reduction were performed under normal parameters.
Assembly: mm10 mouse
Supplementary files format and content: barcodes files, features files, matrix files

molecule: nuclear RNA

organism: Rattus norvegicus

source_name: muscle

growth_protocol: eight-week-old Sprague Dawley (SD) rats were anesthetized with isoflurane using an animal narcotic unit (isoflurane). A 2-cm skin incision was made in the bilateral groin parallel to the inguinal ligament. Subsequently, the inguinal adipose tissues were dissociated from the surrounding tissue except the supplying vessel-a branch of the femoral vessels. Ligated the supplying vessel proximally to the femoral vessels. Then, A blunt-tipped needle was inserted into the distal of the supplying vessel and fixed with 4-0 surgical sutures. The adipose tissues was flushed through the blunt-tipped needle with 10 mL of heparinized saline (25,000 IE/5 mL) to wash out the blood and prevent microthrombus formation.

extract_protocol:
Then the tissue were transferred to cold nuclear lysis buffer (NST with 0.1% NP40, 10 mM Tris-HCl, 146 mM NaCl, 1mM CaCl2, 21 mM MgCl2 and 40 U/mL RNase inhibitor) for 7 min. Add 1 mL ST Wash buffer (10 mM Tris-HCl, 146 mM NaCl, 1 mM CaCl2, 21 mM MgCl2, 0.01% BSA (NEB B9000S) and 40 U/mL RNase inhibitor. Then use 40 um Cell Strainer for collecting nuclear suspension under the 4 ℃, 500 g for 5 min. Then use 100 µL PBS + 1% BSA resuspended the nuclear. After calculating the nuclear number, the nuclear suspension was diluted to 700-1200/µl with PBS + 1% BSA.
We used the MobiCube® Single Cell 3’ Reagent Kits User Guide (PN-S050400301) to construct the cDNA Library and followed by cell counting, quality control, GEMs generation, barcoding, cDNA amplification and gene expression library construction. The data was submit to DNBSEQ-T7 platform (MGI, China) at PE150 Reads Lengths for final sequencing.

treatment_protocol: Perfusion decellularization of the tissue was perfused through the vascular access with 0.5 % Sodium Dodecyl Sulfate (SDS, Solarbio, China) for 24 hours at a constant flow of 3 mL/min. This was followed by a perfusion with deionized water (24 hours) to remove remaining SDS, perfusion with 1% Triton-X 100 (24 hours) and another perfusion with deionized water (24 hours) to remove all remaining reagents. Then, the tissue was perfused with isopropyl alcohol for 72 hours. When the adipose tissue appeared transparent, the adECM was stored with sterile PBS containing 0.1% penicillin-streptomycin at 4℃.

tag: tissue

value: muscle

value: adipose-derived stem cells

value: immune cells, adipose-derived stem cells, skeletal muscle cells, fibro-adipogenic Progenitors, muscle stem cells, vascular smooth muscle cells

value: immune cells (Cd45+/Ptprc+), adipose-derived stem cells (ASCs, Cd45-/Ptprc-, Cd105+/Eng+), skeletal muscle cells (SkM cells, Myh2+, Des+), Fibro-Adipogenic Progenitors (FAPs, Pdgfra+), muscle stem cells (MuSCs, Pax7+), vascular smooth muscle cells (VSMCs, Myh11+Acta2+)

value: adECM+ASCs


title: CRISPRi human, cyno (GEX)

description: 10x Genomics 5' GEX

tag: cell type


title: FT282CTCF-B

value: CTCF (Active Motif 61311)


title: S8, healthy donor, GEX, source: PB, donor: D, sorting: CD34pCD38p

description:
polyA RNA
GEX (3' mRNA) library: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains transcript
S8_mRNA

value: D

value: Male

value: mRNA


title: MCF7, DMSO treated, rep1

value: epithelial cell

value: DMSO


title: siDNAJC9, CENPA, rep1

value: anti-CENP-A antibody, Invitrogen, MA1-20832


title: S7, healthy donor, GEX, source: PB, donor: D, sorting: CD34pCD38n

description:
polyA RNA
GEX (3' mRNA) library: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains transcript
S7_mRNA

value: Peripheral Blood


title: FT33_25_Input

description:
ChIP-Seq for CTCF with Replicate 1 (R1) and Input available. Fastq provided for Replicate 1 (R1) and Input.
FT33-CTCF_5Jan2018_GRCh38_CGC_BWAmem.nodup.tagAlign_x_FT33-25-Input_5Jan2018_GRCh38_CGC_BWAmem.nodup.tagAlign.naive_overlap.filt.regionPeak.narrowpeak.gz

value: Fallopian tube derived epithelial cell


title: siDNAJC9, IgG, rep2

value: IgG negative control, SCBT, sc-2025


title: HFSCs 2, CNR Rarg

first: Matthew

middle: T

last: Tierney

address: 1230 York Ave, Box 300

institute: Rockefeller University

description: CNR Rarg

data_processing:
Reads were trimmed with Skewer, aligned to reference genome (mm10) using Bowtie (v.1.1.2), deduplicated with Java (v.2.3.0) Picard tools, and filtered to ≤120 bp using Samtools (v.1.3.1). BAM files for each replicate were combined using Samtools. Bigwig files were generated using Deeptools (v.3.1.2) with reads per kilobase of transcript per million mapped reads (RPKM) normalization and presented with Integrative Genomics Viewer (IGV) software. CNR peaks were called using SEACR (91) from bedGraph files generated from RPKM-normalized Bigwig files (UCSC Tools) using stringent setting and a numeric threshold of 0.001.
Assembly: mm10
Supplementary files format and content: BIGWIG file generated from combined bamfiles and peak files called from replicate pooled samples in bed format.
Library strategy: CUT&Run

source_name: Telogen (P55) skin mouse 2

extract_protocol:
To resuspend HFSCs, 3D cultures were washed with sterile PBS, dissociated into single cell suspensions using TrpLE-Express (Gibco) for 15min at 37°C. After filtering, cells were pelleted and CNR was performed as previously described in Skene et al., 2018 with minor modifications. Briefly, cells were crosslinked with 1% formaldehyde and quenched with glycine. After washes, nuclei were incubated with concanavalin-A beads, followed by antibody incubation overnight. ConA-bead-bound nuclei were incubated with MNase to cut DNA and the fragments were relaesed by CaCl2 addition.
Sequencing libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina. PCR-amplified libraries were purified using 1× ratio of SPRI beads (Beckman) and eluted in 15 μl EB buffer (Qiagen).

value: Telogen (P55) skin mouse 2

value: Hair follicle stem cells

value: wild-type


title: HFSCs 1, CNR Rxra

description: CNR Rxra

source_name: Telogen (P55) skin mouse 1

value: Telogen (P55) skin mouse 1


title: 7day-adECM+ASC+L6

description: muscle regeneration snNRA-seq data

value: muscle

value: adipose-derived stem cells and L6 myoblasts

value: immune cells, adipose-derived stem cells, skeletal muscle cells, fibro-adipogenic Progenitors, muscle stem cells, vascular smooth muscle cells


title: S6, healthy donor, GEX, source: BM, donor: D, sorting: CD34pCD38p

description:
polyA RNA
GEX (3' mRNA) library: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains transcript
S6_mRNA

value: Progenitor HSPCs

value: Bone Marrow


title: HFSCs 2, CNR Rxra

description: CNR Rxra


title: HFSCs 1, CNR Rarg

description: CNR Rarg


title: Blastocyst-Mural_WT_rep1

city: Munich

first: Francisca

last: Rojas Ringeling

address: Feodor-Lynen-Straße 25, 81377

department: Biochemistry

institute: Ludwig Maximilian University of Munich

data_processing:
Alignment of reads to the genome with the mapper.pl script from MirDeep2 version 2.0.1.2 (options -j -l 17)
Quantification of miRNas with the miRDeep2.pl script, providing the aligned collapsed reads sequences, the mature miRNAs sequence from the organism, the precursor sequences from the organism, as well as precursor sequences from Rattus norvegicus and Homo sapiens. Tabular separated file, one column for miRNA identifier, one column for counts
Assembly: GRCm38
Supplementary files format and content: Tabular separated file, one column for miRNA identifier, one column for counts

source_name: Blastocyst-Mural

extract_protocol:
Normal blastocysts at E4.5, in vivo paused blastocysts at EDG7.5, and mTORi-treated blastocysts were used for microdissection. Laser-assisted separation of ICM and mural trophoblast was performed using a Hamilton Thorne XYRCOS laser system with power setting to 100% and a pulse length of 300 µs (see Supplementary Video 1). For dissection, blastocysts were fixed between two holding pipettes. While the holding pipettes were carefully pulled apart, cellular connections were cut by successive laser pulses, allowing the separation of the blastocyst into pieces containing ICM or mural trophectoderm. Immediately after separation the tissue fragments were transferred into 7 µl PBS and frozen down on dry ice.
Small RNA libraries were prepared using the “TrueQuant small RNA-Seq” kit from GenXPro (Germany) according to the manual.  The method is based on a single-tube protocol for ligation of UMI-containing adapters to RNA molecules followed by Reverse Transcription and PCR48. No size selection of the smallRNAs was performed. The small-RNA was amplified with 12-20 cycles to reach the required amounts for sequencing. Sequencing was performed on an Illumina NextSeq500 instrument with 1 x75 bps.

value: Blastocyst-Mural

value: WT


title: Blastocyst-Mural_WT_rep2


title: Blastocyst-Polar_WT_rep2

source_name: Blastocyst-Polar

value: Blastocyst-Polar


title: FT246_25_Input

description:
ChIP-Seq for CTCF with Replicate 1 (R1) and Input available. Fastq provided for Replicate 1 (R1) and Input.
FT246-CTCF_5Jan2018_GRCh38_CGC_BWAmem.nodup.tagAlign_x_FT246-25-Input_5Jan2018_GRCh38_CGC_BWAmem.nodup.tagAlign.naive_overlap.filt.regionPeak.narrowpeak.gz


title: FT246_CTCF

value: CTCF (Active Motif 61311)


title: S5, healthy donor, GEX, source: BM, donor: D, sorting: CD34pCD38n

description:
polyA RNA
GEX (3' mRNA) library: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains transcript
S5_mRNA

value: Primitive HSPCs

value: D

value: Male

value: mRNA


title: PERFFseq_Mobpplus

source_name: Mouse frozen cerebellum

value: Mouse frozen cerebellum

value: Mobp

value: brain


title: FT282_CTCF-A

value: Fallopian tube derived epithelial cell


title: Blastocyst-Polar_WT_rep1


title: Blastocyst-mTORi_diapaused_rep3

value: mTOR inhibited pause


title: Blastocyst-mTORi_diapaused_rep2


title: PERFFseq_Mobpminus


title: HFSCs, CNR IgG

description: CNR IgG

value: Telogen (P55) skin mouse 1

value: Hair follicle stem cells

value: wild-type


title: S3, healthy donor, GEX, source: BM, donor: C, sorting: CD34pCD38n

description:
polyA RNA
GEX (3' mRNA) library: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains transcript
S3_mRNA

value: Bone Marrow

value: C

value: Female


title: Blastocyst-mTORi_diapaused_rep1

value: Blastocyst-Mural


title: FT33_CTCF

value: CTCF (Active Motif 61311)


title: Blastocyst-Polar_mTORi_rep3

value: Blastocyst-Polar


title: S4, healthy donor, GEX, source: BM, donor: C, sorting: CD34pCD38p

description:
polyA RNA
GEX (3' mRNA) library: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains transcript
S4_mRNA

value: Progenitor HSPCs


title: S1, healthy donor, GEX, source: PB, donor: D, sorting: CD34pCD38n

description:
polyA RNA
GEX (3' mRNA) library: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains transcript
S1_mRNA

value: Primitive HSPCs

value: Peripheral Blood

value: D

value: Male


title: P4, healthy donor, GEX, source: PB, donor: G, sorting: CD34pCD38n

description:
polyA RNA
GEX (3' mRNA) library: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains transcript
P4_mRNA

value: G

value: mRNA


title: Blastocyst-Polar_diapaused_rep3

value: diapaused


title: Blastocyst-Polar_diapaused_rep2


title: Blastocyst-Polar_mTORi_rep1

value: mTOR inhibited pause


title: Blastocyst-Polar_mTORi_rep2


title: Blastocyst-Mural_diapaused_rep2


title: Blastocyst-Mural_diapaused_rep3


title: P3, healthy donor, GEX, source: PB, donor: G, sorting: CD34p

description:
polyA RNA
GEX (3' mRNA) library: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains transcript
P3_mRNA

value: HSPCs


title: Blastocyst-Polar_diapaused_rep1


title: WT, paused, replicate 4

data_processing:
Transcript abundance estimations per sample were obtained with kallisto and imported to R with the Bioconductor package tximport
Assembly: GRCm38
Supplementary files format and content: transcript abundance estimations from kallisto

source_name: ESC

extract_protocol:
Total RNA was extracted using the RNeasy extraction kit (Qiagen, 74104)
1 µg of total RNA was used for standard library preparation using NEBNext PolyA mRNA magnetic isolation module (NEB, E7490).

treatment_protocol: 800,000 wild-type or Dgcr8 KO24 mouse ESCs in normal or mTORi culture (day 2) were used.

value: ESC

value: WT

value: mTORi culture


title: WT, paused, replicate 1


title: WT, paused, replicate 3


title: B3, healthy donor, GEX, source: BM, donor: B, sorting: CD34p

description:
polyA RNA
GEX (3' mRNA) library: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains transcript
B3_mRNA

value: Bone Marrow

value: B

value: Female


title: P2, healthy donor, GEX, source: PB, donor: F, sorting: CD34pCD38n

description:
polyA RNA
GEX (3' mRNA) library: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains transcript
P2_mRNA

value: F


title: P1, healthy donor, GEX, source: PB, donor: F, sorting: CD34p

description:
polyA RNA
GEX (3' mRNA) library: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains transcript
P1_mRNA


title: WT, paused, replicate 2


title: B2, healthy donor, GEX, source: BM, donor: A, sorting: CD34pCD38n

description:
polyA RNA
GEX (3' mRNA) library: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains transcript
B2_mRNA

value: A


title: WT, not paused, replicate 2

value: normal ESC culture conditions


title: WT, not paused, replicate 4


title: WT, not paused, replicate 1


title: S2, healthy donor, GEX, source: PB, donor: D, sorting: CD34pCD38p

description:
polyA RNA
GEX (3' mRNA) library: index1 file contains library index; read1 file contains cell barcode and UMI; read2 file contains transcript
S2_mRNA

value: Progenitor HSPCs

value: Peripheral Blood


title: WT, not paused, replicate 3


title: DGRC8 KO, paused, replicate 4

value: DGCR8 KO


title: Sample_J_FRE

city: Charlestown

first: Mahesh Chandra

last: Kodali

state: MA

department: Neurology

institute: Massachusetts General Hospital / Harvard Medical School

description: 10x Genomics

data_processing:
Reads were aligned to reference 2020-A (Ensembl 98) transcriptome 156 and quantified using Cell Ranger v6.0.2 multipipeline.
Assembly: reference 2020-A (Ensembl 98) transcriptome
Supplementary files format and content: 10X Cell Ranger Outputs

source_name: Cerebrospinal Fluid Cells

extract_protocol:
Fresh or thawed cryopreserved CSF mixed with 10x 5’ v2 RT Reagent Master Mix were immediately processed with the 10x Genomics Chromium Next GEM Single Cell 5’ v2 kit (10x Genomics, Pleasanton, CA), cDNA amplified, and library constructed per the manufacturer’s protocol. Library quality control (QC) was based on Agilent Tapestation 4200 HS D1000 screentapes (Agilent Technologies, Waldbronn, Germany). Multiplexed library pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms (Kapa BioSystems, Boston, MA) and sequenced at shallow depths on Illumina’s iSeq 100 v2 flow cell for 26x10x10x90 cycles for estimated reads per cell. After demultiplexing,  libraries were rebalanced based on reads per cell. Normalized pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms and high depth sequenced on Illumina’s NovaSeq 6000 S4 v1.5 flow cell for 26x10x10x90 cycles, to obtain a sequencing depth of 50K reads/cell (whole transcriptome libraries). Reads were aligned to reference 2020-A (Ensembl 98) transcriptome and quantified using Cell Ranger v6.0.2 multipipeline.
Fresh or thawed cryopreserved CSF mixed with 10x 5’ v2 RT Reagent Master Mix were immediately processed with the 10x Genomics Chromium Next GEM Single Cell 5’ v2 kit (10x Genomics, Pleasanton, CA), cDNA amplified, and library constructed per the manufacturer’s protocol. Library quality control (QC) was based on Agilent Tapestation 4200 HS D1000 screentapes (Agilent Technologies, Waldbronn, Germany). Multiplexed library pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms (Kapa BioSystems, Boston, MA) and sequenced at shallow depths on Illumina’s iSeq 100 v2 flow cell for 26x10x10x90 cycles for estimated reads per cell. After demultiplexing,  libraries were rebalanced based on reads per cell. Normalized pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms and high depth sequenced on Illumina’s NovaSeq 6000 S4 v1.5 flow cell for 26x10x10x90 cycles, to obtain a sequencing depth of 50K reads/cell (whole transcriptome libraries). Reads were aligned to reference 2020-A (Ensembl 98) transcriptome and quantified using Cell Ranger v6.0.2 multipipeline.
Fresh or thawed cryopreserved CSF mixed with 10x 5’ v2 RT Reagent Master Mix were immediately processed with the 10x Genomics Chromium Next GEM Single Cell 5’ v2 kit (10x Genomics, Pleasanton, CA), cDNA amplified, and library constructed per the manufacturer’s protocol. Library quality control (QC) was based on Agilent Tapestation 4200 HS D1000 screentapes (Agilent Technologies, Waldbronn, Germany). Multiplexed library pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms (Kapa BioSystems, Boston, MA) and sequenced at shallow depths on Illumina’s iSeq 100 v2 flow cell for 26x10x10x90 cycles for estimated reads per cell. After demultiplexing,  libraries were rebalanced based on reads per cell. Normalized pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms and high depth sequenced on Illumina’s NovaSeq 6000 S4 v1.5 flow cell for 26x10x10x90 cycles, to obtain a sequencing depth of 50K reads/cell (whole transcriptome libraries). Reads were aligned to reference 2020-A (Ensembl 98) transcriptome and quantified using Cell Ranger v6.0.2 multipipeline.

value: Cerebrospinal Fluid Cells

value: Primary

tag: protocol

value: FRE


title: DGRC8 KO, paused, replicate 1


title: DGRC8 KO, paused, replicate 3


title: DGRC8 KO, paused, replicate 2


title: Sample_J_FBS

description: 10x Genomics

value: FBS


title: Blastocyst-Mural_diapaused_rep1

value: Blastocyst-Mural

value: diapaused


title: DGRC8 KO, not paused, replicate 2

value: ESC


title: DGRC8 KO, not paused, replicate 1


title: DGRC8 KO, not paused, replicate 4


title: RNA-seq,Trp53_WT,Rep3

city: Toronto

first: Sajid

middle: A

last: Marhon

state: ON

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre

description:
Trp53_WT.Neg.Abs.bw
Trp53_WT.Pos.Abs.bw

data_processing:
Raw reads were trimmed to remove adapters and low quality bases. Trimmed reads were aligned to the mouse genome mm10 using the STAR pipeline. Read counts were calculated for genes and repeat elements using featureCount tool. Differential analysis was performed using edgeR tool.
Assembly: mm10
Supplementary files format and content: Bigwig files include genome track signal of the normalized reads.

source_name: ovarian surface epithelium

growth_protocol: Asynchronous growth

extract_protocol:
total RNA isolation and DNaseI treatment was performed using RNeasy Mini Kit (Qiagen) as per manufacturer’s protocol
TruSeq® Stranded Total RNA Library Prep Gold (96 Samples) kit (Illumina, 20020599)

tag: strain

value: ovarian surface epithelium

value: epithelial

value: immortalized, untreated

tag: time


title: RNA-seq,Trp53_WT,Rep2

description:
Trp53_WT.Neg.Abs.bw
Trp53_WT.Pos.Abs.bw


title: DGRC8 KO, not paused, replicate 3


title: Sample_H_REC

description: 10x Genomics

value: REC


title: Sample_I_FBS_2

description: 10x Genomics


title: Sample_I_FBS_1

description: 10x Genomics


title: RNA-seq,Trp53_WT,Rep1

description:
Trp53_WT.Neg.Abs.bw
Trp53_WT.Pos.Abs.bw


title: RNA-seq,Trp53_KO,Rep3

description:
Trp53_KO.Neg.Abs.bw
Trp53_KO.Pos.Abs.bw