title: SPATAC-seq with mouse organogenesis well-E2G


title: SPATAC-seq with zebrafish embryogenesis well-ZSH5 (DNBSEQ-T7)

status: Public on Apr 14 2024

type: SRA

city: beijing

first: Keyong

last: Sun

address: Hai Dian street

department: School of Medicine

country: China

institute: tsinghua university

description:
ZSH5_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file

library_source: genomic

data_processing:
Raw Read1 Fastq files within genome DNA (position from 66-121 nucleotide) were extracted and renamed as new Read1 file. Similarly, raw Read2 Fastq files within genome DNA (position from 51-101 nucleotide) were extracted and renamed as new Read2 file. Round 1, round2 and round3 barcodes are extracted from Read1 and Read2 Fastq files, and are merged and were added into the header of new Read1 and Read2 files. New Read1 and Read2 files were aligned to the reference zebrafish GRCz11 genome assemblyby BWA. The scATAC-seq fragment files were created by sinto (https://timoast.github.io/sinto/index.html) according to standard procedure. Barcodes in fragment file of each sublibrary were tagged with Round4 barcodes (PCR wells), then all sublibrary fragment files were merged into one big fragment file, which were further split into stage-specific fragment files based on Round1 barcodes. For the bulk ATAC-seq data from zebrafish embryos, reads were trimmed with to remove the Nextera sequencing adaptors by trim_galore. The trimmed reads were mapped to the reference zebrafish (GRCz11) genome using BWA. Reads with mapping quality less than 30 and duplication were removed by samtools. BigWig files were generated by bamCoverage.  Fastq files of 10x Genomics scATAC-seq were processed Cell Ranger ATAC Pipeline (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac, v.1.2.0).
Assembly: GRCz11
Supplementary files format and content: bed files, the fragment file of SPATAC-seq, the information of each unique fragment of SPATAC within each sublibrary, including the chromsome number, start site, end site and frequency.
Supplementary files format and content: bed files, the fragment file of 10x Genomics scATAC-seq, the information of each unique fragment within each sample, including the chromsome number, start site, end site and frequency.
Supplementary files format and content: bed files, the fragment file of bulk ATAC-seq, the information of each unique fragment, including the chromsome number, start site, end site
Supplementary files format and content: excel file, cell metadata information for the atlas of zebrafish development, including cell types, coordinate and quality metric of each cell
Supplementary files format and content: bigWig file, genome-wide signal for 604 cell types of scATAC-seq datasets
Supplementary files format and content: bigWig file, genome-wide signal for bulk ATAC-seq of zebrafish embryos

molecule: genomic DNA

organism: Danio rerio

source_name: zebrafish embryos

extract_protocol:
Embryo nuclei were extracted via previously described methods (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019) with some modifications. Briefly, frozen embryos were transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 1 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 200 μl NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB.
Bulk ATAC-seq, 10x Genomics scATAC-seq, and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details.

tag: tissue

value: zebrafish embryos


title: Patient-derived GBM cell line-19

city: Seoul

first: Sun Ha

last: Paek

address: 101, Daehak-ro, Jongno-gu

department: Department of Neurosurgery

country: South Korea

institute: Seoul National University College of Medicine, Seoul National University Hospital

library_source: transcriptomic

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean
Sequenced reads were mapped to GRCh38 whole genome by using HISAT2 version 2.1.0 with parameter -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 1.3.4d, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Brain

growth_protocol: Patient-derived primary GBM cell lines were cultured in Dulbecco’s modified Eagle’s high glucose medium (SH30243.01, Hyclone) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (2357664RP, Gibco) and 1% antibiotic-antimycotic (15240062, Gibco). All cells were maintained at 37 °C in a 5% CO2 incubator and tested regularly for mycoplasma contamination by Mycoplasma Detection Kit (rep-mys-20, InvivoGen).

extract_protocol:
Total RNA extraction was performed using the RNeasy Mini Kit (74106, QIAGEN) according to the manufacturer’s instructions
Libraries for bulk RNA-seq were prepared using the TruSeq Stranded Total RNA Library Prep Kit

value: Brain

tag: cell line

value: Primary

tag: cell type

value: Human glioblastoma multiforme

tag: treatment

value: Untreated

tag: sex/age


title: Beta cells, control, biol rep 2

city: Rijeka

first: Felix

middle: Martinus

last: Wensveen

address: Braće Branchetta 20

department: Histology & Embryology

country: Croatia

institute: University of Rijeka faculty of medicine

data_processing:
Sequence reads were mapped to the mouse GRCm38/mm10 genome with TopHat2 in very-sensitive settings for Bowtie2 (Langmeadand Salzberg, 2012) and EnsEMBL annotation release 67.
Gene expression was quantified by featureCounts and analyzed using DESeq2 within R based on an adjusted P (padj) < 0.05 and, where applied, fold change > 1.2.
As an input for the analysis the raw counts table was used.
Assembly: mm10
Supplementary files format and content: tab-delimited .tsv file contains raw counts for each sample
Supplementary files format and content: Tab-delimited .xlsx file includes comparison between IFNg/IL-1b treated and untreated samples

organism: Mus musculus

source_name: Pancreas

growth_protocol: After purification, beta cells were cultured for 48h in complete RPMI medium (supplemented with 10% FBS, 1% HEPES, sodium pyruvate, glutamine, streptomycin and penicillin).

extract_protocol:
RNA was extracted using standard TRIzol (Invitrogen) protocol
Sequencing libraries were generated using the CEL-seq2 protocol, rendering barcoded samples.

treatment_protocol: 3x104 beta cells were incubated with 10ng/ml of IFNg and 2ng/ml of IL-1b. 4h later, cells were incubated for 1h in KBR medium (115mM Nacl, 4.7mM of KCl, 2.6mM CaCl2x2H2O, 1.2mM KH2PO4, 1.2mM MgSO4x2H2O, 10mM of Hepes,0.5% of BSA and with 2.8mM of Glucose), after which cells were harvested

value: Pancreas

value: beta cells

tag: genotype

value: WT

value: glucose only


title: SPATAC-seq with zebrafish embryogenesis well-ZSH4 (DNBSEQ-T7)

description:
ZSH4_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with mouse organogenesis well-E2F

data_processing:
Raw Read1 Fastq files within genome DNA (position from 66-121 nucleotide) were extracted and renamed as new Read1 file. Similarly, raw Read2 Fastq files within genome DNA (position from 51-101 nucleotide) were extracted and renamed as new Read2 file of Cell Ranger ATAC format. Round 1, Round2 and Round3 barcodes are extracted from raw Read1 and Read2 Fastq files, are merged after correcting 1bp mismatch. Then merged barcodes were attached in the read name of new Read1 and Read2 fastq files by software sinto (https://timoast.github.io/sinto/index.html), which were aligned to the reference mouse (mm10) genome (https://cf.10xgenomics.com/supp/cell-atac/refdata-cellranger-atac-mm10-1.2.0.tar.gz) using BWA. The bam file of each sublibrary was converted to scATAC-seq fragment file by sinto according to standard procedure. Finnaly, the barcodes in fragment file of each sublibrary were tagged with Round4 barcodes (PCR wells).
Assembly: mm10
Supplementary files format and content: bed files, the fragment file of SPATAC-seq, the information of each unique fragment of SPATAC within each sublibrary, including the chromsome number, start site, end site and frequency.
Supplementary files format and content: CSV file, cell metadata information for the atlas of zebrafish development, including cell types, coordinate and quality metric of each cell

source_name: mouse embryo

extract_protocol:
Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment.
Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details.

value: mouse embryo


title: SPATAC-seq with mouse organogenesis well-E7A


title: Patient-derived GBM cell line-18


title: Beta cells, control, biol rep 1


title: SPATAC-seq with zebrafish embryogenesis well-ZSH3 (DNBSEQ-T7)

description:
ZSH3_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with mouse organogenesis well-E2H


title: Beta cells, IFNg/IL1b, biol rep 1


title: SPATAC-seq with zebrafish embryogenesis well-ZSH2 (DNBSEQ-T7)

description:
ZSH2_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Patient-derived GBM cell line-16


title: SPATAC-seq with mouse organogenesis well-E2C


title: Patient-derived GBM cell line-14


title: GMP cells, Enl-T1, TDI11055, Rep1

city: Philadelphia

first: Liling

last: Wan

state: PA

address: 421 Curie Blvd

department: Cancer Biology

country: USA

institute: University of Pennsylvania

data_processing:
RNA-seq samples were sequenced using Illumina NextSeq 500.
Raw reads were mapped to the mouse reference genome (mm10) and transcriptome using HISAT2 v 2.2.1 with default parameters.
The raw counts for gene were calculated by featureCounts v2.0.2.
Differentially expressed genes between conditions were statistically determined using R package DESeq2 v1.40.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene raw count number for each sample

source_name: Blood

growth_protocol: LSK, GMP, L-GMP, cKit+Mac1+ and cKit-Mac1+ cells were fresh sorted from bone marrow ofEnl-WT or T1 mice.

extract_protocol:
RNeasy UCP Micro kit (Qiagen, #73934) was used to extract total RNA and remove genomic DNA.
500ng total RNA was used for library preparation using polyA mRNA magnetic Isolation module (NEB, #E7490) and RNA library prep kit (NEB, #7770) following manufacturer’s instructions. The library quality was assessed on an Agilent Bioanalyzer DNA chip (Agilent, #5067-1504). RNA-seq samples were sequenced using Illumina NextSeq 500.

treatment_protocol: LSK, GMP cells were treated with DMSO or 10 uM TDI-11055 for 48 hours.

value: Blood

value: GMP

value: hematopoietic progenitor cell


title: GMP cells, Enl-T1, DMSO, Rep2

value: DMSO


title: SPATAC-seq with mouse organogenesis well-E2E


title: SPATAC-seq with zebrafish embryogenesis well-ZSH1 (DNBSEQ-T7)

description:
ZSH1_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Patient-derived GBM cell line-15


title: SPATAC-seq with zebrafish embryogenesis well-ZSG7 (DNBSEQ-T7)

description:
ZSG7_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Patient-derived GBM cell line-12


title: SPATAC-seq with mouse organogenesis well-E2B


title: SPATAC-seq with mouse organogenesis well-E1H


title: GMP cells, Enl-WT, DMSO, Rep1


title: LSK cells, Enl-T1, TDI11055, Rep2

value: LSK

value: hematopoietic stem cell


title: Patient-derived GBM cell line-11


title: GMP cells, Enl-T1, DMSO, Rep1


title: GMP cells, Enl-T1, TDI11055, Rep2


title: Patient-derived GBM cell line-13


title: SPATAC-seq with mouse organogenesis well-E2D


title: SPATAC-seq with mouse organogenesis well-E1G


title: LSK cells, Enl-T1, TDI11055, Rep1


title: SPATAC-seq with zebrafish embryogenesis well-ZSG6 (DNBSEQ-T7)

description:
ZSG6_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with mouse organogenesis well-E2A


title: SPATAC-seq with zebrafish embryogenesis well-ZSG4 (DNBSEQ-T7)

description:
ZSG4_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZSG8 (DNBSEQ-T7)

description:
ZSG8_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Patient-derived GBM cell line-10


title: SPATAC-seq with mouse organogenesis well-E1F


title: SPATAC-seq with zebrafish embryogenesis well-ZSG3 (DNBSEQ-T7)

description:
ZSG3_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: LSK cells, Enl-T1, DMSO, Rep2


title: Patient-derived GBM cell line-8


title: LSK cells, Enl-T1, DMSO, Rep1


title: Patient-derived GBM cell line-9

value: Recurrent


title: SPATAC-seq with mouse organogenesis well-E1E


title: SPATAC-seq with mouse organogenesis well-E1D


title: SPATAC-seq with zebrafish embryogenesis well-ZSG2 (DNBSEQ-T7)

description:
ZSG2_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file

value: zebrafish embryos


title: LSK cells, Enl-WT, DMSO, Rep1


title: Patient-derived GBM cell line-7

value: Brain


title: SPATAC-seq with mouse organogenesis well-E1C


title: SPATAC-seq with zebrafish embryogenesis well-ZSG1 (DNBSEQ-T7)

description:
ZSG1_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZSG5 (DNBSEQ-T7)

description:
ZSG5_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with mouse organogenesis well-E1B


title: SPATAC-seq with zebrafish embryogenesis well-ZSF8 (DNBSEQ-T7)

description:
ZSF8_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Patient-derived GBM cell line-6

value: Primary


title: cKit-Mac1+ cells, Enl-T1, Rep1

value: hematopoietic myeloid cell

value: No


title: SPATAC-seq with zebrafish embryogenesis well-ZSF7 (DNBSEQ-T7)

description:
ZSF7_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Patient-derived GBM cell line-5

value: Human glioblastoma multiforme

value: Untreated


title: SPATAC-seq with mouse organogenesis well-E1A


title: cKit-Mac1+ cells, Enl-WT, Rep2

value: WT


title: Patient-derived GBM cell line-4


title: SPATAC-seq with zebrafish embryogenesis well-ZSF6 (DNBSEQ-T7)

description:
ZSF6_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZSF4 (DNBSEQ-T7)

description:
ZSF4_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with mouse organogenesis well-E19H


title: Patient-derived GBM cell line-2


title: cKit+Mac1+ cells, Enl-T1, Rep2


title: cKit-Mac1+ cells, Enl-WT, Rep1


title: Patient-derived GBM cell line-3


title: SPATAC-seq with zebrafish embryogenesis well-ZSF3 (DNBSEQ-T7)

description:
ZSF3_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: cKit+Mac1+ cells, Enl-T1, Rep1


title: SPATAC-seq with zebrafish embryogenesis well-ZSF5 (DNBSEQ-T7)

description:
ZSF5_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with mouse organogenesis well-E19G


title: SPATAC-seq with mouse organogenesis well-E19F


title: SPATAC-seq with mouse organogenesis well-E19E


title: Patient-derived GBM cell line-1


title: cKit+Mac1+ cells, Enl-WT, Rep1


title: SPATAC-seq with zebrafish embryogenesis well-ZSF2 (DNBSEQ-T7)

description:
ZSF2_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: cKit-Mac1+ cells, Enl-T1, Rep2


title: SPATAC-seq with zebrafish embryogenesis well-ZSF1 (DNBSEQ-T7)

description:
ZSF1_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: cKit+Mac1+ cells, Enl-WT, Rep2


title: hinput

city: Jinan

first: Nianyu

last: Li

state: ShanDong

address: 44 wenhua xi road

institute: Shandong University

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11) software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA (v 0.7.12) and clean reads were aligned to the reference genome using BWA mem (v 0.7.12).
For a specific ChIP-seq binding site, individual reads mapping to the plus or minus strand and present significant enrich. For single-end sequencing, the fragment size was estimated with MACS2 predicted method with default parameters. MACS2 scan all the genome with a specific window size and calculate the reads enrichment level. A particular number of windows were used as samples to build enrichment model and to predict fragment size. The following peak calling analysis was based on this predicted fragment size.
After mapping reads to the reference genome, we used the MACS2 (version 2.1.0) peak calling software to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for all data sets. After peak calling, the distribution of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed.
The interaction between transcript factor or chromatin histone modification and DNA were not random, while they show some specific sequence preference. Homer was used to detect the denovo sequence motif and the matched known motifs.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

source_name: Ovary

growth_protocol: DMEM/F12, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37℃ at 5% CO2.

extract_protocol:
ChIP DNA degradation and contamination was monitored on agarose gels. DNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). DNA concentration was measured using Qubit® DNA Assay Kit in Qubit® 3.0 Flurometer (Life Technologies, CA, USA).
The purified DNA was used for ChIP-seq library preparation. The library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Ovary

value: KGN cell

value: human granulosa cells


title: hG3BP1

tag: antibody

value: G3BP1 antibody


title: SPATAC-seq with mouse organogenesis well-E19C

value: mouse embryo


title: SPATAC-seq with mouse organogenesis well-E19B


title: Liver, explant, Healthy_2

city: Kansas City

first: David

middle: S

last: Umbaugh

email: dumbaug@gmail.com, hjaeschke@kumc.edu

state: KS

address: 3901 Rainbow Blvd

institute: University of Kansas Medical Center

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, mapped to GRCH38 genome using Hisat2
Read counts were generated using subread with parameters -t exon - g gene_id
Assembly: GRCH38
Supplementary files format and content: Matrix csv with raw or edgeR normalized (CPM) gene coutns for every sample

source_name: liver

extract_protocol:
Liver explant, RNA extracted using TRIZOL
RNA libraries were prepared for sequencing using standard Illumina protocols. TruSeq Total Stranded RNA

value: liver

tag: condition

value: Healthy


title: SPATAC-seq with zebrafish embryogenesis well-ZSE8 (DNBSEQ-T7)

description:
ZSE8_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Liver, explant, Healthy_1


title: SPATAC-seq with zebrafish embryogenesis well-ZSE6 (DNBSEQ-T7)

description:
ZSE6_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Liver, explant, APAP

value: APAP-ALF liver


title: L-GMP cells, Enl-T1, Rep1

value: Blood

value: L-GMP

value: hematopoietic progenitor cell


title: L-GMP cells, Enl-T1, Rep2


title: SPATAC-seq with mouse organogenesis well-E19A


title: SPATAC-seq with mouse organogenesis well-E18H


title: GMP cells, Enl-T1, Rep2

value: GMP


title: SPATAC-seq with zebrafish embryogenesis well-ZSE7 (DNBSEQ-T7)

description:
ZSE7_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file

value: zebrafish embryos


title: Pt_22_Normal_IORT

city: Santa Monica

first: Javier

last: Orozco

state: CA

address: 2200 Santa Monica Blvd

institute: Saint John's Cancer Institute

data_processing:
Raw RNA-seq reads were checked for quality using FastQC
Filtered for adapters using Trimmomatic
Mapped to the human genome and annotation references GRCh38 using the STAR aligner (v.2.7.2b)
Read counts were generated by the DESeq2 R Bioconductor package
Assembly: GRCh38
Supplementary files format and content: Non-Normalized Counts per gene (.csv file)

source_name: Breast tissue

extract_protocol:
After deparaffinization, 8-10 μm-thick serial tissue sections were micro-dissected using labeled 4-μm thick H&E slides as a template. RNA was purified from the breast re-excision specimens from regions containing normal breast tissue, SM, and SMwA using the Quick-RNA FFPE kit (# R1008, Zymo Research).
RNA samples with high quality (RIN ≥8.0) and high purity (A260/280 >1.8) were used to generate libraries using KAPA HyperPrep Kit with RiboErase (rRNA depletion kit) for FFPE tissues

tag: patient id

value: Breast tissue

tag: breast tissue_type

value: Normal

tag: Sex

value: Female

value: IORT


title: SPATAC-seq with mouse organogenesis well-E19D


title: GMP cells, Enl-T1, Rep1

value: No


title: SPATAC-seq with mouse organogenesis well-E18G


title: SPATAC-seq with zebrafish embryogenesis well-ZSE5 (DNBSEQ-T7)

description:
ZSE5_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Pt_21_Normal_non-IORT

value: non-IORT


title: GMP cells, Enl-WT, Rep2

value: WT


title: GMP cells, Enl-WT, Rep1


title: Pt_21_SM_non-IORT

value: SM


title: SPATAC-seq with zebrafish embryogenesis well-ZSE4 (DNBSEQ-T7)

description:
ZSE4_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Pt_20_SM_IORT


title: SPATAC-seq with zebrafish embryogenesis well-ZSE3 (DNBSEQ-T7)

description:
ZSE3_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with mouse organogenesis well-E18F

value: mouse embryo


title: SPATAC-seq with mouse organogenesis well-E18E


title: LSK cells, Enl-T1, Rep1

value: LSK

value: hematopoietic stem cell


title: SPATAC-seq with zebrafish embryogenesis well-ZSE2 (DNBSEQ-T7)

description:
ZSE2_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with mouse organogenesis well-E18C


title: Pt_20_Normal_IORT


title: LSK cells, Enl-T1, Rep2


title: Pt_18_Normal_non-IORT


title: SPATAC-seq with zebrafish embryogenesis well-ZSE1 (DNBSEQ-T7)

description:
ZSE1_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: LSK cells, Enl-WT, Rep2


title: LSK cells, Enl-WT, Rep1


title: SPATAC-seq with mouse organogenesis well-E18B


title: SPATAC-seq with mouse organogenesis well-E18A


title: SPATAC-seq with mouse organogenesis well-E18D


title: control_uterus

city: Guangzhou

first: Ji-Long

last: Liu

address: 483 Wushan Rd

institute: South China Agricultural University

data_processing:
Clean reads were mapped to mouse genome (UCSC mm9) by using HISAT v2.2.1
Mapped reads were assembled by using Cufflinks v2.2.1
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample

molecule: polyA RNA

source_name: whole uterus

extract_protocol:
TRIzol reagent (Invitrogen) was used to extract total RNAs according to manufacturers’ instructions.
RNA-seq libraries were created by using the TruSeq RNA sample preparation kit (Illumina).

treatment_protocol: Female mice aged 6-8 weeks were mated with fertile males to induce pregnancy. The appearance of the vaginal plug was designated as gestation day (GD) 1. Pregnant females were sacrificed on GD8.

value: whole uterus

tag: time

value: gestational day 8

value: mixed


title: Pt_17_SMwA_IORT

value: SMwA


title: SPATAC-seq with zebrafish embryogenesis well-ZSD6 (DNBSEQ-T7)

description:
ZSD6_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with mouse organogenesis well-E17H


title: SPATAC-seq with mouse organogenesis well-E17G


title: SPATAC-seq with zebrafish embryogenesis well-ZSD5 (DNBSEQ-T7)

description:
ZSD5_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: H3.3G34R_input

city: Shanghai

first: Yang

last: Shi

address: NO. 138, Yi-Xue-Yuan Road

institute: Fudan university

data_processing:
base_calling: CASAVA package (Illumina v1.7)
alignment: bowtie (version 1.0.0)
peak_calling: macs14 (version 1.4)
Genome_build: mm9

extract_protocol:
Chromatin samples were incubated with specific antibodies in ChIP Lysis buffer (50mM HEPES pH7.5, 500mM NaCl, 1mM EDTA, 1%Triton, 0.1%Na-deoxylcholate, 0.1% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on protein A/G beads (10μl per reaction). The bound fractions were washed 3 times with Lysis buffer, and 3 times with RIPA buffer (50mM Hepes, 300mM LiCl, 1mM EDTA, 0.5%NP-40, 0.7%Nadeoxylcholate), and once with TE. Elution and Reverse crosslinking were carried out in Elution buffer (50mM Tris, PH8.0, 1mM EDTA, 1% SDS) 65℃ for 6 hours. After RNase A and protease K digestion, DNA fraction was purified using PCR extraction kit (QIAGEN).
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols.

value: Neural stem cell line established from cerebral vesicles of 9-day-old mouse embryos lacking a functional p53 gene

value: NE-4C H3,3A KO,H3.3G34R-HA


title: SPATAC-seq with zebrafish embryogenesis well-ZSD3 (DNBSEQ-T7)

description:
ZSD3_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file

value: zebrafish embryos


title: SPATAC-seq with mouse organogenesis well-E17F


title: H3.3WT_input

value: NE-4C H3,3A KO,H3.3WT-HA


title: Patient-derived GBM cell line-17

value: Brain

value: Primary

value: Human glioblastoma multiforme

value: Untreated


title: Pt_16_Normal_non-IORT

value: Breast tissue

value: Normal

value: Female

value: non-IORT


title: Pt_15_Normal_non-IORT


title: SPATAC-seq with mouse organogenesis well-E17E

value: mouse embryo


title: Pt_14_Normal_non-IORT


title: Pt_19_Normal_IORT

value: IORT


title: H3.3G34R_H3K27Ac_ChIP

value: Millpore 07-360


title: SPATAC-seq with zebrafish embryogenesis well-ZSD7 (DNBSEQ-T7)

description:
ZSD7_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with mouse organogenesis well-E17D


title: SPATAC-seq with zebrafish embryogenesis well-ZSD1 (DNBSEQ-T7)

description:
ZSD1_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: H3.3WT_H3K27Ac_ChIP


title: Pt_13_SMwA_IORT


title: Pt_13_SM_IORT

value: SM


title: SPATAC-seq with zebrafish embryogenesis well-ZSC8 (DNBSEQ-T7)

description:
ZSC8_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Pt_17_SM_IORT


title: SPATAC-seq with mouse organogenesis well-E17B


title: SPATAC-seq with mouse organogenesis well-E17C


title: H3.3G34R_H3K4me1_ChIP

value: Active Motif 39297


title: METTL3OE_uterus

value: whole uterus

value: gestational day 8

value: mixed


title: SPATAC-seq with zebrafish embryogenesis well-ZSD4 (DNBSEQ-T7)

description:
ZSD4_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file

value: zebrafish embryos


title: H3.3WT_H3K4me1_ChIP

value: Neural stem cell line established from cerebral vesicles of 9-day-old mouse embryos lacking a functional p53 gene

value: NE-4C H3,3A KO,H3.3WT-HA


title: Pt_12_Normal_non-IORT


title: H3.3G34R_Rack7_ChIP

value: NE-4C H3,3A KO,H3.3G34R-HA

value: Bethyl A302-089A


title: SPATAC-seq with zebrafish embryogenesis well-ZSC7 (DNBSEQ-T7)

description:
ZSC7_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Pt_11_Normal_IORT

value: Breast tissue


title: H3.3WT_Rack7_ChIP


title: SPATAC-seq with mouse organogenesis well-E17A


title: SPATAC-seq with zebrafish embryogenesis well-ZSC6 (DNBSEQ-T7)

description:
ZSC6_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Pt_11_SMwA_IORT

value: SMwA


title: SPATAC-seq with mouse organogenesis well-E155


title: Pt_11_SM_IORT

value: Female


title: H3.3G34R_HA_ChIP

value: Santa Cruz Bio sc-7392Ac


title: SPATAC-seq with mouse organogenesis well-E154

value: mouse embryo


title: SPATAC-seq with zebrafish embryogenesis well-ZSD2 (DNBSEQ-T7)

description:
ZSD2_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Pt_10_Normal.region_2_IORT

value: IORT


title: H3.3WT_HA_ChIP


title: SPATAC-seq with mouse organogenesis well-E153


title: SPATAC-seq with zebrafish embryogenesis well-ZSC3 (DNBSEQ-T7)

description:
ZSC3_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Grape berry. Cabernet sauvignon genotype, Sicily site rep3

city: Catania

first: Angela Roberta

last: Lo Piero

state: CT

address: Via S. Sofia 98

country: Italy

institute: University of Catania

data_processing:
Base calling, base quality and Phred score relationship performed with the Illumina CASAVA v1.8 software
Raw reads are filtered to remove reads containing adapters or reads of low quality
The annotated sequences not corresponding with plant species were filtered out.
In the absence of a reference genome clean reads have been assembled using Trinity software (2.6.6 version) ( Kmer coverage = 3, min glue = 4). Corset software (4.6 version) was used for hierarchical clustering (parameter -m 10)
The assembly assessment and gene prediction were evaluated by comparing the Unigenes to the set of Embryophyta genes using the BUSCO quality assessment tool coupled with the OrthoDB (9.0 version) database of orthologs
Seven databases have been applied for gene functional annotation: Nr, Nt, Pfam, KOG/COG, Swiss-Prot, KEGG and GO.
CDS preduction using blast and EST-scan
De novo transcriptome filtered by Corset used as a reference for mapping reads back to transcriptome and quantify the expression level using RSEM.
DESeq2 used for gene expression difference analysis
Assembly: De novo assembly
Supplementary files format and content: raw_counts: txt format, contains read counts of all the unigenes in all the samples
Supplementary files format and content: Unigene: FASTA format, contaiins coding sequences of the assembled unigenes

organism: Vitis vinifera

source_name: fruit

growth_protocol: Vines were bush trained at 0.5 m height, with two to six main branches, each branch spur-pruned to one spur and two buds per spur

extract_protocol:
Ten berries from each biological replicate, kept frozen by continuously liquid nitrogen adding, were ground using a precooled mortar and pestle. Total RNA was isolated from ground whole berries, excluding seeds, by using a slight modification of the method described by Japelaghi and co-workers (Japelaghi et al., 2011). Briefly, a scale-up of the ground tissue was needed: in detail 1 g of sample was added to 10 ml of extraction buffer. Furthermore, three steps of the chloroform: isoamyl alcohol (24:1) extraction were performed.
Sequen_x0002_cing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, Ips_x0002_wich, MA, USA) following manufacturer’s recommenda_x0002_tions. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using ran_x0002_dom hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subse_x0002_quently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3′ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, MA, USA). Then 3 μl USER Enzyme by NEB was used with size-se_x0002_lected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: fruit

tag: location

value: Sicily site

value: Cabernet sauvignon


title: SPATAC-seq with zebrafish embryogenesis well-ZSC2 (DNBSEQ-T7)

description:
ZSC2_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Pt_10_Normal.region_1_IORT


title: Grape berry. Cabernet sauvignon genotype, Sicily site rep2


title: SPATAC-seq with mouse organogenesis well-E11H


title: Pt_10_SM_IORT

value: SM


title: SPATAC-seq with zebrafish embryogenesis well-ZSC1 (DNBSEQ-T7)

description:
ZSC1_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with mouse organogenesis well-E11G


title: Grape berry. Cabernet sauvignon genotype, Sicily site rep1


title: SPATAC-seq with mouse organogenesis well-E156


title: SPATAC-seq with zebrafish embryogenesis well-ZSC5 (DNBSEQ-T7)

description:
ZSC5_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZSB8 (DNBSEQ-T7)

description:
ZSB8_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Pt_9_SM_IORT


title: Grape berry. Cabernet sauvignon genotype, Molise site rep3

value: Molise site


title: SPATAC-seq with mouse organogenesis well-E11F


title: SPATAC-seq with mouse organogenesis well-E11E


title: SPATAC-seq with zebrafish embryogenesis well-ZSC4 (DNBSEQ-T7)

description:
ZSC4_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Pt_9_Normal_IORT

value: Normal


title: Grape berry. Cabernet sauvignon genotype, Molise site rep2


title: SPATAC-seq with zebrafish embryogenesis well-ZSB7 (DNBSEQ-T7)

description:
ZSB7_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file

value: zebrafish embryos


title: SPATAC-seq with zebrafish embryogenesis well-ZSB6 (DNBSEQ-T7)

description:
ZSB6_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Pt_8_Normal.region_2_non-IORT

value: non-IORT


title: SPATAC-seq with mouse organogenesis well-E11D


title: Grape berry. Cabernet sauvignon genotype, Molise site rep1


title: SPATAC-seq with zebrafish embryogenesis well-ZSB5 (DNBSEQ-T7)

description:
ZSB5_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with mouse organogenesis well-E11C


title: Grape berry. Cabernet sauvignon genotype, Campania site rep3

value: Campania site


title: SPATAC-seq with zebrafish embryogenesis well-ZSB4 (DNBSEQ-T7)

description:
ZSB4_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with mouse organogenesis well-E11B


title: Pt_8_Normal.region_1_non-IORT


title: Grape berry. Cabernet sauvignon genotype, Campania site rep2


title: Pt_7_Normal_non-IORT


title: SPATAC-seq with zebrafish embryogenesis well-ZSB3 (DNBSEQ-T7)

description:
ZSB3_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with mouse organogenesis well-E11A


title: Grape berry. Cabernet sauvignon genotype, Campania site rep1


title: Pt_6_Normal_IORT


title: SPATAC-seq with zebrafish embryogenesis well-ZSB2 (DNBSEQ-T7)

description:
ZSB2_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Baseline, Csf1r∆FIRE/∆FIRE, FIRE_NI_KO R3

city: Munich

first: Markus

last: Joppich

state: Bavaria

address: Amalienstr. 17

department: Department of Informatics

country: Germany

institute: LMU Munich

description:
10x genomics
FIRE_NI_KO Rep 3

library_source: transcriptomic single cell

data_processing:
The six mouse samples FIRE_NI (baseline condition of Csf1r∆FIRE/+ and Csf1r∆FIRE/∆FIRE), were processed using Cellranger 4.0.0 using the 2020A mm10 reference.
The 4 mouse samples (FIRE_IF, infarct condition of Csf1r∆FIRE/+ and Csf1r∆FIRE/∆FIRE), were sequenced with 4 technical sequencing replicates and pooled using the cellranger (v4.0.0, 10x Genomics) pipeline. Cellranger 4.0.0 was called with default parameters and the 2020A mm10 reference for gene expression.
The reads of heart1 sample (Tnfsf11aCreRosa26fs-eYFP, supplementary file) were demultiplexed using Je-demultiplex-illu (Girardot et al, 2016) and mapped against a customized mouse reference genome (GRCm38.p6, Gencode annotation M24) including eYfp sequence using CellRanger (v3.1.0, 10x Genomics).
Assembly: 10X genomics mm10 mouse reference 2020A
Supplementary files format and content: Raw feature-barcode matrix in h5 format

extract_protocol:
Heart tissue was dissected into remote and ischemic tissue as described above and minced into small pieces using forceps and a scalpel. When comparing baseline and I/R injury in FACS analysis, basal heart tissue was used for comparison with remote tissue and apical heart tissue for comparison with ischemia tissue. After enzymatic digestion (Collagenase XI 1200 U/mg, Collagenase I 125 U/mg, Hyaluronidase 500 U/mg, DNase I 1836 U/mg; Sigma Aldrich®) for 30 min at 37°C cells were washed and incubated with purified anti-CD16/32 (FcγRIII/II; dilution 1/50) for 10 min.
After sorting, cells were proceeded for single cell capture, barcoding and library preparation using Chromium Next GEM single cell 3’ (v3.1, 10x Genomics) according to manufacturer’s specifications. Pooled libraries were sequenced on an Illumina HiSeq1500 sequencer (Illumina, San Diego, USA) in paired-end mode with asymmetric read length of 28+91 bp and a single indexing read of 8bp.

value: Heart

value: leukocytes (CD45+ cells)

value: non-infarcted


title: Grape berry. Aglianico genotype, Sicily site rep3

value: Aglianico


title: SPATAC-seq with zebrafish embryogenesis well-ZSB1 (DNBSEQ-T7)

description:
ZSB1_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Baseline, Csf1r∆FIRE/∆FIRE, FIRE_NI_KO R2

description:
10x genomics
FIRE_NI_KO Rep 2


title: Pt_8_SM_non-IORT

value: Breast tissue

value: Female


title: Pt_6_SMwA_IORT

value: SMwA


title: Pt_6_SM_IORT

value: IORT


title: SPATAC-seq with zebrafish embryogenesis well-ZSA7 (DNBSEQ-T7)

description:
ZSA7_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Grape berry. Aglianico genotype, Sicily site rep2

value: fruit


title: Baseline, Csf1r∆FIRE/∆FIRE , FIRE_NI_KO R1

description:
10x genomics
FIRE_NI_KO Rep 1


title: SPATAC-seq with zebrafish embryogenesis well-ZSA8 (DNBSEQ-T7)

description:
ZSA8_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Grape berry. Aglianico genotype, Molise site rep3


title: Pt_5_SM_IORT


title: Baseline, Csf1r∆FIRE/+, FIRE_NI_CTRL R2

description:
10x genomics
FIRE_NI_CTRL Rep 2


title: SPATAC-seq with zebrafish embryogenesis well-ZSA5 (DNBSEQ-T7)

description:
ZSA5_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Baseline, Csf1r∆FIRE/+, FIRE_NI_CTRL R3

description:
10x genomics
FIRE_NI_CTRL Rep 3


title: Pt_4_SM_non-IORT


title: MI d2, Csf1r∆FIRE/+, FIRE_IF_WT R2

description:
10x genomics
FIRE_IF_WT Rep 2

value: 2 days after I/R injury


title: Grape berry. Aglianico genotype, Molise site rep1


title: SPATAC-seq with zebrafish embryogenesis well-ZSA4 (DNBSEQ-T7)

description:
ZSA4_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZSA3 (DNBSEQ-T7)

description:
ZSA3_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Baseline, Csf1r∆FIRE/+, FIRE_NI_CTRL R1

description:
10x genomics
FIRE_NI_CTRL Rep 1


title: Grape berry. Aglianico genotype, Campania site rep3


title: Pt_2_Normal.region_2_non-IORT


title: Pt_2_Normal.region_1_non-IORT


title: Grape berry. Aglianico genotype, Campania site rep2


title: Pt_1_Normal_non-IORT


title: MI d2, Csf1r∆FIRE/+, FIRE_IF_WT R1

description:
10x genomics
FIRE_IF_WT Rep 1


title: SPATAC-seq with zebrafish embryogenesis well-ZSA2 (DNBSEQ-T7)

description:
ZSA2_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Grape berry. Aglianico genotype, Sicily site rep1

value: Sicily site


title: Grape berry. Aglianico genotype, Molise site rep2


title: MI d2, Csf1r∆FIRE/∆FIRE, FIRE_IF_KO R2

description:
10x genomics
FIRE_IF_KO Rep 2


title: SPATAC-seq with zebrafish embryogenesis well-ZSA6 (DNBSEQ-T7)

description:
ZSA6_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: SPATAC-seq with zebrafish embryogenesis well-ZSA1 (DNBSEQ-T7)

description:
ZSA1_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file


title: Pt_4_Normal_non-IORT


title: MI d2, Csf1r∆FIRE/∆FIRE, FIRE_IF_KO R1

description:
10x genomics
FIRE_IF_KO Rep 1


title: Pt_3_SMwA_IORT


title: AM46

status: Public on Apr 13 2024

city: Córdoba

first: Antonio

last: Rodriguez Ariza

state: Córdoba

address: Av. Meléndez Pidal S/N

department: Medical Oncology

country: Spain

institute: Maimonides Institute of Biomedical Research of Cordoba

data_processing:
STAR
Assembly: hg38
Supplementary files format and content: Tab-delimited raw counts.

source_name: Colorectal cancer tumour

extract_protocol:
RNeasy Mini Kit
RNA libraries were constructed according to CRG.

value: Colorectal cancer tumour

value: mesenchymal cells

tag: phenotype

value: LOW GSNOR


title: AM36


title: AM37


title: AM47


title: AM41


title: AM33


title: AM24


title: AM27


title: Grape berry. Aglianico genotype, Campania site rep1


title: AM19


title: AM18


title: AM16


title: AM14


title: AM48

value: HIGH GSNOR


title: AM43


title: AM45


title: AM44


title: AM42


title: AM35


title: AM38


title: AM39


title: AM40


title: AM26


title: AM30


title: AM29


title: Neuron_IMP1_miCLIP_no_XL

city: London

first: Pierre

last: Klein

address: Gower Street

department: Institute of Structural and Molecular Biology

country: United Kingdom

institute: University College London

data_processing:
library strategy: miCLIP
miCLIP reads were processed according to iCLIP analysis methods using the iMaps webserver (https://imaps.genialis.com/iclip ) for standardised primary analysis. iMaps is based on the icount package. Briefly, the following steps were performed: demultiplexing using experimental barcodes, UMI identification, adapter trimming, STAR pre-mapping to rRNAs and tRNAs, STAR alignment to genome, crosslink site assignment using icount package, duplicate removal by UMI sequence. Control quality checks (FastQC 0.11.7, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/, PCR duplication ratio, quality of sequencing and alignment statistics from iMaps) were performed on each individual sample.
Mutation (CIMS) and Truncation (CITS) site calling was performed as previously described (Weyn-Vanhentenryck et .al, 2014). Briefly, low-quality bases and adaptor sequences were all removed using FLEXBAR tool   (-f i1.8 -as AGATCGGAAGAGCGGTTCAG --pre-trim-phred 30 -s -t sample). Reads were demultiplexed based on 5′ barcodes for individual replicates using pyCRAC. Reads were processed in pooled or separate replicate modes using the CTK package  (https://zhanglab.c2b2.columbia.edu/index.php/CTK_Documentation).  In brief the barcode was stripped and added to the name of the read. Biological and technical replicates were concatenated (CIMS analysis). PCR duplicates were collapsed using pyFastqDuplicateRemover.py script from pyCRAC. The header was transformed to be compatible with CTK analysis (mawk -F ‘[_/]’ ‘/^>/{print $1”_”$2”_”$3”/”$4”#”$3”#”$2; getline($9); print $9}’ ). Reads were aligned to the human genome (hg38) using bwa (aln -t 4 -n 0.06 -q 20). Positions of C → T from mapped reads were obtained using the CIMS software package 45. Briefly, aligned reads were parsed using parseAlignment.pl to generate a bed file of read coordinates and mutation coordinates. PCR duplicates were collapsed based on read coordinated and barcode identities using tag2collapse.pl script. To get the mutations in unique tags joinWrapper.py script was used. C to T transitions were extracted and a bed file generated. Mutation reproducibility was evaluated using CIMS.pl script. For each mismatch position, the unique tag coverage (k) and the number of C→T transitions (m) were determined. C→T transitions located in DRACH motifs were called using kmer.annotate.cims.sh script based on (m ≥ 2) and transition frequency (1% ≥ m/k ≤ 50%). Position of truncations from mapped reads were obtained using the CITS software package. Briefly, after the mutation removal step from PCR duplicates in the CIMS strategy, deletions were obtained from the mutation file using getMutationType.pl on each individual sample. Truncations events were then identified using CITS.pl script. Technical and biological replicates were then concatenated. CITS and CIMS final bed files were merged using Bedtools’s mergeBed function.
Assembly: GRCh38.p13 human genome
Supplementary files format and content: Bed file containing crosslink sites
Supplementary files format and content: Bed file containing called m6A sites

source_name: hIPSC_derived NPC and Neurons

extract_protocol:
Cell were washed with PBS 1X on ice. Content of 80 to 100% of two 6-well plate was lysed in 1.5 mL TRIzol reagent and total RNA was extracted using manufacturer’s instruction (all volumes were scaled up according to the initial volume TRIzol). RNA was resuspended in 30μl of RNase free water. RNA concentration and the 260/280 ratio were assessed using Nanodrop, and the Agilent 2400 Bioanalyser was used to assess quality. RNA integrity (RIN) scores were used to quality check samples.  Total RNA was treated with DNAse I (TURBO DNAse, ambion, AM2238) using rigorous DNAse treatment conditions according to manufacturer’s instructions. DNAse free Poly(A)+ RNA was prepared using oligo dt dynabeads (NEB S1419S) using the following protocol: 1mg of dynabeads were washed with binding buffer and resuspended in 100μl of binding buffer (20 mM Tris-HCl, pH 7.5, 1.0 M LiCl, 2 mM EDTA). Volume of RNA was adjusted to 100µl in RNAse free water and mixed with 100µl of binding buffer. Samples were incubated at 65°C for 2 min and immediately put on ice. RNA was thoroughly mixed with washed beads and tubes were rotating head over tail for 5 min at RT. Two washes with wash buffer A (10 mM Tris-HCl, pH 7.5 ,0.15 M LiCl, 1 mM EDTA 10 mM Tris-HCl, pH 7.5) were performed followed by elution with 50μl of elution buffer (20 mM Tris-HCl, pH 7.5, 1 mM EDTA). Samples were then incubated at 80°C for 2 min under gentle agitation and placed on a magnetics rack. Supernatant was reused for another round of purification after beads were washed with 100µl of elution buffer and 200µl of wash buffer.  RNA concentration was assessed using Nanodrop.
miCLIP was performed as previously described (Hawley et al. 2019) with minor modifications.  PolyA RNA (1μg) was brought to 30μl water and incubated with 3μl of 10X Fragmentation Buffer (Thermoscientific) at 60°C for 15min. Samples were immediately placed on ice and 3.3 μl of Stop Solution was added. Samples were incubated with 10μl of 1 μg/μl of anti-m6A antibody in 500μl IP buffer (50 mM Tris-HCL, pH 7.4, 100mM NaCl, 0.05% NP-40) for 2h at 4°C rotating head over tail. RNA-anti m6A antibody complexes were crosslinked in a 6-well plate on ice twice with 0.3 J/cm-2 UV light (254 nm) in a stratalinker. Negative controls (non-crosslink and anti-IgG antibodies) were also prepared. Crosslinked RNA-anti-m6A complexes were mixed with 30μl of washed Protein G Dynabeads (Dynal) and incubated at 4°C for 2 hours rotating head over tail.  Librarires were prepared by ligating RNA to a pre-adenylated infrared labelled IRL3 adaptor (Zarnegar et al., 2016) with the following sequence:  /5rApp/AG ATC GGA AGA GCG GTT CAG AAA AAA AAA AAA /iAzideN/AA AAA AAA AAA A/3Bio/. The protein-RNA complexes were then size-separated by SDS-Page, blotted onto nitrocellulose and visualised by Odyssey scanning (LI-COR). The correct region from the nitrocellulose membrane was cut according to previously published protocol (Grozhik et al., 2017) and RNA was released from the membrane by proteinase K (Roche, 03115828001) digestion and incubation at 60 min at 50°C. RNA was recovered by Phenol Chloroform precipitation. cDNA was synthesised with Superscript IV Reverse Transcriptase (Life Technologies). Reverse transcription was performed with primers containing UMIs and barcode (XXXXX) to allow multiplexing: /5Phos/ WWW XXXXX NNNN AGATCGGAAGAGCGTCGTGAT /iSp18/ GGATCC /iSp18/ TACTGAACCGC. cDNA molecules were purified using AMPure XP beads (Beckman-Coulter, USA), then circularised using Circligase II (Epicenter) followed by AMPure XP beads purification. After PCR amplification, libraries were size-selected by gel-purification and size distribution was assessed using Agilent 2400 Bioanalyser. Libraries were quantified by QuBit dsDNA HS Assay. Library composed of the same quantity of cDNA for each sample was sequenced as single-end 100bp reads on Illumina HiSeq 4000

value: hIPSC_derived NPC and Neurons

value: Neurons

value: mouse anti-m6A (Abcam, ab151230)

value: Neuronal differentiation protocol


title: AM25


title: AM32


title: AM28


title: Neuron_IMP1_miCLIP_tech_replicate_2_bio_rep4

source_name: hIPSC_derived Neurons

value: hIPSC_derived Neurons


title: Neuron_IMP1_miCLIP_tech_replicate_2_bio_rep3


title: AM22


title: AM23


title: Neuron_IMP1_miCLIP_tech_replicate_1_bio_rep3


title: Neuron_IMP1_miCLIP_tech_replicate_1_bio_rep4


title: AM21


title: AM20


title: Neuron_IMP1_miCLIP_tech_replicate_2_bio_rep2


title: SPATAC-seq with zebrafish embryogenesis well-ZSD8 (DNBSEQ-T7)

description:
ZSD8_SPATACseq_Batch1_MGI
Used to produce the ZEPA_metadata.xlsx, ZEPA.All.sample.bed.gz and all BigWig files in the section of Supplementary file

value: zebrafish embryos


title: Neuron_IMP1_miCLIP_tech_replicate_1_bio_rep2


title: AM17


title: NPC_IMP1_miCLIP_tech_replicate_2_bio_rep4

source_name: hIPSC_derived NPC

value: hIPSC_derived NPC

value: Neuronal progenitor


title: Neuron_IMP1_miCLIP_tech_replicate_1_bio_rep1


title: AM13


title: R106, Day 7 Intact, rep 2

city: Leiden

first: Françoise

last: Carlotti

address: Albinusdreef 2

country: Netherlands

institute: Leiden University Medical Center

description: Experimental setup 2

data_processing:
For the mapping of the sequenced reads and quantification of the number of transcripts reads 2 from the fastq files were mapped to the human reference transcriptome with BWA and reads 1 were used to extract the cell-barcode sequences and unique molecular identifiers (UMI). UMI-correction was performed to the read and barcode counts resulting in unique transcript count tables. Spike-in reads were removed from the dataset.
Assembly: hg19
Supplementary files format and content: Comma-separated values (csv) files containing cell barcodes, read counts and transcript counts

source_name: Pancreatic islets

extract_protocol:
Islets were briefly washed in PBS and dispersed into single cells. Cells were sorted using a FACS Jazz or FACS Aria III (BD Biosciences, Franklin Lakes, NJ, USA). Live single cells were selected based on DAPI exclusion and FSC, sorted into 384-well hard shell plates (BioRad, Hercules, CA, USA) and further processed with SORTseq (SOrting and Robot-assisted Transcriptome sequencing) as previously described (Muraro, et al 2016).
Mapping of the sequenced reads and quantification of the number of transcripts reads 2 from the fastq files were mapped to the human reference transcriptome with BWA and reads 1 were used to extract the cell-barcode sequences and unique molecular identifiers (UMI). UMI-correction was performed to the read and barcode counts resulting in unique transcript count tables. Spike-in reads were removed from the dataset.

value: Pancreatic islets


title: Neuron_IMP1_miCLIP_tech_replicate_2_bio_rep1


title: NPC_IMP1_miCLIP_tech_replicate_1_bio_rep4


title: NPC_IMP1_miCLIP_tech_replicate_1_bio_rep3


title: NPC_IMP1_miCLIP_tech_replicate_2_bio_rep3


title: R106, Day 7 Aggregated, rep 2

description: Experimental setup 2


title: NPC_IMP1_miCLIP_tech_replicate_2_bio_rep2


title: R106, Day 2 Intact, rep 2

description: Experimental setup 2


title: R106, Day 7 Aggregated, rep 1

description: Experimental setup 2


title: NPC_IMP1_miCLIP_tech_replicate_1_bio_rep2


title: R106, Day 7 Intact, rep 1

description: Experimental setup 2


title: NPC_IMP1_miCLIP_tech_replicate_2_bio_rep1


title: R106, Day 2 Aggregated, rep 2

description: Experimental setup 2


title: R102, Day 3 Intact, rep 2

description: Experimental setup 2


title: R106, Day 2 Intact, rep 1

description: Experimental setup 2


title: NPC_IMP1_miCLIP_tech_replicate_1_bio_rep1


title: R102, Day 3 Intact, rep 1

description: Experimental setup 2


title: R106, Day 2 Aggregated, rep 1

description: Experimental setup 2


title: Neuron_IMP1_iCLIP_tech_replicate_1_bio_rep3

data_processing:
library strategy: iCLIP
iCLIP reads were processed according to iCLIP analysis methods using the iMaps webserver (https://imaps.genialis.com/iclip ) for standardised primary analysis. iMaps is based on the icount package. Briefly, the following steps were performed: demultiplexing using experimental barcodes, UMI identification, adapter trimming, STAR pre-mapping to rRNAs and tRNAs, STAR alignment to genome and crosslink sites assignment. Significant crosslink sites were defined using the ‘iCount peaks’ tool on the iMaps web server while
Peaks were called using the paraclu package. Peaks were defined by clustering the significant crosslink sites using iMAPS default parameters
Control quality checks (FastQC 0.11.7, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/, PCR duplication ratio, quality of sequencing and alignment statistics from iMaps) were performed on each individual sample.
Assembly: GRCh38.p13 human genome
Supplementary files format and content: Bed file containing crosslink sites
Supplementary files format and content: Bedgraph file containing peaks

extract_protocol:
iCLIP was performed as previously described (Huppertz et al. 2014) with minor modifications. Briefly, three biological and three technical replicates for NPCs and neurons were cross-linked at 300mJ and then lysed in 1ml of IP lysis buffer. RNA fragmentation was performed with 0.4 units of RNase I (Thermo Scientific, EN0602) and 4μl Turbo DNase I (Ambion, AM223) added to 1mL of protein lysate at a concentration of 1mg/mL. Ideal RNAse concentration was previously determined using a concentration gradient: low (0.4U), medium (0.8U) high (2.5 U) to 1 mg of protein lysate from NPC and neuron. Ideal IMP1 antibody was previously determined using 1μg or 5μg of antibody to 1 mg of protein lysate. To separate protein-RNA complexes, samples were incubated with 5μg of anti-IMP1 antibody or 5μg of anti-IgG (negative control) coupled to Protein G beads (Dynal) at 4°C ON rotating head over tail.
Librarires were prepared by ligating RNA to a pre-adenylated infrared labelled IRL3 adaptor (Zarnegar et al., 2016) with the following sequence:  /5rApp/AG ATC GGA AGA GCG GTT CAG AAA AAA AAA AAA /iAzideN/AA AAA AAA AAA A/3Bio/. The protein-RNA complexes were then size-separated by SDS-Page, blotted onto nitrocellulose and visualised by Odyssey scanning (LI-COR). Desired region (determined from the RNAse gradient experiment) was cut from the membrane in small pieces and RNA was released from the membrane by proteinase K (Roche, 03115828001) digestion and incubation at 60 min at 50°C. RNA was recovered by Phenol Chloroform precipitation. cDNA was synthesised with Superscript IV Reverse Transcriptase (Life Technologies). Reverse transcription was performed with primers containing UMIs and barcode (XXXXX) to allow multiplexing: /5Phos/ WWW XXXXX NNNN AGATCGGAAGAGCGTCGTGAT /iSp18/ GGATCC /iSp18/ TACTGAACCGC. cDNA molecules were purified using AMPure XP beads (Beckman-Coulter, USA), then circularised using Circligase II (Epicenter) followed by AMPure XP beads purification. After PCR amplification, libraries were size-selected by gel-purification and size distribution was assessed using Agilent 2400 Bioanalyser. Libraries were quantified by QuBit dsDNA HS Assay. Library composed of the same quantity of cDNA for each sample was sequenced as single-end 100bp reads on Illumina HiSeq 4000

value: Rabbit anti-IMP1 (MBL, RN007P)


title: Neuron_IMP1_iCLIP_tech_replicate_3_bio_rep3


title: R102, Day 3 GFP, rep 2

description: Experimental setup 2


title: IgG_iCLIP

value: NPC + Neurons

value: rabbit anti-IgG (Proteintch 30000-0-AP)


title: AM15


title: Neuron_IMP1_iCLIP_tech_replicate_3_bio_rep2


title: Neuron_IMP1_iCLIP_tech_replicate_2_bio_rep3


title: R102, Day 3 GFP, rep 1

description: Experimental setup 2


title: Neuron_IMP1_iCLIP_tech_replicate_2_bio_rep2


title: P479, Day 7 GFP, rep 4

description: Experimental setup 1


title: P479, Day 7 Intact, rep 1

description: Experimental setup 1


title: P479, Day 7 Intact, rep 2

description: Experimental setup 1


title: Neuron_IMP1_iCLIP_tech_replicate_3_bio_rep1


title: Neuron_IMP1_iCLIP_tech_replicate_1_bio_rep2


title: Neuron_IMP1_iCLIP_tech_replicate_2_bio_rep1


title: P479, Day 7 GFP, rep 2

description: Experimental setup 1


title: Neuron_IMP1_iCLIP_tech_replicate_1_bio_rep1


title: NPC_IMP1_iCLIP_tech_replicate_3_bio_rep3


title: P479, Day 7 GFP, rep 1

description: Experimental setup 1


title: NPC_IMP1_iCLIP_tech_replicate_2_bio_rep3


title: P479, Day 7 Aggregated, rep 2

description: Experimental setup 1


title: P479, Day 7 Aggregated, rep 1

description: Experimental setup 1


title: NPC_IMP1_iCLIP_tech_replicate_1_bio_rep3


title: NPC_IMP1_iCLIP_tech_replicate_3_bio_rep2


title: P479, Day 5 GFP, rep 4

description: Experimental setup 1


title: NPC_IMP1_iCLIP_tech_replicate_2_bio_rep2


title: NPC_IMP1_iCLIP_tech_replicate_1_bio_rep2


title: P479, Day 5 GFP, rep 3

description: Experimental setup 1


title: P479, Day 5 GFP, rep 2

description: Experimental setup 1


title: NPC_IMP1_iCLIP_tech_replicate_3_bio_rep1


title: P479, Day 2 GFP, rep 4

description: Experimental setup 1


title: Neuron_CTRL_KD_biological_rep3

data_processing:
Raw mRNA sequencing reads were trimmed using TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore),
Quality was evaluated using FastQC 0.11.7, (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Rreads were aligned to GRCh38.p13 human genome using splice-aware aligner STAR v2.6.1 40 with default parameters.
Aligned reads were quantified using --quantMode (TranscriptomeSAM GeneCounts) function.
Differential gene expression was measured using DESeq2 41 using STAR count matrix as an input (DESeqDataSetFromMatrix function).
Assembly: GRCh38.p13 human genome
Supplementary files format and content: raw count table from Deseq2

extract_protocol:
NPC and neurons were washed with PBS 1X and harvested by centrifugation. Total RNA was extracted using Maxwell RSC simplyRNA cells kit including DNase treatment in the Maxwell RSC instrument following manufacturer’s instructions. RNA concentration and the 260/280 ratio were assessed using Nanodro
Poly(A)+ selected reverse stranded RNA sequencing libraries were prepared from total RNA using KAPA mRNA HyperPrep Library kit for Illumina® kit, with 200 ng of total RNA as input


title: P479, Day 5 GFP, rep 1

description: Experimental setup 1


title: P479, Day 2 GFP, rep 3

description: Experimental setup 1


title: P479, Day 0, rep 3

description: Experimental setup 1


title: P479, Day 0, rep 2

description: Experimental setup 1


title: Neuron_CTRL_KD_biological_rep2


title: Neuron_CTRL_KD_biological_rep1


title: P479, Day 7 GFP, rep 3

description: Experimental setup 1


title: P479, Day 0, rep 1

description: Experimental setup 1


title: Neuron_IMP1_KD_biological_rep3


title: sample2_wnt3 (biol rep 3)

city: Tel Aviv

first: Rina

last: Rosin-Arbesfeld

address: Haim Levanon

department: Clinical Microbiology and Immunology

country: Israel

institute: Tel Aviv University

data_processing:
Twelve FastQ files were uploaded to Partek Flow (Build version 10.0.21.1116; https://www.partek.com) for processing. Poly-A/T stretches and Illumina adapters were trimmed from the reads. Resulting reads with Phred score < 20 were filtered. Reads were mapped to the human GRCh38.p13 reference genome using STAR 2.7.8a with default parameters to reveal ~ 20 million reads per sample. Quantification to annotation model was performed using Partek Expectation/Maximization (E/M) algorithm  obtaining 33,331 genes.
Assembly: human GRCh38.p13
Supplementary files format and content: Count matrix of gene expression 33,331 genes
Supplementary files format and content: Differential expression analysis using DESeq2
Supplementary files format and content: gene ontology analysis using goseq

source_name: Whole blood

extract_protocol:
Freshly isolated primary human classical monocytes (CD14+CD16-) from two donors were cultured for 8 hours in triplicates in cell repellent plates in the presence of control or Wnt-3a conditioned media.   Media were comprised of 80% L- or L-Wnt-3a- CM and 20% RPMI-1640 (both containing 10% FBS and 1% Penicillin/Streptomycin) at 37°C in 5% CO2. L cells and L-Wnt-3a cells were propagated according to the ATCC guidelines and CM were produced according to the ATCC protocols.
Total RNA was extracted using the Direct-zol RNA MiniPrep kit. Replicates of high RNA integrity (RIN ≥ 7.8) were processed. Libraries were prepared using the NEBNext Ultra II RNA Library Prep kit with the NEBNext Poly(A) mRNA Magnetic Isolation Module, starting with ~ 500 ng of total RNA. Ten PCR cycles were performed during library amplification. Libraries were quantified by Qubit and TapeStation and sequenced on a NextSeq 500 instrument using a NextSeq 500/550 High Output Kit v2.5 (75 Cycles) kit.

value: Whole blood

value: primary human

value: CD14+CD16- monocytes

value: donor 2


title: sample2_wnt2 (biol rep 2)


title: Neuron_IMP1_KD_biological_rep2


title: sample2_wnt1 (biol rep 1)


title: NPC_CTRL_KD_biological_rep3


title: Neuron_IMP1_KD_biological_rep1


title: NPC_CTRL_KD_biological_rep2


title: NPC_IMP1_iCLIP_tech_replicate_2_bio_rep1


title: sample2_control2 (biol rep 2)

value: control


title: NPC_CTRL_KD_biological_rep1


title: sample2_control1 (biol rep 1)


title: sample1_wnt2 (biol rep 2)

value: donor 1


title: P479, Day 0, rep 4

description: Experimental setup 1


title: sample1_wnt3 (biol rep 3)


title: NPC_IMP1_KD_biological_rep1


title: NPC_IMP1_iCLIP_tech_replicate_1_bio_rep1


title: NPC_IMP1_KD_biological_rep3


title: NPC_IMP1_KD_biological_rep2


title: sample1_wnt1 (biol rep 1)


title: sample1_control3 (biol rep 3)


title: sample1_control1 (biol rep 1)


title: m244_WT_CRBM

city: CABA

first: Damian

last: Refojo

state: CABA

address: Godoy Cruz 2390

country: Argentina

institute: Biomedicine Research Institute of Buenos Aires (IBioBA)

data_processing:
Raw reads were aligned to the Mus musculus genome (version mm10) using STAR(76)
Reads were quantified using End Sequence Analysis Toolkit(77) for 3' RNA libraries.
Differential gene expression analysis was done with edgeR
Libraries were sequenced 2 times to increase coverage. Fastq files were merged and processed together afterwards (we are providing both sequenced runs separately in the folders "Run2" and "Run 3")
Assembly: mm10

source_name: Cerebellum

extract_protocol:
RNA was extracted using the RNeasy mini kit with in-column DNase treatment
30ng of RNA was used as input for preparing 3' RNA sequencing libraries following CelSeq2 protocol

value: Cerebellum

value: WT


title: m242_CD_CRBM

value: circTulp4-deficient (CD) mouse model


title: HCT116 - control-rep2

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description:
HCT116-control-rep2
read_counts_SAE_KD.txt

data_processing:
Reads were aligned to hg19 Genome Assembly using Tophat2 with default settings
Gene expression level of UCSC known genes were quantified using HTseq-count v0.9.1
Genome_build: hg19
Supplementary_files_format_and_content: text files containing raw gene level counts

source_name: HCT 116  Cells

growth_protocol: HCT116 cells stably expressing Tet-On shSAE2 were grown in DMEM at 370C with 5% CO2. Media was supplemented with 10% Tet System Approved FBS, 100 U/ ml-penicillin, and 100 mg/ml streptomycin.

extract_protocol:
Total RNA was extracted from cells using miRNeasy RNA isolation kit (Qiagen) per manufacturer's protocol.
Kapa mRNA-seq library prep kit

value: colon

value: shSAE2-stable expression

value: DMSO for 5 days


title: sample2_control3 (biol rep 3)


title: HCT116 - control-rep1

description:
HCT116-control-rep1
read_counts_SAE_KD.txt


title: HCT116 - SAE2 kd-rep1

description:
HCT116-SAE2 kd-rep1
read_counts_SAE_KD.txt

value: doxycyclin 1ug/mL for 5 days


title: HCT116 - TFAP2C siRNA-rep2

description:
HCT116 -TFAP2C siRNA- rep2
read_count_TFAP2C.txt

value: siRNA for 48 hrs


title: HCT116 - SAE2 kd-rep2

description:
HCT116-SAE2 kd-rep2
read_counts_SAE_KD.txt


title: HCT116 - TFAP2C siRNA-rep1

description:
HCT116 -TFAP2C siRNA- rep1
read_count_TFAP2C.txt


title: m240_WT_CRBM


title: HCT116 - control siRNA-rep2

description:
HCT116 -control siRNA- rep2
read_count_TFAP2C.txt

source_name: HCT 116 Cells


title: m190_CD_CRBM


title: m162_WT_CRBM


title: m164_WT_CRBM


title: HCT116 cells (SAE2 kd) - HA(TFAP2C)-rep2

data_processing:
Sequences were aligned to mm9 genome using Novoalign, only unique aligned reads were kept
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files were generated using in house R scripts

source_name: HCT116 cells

extract_protocol:
Chromatin was extracted and digested using SimpleChIP® Plus Enzymatic Chromatin IP Kit (Cell Signaling Technology) according to the manufacturer’s protocol. Histone-DNA complexes were isolated with antibody.
Kapa DNA library prep kit

treatment_protocol: Cells were treated with 1ug/mL doxycyclin for 5 days to knock down SAE2

value: colon carcinoma

tag: chip antibody

value: Cell Signaling Cat# 3724S

value: Doxycyclin 1ug/mL for 5 days


title: HCT116 - control siRNA-rep1

description:
HCT116 -control siRNA- rep1
read_count_TFAP2C.txt


title: HCT116 cells (SAE2 kd) - input DNA-rep2


title: HCT116 cells (SAE2 kd) - input DNA-rep1


title: m244_WT_Cx

source_name: Cortex

value: Cortex


title: HCT116 cells - HA(TFAP2C)-rep2

value: untreated


title: m240_WT_Cx


title: m118_CD_CRBM


title: HCT116 cells (SAE2 kd) - HA(TFAP2C)-rep1


title: HCT116 cells - input DNA-rep2


title: sample1_control2 (biol rep 2)

value: Whole blood

value: primary human

value: CD14+CD16- monocytes


title: HCT116 cells - HA(TFAP2C)-rep1


title: m190_CD_Cx


title: m164_WT_Cx


title: HCT116 cells - input DNA-rep1


title: WT_2

city: Dalian

first: Jinsong

last: Yan

address: 9 west section, Lvshun south road, Dalian, Liaoning Province, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

data_processing:
For the gene expression, we mapped the sequencing data to reference genome (hg38) using STAR, and defined transcript coordinates according to the gene annotation format file (GTF file) from GENCODE (Release 33, GRCh38).
The Gene abundances are given as read counts with “--quantMode GeneCounts” parameter using the STAR.
Assembly: hg38
Supplementary files format and content: Excel file include gene counts for each Sample …

source_name: wild type

extract_protocol:
Total RNAs of the wild type and IRAIN over-expression K562 cells were extracted using the QIAamp AllPrep RNA Mini Kit (Cat# 80204, QIAGEN), according to the manufacturer's specifications.
Libraries were constructed using the TruSeq RNA Sample Preparation Kits (Illumina), and the quality of the library was assessed using Bioanalyzer 2100 (Agilent Technologies).

value: wild type


title: WT_1


title: IRAIN_3

source_name: IRAIN over-expression

value: IRAIN over-expression


title: m162_WT_Cx

value: WT


title: HCT116 cells (SAE2-kd) - Med1

value: Bethyl Cat# A300-793A


title: m138_CD_Cx

value: circTulp4-deficient (CD) mouse model


title: m244_WT_HPC

source_name: hippocampus

value: hippocampus


title: IRAIN_2


title: HCT116 cells (SAE2-kd) - H3K27me3

value: Abcam Cat# ab 6002

value: shSAE2-stable expression


title: m242_CD_Cx


title: HCT116 cells (SAE2-kd) - H3K4me3

value: Abcam Cat# 04-745


title: 7CD14-Monocytes-1

city: Nanjing

first: Wang

last: Yafeng

address: Puzhuzhonglu

institute: Nanjing Drum Tower Hospital, Medical School, Nanjing University

data_processing:
The clean reads were mapped against the GRCh38 genome assembly (Homo sapiens)
Assembly: GRCh38
Supplementary files format and content: Excel contain PFKM value for each sample

source_name: Blood

extract_protocol:
The total RNA was isolated with Takara RNAiso Plus.
The libraries were sequenced using Strategy PE150

value: Blood

value: primary cells

value: PBMC

value: healthy donor

value: Control


title: HCT116 cells (SAE2-kd) - H3K27Ac

value: colon carcinoma

value: Abcam Cat# ab 4729

value: Doxycyclin 1ug/mL for 5 days


title: 8CD14-Monocytes-2


title: 6CD4-T-2

value: CD3/CD28 activated


title: IRAIN_1

value: IRAIN over-expression


title: m242_CD_HPC


title: WT_3

value: wild type


title: m118_CD_Cx

value: Cortex


title: HCT116 cells (SAE2-kd) - SUMO2/3

value: MBL International Cat# M114-3


title: 3CD8-T-3


title: 4CD4-T-1


title: 9CD14-Monocytes-3


title: 2CD8-T-2


title: 5CD4-T-2


title: m240_WT_HPC

value: hippocampus

value: WT


title: m190_CD_HPC

value: circTulp4-deficient (CD) mouse model


title: IGHM6_Bait_gIGHM6_gCRLF2

city: Stanford

first: Richard

middle: L

last: Frock

state: California

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford University

data_processing:
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203) and Liang et al., 2021 PNAS (PMC8166026)
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the hg38 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2 and filtered to identify rejoining events and then combined to translocations using JoinT
Assembly: hg38
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)
Library strategy: JoinT-seq

growth_protocol: Nalm6 cells were grown in RPMI-1640 supplemented with 10% FBS, 1% Penicillin/Streptomycin, 1% Glutamax (Gibco), and 50 M -mercaptoethanol.

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step being omitted - PMID: 34006647, using primers associated with the target locus for Illumina Novaseq sequencing

treatment_protocol: Cells were nucleofected (T-001; amaxa Ii system) with SpgRNA vectors as described - PMID: 23892895

value: cell line

tag: read normalization


title: HCT116 cells (SAE2-kd) - SUMO1

value: Abcam Cat# 4940S

value: shSAE2-stable expression


title: 1CD8-T-1

value: Blood

value: primary cells

value: PBMC


title: HCT116 cells (SAE2-kd) - input DNA

value: colon carcinoma


title: IGHM6_Bait_Control_gCRLF2


title: HCT116 cells - Med1

value: Bethyl Cat# A300-793A

value: untreated


title: Cracd KO, scRNAseq

city: Houston

first: Bongjun

last: Kim

state: Texas

address: 6565 MD Anderson BLVD

department: Experimental Radiation Oncology

institute: MD Anderson Cancer Center

data_processing:
The Cell Ranger was used for demultiplexing, barcoded processing, and gene counting. The loom files were generated using velocyto package 32. The R package Seurat33 and Python package Scanpy34 were used for pre-processing and clustering of scRNA-seq data with the loom files. UMAP was used for dimensional reduction, and cells were clustered in Seurat or Scanpy. Datasets were pre-processed, normalized separately. Each dataset was normalized separately and clustered by the “Leiden” algorithm 35. Cracd WT and Cracd KO datasets were combined using “ingest” function in Scanpy. Scanpy was used to concatenate the Cracd WT vs. KO dataset and preSC Cracd WT vs. KO samples. Cells with more than 7000 counts reads were removed. Gene expression for each cell was normalized and log-transformed. The percentages of mitochondrial reads were regressed before scaling the data. Dimensionality reduction and Leiden clustering (resolution 0.5 ~ 1) was carried out, and cell lineages were annotated based on algorithmically defined marker gene expression for each cluster (sc.tl.rank_genes_groups, method=‘wilcoxon’). The list of differentially expressed genes (DEGs) in Cracd WT and Cracd KO was generated by comparing Cracd KO vs. Cracd WT (sc.tl.rank_genes_groups, groups=[' Cracd KO '], reference= ‘Cracd WT’, method='wilcoxon').
Assembly: mm10
Supplementary files format and content: h5ad anndata

source_name: Lung

extract_protocol:
Lungs were harvested from euthanized mice (Cracd WT or Cracd KO) after perfusing 10 ml of cold phosphate-buffered saline (PBS) into the right ventricle. The lung was digested in Leibovitz’s medium (Invitrogen) with 2 mg/mL Collagenase Type I (Worthington), 2 mg/mL Elastase (Worthington), and 2 mg/mL DNase I (Worthington) at 37 °C for 45 min. The tissue was triturated with a pipet every 15 min of digestion until homogenous. The digestion was stopped with FBS (Invitrogen) to a final concentration of 20%. The cells were filtered with a 70 μm cell strainer (Falcon) and spun down at 5,000 r/min for 1 min. The cell pellet was resuspended in red blood cell lysing buffer (Sigma) for 3 min, spun down at 5,000 r/min for 1 min, and washed with 1 mL ice-cold Leibovitz’s medium with 10% FBS. In single-cell RNA sequencing (scRNA-seq), digested lung cells were resuspended in 400 μl of buffer with 5 μl of anti-CD31-FITC (BD Biosciences, CA, USA), 5 μl of anti-CD45-APC (BD Biosciences), and 5 μl of anti-CD326 (EpCAM)-PE-Cy7 (BD Biosciences) and incubated for 30 min at 4 C. Cells were then washed twice, followed by sorting of the epithelial cells (EpCAM+ / CD31- / CD45-) by fluorescence-activated cell sorting at the Cytometry and Cell Sorting Core at BCM.
Single-cell Gene Expression Library was prepared according to the guideline for the Chromium Single Cell Gene Expression 3v3.1 kit (10X Genomics). Briefly, single cells, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10 Genomics) to generate single-cell GEMS (Gel Beads-In-Emulsions), where full-length cDNA was synthesized and barcoded for each single cell. Subsequently, the GEMS were broken and cDNAs from each single cell were pooled, followed by cleanup using Dynabeads MyOne Silane Beads and cDNA amplification by PCR. The amplified product was then fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. The final library was generated by amplification. The library was performed at the Single Cell Genomics Core at BCM.

value: Lung

value: Epithelial cell

value: Cracd KO


title: m138_CD_HPC


title: m162_WT_HPC


title: Cracd WT, scRNAseq

value: Cracd WT


title: HCT116 cells - H3K27me3

value: Abcam Cat# ab 6002


title: IGHM1 Bait_gIGHM1_gBCL2(D03.2)


title: IGHM1_Bait_gIGHM1


title: HCT116 cells - H3K4me3

value: Abcam Cat# 04-745


title: WT-44

first: Hongxi

state: Jiangsu

address: No. 639, LongMian Road, Jiangning District, Nanjing

institute: China Pharmaceutical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited excel files include readcount values for each sample
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: liver tissues of wild type mice  after liver ischemia/reperfusion injury

growth_protocol: The hepatocyte-specific IRF8-deficient mice(IRF8-cKO) mice and wild type (WT) mice were housed in an_x000D_environment with controlled light (12 h light/12 h dark), temperature, and humidity;_x000D_food and water were available ad libitn)

extract_protocol:
RNA was harvested using Trizol reagent. RNA purity was checked using the NanoPhotomete spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The hepatocyte-specific IRF8-deficient mice(IRF8-cKO) mice and wild type (WT) mice were subjected to warm ischemia/reperfusion(I/R) injury (1 hour ischemia and 12 hour  reperfusion)and the ischemic injury lobe of liver tissues were isolated for deep sequencing.

tag: strain

value: C57bl/6 mice of wild type

value: ischemic injury lobe of liver tissues

value: 1 hour ischemia and 12 hour  reperfusion


title: WT-77

tag: tissue


title: IGHM1_Bait_no_gRNA

tag: cell line

value: cell line

value: WT


title: IRF8-cKO-106

source_name: liver tissues of  mice with hepatocyte-specific IRF8-deficient mice (IRF8-cKO) after liver ischemia/reperfusion injury

value: C57bl/6 mice with hepatocyte-specific IRF8-deficient mice (IRF8-cKO)


title: Smchd1 MommeD1 mut repeat 1

city: Jerusalem

first: Eden

last: Engal

address: Ein Kerem

department: Faculty of Medicine

institute: Hebrew University of Jerusalem

data_processing:
Reads were aligned to the mm10/GRCm38 genome using STAR version 2.7.10 with default parameters.
Gene read count was peroformed using feauteCounts version 2.0.1.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file include gene count values for each sample

source_name: Neural stem cells

growth_protocol: We derived WT and Smchd1-null (Smchd1MommeD1/MommeD1) NSCs from embryonic day 14.5 (E14.5) mouse brains. Only male cell lines were used in this study because Smchd1-null female embryos die around E10.5.

extract_protocol:
We extracted RNA from NSCs and performed next-generation sequencing, using RNA ScreenTape kit (catalog #5067-5576; Agilent Technologies), D1000 ScreenTape kit (catalog #5067-5582; Agilent Technologies), Qubit RNA HS Assay kit (catalog # Q32852; Invitrogen), and Qubit DNA HS Assay kit (catalog #32854; Invitrogen) were used for each specific step for quality control and quantity determination of RNA and library preparation
For mRNA library preparation: TruSeq RNA Library Prep Kit v2 was used (Illumina). In brief, 1 µg was used for the library construction; library was eluted in 20 µL of elution buffer. Libraries were adjusted to 10 mM, and then 10 µL (50%) from each sample was collected and pooled in one tube

value: Neural stem cells

tag: cell type

value: Smchd1 null MommeD1


title: Smchd1 MommeD1 mut repeat 2

tag: treatment


title: Donor 2 (DN2)

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

institute: Consiglio Nazionale delle Ricerche

data_processing:
Preliminary analysis using the 10X Genomics pipeline relying on cellranger (base calling, alignment, feature count) using default parameters
Filtering, Normalization, Scaling using the R package Seurat
Identification of clusters using the Louvin algorithm privded by the R package Seurat
Identification of differentially expressed genes using the MAST algorithm provided by the R package Saurat
Genome_build: GRCh38
Supplementary_files_format_and_content: 10X Genomics - Cellranger matrix

source_name: FACS sorted primitive HSPC cells

extract_protocol:
Droplet-based digital 5’scRNA-seq was performed on A Chromium Single-Cell Controller (10x Genomics, Pleasanton, CA) using the Chromium Single Cell 5’ Reagent Kit v2 coupled to feature barcoding technology for cell surface protein according to the manufacturer’s instructions.
scRNA-Seq libraries were prepared according to the manufacturer’s instructions
2x150nt of length through NovaSeq_6000_S1_300_cycles

tag: time point

value: 24h upon ZFN nuclease delivery

value: Cord blood derived CD34+ cells


title: HCT116 cells - SUMO1

value: colon carcinoma

value: Abcam Cat# 4940S

value: untreated

value: shSAE2-stable expression


title: Donor 3 (DN3)


title: HCT116 cells - SUMO2/3

value: MBL International Cat# M114-3


title: Smchd1 MommeD1 mut repeat 3

tag: genotype


title: Smchd1 Wt repeat 2

value: Smchd1 wt


title: IRF8-cKO-71


title: Smchd1 Wt repeat 1


title: HCT116 cells - input DNA


title: Donor 1 (DN1)


title: IRF8-cKO-88


title: IGHM6_Bait_gIGHM6


title: BMDM, KO, biol. Rep 3, LPS

status: Public on Apr 12 2024

city: Mainz

first: Matthias

last: Bros

address: Langenbeckstrasse 1

department: Dermatology

institute: University Medical Center Mainz

data_processing:
RNA-Seq reads were aligned with STAR aligner (v2.7.3a) to the GRCm39 genome with the parameters --outStd SAM --outMultimapperOrder Random --outSAMattributes NH HI AS nM MD --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04.
Using the featureCounts program of subread software (v2.0.0) the primary alignments were assigned to exons with default parameters.
The GENCODE mouse annotation release M26 was used in all the steps.
Further, with only the uniquely mapped reads differential expression analysis was performed using the bioconductor release 3.14 and DESeq2 (v1.34.0) where genes showing a Benjamini-Hochberg adjusted FDR < 0.1 were considered differentially expressed.
Assembly: GRCm39 (v M26)
Supplementary files format and content: fastq.gz

source_name: bone marrow-derived macrophages

growth_protocol: Bone marrow cells (4×105/ml) were seeded in 12-well cell cluster plates (1 ml) in IMDM-based culture medium containing 5% FCS, 2 mM L-glutamine, 100 U/mL penicillin, 100 µg/mL streptomycin, 50 µM ß-mercaptoethanol, and supplemented with 10 ng/ml recombinant murine GM-CSF. Culture media was replenished every 3 days of culture. BMDM were subjected to experiments on day 7.

extract_protocol:
RNA was purified with the RNeasy Plus Mini Kit according to the manufacturer’s protocol.
NGS library prep was performed with Lexogen`s QuantSeq 3´mRNA-Seq Library Prep Kit FWD following Lexogen`s standard protocol with modifications for low Input RNA (≤10ng) (015UG009V0260). Libraries were prepared with a starting amount of 6.9ng and amplified in 22 PCR cycles.
Libraries were profiled in a High Sensitivity DNA chip on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit Flex Fluorometer (Life technologies).
All 12 samples were pooled together with 12 samples from another project in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput Flowcell, SR for 1x 85 cycles plus 6 cycles for the index read.

treatment_protocol: 4x105 BMDM of WT and KSRP-KO mice were cultured with LPS (1µg/ml) for 6h.

value: bone marrow-derived macrophages

value: KSRP-/-

value: 1 ug/ul LPS


title: BMDM, KO, biol. Rep 1, LPS


title: m118_CD_HPC

value: hippocampus

value: circTulp4-deficient (CD) mouse model


title: BMDM, WT, biol. Rep 2, LPS

value: KSRP+/-


title: HCT116 cells - H3K27Ac

value: Abcam Cat# ab 4729


title: BMDM, WT, biol. Rep 1, LPS


title: BMDM, KO, biol. Rep 3


title: WT-14

value: C57bl/6 mice of wild type

value: ischemic injury lobe of liver tissues

value: 1 hour ischemia and 12 hour  reperfusion


title: BMDM, KO, biol. Rep 2


title: BMDM, KO, biol. Rep 1


title: BMDM, WT, biol. Rep 2


title: BMDM, WT, biol. Rep 1


title: BMDM, WT, biol. Rep 3


title: BMDM, WT, biol. Rep 3, LPS


title: BMDM, KO,  biol. Rep 2, LPS


title: THP-1 with LPS only Replicate 3

type: RNA

city: Oshawa

first: Michael

middle: P

last: Jeffrey

state: Ontario

address: 2000 Simcoe St N

department: Faculty of Science

country: Canada

institute: Ontario Tech University

description: Biological Replicate 3 of 4

hyb_protocol: Cy3 and Cy5 labelled cDNA were mixed and hybridized at 50C for 18h on the Agilent whole human gene expression microarray (GE 4x44K; GPL10332).

scan_protocol: Each array was scanned with a ScanArray 5000 instrument (Perkin Elmer, Waltham, MA) and acquired images were quantified with ImaGene® microarray analysis software.

data_processing: Global LOWESS normalization was conducted with ImaGene® microarray analysis software.

source_name: THP-1 Control Rep3

label_protocol: Poly A mRNA were reverse transcribed from 15 µg of total RNA with SuperScript IV (Invitrogen) and labelled with either Cy3 or Cy5 (GE Healthcare Life Sciences, Buckinghamshire, England) before cDNA purification with PCR Purification Kit (QIAGEN).

growth_protocol: The THP-1 human peripheral blood monocyte cell line (ATCC #TIB-202) was maintained in an undifferentiated state using RPMI-1640 medium supplemented with 0.05 mM β-mercaptoethanol, 10% calf serum and 0.05 mg/mL gentamicin and cultured in a humidified incubator at 37oC and 5% CO2

extract_protocol: Total RNA was extracted by using TRIzol Reagent (ThermoFisher Scientific, MA, USA) following manufacturer's protocol with PhaseLock tubes (5 Prime, MD). Total extracted RNA was then purified using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany). The purity and quality of RNA was determined using both the ND100 NanoDrop and an Agilent 2000 Bioanalyzer, respectively. Only samples with an RNA Integrity Number (RIN) greater than 9.0 were used for microarray analysis.

treatment_protocol: THP-1 cells were incubated for 24-, 48-, or 72-hrs with either the Lacticaseibacillus rhamnosus R0011 secretome (LrS) (20% v/v) or a matched L-lactic acid control (LA). For some experiments, THP-1 cells were challenged with LPS (125ng/mL) alone for 6 hours or after 72-hrs of conditioning with the LrS.

value: THP-1 (ATCC #TIB-202)

value: Peripheral Blood Monocyte

source_name: THP-1 with LPS Rep3


title: THP-1 with LPS only Replicate 2

description: Biological Replicate 2 of 4

source_name: THP-1 with LPS Rep2

source_name: THP-1 Control Rep2


title: THP-1 with LrS + LPS Replicate 2

description: Biological Replicate 2 of 4

source_name: THP-1 with LrS + LPS Rep2


title: THP-1 conditioned with LA for 72hrs Replicate 2

description: Biological Replicate 2 of 4

source_name: THP-1 with LA for 72hrs Rep2

source_name: THP-1 72hr Control Rep2


title: THP-1 conditioned with LA for 48hrs Replicate 1

description: Biological Replicate 1 of 4

source_name: THP-1 with LA for 48hrs Rep1

source_name: THP-1 48hr Control Rep1


title: THP-1 with LrS + LPS Replicate 1

description: Biological Replicate 1 of 4

source_name: THP-1 with LrS + LPS Rep1

source_name: THP-1 Control Rep1


title: THP-1 with LrS + LPS Replicate 4

description: Biological Replicate 4 of 4

source_name: THP-1 Control Rep4

source_name: THP-1 with LrS + LPS Rep4


title: THP-1 conditioned with LA for 48hrs Replicate 2

description: Biological Replicate 2 of 4

source_name: THP-1 with LA for 48hrs Rep2

source_name: THP-1 48hr Control Rep2


title: THP-1 with LrS + LPS Replicate 3

description: Biological Replicate 3 of 4

source_name: THP-1 with LrS + LPS Rep3


title: THP-1 conditioned with LA for 72hrs Replicate 1

description: Biological Replicate 1 of 4

source_name: THP-1 with LA for 72hrs Rep1

source_name: THP-1 72hr Control Rep1


title: THP-1 conditioned with LA for 72hrs Replicate 4

description: Biological Replicate 4 of 4

source_name: THP-1 72hr Control Rep4

source_name: THP-1 with LA for 72hrs Rep4


title: THP-1 conditioned with LA for 24hrs Replicate 1

description: Biological Replicate 1 of 4

source_name: THP-1 with LA for 24hrs Rep1

source_name: THP-1 24hr Control Rep1


title: THP-1 conditioned with LA for 24hrs Replicate 4

description: Biological Replicate 4 of 4

source_name: THP-1 24hr Control Rep4

source_name: THP-1 with LA for 24hrs Rep4


title: THP-1 conditioned with LrS for 72hrs Replicate 4

description: Biological Replicate 4 of 4

source_name: THP-1 with LrS for 72hrs Rep4