title: EEC, rbIgg, 12, veh

data_processing:
Paired-end reads from the FASTQ files were aligned using Bowtie2 (version 2.4.2) to the Genome Reference Consortium Mouse Build 38 (mm10).
Alignment to the iGenomes Escherichia coli strain K12, MG1655 Build 2001-10-15 (Illumina) allowed for calibration based on carry over E.coli DNA introduced with the pA/G MNase using the py_sam_2_spikenormbg.py script available at https://github.com/peteskene/py_sam_2_spikenormbg
Peak calling was performed using the py_peak_calling.py script. Both the normalization and peak calling scripts are available at https://github.com/peteskene and have been previously published with the CUT&RUN methodology.
Peaks were required to be present in a minimum of 4 peaksets
Differential binding analysis was performed using the Bioconductor package DiffBind (version 2.15.1) on peaks with score=DBA_SCORE_TMM_MINUS_FULL set in dba.count, using method=DBA_EDGER in dba.analyze.
Assembly: mm10
Supplementary files format and content: The processed file containes the bigwig file that allows for a display of dense, continuous data in a genome browser track.
Library strategy: CUT&RUN-seq

extract_protocol:
500k cells were collected for each antibody incubation (anti-H3K27me3 antibody, Sigma, 07-499; anti-Rabbit IgG, Antibodies Online, ABIN101961). Cells were bound to concanavalin-A coated beads (Bangs Labs, BP531) and incubated with antibody overnight. On the second day, pA/G MNase fusion protein (Cell Signaling, 40366S) was bound during an hour-long incubation at 4°C and activated with 2 mM CaCl¬¬¬2 during a 30 min incubation at 0°C.Samples were incubated for 30 min at 37°C to release chromatin fragments into the supernatant. Supernatant was collected and DNA was extracted using phenol:chloroform:isoamyl alcohol. DNA concentration was determined using the High Sensitivity dsDNA Qubit Assay (Invitrogen, Q32851) and fragment sizes were determined using the High Sensitivity D1000 ScreenTape Assay (Agilent, 5067-5584 and 5067-5585).
DNA libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645) with the NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set I) (NEB, E7600S). All library sizes and concentrations were confirmed on a TapeStation 4200 (Agilent) and Qubit 3.0 Fluorometer (Thermo Fisher). Individually barcoded libraries were pooled and sequenced on an Illumina NextSeq 500 (75-bp paired-end).

treatment_protocol: At monolayer confluency, the media was replaced, and cells were either treated with 1:1000 vehicle (ethanol; resulting in 0.1% ethanol) or 1:1000 corticosterone in ethanol (Cayman Chemical, 16063; 1.4mM, resulting in 500 ng/ml of corticosterone). The media was replaced 72 hours (day 3) and 144 h (day 6) following the treatment. Cells were collected at day 9 (six days after treatment ended).

tag: cut&run antibody


title: 2dpi ATAC

status: Public on Aug 19 2024

type: SRA

city: Toronto

first: Jeff

last: Wrana

state: Ontario

address: 600 University Avenue

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

description:
10x Genomics Multiome
clu_0_2_dpi_dblt_filtd_final_seuratobj_apr242023.RData

library_source: genomic

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm39
Supplementary files format and content: clu_0_2_dpi_dblt_filtd_final_seuratobj_apr242023.Rdata: processed R data file containing both samples.
Supplementary files format and content: A11C3_atac_fragments.tsv.gz: atac fragments file for A11
Supplementary files format and content: A11C3_atac_fragments.tsv.gz.tbi: atac fragments index file for A11
Supplementary files format and content: A11C3_filtered_feature_bc_matrix.h5: feature matrix file for C3
Supplementary files format and content: A9C1_atac_fragments.tsv.gz: atac fragments file for A9
Supplementary files format and content: A9C1_atac_fragments.tsv.gz.tbi: atac fragments index file for A9
Supplementary files format and content: A9C1_filtered_feature_bc_matrix.h5: feature matrix file for C1

molecule: genomic DNA

organism: Mus musculus

source_name: Small intestine

extract_protocol:
Small intestines were flushed with ice-cold PBS, cut longitudinally into roughly 2-mm-long pieces, rinsed with ice-cold PBS, and incubated in 2mM EDTA at 4°C for 40min with continuous shaking. The whole-epithelial segments were isolated by vigorous shaking in ice-cold PBS, and enriched for crypts by passing dissociated epithelial segments through a 70µm mesh cell strainer.
10x Genomics Single Cell Multiome (ATAC + Gene Expressoin)

tag: tissue

value: Small intestine

tag: treatment

value: 12Gy irradiation (48hr)


city: Amsterdam

first: Christina

last: Moene

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description:
Sox2P-reporter -116 kb, population P5 pool4 rep1
E2138 Sox2P-reporter -116 kb, population P5 pool4 rep1 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

data_processing:
The full protocol is described in the corresponding manuscript. In short, reads overlapping the SB-genome junction were selected, SB-sequences were trimmed off (using an adapted version of cutadapt) and reads were mapped to the genome (mm10 or an in silico version of mm10 including the hopping launch pad at -116 kb), filtering for mapq >=10. All putative integrations are lifted over to mm10.
Assembly: mm10
Supplementary files format and content: The processed data file reports all putative integrations mapped in a pool or clone (supported by at least one mapping read, filtering in the manuscript can be more strict). Columns: chr = chromosome; start, end = integration location; seq = dinucleotide at integration site (expected for SB: TA); strand = strand of integration (orientation); read_count = total read count, mapq = total mapping quality (of all reads); read_count_1/mapq_1 = forward mapping reads (3' ITR); read_count_2/mapq_2 = reverse mapping reads (5' ITR); all other columns specify and annotate the sequenced sample. There is one processed data file per founder cell line (pool-based experiments) and one for the isolated clones.

source_name: F1 hybrid 129/Sv:CAST/EiJ

growth_protocol: F121/9 (CAST/EiJ x S129/Sv) Sox2 mCherry+/eGFP+ were cultured in Serum+Lif+2i condition. Briefly, cells were cultured on gelatin-coated (0.1%) culture plates in Glasgow minimum essential medium (Sigma-Aldrich, G5154) supplemented with 15% fetal bovine serum (Thermo Fisher Scientific, 10270-106), 1% L-glutamine (Thermo Fisher Scientific, 25030024), 1% sodium pyruvate (Thermo Fisher Scientific, 11360-70), 1% MEM non-essential amino acids (Thermo Fisher Scientific, 11140-50), 1% penicillin-streptomycin (Thermo Fisher Scientific, 15070063), 100 µM ß-mercaptoethanol, 10 x 4 U leukemia inhibitory factor (LIF; esg1107, Millipore), 1 μM MEK inhibitor PD0325901 (Mirdametinib, MedChemExpress), 3 μM GSK-3β inhibitor CHIR99021 (Laduviglusib, MedChemExpress) in 5% CO2 at 37°C. Cells were passaged every 2 days.

extract_protocol:
Sorted pools and clones were expanded and crude lysates were obtained from a full 96 well plate by lysing with 50 µL DirectPCR Lysis Reagent (102-T, Viagen Biotec) supplemented with 100 µg/mL proteinase K, and incubating 2.5 h at 55 °C and 45 min at 85 °C. For unsorted control cell pools, gDNA was extracted after expansion using the ISOLATE II Genomic DNA Kit (BIO-52067, Bioline).
SBt integrations were mapped by amplifying and sequencing the ITR-genome junction using a tagmentation-based approach. The procedure was similar to {Schep, 2021, 33848455}, but using the following SB-ITR specific primers: MEP009 (5′ ITR, reverse) or LD027 (3′ ITR, forward) for the linear enrichment and MEP011 (5′ ITR, reverse) or MEP034 (3′ ITR, forward) for PCR.Input for one tagmentation reaction was either 100ng gDNA or 3 µL crude lysate. The 72 °C extension times of all PCRs were increased to 1 min. In addition, the composition of the linear enrichment PCR was changed to 10 μL of tagmented DNA, 2 μL of 1 μM primer, 4 μL dNTPs (10mM), 8 μL 5x Phusion® HF Buffer (NEB), 0.5 μL Phusion® HS Flex polymerase (2 U/μL - NEB), in a final volume of 40 μL. For all clones and some experiments with sorted pools (proof-of-principle experiment, third replicate of the reporter hopping) we halved this reaction to a final volume of 20 µL. For the unsorted control pools, 10 separate tagmentation reactions and library preparations were performed, usually using one set of sequencing indices. Libraries were sequenced with 150 bp paired-end reads using either an Illumina MiSeq system (reagent kit v2) or  Illumina NextSeq 550 system (mid-output kit) including 10% of PhiX spike-in.  Primers are described in the corresponding manuscript.

treatment_protocol: SB hopping was induced by transfecting 2.5 to 5 million cells with the bicistronic plasmid (pME07) encoding SB transposase SB100x and the human nerve growth factor receptor (LNGFR), using Lipofectamine 2000 (Invitrogen, 11668019) and 5 µg of plasmid per million cells. After 30 hours, transfected cells were enriched using MACS MS columns (130-042-201, Miltenyi Biotec) and LNGFR MicroBeads (130-091-330, Miltenyi Biotec) according to the manufacturer’s protocol. One week after transfection, 0.2 million SB-transposase-transfected cells were set apart as an unsorted pool and the remaining cells were FACS sorted into pools (of up to 1000 cells) based on reporter expression. Clones were obtained by sorting single cells from previously obtained pools, or sorted directly from the full pool of SB-transposase-transfected cells.

tag: cell line

value: F1 hybrid 129/Sv:CAST/EiJ

tag: cell type

value: mESC

tag: genotype

value: WT

tag: launch pad_location

tag: insert

tag: sorted gate

tag: sample type

value: sorted pool


title: D2 UT

city: Badalona

first: LUCIA

last: LORENZI

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute

data_processing:
Reads were aligned to human genome hg38 and to fruit fly genome fruit dm6 using Bowtie2 version 2.4.4 with ‘--very-sensitive’ flag set and a minimum fragment length (-X flag) of 1000bp, all other parameters set to default.
Duplicate reads were identified using Picard MarkDuplicates and excluded from the downstream analysis
Genome wide coverage tracks in bigwig format were generated using DeepTools bamCoverage (v. 3.3.1).
ChIP-Seq Peaks were identified by MACS2 (v. 2.2.5) using input libraries as control.
Assembly: hg38
Supplementary files format and content: tab-delimited narrowPeak files contain macs2 called peaks for each sample (except for input files)

organism: Homo sapiens

source_name: GM-MDM

growth_protocol: Primary human macrophages were generated through differentiation of CD14+ monocytes with 500 U/mL of recombinant human GM-CSF  in RPMI 1640 medium  containing 10% FBS , 1% penicillin/streptomycin, 1x GlutaMAX, and 1x sodium pyruvate  for 3 days.

extract_protocol:
Cells were cross-linked with 1% formaldehyde, lysed and sonicated in 1% Triton, 0.1% sodium deoxycholate, 0.5% SDS, 0.2M NaCl, 10mM Tris, pH 7.5, 10mM EDTA, and 1X protease inhibitor cocktail.
Libraries were prepared using the NEBNext Ultra DNA Library Prep kit (E7645, New England Biolabs).

treatment_protocol: GM-MDMs were treated with LPS (1 ng/ml) in the presence or absence of butyrate (10 mM) for 16 hours

value: GM-MDM

tag: chip antibody

value: H3K27ac antibody (Abcam ab4729)

value: UT


description:
Sox2P-reporter -116 kb, population P6 pool1 rep1
E2138 Sox2P-reporter -116 kb, population P6 pool1 rep1 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: D1 LPS

value: LPS


title: D1 UT


title: 2dpi RNA

library_source: transcriptomic

molecule: total RNA


title: 0dpi ATAC


title: EEC, rbIgg, 9, cort

city: Aurora

first: Nickole

last: Moon

state: CO

address: 12700 East 19th Avenue, RC2, Rm 9480

country: USA

institute: University of Colorado

growth_protocol: Cells were seeded in on plates coated collagen type 1, rat tail (Millipore, C3867). Cells were grown in Iscove’s Modified Dulbecco’s Medium (IMDM) (Gibco, 12440061) supplemented with 10% fetal bovine serum (Gibco, 26140079) and 1% penicillin-streptomycin (Gibco, 15070063).

value: epididymal epithelial cell

value: anti-Rabbit IgG, Antibodies Online, ABIN101961

value: corticosterone


title: 6_5085wt_CCR20_CD45_cells

city: Gent

first: Lars

last: Vereecke

address: Technologiepark-Zwijnaarde 927

department: IRC

country: Belgium

institute: VIB

data_processing:
Sequence reads were extracted from UMI’s and deduplicated using UMI-Tools v1.14 (BCPattern:"(?P<umi_1>.{6})(?P<discard_1>.{4}).*") as recommended by the Library Prep Kit
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.39 (Leading:20 , Trailing:20, SlidingWindow:4:20, MinLen:37,-phred33, IlluminaClip:Trimmomatic-0.39/adapters/TruSeq3-SE.fa:2:30:10)
Trimmed reads were mapped to GRCm39 using STAR v2.7.10b (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMultimapNmax 20 --outFilterType BySJout --outFilterMismatchNoverLmax 0.1 --clip3pAdapterSeq AAAAAAAA) as recommended by the Library Prep Kit
Read count extraction was done using FeatureCounts v2.0.6
Assembly: GRCm39 (Ensembl release 109)
Supplementary files format and content: comma-seperated file includes raw deduplicated counts for each Sample

source_name: colon

growth_protocol: Mice were housed in individually ventilated cages at the VIB Center of Inflammation Research in a specific pathogen-free animal facility.

extract_protocol:
RNA was extracted by Trizol (Invitrogen) and 12 ng input RNA was used for library preparation.
RNA libraries for RNA-seq were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD by NXTGNT following manufacturer’s protocols

treatment_protocol: 6 week old mice were administered 20 mg streptomycin by oral gavage 24h before infection. Mice were orally challenged with 10^8 CFU of Nisse or 11G5 and followed up for 28 days. Colon was dissected and flushed with 1x PBS and tumors were dissociated using a mouse tumor dissociation kit (Miltenyi) according to the manufacturer's instructions. Total viable cells were sorted using anti-CD326 and anti-CD45 antibodies.

value: colon

value: immune cells

tag: condition


description:
Sox2P-reporter -116 kb, population P4 pool1 rep1
E2138 Sox2P-reporter -116 kb, population P4 pool1 rep1 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: EEC, rbIgg, 8, cort


description:
Sox2P-reporter -116 kb, population P5 pool3 rep1
E2138 Sox2P-reporter -116 kb, population P5 pool3 rep1 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: EEC, rbIgg, 10, veh

value: vehicle


title: 0dpi RNA


title: SAMPLE_00000002_R04_C04

city: Kiel

first: Matthias

last: Hübenthal

state: SH

address: Rosalind-Franklin-Str. 9

department: Dermatology, Venereology and Allergy

country: Germany

institute: University Hospital Schleswig-Holstein

description: counts.csv

data_processing:
Illumina standard primers were trimmed using trim_galore (version 0.6.6)
Reads were mapped to the human reference genome (GRCh38, Ensembl release 103) using hisat2 (version 2.2.1)
Mapped reads were cleaned and sorted using samtools (version 1.11)
Number of reads for each gene was counted using rsubread (version 2.2.6)
Assembly: GRCh38, Ensembl release 103
Supplementary files format and content: Tab-delimited text file including raw counts of sequencing reads for each gene and sample

molecule: polyA RNA

source_name: Personalized skin model

growth_protocol: Cultured hair follicle-derived human keratinocytes were seeded onto a collagen/fibroblast matrix and allowed to develop a multilayered stratified epidermis through incubation for one week at the air/medium interface

extract_protocol:
Total RNA was isolated using the NucleoSpin RNA Kit (Macherey-Nagel, Düren, Germany)
RNA samples were prepared for sequencing using the Illumina Truseq® mRNA Protocol and sequenced on the NovaSeq6000 with 2x50bp

treatment_protocol: 3D skin models generated from hair follicle-derived human keratinocytes obtained from two atopic dermatitis patients were left unstimulated or stimulated with medium alone, IL-4 (5 ng/mL) and IL-13 (50 ng/mL) alone as well as in combination

value: Personalized skin model

tag: patient

value: donor 2

value: atopic dermatitis

tag: replicate


description:
Sox2P-reporter -116 kb, population P1 pool1 rep1
E2138 Sox2P-reporter -116 kb, population P1 pool1 rep1 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ


title: SAMPLE_00000002_R04_C02

description: counts.csv


title: HEPG2 ERCC spike-in, full-length transcripts

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description: Instrument model: Element Biosciences AVITI

data_processing:
Long reads were first assembled using tool SPADES
Then the long reads were aligned to ERCC reference genome by Minimap2 aligner
Transcript counts were collected based on the alignment and the count per million (CPM) was calculated for transcript quantification.
BCFtools were applied on the aligned file to call the variant sites.
Assembly: ERCC
Supplementary files format and content: BCFtool variant calling file in TXT format

organism: synthetic construct

source_name: ERCC

extract_protocol:
1% dilution of ERCC RNA Spike-In Mix (4456740, ThermoFisher)
LoopSeq preparation of ThermoFisher ERCC RNA Spike-in Mix (Cat#: 4456740) was executed as follows. First, reverse transcription of 11ul ERCC RNA of a 1% diluted template was performed, using a prepared mix of Maxima H Minus RT Buffer and Reverse Transcriptase 200U/µl (Cat#: EP0752, ThermoFisher), RiboLock RNAse inhibitor 40U/µl (Cat#: EO0381, ThermoFisher), 10mM dNTP (Cat#: N0447L, New England Biolabs), LoopSeq specific 100uM Template Switching Oligo (IDT), and a LoopSeq specific 10uM polyTVN UMI-tagging primer oligo (IDT). Incubation conditions were 50°C for 90 min followed by 85°C for 5 min.
UMI diversity in the RT product was then quantified by qPCR. As the RT polyTVN primer oligo includes a UMI sequence, each first strand generated by RT was uniquely UMI-tagged, allowing quantification by qPCR using LoopSeq Amp Mix S and LoopSeq Amp Additive from the Amplicon LoopSeq kit (# 840-10002, Element Biosciences). A master mix of Amp Mix S and Amp Additive was generated following manufacturer instructions and was spiked with 50X SYBR Green (# S7585, Invitrogen) to final concentration of 0.5X SYBR. A dilution series of the RT product was created and quantified by qPCR to determine the dilution needed for an optimized concentration of 15,000 UMIs/µl. PCR was performed for 22 cycles using PCR cycling conditions of 95°C for 3 min, 95°C 30s, 60°C 45s, 72°C 8 min, and a 10°C hold.
After the appropriate dilution was determined by qPCR, twelve replicate 20µl PCR reactions were prepared using LoopSeq Amp Mix S, LoopSeq Amp Additive, and RT product diluted to 15,000 UMIs/µl as template. PCR was performed as described above. 0.6x SPRISelect (Cat#: B23319, Beckman-Coulter) was used for cleanup and generation of a final pool of 20µl. Pooled PCR product was used as input into the Extension LoopSeq kit (Cat#: 840-10003, Element Biosciences).
Circularization of the synthetic long read transcriptome library prepared above was performed using the Adept Library Compatibility Kit v1.1 (Cat#: 830-00007, Element Biosciences) according to manufacturer instructions. The circularized library was quantified using qPCR with the provided standard before being sequenced on the AVITI system with 2 x 150 length paired end reads.
Element Biosciences AVITI, bulk long-read RNA-seq

value: ERCC


title: HEPG2 ERCC spike-in

data_processing:
The raw RNA-seq data were pre-processed by FastQC and Trimmomatic for quality control and trimming.
Then the reads were aligned to ERCC reference genome by STAR aligner
Transcript counts were collected based on the alignment and the count per million (CPM) was calculated for transcript quantification.
BCFtools were applied on the aligned file to call the variant sites.
Assembly: ERCC
Supplementary files format and content: Element.HEPG2-ERCC-spike-in-1.STAR.ReadsPerGene.out.tab: transcript count file in TAB format
Supplementary files format and content: Element.mpileup.txt: BCFtool variant calling file in TXT format

extract_protocol:
1% dilution of ERCC RNA Spike-In Mix (4456740, ThermoFisher)
The linear library pool prepared above was amplified with the KAPA HiFi HotStart Library Amplification kit with Primer Mix (#KK2621) to ensure blunt-end products prior to circularization (90s at 98°C; 5 cycles of 30s at 98°C, 30s at 60°C, 30s at 72°C; and 60s at 72°C). Circularization was performed using the Element Biosciences Adept Library Compatibility Kit v1.1 (Cat#: 830-00007) according to manufacturer instructions. The circularized library was quantified using qPCR with the provided standard before being sequenced on the AVITI system with 2 x 150 length paired end reads.
Element Biosciences AVITI, bulk short-read RNA-seq


extract_protocol:
1% dilution of ERCC RNA Spike-In Mix (4456740, ThermoFisher)
LoopSeq preparation of ThermoFisher ERCC RNA Spike-in Mix (Cat#: 4456740) was executed as follows. First, reverse transcription of 11ul ERCC RNA of a 1% diluted template was performed, using a prepared mix of Maxima H Minus RT Buffer and Reverse Transcriptase 200U/µl (Cat#: EP0752, ThermoFisher), RiboLock RNAse inhibitor 40U/µl (Cat#: EO0381, ThermoFisher), 10mM dNTP (Cat#: N0447L, New England Biolabs), LoopSeq specific 100uM Template Switching Oligo (IDT), and a LoopSeq specific 10uM polyTVN UMI-tagging primer oligo (IDT). Incubation conditions were 50°C for 90 min followed by 85°C for 5 min.
UMI diversity in the RT product was then quantified by qPCR. As the RT polyTVN primer oligo includes a UMI sequence, each first strand generated by RT was uniquely UMI-tagged, allowing quantification by qPCR using LoopSeq Amp Mix S and LoopSeq Amp Additive from the Amplicon LoopSeq kit (# 840-10002, Element Biosciences). A master mix of Amp Mix S and Amp Additive was generated following manufacturer instructions and was spiked with 50X SYBR Green (# S7585, Invitrogen) to final concentration of 0.5X SYBR. A dilution series of the RT product was created and quantified by qPCR to determine the dilution needed for an optimized concentration of 15,000 UMIs/µl. PCR was performed for 22 cycles using PCR cycling conditions of 95°C for 3 min, 95°C 30s, 60°C 45s, 72°C 8 min, and a 10°C hold.
After the appropriate dilution was determined by qPCR, twelve replicate 20µl PCR reactions were prepared using LoopSeq Amp Mix S, LoopSeq Amp Additive, and RT product diluted to 15,000 UMIs/µl as template. PCR was performed as described above. 0.6x SPRISelect (Cat#: B23319, Beckman-Coulter) was used for cleanup and generation of a final pool of 20µl. Pooled PCR product was used as input into the Extension LoopSeq kit (Cat#: 840-10003, Element Biosciences).
Then the library is constructed following the standard protocal for Illumina NextSeq
Illumina NextSeq, bulk long-read RNA-seq


title: SAMPLE_00000002_R04_C03

description: counts.csv


title: EEC, rbIgg, 5, veh


title: HEPG2 ERCC spike-in, all


title: SAMPLE_00000002_R04_C01

description: counts.csv

value: Ctrl


title: HEPG2 ERCC spike-in, all


title: MZM_0410_127

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2FastQ v2.20.0.422
Reads were mapped using TopHat2 v2.1.0 (--no-convert-bam --no-coverage-search -x 1 -g 1)
Counting of reads per gene was done using featureCounts v1.6.5 (-s 2)
Genome_build: genome v20150522 and annotation v20150922 can be downloaded from the Nothobranchius furzeri Information Network Genome Browser (http://nfingb.fli-leibniz.de/)
Supplementary_files_format_and_content: xls file containing read counts/RPMs/RPKMs per gene

organism: Nothobranchius furzeri

source_name: whole brain

extract_protocol:
RNA was extracted with modified Trizol protocol, using Qiazol lysis reagent (Qiagen). In brief, samples were lysed in 1mL QIAzol and 0.2mL of Chloroform was added. Samples were mixed and centrifuged at 20000g for 20 minutes at 4°C in a tabletop centrifuge. After the centrifugation, the upper aqueous phase was withdrawn and mixed with 1.1 volumes (550µl) of isopropyl alcohol, 0.16 volumes (80µl) of 2M, pH 4.2 Sodium acetate and 1µL (10µg) of GlycoBlue to precipitate RNA. Samples were then centrifuged at 20000g for 30 minutes at 4°C, washed twice with 80% ethanol and centrifuged at 7500g for 5 minutes at 4°C. The resulting pellet was dried for no more than 5 minutes and dissolved in nuclease-free water.
Preparation of libraries was done using NEBNext Ultra II directional library preparation kit including enrichment of polyA RNAs using NEBNext Poly(A) mRNA Magnetic Isolation Module  New England Biolabs)  according the manufacturer‘s description.

tag: strain

tag: Sex

value: male

tag: age

value: 35 dph


title: EEC, rbIgg, 4, veh

tag: cut&run antibody


title: UHR ERCC spike-in BS-L017_28

description: Element Biosciences AVITI, bulk short-read RNA-seq

data_processing:
The raw RNA-seq data were pre-processed by FastQC and Trimmomatic for quality control and trimming.
Then the reads were aligned to ERCC reference genome by STAR aligner
Transcript counts were collected based on the alignment and the count per million (CPM) was calculated for transcript quantification.
BCFtools were applied on the aligned file to call the variant sites.
Assembly: ERCC
Supplementary files format and content: TAB files: transcript count file in TAB format
Supplementary files format and content: mpileup files: BCFtool variant calling file in TXT format

source_name: External RNA Controls Consortium (ERCC)

extract_protocol:
1% dilution of ERCC RNA Spike-In Mix (4456740, ThermoFisher)
The linear library pool prepared above was amplified with the KAPA HiFi HotStart Library Amplification kit with Primer Mix (#KK2621) to ensure blunt-end products prior to circularization (90s at 98°C; 5 cycles of 30s at 98°C, 30s at 60°C, 30s at 72°C; and 60s at 72°C). Circularization was performed using the Element Biosciences Adept Library Compatibility Kit v1.1 (Cat#: 830-00007) according to manufacturer instructions. The circularized library was quantified using qPCR with the provided standard before being sequenced on the AVITI system with 2 x 150 length paired end reads.

tag: tissue

value: Universal Human Reference with ERCC spike-in


title: EEC, rbIgg, 3, cort

tag: treatment


title: UHR ERCC spike-in BS-L017_27


title: MZM_0410_125


title: MZM_0410_126


title: EEC, rbIgg, 2, cort

tag: cell line


title: EEC, H3k27me3, 12, veh

tag: cell type


title: SAMPLE_00000002_R03_C02

description: counts.csv


title: MZM_0410_124


title: SAMPLE_00000002_R03_C01

description: counts.csv


title: UHR ERCC spike-in BS-L017_25


title: A41_A_11m

value: 39 dph


title: EEC, H3k27me3, 10, veh


title: SAMPLE_00000002_R03_C03

description: counts.csv


title: UHR ERCC spike-in BS-L017_26


title: EEC, H3k27me3, 9, cort


title: A41_A_7m


title: SAMPLE_00000001_R02_C02

description: counts.csv

value: donor 1


title: normal runID=BL90bb7c13

data_processing:
The long-read transcripts were assembled using SPADES from a python script
Single-cell transcriptome long reads were aligned to human reference genome hg38 by long-read aligner Minimap2
LOOPseq long-reads were analyzed by the tool SQANTI on full and trimmed dataset
Assembly: hg38
Supplementary files format and content: TXT for long-read annotation file

source_name: liver

extract_protocol:
HCC samples and benign liver samples were freshly dissected from a patient who underwent liver transplantation. The procurement procedure was approved by the institution review board of University of Pittsburgh. The procedure was compliant with all regulations related to the protocol. The dissected tissues were minced by scalpel and digested with collagenase/protease solution (VitaCyte, 007-1010) until the tissue was fully digested. The digestion time for each preparation was in a range 45-60 min. The digested tissue was removed and immediately cooled with ice-cold Leibovitz's L-15 Medium (Invitrogen, 11415114) supplemented with 10% fetal bovine serum (Sigma, F4135). The single-cell suspension was verified under the microscope. The number of live cells was estimated by trypan blue staining using a hemacytometer.
Follow pipelines for 10x Genomic single-cell and unique molecular index (UMI) barcoding, and LOOP UMI distribution and library construction
Circularization of the synthetic long read single cell transcriptome library prepared above was performed using the Adept Library Compatibility Kit v1.1 (#830-00007, Element Biosciences) according to manufacturer instructions. The circularized library was quantified using qPCR with the provided standard before being sequenced on the AVITI system with 2 x 150 length paired end reads.
Element Biosciences AVITI, single-cell long-read RNA-seq, 10X scRNA-seq + LOOP

value: liver

value: benign


title: EEC, rbIgg, 7, cort

value: epididymal epithelial cell

value: anti-Rabbit IgG, Antibodies Online, ABIN101961

value: corticosterone


title: A41_A_5m


title: EEC, H3k27me3, 8, cort


title: SAMPLE_00000002_R03_C04

description: counts.csv


title: SAMPLE_00000001_R02_C04

description: counts.csv


title: benign runID=BLfbcc2e6f


title: SAMPLE_00000001_R02_C03

description: counts.csv


title: A41_A_3m


title: SAMPLE_00000001_R02_C01

description: counts.csv


title: benign runID=BLd2616eee


title: EEC, H3k27me3, 5, veh

value: vehicle


title: SAMPLE_00000001_R01_C04

description: counts.csv

value: Personalized skin model


title: benign runID=BL56fa5485


title: Old_Ctr

city: Tsukuba

first: Isao

last: Matsumoto

state: Ibaraki

address: 1-1-1 Tennodai

department: Department of Rheumatology

country: Japan

institute: University of Tsukuba

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-ranger)
Assembly: mm10 2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: inguinal lymph node

extract_protocol:
Inguinal lymph nodes (LNs) were harvested from young (8 weeks) and old (14-15 months) DBA/1 mice 14 days after GIA induction (GIA groups) or PBS injection (control groups). The LNs were homogenized and filtered 40um cell strainer and washed with PBS. All cells from LNs were stained with Pacific blue-conjugated anti-mouse CD4 antibody and CD4+ T cells were sorted on a Moflo XDP cell sorter (Beckman Coulter) . CD4+ T cells were collected equally from four mice in each of the four groups, each with 10,000 cells. CD4+ T cells were washed with PBS and resuspended in 0.04% w/v BSA.
Library was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1, 10x Genomics). Briefly, CD4+ T cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: inguinal lymph node

value: CD4+ T cells


title: EEC, H3k27me3, 3, cort


title: Young_Ctr

description: 10x Genomics


title: tumor runID=BL23e56d74

value: tumor


title: SAMPLE_00000001_R01_C03

description: counts.csv

value: atopic dermatitis


title: Young_GIA

description: 10x Genomics


title: tumor runID=BL7d804c10


title: tumor runID=BLe6fb7832


title: SAMPLE_00000001_R01_C01

description: counts.csv

value: Ctrl


title: Old_GIA

description: 10x Genomics


title: EEC, H3k27me3, 7, cort


title: plankton_O3_S14

status: Public on Aug 18 2024

city: Sydney

first: Catherine

middle: Rose

last: Gatt

state: NSW

address: UNSW Sydney High St Kensington

department: School of Clinical Medicine

country: Australia

institute: University of New South Wales

data_processing:
Paired forwards and reverse reads from all wells were combined into two single files and these combined reads were assembled into contigs using rnaspades  (v3.15.5) with default parameters [31]. Bowtie2 [32] was used to map all the paired and unpaired reads of each well individually against the contigs assembled above. Then, pileup.sh from BBMap (v38.18)  [20] was run on individual bam files to count the number of forward and reverse reads from each individual well that map to each contig . An expression matrix of all contigs in the combined rnaSpades assembly, and the total number of reads (forwards plus reverse) from each well mapping to that contig was generated. The top five contigs with the highest number of reads mapped to them from each well were visualised in Python 3.11.6 using double hierarchical clustering.
Assembly: custom assembly (see data processing step)
Supplementary files format and content: csv with counts against every assembled contig

organism: marine plankton environmental sample

source_name: plankton

extract_protocol:
Cells were captured using the CellCelector platform (ALS Automation GmbH/Sartorius) with a glass capillary tube (inner diameter:  150 μm) using the manual picking mode. The cells were dispensed into  a 384-well Frame-Star plate (4titude Ltd, Surrey, UK) containing 1 μL lysis buffer, which was cooled to  4 ºC  for the duration of the capture. For the first batch of samples, a brightfield image of each cell was recorded before capture. For the second batch of samples, brightfield and epifluorescence images (emission spectrums 515, 595 and 681 nm) of each cell were taken before each capture. For both batches, a brightfield image was taken after each cell capture to confirm successful picking. Two of the wells included in the following cDNA synthesis, library preparation and sequencing did not have cells placed into them, to act as a control for background contamination originating from the laboratory equipment used. Following cell capture, the lysis plate was stored at –80 C for one month
cDNA synthesis was performed following the Smart-seq2 protocol [29]. In brief, 1.8μl of reaction mix (SmartScribe, Rnase Inhibitor, 5x First Strand Buffer, DDT (100mM), Betaine (5M), MgCl2 (1M), TSO (100uM), H2O) was added to each well containing a single cell lysate using the MANTIS automated liquid handler and reverse transcription was performed by incubating the plate at 42 C for 90 minutes, then 70 C for 5 minutes using a thermal cycler (check brand). Following this, 4.2μl of PCR mix (H2O, Kapa Buffer (5x), dNTP (10mM), Polymerase (1U/ul), IS_PCR (10uM)) was added to each well using the MANTIS automated liquid handler (brand) and PCR was performed according to the following cycle: 1) 95 C for 3 minutes, 2) 26 cycles of 98 C for 20 seconds, 67 C for 15 seconds, 72 C for 5 minutes, and 3) 72 C for 5 minutes. A mean concentration of the cDNA in each well was calculated using measurements from the Bioanalyzer 2100 (Agilent Technologies, Waldbronn, Germany) and cDNA concentrations were normalised to 1.4 ng/µl with nuclease-free water using the automated liquid handler Mosquito. The plate was stored at 4C until library preparation. The Nextera XT kit (Illumina, San Diego, CA, USA) was used for tagmentation using 15 cycles of PCR. Bead purification was carried out using Agencourt Ampure XP (Beckman Coulter, Brea CA, USA) magnetic beads. One sample was purified at a ratio of 0.7X for two cycles and a second sample was purified using an additional reverse purification at a ratio of 0.5X for one cycle. Library concentration and size were compared between the two samples using the High-Sensitivity D1K TapeStation (Agilent 2200 TapeStation).

value: plankton


title: plankton_O6_S56


title: plankton_N7_S69


title: plankton_M6_S54


title: plankton_O4_S28


title: plankton_N3_S13


title: plankton_O5_S42


title: SAMPLE_00000001_R01_C02

description: counts.csv


title: tumor runID=BL972f8fba


title: plankton_O7_S70


title: plankton_M4_S26


title: plankton_N5_S41


title: EEC, H3k27me3, 2, cort


title: plankton_M3_S12


title: plankton_L4_S25


title: plankton_L5_S39


title: plankton_L3_S11


title: plankton_L6_S53


title: plankton_K7_S66


title: plankton_K6_S52


title: plankton_N4_S27


title: plankton_N6_S55


title: plankton_K5_S38


title: EEC, H3k27me3, 4, veh


title: plankton_K4_S24


title: plankton_M5_S40


title: plankton_M7_S68


title: plankton_J3_S9


title: plankton_J7_S65


title: plankton_K3_S10


title: plankton_H7_S63


title: plankton_J6_S51


title: plankton_G5_S34


title: plankton_J4_S23


title: plankton_J5_S37


title: plankton_L7_S67


title: plankton_G4_S20


title: plankton_I6_S50


title: plankton_F5_S33


title: plankton_I5_S36


title: plankton_I4_S22


title: plankton_H6_S49


title: plankton_H5_S35


title: plankton_F3_S5


title: plankton_E6_S46


title: plankton_I3_S8


title: plankton_H4_S21


title: plankton_E5_S32


title: plankton_I7_S64


title: plankton_G7_S62


title: plankton_H3_S7


title: plankton_G3_S6


title: plankton_F6_S47


title: plankton_G6_S48


title: plankton_E3_S4


title: plankton_D7_S59


title: plankton_D4_S17


title: plankton_F7_S61


title: plankton_F4_S19


title: plankton_E4_S18


title: plankton_D6_S45


title: plankton_D5_S31


title: plankton_D3_S3


title: plankton_C7_S58


title: plankton_C5_S30


title: plankton_C6_S44


title: plankton_B4_S15


title: plankton_C4_S16


title: RC37_rep3

city: Basel

first: Grégoire

middle: M

last: Vernaz

address: Vesalgasse 1

country: Switzerland

institute: University of Basel

description:
Total RNA from homogenised whole embryo tissues
GeneCount_ensembl_deseq2Norm.txt.gz
TEquant_deseq2Norm_transposonOnly.txt.gz
lncR_deseq2Norm.txt.gz

data_processing:
Sequenced reads were trimmed for adapter sequence and low-quality sequence using TrimGalore
Reads were then mapped to the A.calliptera 1.2 ref genome assembly (Ensembl) using STAR
A gene count matrix was generated using STAR-in built HTSeq and gene count were normalised using DESeq2
Transposon expression was quantified using STAR and TEcount (deseq2 normalised count)
lncRNA were quantified using STAR/HTseq2 (deseq2 normalised count)
Assembly: AstCal1.2_ensembl_GCA_900246225.3, Astatotilapia_calliptera.fAstCal1.2.105.gff3, GCF_900246225.1_fAstCal1.2_genomic.gff
Supplementary files format and content: GeneCount_ensembl_deseq2Norm.txt.gz: tab-sep text files with DESeq2-normalised protein-coding gene count for each sample (column) and each gene (row)
Supplementary files format and content: TEquant_deseq2Norm_transposonOnly.txt.gz: tab-sep text files with DESeq2-normalised TE gene count for each sample (column) and each gene (row)
Supplementary files format and content: lncR_deseq2Norm.txt.gz: tab-sep text files with DESeq2-normalised long-non-coding gene count for each sample (column) and each gene (row)

organism: Rhamphochromis sp. 'chilingali'

source_name: whole embryo

extract_protocol:
RNA was extracted using Direct-Zol RNA Microprep Kit (Zymo) according to manufacturer's instruction
RNA libraries were preped (stranded, polyA enriched) and sequenced on NovaSeq6000 (paired end 150bp)

value: whole embryo

tag: developemental stage

value: whole embryo ; somite stage 37

tag: genotype

value: wild-type

value: tank-reared


title: plankton_E7_S60


title: RC37_rep1


title: plankton_B7_S57


title: plankton_B6_S43


title: plankton_B5_S29


title: plankton_C3_S2


title: P7-Retina-EC-ATACseq-KO-rep1

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

institute: Medical Faculty Mannheim/University of Heidelberg

description:
littermates 2
RetinaEC_RNF20_ATAC_seq_diff_peak.xls
Retina_EC_RNF20_KO_Merge.bw

data_processing:
BGI100
P7_Retina_EC_ATAC-seq paired-end sequencing reads were trimmed of adapters using Trimmomatic-0.36 and then mapped to mm10 mouse genome with Bowtie2 (default settings) (Langmead and Salzberg, 2012b).
Following removal of unmapped reads by SAMtools (-F 1804 -f 2) (Li et al., 2009a), PCR artefacts were excluded by the MarkDuplicates.jar from Picard-tools-1.119 (Tools, 2015).
BamCoverage function of deepTools (Ramírez et al., 2014) with normalization to the reads per genomic content was used to generate the bigwig files for visualization of P7_Retina_EC_ATAC-seq reads in the genome browser IGV (-bs 20 --smoothLength 40 --normalizeUsing RPGC --effectiveGenomeSize 2150570000 -e). Therefore, bam files of each 3 replicates were merged by BamTools (Barnett et al., 2011) and processing was performed like described.
Peak calling was applied from merged bam-files with MACS2 (--nomodel --shiftsize 73)
Called peaks from merged files and individual bam files were further used to quantify and normalize counts as well as calculating differentially accessible chromatin regions upon the different treatments using the R package DiffBind (Stark and Brown) with an edgeR based TMM normalization using read counts and effective library size and an edgeR method to perform differential binding affinity analysis. Peaks were annotated by a custom R script combining ChIPseeker (Yu et al., 2015) and rtracklayer packages (Lawrence et al., 2009b).
Differentially accessible peaks were filtered by R for a p-value of 0.05 and a Log2(FoldChange) of ≥ 0.58 and ≤ -0.58.
indivicual bam files were mergeed by using bamtools merge and merged files were converted to BigWig files using bamCoverage (-bs 20 --smoothLength 40 -p max  --normalizeUsing RPKM -e 150 -o ouput.bw)
mm10
Supplementary files format and content: diff_peaks and BigWig files (In principle, both the xls and txt files are the same, only different format so that users can work with their preferred format.)

growth_protocol: Mice were kept according to the standard of the animal facility of the University of Heidelberg, Medical Faculty of Mannheim.

extract_protocol:
At P7 mice were sacrificed and Retina were dissected followed by digestion with Enzyme solution (Collagenase I 1mg/ml, DNAse I 0.1 mg/ml in HBSS w/o Mg/Cl) for 45 min at 37°C with agitation. The digestion was stopped by addigng Basal Medium (DMEM high glucose, 20% FCS, 1xP/S, 1xGlutamin, 25mM HEPES) and filtering the cell suspension trough a 70 µm cell strainer. After centrifugation the cell pellet was resuspended in 1 ml Basal medium and bound with CD31-coupled magnetic Dynabeads (eBioscience #17031180) for 30 min at RT with agitaion. After washing 5 times on a magnetic rack, EC were counted and max 50.000 cells were used for ATAC.
tagmented DNA; Illumina Nextera Tagmentation kit; IDT-ILMN Nextera DNA UD Indexes (384) Plate C;

treatment_protocol: Pdgfb-iCRE-ERT2_RNF20floxed mice were injected daily from P1 to P4 with 75µg (Z)-4-HO-Tamoxifen (H7904, Sigma Aldrich)

value: Retina

value: EC

value: Pdgf{beta}CreERT2pos Rnf20p/p


title: plankton_B3_S1


title: RC30_rep3

value: whole embryo ; somite stage 30


title: RC37_rep2


title: RC30_rep2


title: thymus_#8_S4

type: RNA

city: Miyazaki

first: Shoichi

last: Wakitani

address: 1-1 Gakuenkibanadai-nishi

department: Faculty of Agriculture

institute: University of Miyazaki

description: Gene expression in thymus

hyb_protocol: Hybridisation was performed using the Gene Expression Hybridization Kit (Agilent, #5188-5242). 1. 600ng of Cy3-labelled cRNA was incubated at 60°C for 30 minutes in a reaction volume of 25 uL containing 25×Fragmentation Buffer and 10x GE Blocking Agent  following the manufacturers instructions. 2. incubated in a water bath at 60°C for 30 minutes, then cooled in ice water for 1 minute   3. spun down quickly and mixed 25uL of 2xHybridization Buffer HI-RPM by pipetting.   4. 40uL was applied to a gasket slide and the array slide was loaded on top of it.  5. hybridized at 65°C for about 17 hours with stirring in a hybridization oven. After Hybridization, The glass slides were washed using the Gene Expression Wash Pack (Agilent, #5188-5327).    After hybridization, the gasket and array slides were disassembled with the microarrays on GE Wash Buffer 1 (Agilent), washed at room temperature for 1 minute with 37Â°C GE Wash buffer 2 (Agilent) for 1 minute, and the slide rack was pulled to dry.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green).

data_processing: The fluorescence signal at each spot was quantified using Agilent Feature Extraction ver. 12.0.3.1. The R package limma was used to normalize the entire data.

organism: Bos taurus

source_name: thymus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50ng RNA using the Low Input Quick Amp Labeling Kit (Agilent, #5190-2305) according to the manufacturer's instructions, followed by RNeasy Mini Kit (QIAGEN, #74104) . Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from thymus tissue frozen at -80°C using ISOGEN II (Nippon Gene, Tokyo, Japan).The NanoDrop 1000 (Thermo Fisher Scientific) was used to measure RNA concentration and purity in Nucleic Acid measurement mode.

treatment_protocol: Thymus lobes were removed at necropsy from black calves with poor prognosis on each farm.

tag: breed

value: Japanese Black calf

value: thymus

tag: gender

value: male


title: thymus_#6_S3

description: Gene expression in thymus


title: P7-Retina-EC-ATACseq-CTR-rep2

description:
littermates 2
RetinaEC_RNF20_ATAC_seq_diff_peak.txt
Retina_EC_RNF20_KO_Merge.bw


title: RC30_rep1


title: RC26_rep2

value: whole embryo ; somite stage 26


title: P7-Retina-EC-ATACseq-KO-rep2

description:
littermates 2
RetinaEC_RNF20_ATAC_seq_diff_peak.xls
Retina_EC_RNF20_CTR_Merge.bw

value: Pdgf{beta}CreERT2neg Rnf20p/p


title: RC26_rep3


title: thymus_#7_S4

description: Gene expression in thymus


title: P7-Retinal-EC-Rnf20-KO-RNAseq-Rep3

description: RetinaEC_P7_RNF20_RNA-seq_differential_expression_Deseq2.xls

data_processing:
Raw reads were Trimmed with trimmomatic-0.36.jar (ILLUMINACLIP:<Truseq_SE.fa>}:2:30:10  LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:15 CROP:48 HEADCROP:7
The trimmed reads were mapped to the mm10 reference genome using STAR (−alignIntronMin 20 −alignIntronMax 500000)
Samples were quantified using analyzeRepeats.pl (mm10 –count exons –strand both –noadj).
Differential expression was quantified and normalized using DESEq2. Reads per kilobase per millions mapped (rpkm) was determined using rpkm.default from EdgeR.
Excel was used to filter differentially regulated genes (fold change ≥1.5; log2 fold change ≤-0.58, ≥0.58; p-value < 0.05.)
mapped bam files were converted to bigWig files by using bamCoverage (-bs 20 --smoothLength 40 -p max  --normalizeUsing RPKM -e 150 -o ouput.bw)
Assembly: mm10
Supplementary files format and content: RPKMs and differential expression data (In principle, both the xls and txt files are the same, only different format so that users can work with their preferred format.)

source_name: PRnf91 Pup 4

growth_protocol: Pups were injected daily from P1 to P4 with 75µg Z-4-HO-Tamoxifen (H7904, Sigma Aldrich)

extract_protocol:
PolyA RNA was isolated using Rneasy Universal Mini Kit from Qiagen
BGI: BGISEQ-500 Ultra Low Input RNA Sample Library Construction Protocol:
1. Amplification
Mix the PolyA RNA sample（more than 200 pg, good-quality）with oligo-dT and dNTPs. Incubate
at 72℃ and immediately put it back on ice. Spin down the samples and reverse transcribed to cDNA based on polyA tail. Switch template at 5' end of the RNA and amplify the full-length cDNA by PCR.
2. Quality Control of Amplification Products
Determine the average molecule length using the Agilent 2100 bioanalyzer instrument (Agilent
High Sensitivity DNA Reagents).
3. Library Construction
Follow Tagmentation-based library construction protocol. PCR products were purified and
selected with the Agencourt AMPure XP-Medium kit. DNA was quantified by Agilent Technologies 2100 bioanalyzer.
4. Circularization
The double stranded PCR products were heat denatured and circularized by the splint oligo
sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library.
5. Library quality control
Library was qualified by the Agilent Technologies 2100 bioanalyzer.
6. Sequencing
The library was amplified to make DNA nanoball (DNB) which had more than 300 copies of
one molecular. The DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated in the way of sequenced by combinatorial Probe-Anchor Synthesis (cPAS)
SMART-Seq Ⅱ

treatment_protocol: At P7 Retina were dissected and digested with Enzyme solution (Collagenase I 1mg/ml, DNAse I 0.1 mg/ml in HBSS w/o Mg/Cl) The digestion was stopped by adding Basal Medium (DMEM high glucose, 20% FCS, 1xP/S, 1xGlutamin, 25mM HEPES) and filtering the cell suspension trough a 70 µm cell strainer. After centrifugation the cell pellet was resuspended in 1 ml Basal medium and bound with CD31 Antibody (eBioscience #17031180) for 30 min and cells were sorted by FACS for CD31+ cells


title: P7-Retina-EC-ATACseq-CTR-rep1

description:
littermates 2
RetinaEC_RNF20_ATAC_seq_diff_peak.txt
Retina_EC_RNF20_CTR_Merge.bw


title: thymus_#5_S2

description: Gene expression in thymus

value: female


title: RC22_rep3

value: whole embryo ; somite stage 22


title: thymus_#3_S1

description: Gene expression in thymus


title: thymus_#4_S2

description: Gene expression in thymus


title: thymus_#1_S0

description: Gene expression in thymus


title: thymus_#2_S0

description: Gene expression in thymus


title: RC22_rep2


title: RC20_rep2

value: whole embryo ; somite stage 20


title: RC22_rep1


title: RC20_rep3


title: P7-Retinal-EC-Rnf20-Ctrl-RNAseq-Rep2

source_name: PRnf91 Pup 9


title: P7-Retinal-EC-Rnf20-KO-RNAseq-Rep1

source_name: PRnf91 Pup 1


title: HUV_ERG_OE_Inp_r2

data_processing:
Visualization of raw reads was done using FASTX-ToolKit, trimmed of the raw reads using Trimmomatic (Bolger et al. 2014), min lengh of 60 bp and Quality score of minimum 15, remove Illumina Adapters TruSeq3
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 default settings
mapped bam files were merged with bamtools merge (default settings) and used to calculate the Pol2 Index
Bam files were merged with bamtools merge (v. 2.5.1) (default settings) and converted to BigWig files with the help of bamCoverage (v. 3.5.1) settings (-bs 20 --smoothLength 40 -p max  --normalizeUsing RPKM -e 150)
Assembly: mm10
Supplementary files format and content: BigWig files

source_name: Human Umbilical Vein Endothelial Cells

growth_protocol: HUVECS (Lonza, pooled donor) were cultured in EGM-MV2 medium

extract_protocol:
72h after infection, when cells were fully confluent, cells were fixed on the plate with 1% Formaldehyde for 10 min at RT then fixation was stopped with 125 mM Glycin for 5 min at RT followed by ChIP for Pol II
Libraries were constructed with the NEB Ultra DNA II Library Kit for Illumina (#E7103S/L)

treatment_protocol: HUVECs were infected with a lentivirus OE ERG or STAT3

value: Human Umbilical Vein Endothelial Cells

value: HUVEC

value: Primary cell

value: lentiviral ERG OE


title: P7-Retinal-EC-Rnf20-Ctrl-RNAseq-Rep1

description: RetinaEC_P7_RNF20_RNA-seq_differential_expression_Deseq2.txt

source_name: PRnf91 Pup 6


title: RC18_rep2

value: whole embryo

value: whole embryo ; somite stage 18

value: wild-type

value: tank-reared


title: HUV_ERG_OE_Inp_r1


title: P7-Retinal-EC-Rnf20-Ctrl-RNAseq-Rep3

source_name: PRnf91 Pup 11

value: Retina

value: EC


title: RC18_rep3


title: HUV_PLKO_Ctr_Inp_r2

value: Ctr

value: lentiviral backbone CTR


title: RC20_rep1


title: HUV_PLKO_Ctr_Inp_r1


title: RC15_rep3

value: whole embryo ; somite stage 15


title: P7-Retinal-EC-Rnf20-KO-RNAseq-Rep2

source_name: PRnf91 Pup 2

value: Pdgf{beta}CreERT2pos Rnf20p/p


title: RC26_rep1

value: whole embryo ; somite stage 26


title: RC15_rep2


title: HUV_ERG_OE_P2t_IP_ChiP_r1

description: Rpb1 NTD (D8L4Y) Cell Signalling


title: RC10_rep3

value: whole embryo ; somite stage 10


title: RC15_rep1


title: RC10_rep1


title: RC10_rep2


title: HUV_PLKO_Ctr_P2t_IP_ChiP_r1

description: Rpb1 NTD (D8L4Y) Cell Signalling


title: HUVEC_siRN20_60h_ATAC_r4

description: Primary cell

data_processing:
Ngmerge was used to trim the paired fastq files.
The trimmed reads were mapped to the human hg38 genome using botwie2 (v. 2.4.4) (-t -X2000 --no-mixed –no-discordant).
samtools view -F 1804 -f 2 -u and MarkDuplicates.jar was used to remove PCR duplicated from bam files.
Accessible areas were called with macs2 callpeak -t bam -f BAMPE -n name_ouput --broad --nomodel -g hs -q 0.01 --bdg --shift -75 --extsize 150 --keep-dup all
Bam files were merged with bamtools merge (v. 2.5.1) (default settings) and converted to BigWig files with the help of bamCoverage (v. 3.5.1) settings (-bs 20 --smoothLength 40 -p max --normalizeUsing RPKM -e 150).
Assembly: hg38 from UCSC genome.
Supplementary files format and content: BigWig files

source_name: HUVEC

growth_protocol: HUVEC (LONZA, pooled donor) were cultured in EGM-MV2 medium.

extract_protocol:
60h after transfection cells were counted and 50,000 cells were used for ATAC. Starting material: 50,000 cells; Tagmentation: Illumina Nextera Tagmentation kit; Adapters: Dual Index adapters from the IDT for Illumina-Nextera DNA Indexes (Plate C); Size Selection: size selection was performed using Ampure XP beads to select for fragments between200-800 bp; Quality and quantity was assessed using the Agilent Bioanalyzer.
Aim of Sequencing: to asses chromatin accessibility; sample Type: single cell, with 50,000 cells per sample; Sequencing platform: BGI; Read Type: Paired-end; read length: 2x 100 bp; library type: ATAC-seq library; Indexing Strategy: Dual-indexing strategy using the IDT for Illumina-Nextera DNA UD Indexes (Plate C).

treatment_protocol: HUVEC P2 transfected with 28 nM siRNA over night.

value: siRNF20 transfection


title: RC4_rep3

value: whole embryo ; somite stage 4


title: HUVEC_siRN20_60h_ATAC_r3

description: Primary cell

value: HUVEC

value: Human Umbilical Vein Endothelial Cells


title: HUVEC_siRN20_60h_ATAC_r1

description: Primary cell


title: RC4_rep1


title: HUVEC_siCTR_60h_ATAC_r4

description: Primary cell

value: siCTR transfection


title: HUVEC_siRN20_60h_ATAC_r2

description: Primary cell


title: RC18_rep1

value: whole embryo


title: HUVEC_siCTR_60h_ATAC_r2

description: Primary cell


title: H2Bub_IP_siRNF20_HUVEC_r3_ChIP_seq

description: Primary cell

data_processing:
Visualization of raw reads was done using FASTX-ToolKit, trimmed of the raw reads using Trimmomatic (Bolger et al. 2014), min length of 60 bp and Quality score of minimum 15, remove Illumina Adapters TruSeq3.
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 default settings.
Mapped bam files were merged with bamtools merge (default settings).
Bam files were merged with bamtools merge (v. 2.5.1) (default settings) and converted to BigWig files with the help of bamCoverage (v. 3.5.1) settings (-bs 20 --smoothLength 40 -p max --normalizeUsing RPKM -e 150).
Assembly: refdata-gex-mm10-2020-A genome.
Supplementary files format and content: bigWig files

extract_protocol:
60h after transfection cells were counted 2 millions cells were used for ChIP-seq of H2Bub.
Libraries were constructed with the NEB Ultra DNA II Library Kit for Illumina (#E7103S/L).

tag: antibody


title: HUVEC_siCTR_60h_ATAC_r3

description: Primary cell


title: HUVEC_siCTR_60h_ATAC_r1

description: Primary cell


title: Soybean W05 root uninfected control  replicate 3

city: Hong Kong

first: Hon-Ming

last: Lam

state: Hong Kong

address: The Chinese University of Hong Kong

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
The RNA-seq analysis workflow is orchestrated by Nextflow 21.04.3, utilizing the nf-core/rnaseq 3.3 pipeline,firstly，Quality Control and Preprocessing:FastQC 0.11.9 performs initial quality checks and Trim Galore 0.6.6 trims adapter sequences and low-quality bases, using default parameters for Illumina reads.
Read Alignment: STAR 2.7.6a aligns RNA-seq reads with default parameters optimized for paired-end reads andspliced alignments.
Transcript Quantification and Assembly:Salmon 1.4.0 quantifies transcripts using default k-mer-based abundance estimation.Picard 2.23.9 and SAMtools 1.12 are employed for sorting, indexing, and converting the alignment outputs into usable formats.
Transcript Quantification:StringTie or similar tools integrated within the nf-core/rnaseq pipeline estimate the abundance of transcripts.
Assembly: Glycine max Wm82.a4.v1
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv file includes TPM values for each sample

organism: Glycine max

source_name: root

growth_protocol: Soybean was planted in the greeenhouse supplemented with 1X B&D solution

extract_protocol:
Total RNA was extracted using RNAiso plus (Takara, Cat.# 9108/9109). 2ug of total RNA was sent to Novogene Co, Ltd for RNA sequencing
RNA library is performed by polyA capture and reverse transcription of cDNA. Strand-specific polyA-enriched libraries were sequenced on illumina NovaSeq 6000

treatment_protocol: Soybean plantes were incoulated with different Siborhizobium fredii strains

value: root


title: Soybean W05 root uninfected control  replicate 2


title: Soybean W05 root inoculated with Sinorhizobium R2-rhcN  replicate 2


title: H2Bub_IP_siRNF20_HUVEC_r2_ChIP_seq

description: Primary cell


title: HUV_PLKO_Ctr_P2t_IP_ChiP_r2

description: Rpb1 NTD (D8L4Y) Cell Signalling

value: Primary cell


title: Soybean W05 root inoculated with Sinorhizobium R2-rhcN  replicate 3


title: HUV_ERG_OE_P2t_IP_ChiP_r2

description: Rpb1 NTD (D8L4Y) Cell Signalling

value: lentiviral ERG OE


title: Soybean W05 nodule inoculated with Sinorhizobium R2-rhcN  replicate 3

source_name: root nodule

value: root nodule


title: Soybean W05 root inoculated with Sinorhizobium R2-rhcN  replicate 1


title: Soybean W05 nodule inoculated with Sinorhizobium R2-rhcN  replicate 2


title: H2Bub_IP_siRNF20_HUVEC_r1_ChIP_seq

description: Primary cell


title: Soybean W05 nodule inoculated with Sinorhizobium R2-rhcN  replicate 1


title: H2Bub_IP_siCTR_HUVEC_r3_ChIP_seq

description: Primary cell


title: Soybean W05 root inoculated with Sinorhizobium R4p2  replicate 3


title: Soybean W05 root inoculated with Sinorhizobium R4p2  replicate 2


title: H2Bub_IP_siCTR_HUVEC_r1_ChIP_seq

description: Primary cell


title: 01HUVEC-siRNF20-3-60h

description: HUVEC_RNF20_RNA-seq_differential_expression_Deseq2.xls

data_processing:
Raw reads were Trimmed with trimmomatic-0.36.jar (ILLUMINACLIP:<Truseq_SE.fa>}:2:30:10  LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:15 CROP:48 HEADCROP:7
The trimmed reads were mapped to the hg38 reference genome using STAR (−alignIntronMin 20 −alignIntronMax 500000)
Samples were quantified using analyzeRepeats.pl (hg38 –count exons –strand both –noadj).
Differential expression was quantified and normalized using DESEq2. Reads per kilobase per millions mapped (rpkm) was determined using rpkm.default from EdgeR.
Excel was used to filter differentially regulated genes (fold change ≥1.5; log2 fold change ≤-0.58, ≥0.58; p-value < 0.05.)
Assembly: mm10
Supplementary files format and content: RPKMs and differential expression data (In principle, both the xls and txt files are the same, only different format so that users can work with their preferred format.)

source_name: retina

extract_protocol:
Total RNA was isolated with Trizol
BGI_RNA Seq_stranded

treatment_protocol: HUVEC P2 transfected with 20 nM siRNA over night, next day changed to full medium (EGM MV2), next day starved in EGM Basal Medium for 12h, bevor harvesting in Trizol

value: retina

tag: passage


title: H2Bub_IP_siCTR_HUVEC_r2_ChIP_seq

description: Primary cell

value: Ctr


title: Soybean W05 root inoculated with Sinorhizobium R4p2  replicate 1


title: Soybean W05 nodule inoculated with Sinorhizobium R4p2  replicate 3


title: 01HUVEC-siRNF20-1-60h


title: Soybean W05 root uninfected control  replicate 1


title: 01HUVEC-siRNF20-2-60h

description: HUVEC_RNF20_RNA-seq_differential_expression_Deseq2.txt


title: Soybean W05 nodule inoculated with Sinorhizobium R4p2  replicate 1


title: 01HUVEC-siCtr3-60h

value: sCTR


title: Soybean W05 nodule inoculated with Sinorhizobium R4p2  replicate 2


title: Soybean W05 root inoculated with Sinorhizobium R4i2  replicate 3


title: 01HUVEC-siCtr1-60h


title: Soybean W05 root inoculated with Sinorhizobium R4i2  replicate 2


title: 01HUVEC-siCtr2-60h


title: Soybean W05 root inoculated with Sinorhizobium R4i2  replicate 1


title: Soybean W05 nodule inoculated with Sinorhizobium R4i2  replicate 1


title: Soybean W05 nodule inoculated with Sinorhizobium R4i2  replicate 2


title: Soybean W05 root inoculated with Sinorhizobium R4  replicate 3


title: Soybean W05 nodule inoculated with Sinorhizobium R4i2  replicate 3


title: Soybean W05 root inoculated with Sinorhizobium R4  replicate 1


title: Soybean W05 nodule inoculated with Sinorhizobium R4  replicate 3


title: Soybean W05 root inoculated with Sinorhizobium R4  replicate 2


title: Soybean W05 nodule inoculated with Sinorhizobium R4  replicate 2


title: T1 at weeks 3 [Immune]

city: Taipei

first: Chung-Hsing

last: Chen

address: No.1 Ai-Guo West Road

department: Department of Mathematics

country: Taiwan

institute: University of Taipei

hyb_protocol: Hydridized according to the manufacturer's protocol.

scan_protocol: Scanned according to the manufacturer's protocol.

data_processing: We merged these samples in different panels into one dataset for subsequent data normalization. Data normalization similar to that described by the nCounter Advanced Analysis user manual (version 2.0, NanoString Technologies) was applied. Each count was transformed to a log2 scale and then normalized using positive control probes and housekeeping genes identified by geNorm algorithmt to reduce variations. We also calculated means of paired normal mice at weeks 3 and weeks 5 to 7 to scale mice (paired normal, tumor-bearing mice, and recurrence mice) at these two time points.

label: NanoString oligonucleotide probe

source_name: PBMC from tumor-bearing mouse 1 at weeks 3

label_protocol: Labeled according to the manufacturer's protocol.

extract_protocol: Mouse blood was collected with Microtainer® (BD) with EDTA and incubated with 3 ml ACK lysis buffer (Gibco) for 5 min at room temperature to lyse red blood cells. PBMC were spun down by centrifugation at 1500 rpm for 10 min at 4℃ and washed twice with phosphate-buffered saline (PBS). RNA of PBMC was isolated by using Direct-Zol RNA Miniprep Kits (ZYMO RESEARCH) according to manufacturer instructions.

value: BALB/c

tag: group

value: Tumor


title: T3 at weeks 3 [Immune]

source_name: PBMC from tumor-bearing mouse 3 at weeks 3


title: R3 at weeks 5-7 [Immune]

source_name: PBMC from recurrence mouse 3 at weeks 5-7

value: Recurrence


title: R1 at weeks 5-7 [Immune]

source_name: PBMC from recurrence mouse 1 at weeks 5-7


title: R2 at weeks 5-7 [Immune]

source_name: PBMC from recurrence mouse 2 at weeks 5-7


title: Soybean W05 root inoculated with Sinorhizobium R2p4  replicate 3


title: N2 at weeks 3 [Immune]

source_name: PBMC from normal mouse 1 at weeks 3

value: Normal


title: Soybean W05 nodule inoculated with Sinorhizobium R4  replicate 1


title: Soybean W05 root inoculated with Sinorhizobium R2p4  replicate 2


title: N3 at weeks 5-7 [Immune]

source_name: PBMC from normal mouse 3 at weeks 5-7


title: N3 at weeks 3 [Immune]


title: Soybean W05 root inoculated with Sinorhizobium R2p4  replicate 1


title: primary hepatocytes, HKO-2, PA

city: Nanjing

first: ying

last: zheng

address: 639 Longmian Avenue, Chunhua Street, Jiangning District,

country: China

institute: China Pharmaceutical University

data_processing:
CLC Genomics Workbench V11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length faction: 0.8 similarity faction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text fles include RPKM values for each Sample

source_name: liver

growth_protocol: 6-week-old G3bp1-Flox and G3bp1-HKO mice

extract_protocol:
RNA was harvested using RNeasy Plus Mini Kit (Qiagen). 1.3μg total RNA was used for the construction of suquencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufaturer's protocols.

treatment_protocol: primary hepatocytes , rapidly frozen in liquid nitrogen, were stored at -80°C for subsequent RNA extraction

value: liver

value: primary hepatocytes

value: hepatocyte-specific G3bp1-knockout

value: PA


title: Soybean W05 nodule inoculated with Sinorhizobium R2p4  replicate 3


title: N1 at weeks 3 [Immune]


title: T2 at weeks 3 [Immune]

source_name: PBMC from tumor-bearing mouse 2 at weeks 3


title: N1 at weeks 5-7 [Immune]

source_name: PBMC from normal mouse 1 at weeks 5-7


title: Soybean W05 nodule inoculated with Sinorhizobium R2p4  replicate 1


title: primary hepatocytes, Flox-3, PA

value: Flox


title: primary hepatocytes, HKO-3, PA


title: Soybean W05  root inoculated with Sinorhizobium R2i4  replicate 3


title: primary hepatocytes, Flox-1, PA


title: Soybean W05 nodule inoculated with Sinorhizobium R2i4 replicate 3


title: primary hepatocytes, HKO-2, BSA

value: BSA


title: primary hepatocytes, HKO-1, PA


title: primary hepatocytes, HKO-1,BSA


title: Soybean W05  root inoculated with Sinorhizobium R2i4  replicate 1

value: root


title: Soybean W05 nodule inoculated with Sinorhizobium R2i4 replicate 2


title: primary hepatocytes, Flox-3, BSA


title: Soybean W05 root inoculated with Sinorhizobium R2  replicate 3


title: N2 at weeks 5-7 [Immune]

source_name: PBMC from normal mouse 2 at weeks 5-7


title: primary hepatocytes, Flox-1,BSA


title: shSrsf10

city: shanghai

first: JL

last: CAI

address: shanghai

institute: fudan university

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the cell Ranger software v6.1.0(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
Single-cell RNA-seq was performed following the protocol established by Gene Denovo Biotechnology Co. (Guangzhou, China).9 In brief, the cell suspension derived from mouse liver was centrifuged at 50 g for 2 min, resulting in the separation of hepatocytes settling at the bottom, while nonparenchymal cells (NPCs) were mainly remained in the supernatant suspension.9 A small amount of single cell suspension was mixed with equal volume of 0.4% trypan blue staining solution and counted using Counter ® II Automated Cell Counter.
The mixture, including gel beads with barcode, cells, and enzymes, was separated by oil in the reservoir to form GEMs (Gel Beads In Emulations). Subsequently, gel beads dissolved, releasing the captured sequence containing Barcode sequence. RNA was reverse transcribed to produce cDNA, following the 10×Genomics single cell 3’ library construction V3 protocol. Quantification and pooling were carried out using the ABI One-Step Plus Real-Time PCR System (Life Technologies). 9 High-throughput sequencing was performed in PE150 sequencing mode on the Illumina sequencing platform.


title: Soybean W05 nodule inoculated with Sinorhizobium R2p4  replicate 2


title: Soybean W05 root inoculated with Sinorhizobium R2  replicate 2


title: Soybean W05  root inoculated with Sinorhizobium R2i4  replicate 2


title: Soybean W05 nodule inoculated with Sinorhizobium R2i4 replicate 1


title: shCtrl

value: WT


title: Soybean W05 root inoculated with Sinorhizobium R2  replicate 1


title: young_5_DP

city: wuhan

first: huiru

last: jing

address: Donghu Road, No. 115, Wuchang District, Wuhan, Hubei Province

institute: wuhan university

data_processing:
Illumina’s bcl2fastq was used to convert bcl files to FASTQ files and de-multiplex the samples.
Reads were filtered based on a mean base quality score > 20, and adapters were trimmed by “trim_galore” (version 0.4).
The raw reads were filtered by removing adaptor sequences, contamination and low-quality reads. Cleaned reads were mapped to mm10 using STAR aligner (version 2.5.1.)
Subread HTSeq (Version 2.0.3) was applied for gene quantification based on GENCODE annotation (gencode.vM23)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw read count and log2 transformed DESeq2 normalized counts for each sample

source_name: thymus

extract_protocol:
Live cells were collected, and RNA was harvested using Trizol reagent. Direct-zol RNA Microprep Kits (Cat#R2061) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard BGI protocols.

value: thymus

value: 10 weeks

value: wild type


title: young_5_DN


title: primary hepatocytes, Flox-2, PA


title: Soybean W05 nodule inoculated with Sinorhizobium R2  replicate 3

value: root nodule


title: young_4_DP


title: young_4_DN


title: primary hepatocytes, HKO-3, BSA


title: young_3_DP


title: primary hepatocytes, Flox-2,BSA


title: young_3_DN


title: AC27_rep2

organism: Astatotilapia calliptera

source_name: whole embryo

value: whole embryo

value: whole embryo ; somite stage 27

value: wild-type

value: tank-reared


title: AC30_rep1

value: whole embryo ; somite stage 30


title: AC27_rep3


title: AC27_rep1


title: young_2_DN


title: AC22_rep3

value: whole embryo ; somite stage 22


title: young_1_DP


title: Soybean W05 nodule inoculated with Sinorhizobium R2  replicate 2


title: young_1_DN


title: AC22_rep2


title: WT_5_DP

value: Mettl3flox/wt; Cd4Cre


title: WT_4_DP


title: AC22_rep1


title: WT_3_DP


title: AC30_rep2


title: AC20_rep2

value: whole embryo ; somite stage 20


title: WT_4_DN


title: Soybean W05 nodule inoculated with Sinorhizobium R2  replicate 1


title: AC18_rep3

value: whole embryo ; somite stage 18


title: AC18_rep2


title: WT_2_DP


title: WT_2_DN


title: young_2_DP


title: AC18_rep1


title: AC15_rep3

value: whole embryo ; somite stage 15


title: WT_1_DP


title: AC20_rep3


title: AC15_rep2


title: AC20_rep1


title: WT_5_DN


title: KO_4_DP

value: Mettl3flox/flox; Cd4Cre


title: KO_3_DP


title: AC10_rep2

value: whole embryo ; somite stage 10


title: KO_2_DP


title: AC10_rep3


title: AC4_rep2

value: whole embryo ; somite stage 4


title: AC10_rep1


title: KO_5_DP

value: thymus


title: Aged_5_DP

value: 60 weeks


title: AC15_rep1


title: Shade, Input, rep2

city: Shanghai

first: Lin

last: Li

address: 2005 Songhu Road, Yangpu Distric

department: school of life science

institute: Fudan university

data_processing:
Raw sequence reads were initially processed by fastp for quality control, and then adapter sequences and poor quality reads were removed by using trimmomatic software.
Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to reference genome sequences using the bwa program.
Peaks were called uing MACS v2.2.71 with the significance cut-off q-value <=0.05
bigWig files were generated using the deepTools v3.5.0. narrowPeak files were generated using MACS with default settings.
Assembly: Tair10_Ensembl_43
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

organism: Arabidopsis

source_name: whole seedlings

growth_protocol: 7-day-old continuous white light-grown ProbZIP59::bZIP59-GFP/bzip59 seedlings treated with 2 h shade.

extract_protocol:
Seedings were fixed with 1% formaldehyde for 15 minutes under vacuum condition. After grind and lysis, chromatin was sonicated using a Bioruptor Next Gen UCD-300 (Diagenode).
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). Amplified libraries were size selected using 2% gel to capture fragments between 100 and 400 bp. Libraries were quantiﬁed using the Agilent 2100 Bioanalyzer (Agilent Technologies). Samples without antibodies were used as the input control. The sample library was sequenced on NovaSeq6000 PE150.

treatment_protocol: With 2 h shade (R/FR=0.65) treatment

value: whole seedlings

value: 2 h shade (R/FR=0.65)

tag: chip antibody


title: AC4_rep3

value: whole embryo


title: Aged_5_DN

value: wild type


title: AC4_rep1

value: wild-type


title: Aged_4_DP


title: WT_1_DN

value: 10 weeks


title: KO_1_DP


title: Shade, IP, rep2

value: GFP (Abcam, #ab290)


title: Aged_4_DN


title: Shade, Input, rep1


title: Aged_3_DP


title: Aged_3_DN


title: White light, IP, rep2


title: Aged_2_DP


title: White light, Input, rep2


title: White light, Input, rep1


title: Aged_2_DN


title: Aged_1_DP


title: Aged_1_DN


title: White light, IP, rep1


title: Mutant bzip59,shade, replication 3

data_processing:
Raw sequence reads were initially processed by fastp for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filitered reads were then mapped to Tair10 using Hisat2
Differential gene expression analysis was done using R package DESeq2
Assembly: TAIR10
Supplementary files format and content: all_genes_expresson_TPM.csv

growth_protocol: 7-day-old continuous white light-grown Col-0 and bzip59 seedlings treated with 2 h shade.

extract_protocol:
Total RNA was extracted from tissue samples, and the concentration and purity of the extracted RNA were detected by Nanodrop2000. The integrity of RNA was detected by agarose gel, and the RIN value was determined by Agilent 2100. Using magnetic beads with Oligo (dT) and ployA for A-T base pairing, mRNA can be isolated from total RNA for analysis of transcriptome information. Under the action of reverse transcriptase, six random primers were added to reverse synthesize a single strand of cDNA using mRNA as a template, followed by a two-strand synthesis to form a stable double-stranded structure. The structure of double-stranded cDNA is sticky end. Add End Repair Mix to repair it into a flat end, and then add an "A" base at the 3 'end to connect the Y-shaped connector.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Arabidopsis

value: Mutuan, SALK_024459

value: shade


title: Mutant bzip59,shade, replication 2


title: BM lin- Flt3+ Kitint-lo H/H, HTO

city: St. Louis

first: Feiya

last: Ou

state: MO

address: 4939 Children's Place

department: Pathology & Immunology

institute: Washington University in St. Louis

library_source: other

data_processing:
The Cell Ranger pipeline v8.0.0 was used for aligning reads to the mm10 reference genome, single cell counting, barcode processing, and sample demultiplexing.
Assembly: mm10
Supplementary files format and content: TSV files of per biological replicate

molecule: protein

source_name: BM

extract_protocol:
BM and spleens were harvested from two WT and two Irf8 +32H/H mice. The BM samples were depleted of lin+ cells expressing CD3e, CD8b, CD11b, CD19, B220, ly-6G, TER-119, and NK1.1. Each sample was stained with fluorochrome-conjugated antibodies and labeled with a unique Antibody Capture TotalSeq B antibody (Biolegend) before sorting for lin- Flt3+ Kitint-lo cells. Two samples from each genotype were pooled and resuspended in PBS with 0.04% BSA at a final concentration of approximately 1,000 cells/mL. The spleen samples were enriched for CD11c-expressing cells, similarly stained with fluorochrome-conjugated antibodies and labeled with a unique Antibody Capture TotalSeq B antibody (Biolegend), before further sort-purification for CD11c+ cells. All four samples were pooled and resuspended in PBS with 0.04% BSA at approximately 1,000 cells/mL. These were loaded on a 10× Genomics Chromium Single Cell Controller at GTAC@MGI at Washington University School of Medicine.
Library preparation was performed using the 10× Genomics Next GEM Single Cell 3’ Reagents Kit v3. Libraries were sequenced using an Illumina Novaseq 6000 sequencer, producing 150 bp paired-end reads. Sequencing targeted depths of 1B reads for the gene expression (GEX) library and 100M reads for the hashtag oligo (HTO) library, respectively.

value: BM

value: lin- Flt3+ Kitint-lo BM cells

value: H/H


title: Mutant bzip59,shade, replication 1


title: BM lin- Flt3+ Kitint-lo H/H, GEX


title: Spl CD11c+ WT and H/H, HTO

source_name: Spleen

value: Spleen

value: CD11c+ splenocytes

value: WT and H/H


title: Mutant bzip59,whlie light, replication 1

value: white light


title: Spl CD11c+ WT and H/H, GEX


title: Mutant bzip59,whlie light, replication 2

value: whole seedlings


title: Mutant bzip59,whlie light, replication 3


title: BM lin- Flt3+ Kitint-lo WT, HTO

value: WT


title: Shade, IP, rep1

value: 2 h shade (R/FR=0.65)


title: Wild type Col-0,shade, replication 3

value: Wild type


title: BM lin- Flt3+ Kitint-lo WT, GEX


title: Wild type Col-0,shade, replication 2


title: Wild type Col-0,shade, replication 1


title: scRNAseq: PRXTFAMHIF1dPA_Control2

city: Philadelphia

first: Ernestina

last: Schipani

address: 310A Stemmler Hall, 3450 Hamilton Walk

department: McKay Orthopaedic Research Laboratory

institute: University of Pennsylvania

description: 10X Genomics

data_processing:
Libraries were uniquely indexed using the Chromium Dual Index Kit, pooled, and sequenced on an Illumina NovaSeq 6000 sequencer using a paired-end, dual-indexing run strategy. Sequencing for each library aimed for 20,000 mean reads per cell. The data were then processed using the Cell Ranger pipeline (10x Genomics, version 6.1.2) for demultiplexing, alignment of sequencing reads to the mm10 mouse transcriptome, and generation of feature-barcode matrices.
Assembly: mm10
Supplementary files format and content: Processed files are the raw and filtered feature-barcode matrices in Hierarchical Data Format (HDF5, or H5) that are output from Cell Ranger (raw_feature_bc_matrix.h5 and filtered_feature_bc_matrix.h5). For more information, see the Cell Ranger documentation for ‘Outputs’:https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/outputs/cr-outputs-overview.

source_name: Bone

extract_protocol:
Periosteum-derived cells (PDCs) were isolated from hindlimbs of TFAMfl/fl and PRX;TFAMfl/fl mice, as well as from TFAMfl/fl;HIF1dPAfl/fl and PRX;TFAMfl/fl;HIF1dPAfl/fl mice at postnatal day 21 (p21), following an established procedures (Gastel et al., 2012). Briefly, femurs and tibias were dissected to remove muscle and connective tissues under aseptic conditions. The epiphyses were covered with 5% low melting point agarose (SeaPlaque, Lonza, Verviers, Belgium) to protect them from enzymatic degradation. The PDCs were then isolated via collagenase-dispase enzymatic digestion consisting of 3 mg/ml collagenase type IA (MilliporeSigma, Rockville, MD) and 4 mg/ml dispase II (MilliporeSigma) in α-minimal essential medium (α-MEM) with 2 mM glutaMAX-I (Gibco, Invitrogen, Carlsbad, CA). Cells from the initial 10-minute digestion phase were discarded to remove contamination with residual muscle and connective tissue cells. A subsequent one-hour digestion was performed to release the PDCs.
Next-generation sequencing libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent Kit v3 according to the manufacturer's instructions.

value: Bone

value: Periosteal Cell


title: scRNAseq: PRXTFAMHIF1dPA_Mutant2

description: 10X Genomics


title: scRNAseq: PRXTFAMHIF1dPA_Mutant1

description: 10X Genomics


title: Wild type Col-0,whlie light, replication 3


title: scRNAseq: PRXTFAMHIF1dPA_Control1

description: 10X Genomics


title: Wild type Col-0,whlie light, replication 2


title: scRNAseq: PRX1TFAM_Mutant2

description: 10X Genomics


title: Wild type Col-0,whlie light, replication 1


title: scRNAseq: PRX1TFAM_Mutant1

description: 10X Genomics


title: scRNAseq: PRX1TFAM_Control1

description: 10X Genomics


title: H3K27ac ChIP-seq dual 8h 1

city: Rehovot

first: Ido

last: Goldstein

address: POB 12

department: Institute of Biochemistry, Food Science and Nutrition

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Fastq files were mapped to the mm10 mouse genome assembly using Bowtie2
Assembly: mm10
Supplementary files format and content: BAM files contain aligned reads

source_name: primary hepatocytes

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 min at room temperature and quenched with 0.125M glycine. Crosslinked samples were washed in phosphate buffered saline (PBS), resuspended in ChIP lysis (0.5% SDS, 10mM EDTA, 50mM Tris-HCl pH8) buffer and sonicated to release 100-1000 bp fragments. Antibody against H3K27ac was conjugated to magnetic beads for 2 h at 4°C. Chromatin was immunoprecipitated with antibody-bead conjugates for 16 h at 4°C. Immunocomplexes were washed sequentially with the following buffers: low-salt buffer (0.01% SDS, 1% Triton x-100, 2 mM EDTA, 20mM Tris-HCl pH8, 150mM NaCl), high salt buffer (0.01% SDS, 1% Triton x-100, 2mM EDTA, 20mM Tris-HCl pH8, 500mM NaCl), low salt buffer and TE buffer (10mMTris-HCl, 1mM EDTA pH8). Chromatin was de-proteinized with proteinase K for 2 h at 55°C and de-crosslinked for 12 h at 65°C. DNA was subsequently phenol-chloroform purified and ethanol precipitated.
ChIP DNA libraries were prepared using the KAPA HyperPrep Kit (KAPA biosystems, cat# KR0961).

treatment_protocol: Primary hepatocytes were isolated from male, 8-10 weeks-old mice (strain C57BL/6JOlaHsd). Three hours after plating, media was changed to Williams E media. After 18h, the hepatocytes were treated with hormones (corticosterone 1 µM, Wy14643 10 µM or a dual treatment) for 8h.

value: primary hepatocytes

value: wt

value: 1uM cort + 10uM WY 1 8h


title: scRNAseq: PRX1TFAM_Control2

description: 10X Genomics


title: H3K27ac ChIP-seq wy 8h 1

value: 10uM WY 1 8h


title: H3K27ac ChIP-seq cort 8h 3

value: 1uM cort 3 8h


title: H3K27ac ChIP-seq cort 8h 2

value: 1uM cort 2 8h


title: H3K27ac ChIP-seq wy 8h 3

value: 10uM WY 3 8h


title: Ketamine 2

city: Iowa City

first: Michael

middle: S

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

data_processing:
Barcoded samples were pooled and sequenced, using an Illumina NovaSeq 6000 at the Iowa Institute for Human Genomics (IIHG) Core Facility, to obtain an average of 223 million paired-end 100bp reads per sample. Reads were converted from the native Illumina BCL format to fastq format with ‘bcl2fastq’ (v2.20.0.422). Data was processed using nf-core/rnaseq v3.10 (doi: https://doi.org/10.5281/zenodo.1400710) of the nf-core collection of workflows (Ewels et al., 2020). The pipeline was executed with Nextflow v22.10.1 (Di Tommaso et al., 2017) on the University of Iowa’s Argon HPC cluster with the following command:
nextflow run nf-core/rnaseq -r 3.10 -profile argon --igenomes_base /Users/mchiment/igenomes/references --input samplesheet.csv --outdir nf --genome GRCm38 --email michael-chimenti@uiowa.edu --save_merged_fastq FALSE --skip_markduplicates TRUE --skip_preseq TRUE --skip_dupradar TRUE --skip_stringtie TRUE
Alignments were stored as indexed BAM files. QC was performed with MultiQC v3.9.5. All samples passed bioinformatic QC thresholds and were retained for exploratory analysis. Salmon-derived gene-level expression values were imported into an R Studio environment. Variance-stabilized gene-level counts were used for exploratory analysis via principal components analysis and sample-to-sample distance calculations. Non-normalized gene-level counts were used for differential expression analysis with DESeq2  following best practices as described in the DESeq2 vignette. A DESeq2 data object was created and conditioned solely on ‘treatment’ for DE testing. Code used in this analysis is available here.  Raw and processed data were deposited in the NCBI Gene Expression Omnibus. Pathway analysis was carried out using iPathwayGuide software (https://advaitabio.com/ipathwayguide) to perform proprietary “impact analysis” to generate reports describing enriched pathways, GO terms, and upstream regulatory genes. These analyses consider both the direction and type of all signals on a pathway along with the position, role and type of each gene..

source_name: Brain

growth_protocol: We administered saline or ketamine (30 mg/kg/day, i.p.) for 10 consedutive days. Then the brains were extracted and frozen rapidly.

extract_protocol:
To pull down the EGFP-tagged polyribosomes, we used an affinity matrix containing Dynabeads (Thermo Fisher Scientific, Waltham, MA, USA), Biotinylated protein L (Genscript, Piscataway, NJ, USA), and GFP antibodies (HtzGFP-19F7 and HtzGFP-19C8, Heintz Lab, Rockefeller University, New York, NY, USA). The supernatant with EGFP-tagged polyribosomes was incubated with this affinity matrix, and after incubation, the beads (now with EGFP-tagged polyribosomes) were washed in high salt buffer (20 mM HEPES, 10 mM MgCl2, 350 mM KCl, 1% NP-40, 0.5 mM DTT and 100 μg/ml cyclohexamide). RNA from the complex was isolated using the Agilent Absolutely RNA Nanoprep kit (Agilent, Santa Clara, CA, USA) following the manufacturer's instructions. Further, before sequencing the RNA was quantified in Drop Sense (Perkin Elmer, MA, USA) and Qubit HS RNA (Thermo Fisher Scientific) and checked for quality in 2100 Bioanalyzer (Agilent).
The Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus sample preparation kit (Illumina, San Diego, CA, USA) was used for library preparation. Library concentrations were measured, and the average size was determined using the Qubit dsDNA HS kit (Thermo Fisher Scientific) and the 2100 Bioanalyzer (Agilent). The four libraries were then combined equally based on molar concentrations, and the pool's concentration was measured using the KAPA Illumina Library Quantification Kit (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: The lateral septal tissue was collected in an ice-cold dissection buffer (1X HBSS, 2.5 mM HEPES, 35 mM Glucose, 4 mM NaHCO3, and 100 μg/ml cyclohexamide). Since the expected number of activated neurons was relatively low, we pooled five LS tissue punches into one tube. As a result, we created 2 ketamine and 2 saline pooled samples for ribo-TRAP. Next, we homogenized the pooled tissue in a tissue lysis buffer (20 mM HEPES, 10 mM MgCl2, 150 mM KCl, 0.5 mM DTT, 100 μg/ml cyclohexamide, RNase inhibitors and EDTA-free protease inhibitors) using a prechilled micropestle, and the homogenate was centrifuged to obtain the supernatant containing polyribosomes.

value: Brain

value: Fos-iCreER (+/+)

value: Ribo-TRAP


title: H3K27ac ChIP-seq wy 8h 2

value: 10uM WY 2 8h


title: Saline 2


title: Mouse activated PD1+ T cells from total CD4 depleted TDLNS VDJ

city: Atlanta

first: Haydn

last: Kissick

state: Georgia

address: 1462 Clifton Rd

institute: Emory University

description: 10X Genomics of PD1+CD44+ and naïve T cells from CD4 depleted tumor draining lymph nodes of 5-week bearing TRAMPC1-GP mice

data_processing:
Aligned using Cellranger and differential gene expression and clustering performed with Seurat.
Assembly: hg38
Supplementary files format and content: tsv.gz
Supplementary files format and content: input for scRNAseq analysis.

molecule: other

source_name: tumor draining lymph nodes

extract_protocol:
Cells were FACS sorted and used to generate single cell suspensions. RNA was extracted using qiagen all-prep kits. Samples were loaded onto the 10X Genomics Chromium Controller according to manufacturer's protocol.
Library construction was performed using the Chromium Single Cell 5’ Library Construction Kit

value: tumor draining lymph nodes

value: Activated (PD1+CD44+) and naive T cells

value: CD4 depleted by GK1.5 antibody

tag: cancer type

value: TRAMPC1-GP cell line


title: Mouse activated PD1+ T cells from total CD4 depleted TDLNS GEX


title: H3K27ac ChIP-seq nt 8h 3

value: nt


title: Ketamine 1


title: Saline 1


title: H3K27ac ChIP-seq nt 8h 2


title: non-stimulated cardiac fibroblasts, D

city: NYC

first: Izabela

last: Tuleta

state: NY

address: 1300 Morris Park Avenue

department: Cardiology

institute: Albert Einstein College of Medicine

description:
EVD
Mouse cardiac fibroblasts at passage 2 were cultured with empty plasmid.

data_processing:
Raw image data file from high-throughput sequencing was transformed to Sequenced Reads by CASAVA base recognition (Base Calling).
The library preparations were sequenced on Illumina NovaSeq 6000 devices, generating 100 bp paired end reads. Adapter, poly-N and low-quality reads from the raw data were excluded to purify the data analysis
Quality Phred Scores, Q20%, Q30% and GC contents of the clean data were calculated, showing high accuracy of reads (>99%, with 0.02 error rate).
Filtered reads were aligned to the C57BL/6J reference genome (December 2011 release of the mouse musculus reference genome (mm10; GRCm38.p6) from Ensembl) using TopHat2 algorithm alignment program v.2.0.
Mapped reads were assembled using both Scripture (beta2) and Cufflinks v.2.1.1 algorithm
HTSeq software v.0.6.1 was used to count the number of reads mapped to each gene. Read count of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM), was used to calculate gene expression level, which considered the effects of both sequencing depth and gene length
Assembly: mm10
Supplementary files format and content: excel files including raw gene counts for every gene and every sample
Supplementary files format and content: excel files including FPKM values counts for every gene and every sample

source_name: Cardiac fibroblasts

extract_protocol:
RNA was extracted with Trizol reagent.
RNA sequencing was performed by Novogene. RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-seq. Library preparation was performed by Novogene, Inc., using at least 1 ug high-quality total RNA input per sample. mRNA enrichment was performed with poly-T oligo-attached magnetic beads. Libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina.

treatment_protocol: Transformed E. coli bacteria in stab culture were used as a source of plasmids: 1. plasmid containing murine THBS4 ( pAAV.CMV.SV40.THBS4-HA.SV40(polyA), #155193, Addgene, Watertown, MA) and 2. empty plasmid serving as a control (pAAV-CA, #69616, Addgene, Watertown, MA). After transfection, medium with plasmid was discarded and replaced by standard medium without antibiotics for 12 hours. Thereafter, cells were serum deprived for 24h (for RNA) or 48h (for proteins) and collected for subsequent experiments. Efficiency of TSP-4 overexpression was confirmed using western blotting.

value: cardiac fibroblasts

tag: strain

value: Cardiac fibroblasts were cultured in the presence of empty plasmid


title: Mouse activated PD1+ T cells from Treg depleted TDLNS GEX

description: 10X Genomics of PD1+CD44+ and naïve T cells from Treg depleted tumor draining lymph nodes of 5-week bearing TRAMPC1-GP FOXP3-DTR mice

value: Treg depleted by diptheria toxin


title: H3K27ac ChIP-seq dual 8h 3

value: primary hepatocytes

value: wt

value: 1uM cort + 10uM WY 3 8h


title: non-stimulated cardiac fibroblasts, C

description:
EVC
Mouse cardiac fibroblasts at passage 2 were cultured with empty plasmid.


title: H3K27ac ChIP-seq dual 8h 2

value: 1uM cort + 10uM WY 2 8h


title: RNA-seq dual 8h 3

extract_protocol:
Total RNA was isolated from primary mouse hepatocytes using NucleoSpin kit (Macherey-Nagel cat# 740955.25) according to the manufacturer’s protocol.
For quality control of RNA yield and library synthesis products, the RNA ScreenTape and D1000 ScreenTape kits (both from Agilent Technologies), Qubit® RNA HS Assay kit, and Qubit® DNA HS Assay kit (both from Invitrogen) were used for each specific step. mRNA libraries were prepared from 1 µg RNA using the KAPA Stranded mRNA-Seq Kit, with mRNA Capture Beads (KAPA biosystems, cat# KK8421).

treatment_protocol: Primary hepatocytes were isolated from male, 8-10 weeks-old mice (strain C57BL/6JOlaHsd). Three hours after plating, media was changed to Williams E media. After 18 h, hormones (corticosterone 1 µM, Wy14643 10 µM or a dual treatment)  were added for 8h.


title: RNA-seq dual 8h 2


title: non-stimulated cardiac fibroblasts, B

description:
EVB
Mouse cardiac fibroblasts at passage 2 were cultured with empty plasmid.


title: RNA-seq dual 8h 1

value: 1uM cort + 10uM WY 1 8h


title: H3K27ac ChIP-seq cort 8h 1

value: 1uM cort 1 8h


title: RNA-seq wy 8h 3

value: 10uM WY 3 8h


title: Mouse activated PD1+ T cells from Treg depleted TDLNS VDJ


title: Mouse untreated activated PD1+ T cells from TDLNS GEX

description: 10X Genomics of PD1+CD44+ and naïve T cells from untreated tumor draining lymph nodes of 5-week bearing TRAMPC1-GP mice

value: Untreated


title: RNA-seq wy 8h 2

value: 10uM WY 2 8h


title: RNA-seq cort 8h 3

value: 1uM cort 3 8h


title: naah_line,rep1,d15

city: Poznan

first: Ireneusz

last: Stolarek

address: Z. Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry Polish Academy of Sciences

data_processing:
Data were quality trimmed with TrimGalore
FASTQ files were quasialigned to the gencode v39 human reference transcriptome with salmon
Assembly: Gencode v39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: naah

growth_protocol: The Pluripotency rate of the obtained cells was characterized by Sox2 and Nanog immunochemistry. The induced pluripotent stem cells (iPSCs) were cultured on the GeltrexTM (Thermo Fisher Scientific A1413301) coated 12-well plates in Essential 8™ Medium (ThermoFisher Scientific A1517001).

extract_protocol:
The RNA was extracted from the iCMs on day four and day 30. Cells were first washed with PBS and dissociated from the plate either by 3 minutes incubation in 37°C with PBS with EDTA (4 days iCMs) or 5-10 minutes incubation with TrypLE™ (Thermo Fisher Scientific 12604013) (30 days iCMs). Dissociated cells were washed with medium from the plate and collected in 15ml falcon tubes. The centrifugation for 3min/1300rpm/RT allowed us to obtain the cell pellet. The supernatant was discarded, and the cell pellet was washed with cold PBS twice and centrifuged at 4min/2000rpm/4°C. Finally, the cell pellet was resuspended in 1ml of TRIzol™ Reagent (Thermo Fisher Scientific 15596026) or 200µl of RNAlater (Sigma-Aldrich R-0901) and stored at -20°C for further RNA extraction. Standard phenol/chloroform protocol was used to isolate RNA from TRIzol™ Reagent samples. Total RNA isolation from RNAlater collected samples was conducted with mirVana™ miRNA Isolation Kit (Thermo Fisher Scientific AM1561). The obtained RNAs' amount and quality were measured on a Multiskan SkyHigh Microplate Spectrophotometer (Thermo Scientific). The 500ng of RNA was used as a template to generate complementary DNA with SuperScript™ IV First-Strand Synthesis System with ezDNase™ Enzyme (Thermo Fisher Scientific 18091150). Reverse transcription was conducted using a thermal cycling program: 23°C/10 minutes, 55°C/10min, and 80°C/10 min on T100 Thermal Cycler (Bio-Rad).
For each sample, RNA libraries were prepared from 100 ng RNA using the KAPA RNA HyperPrep Kit with RiboErase (Kapa Biosystems) according to manufacturer’s protocol, followed by quality check using Fragment Analyzer (Agilent). The libraries were normalized and pooled, and then sequenced using NovaSeq6000 platform (Illumina) to an average of 120 M 151 bp paired-end reads per sample.

treatment_protocol: iPSCs next differentiated to iCMs using the PSC Cardiomyocyte Differentiation Kit according to the manufacturer's instructions (ThermoFisher Scientific A2921201). After eight days, cells became contracting iCMs and were further cultured in PSC Cardiomyocyte Maintenance Medium (Thermo Fisher Scientific A2920801) for at least 30 days. TNNT2 expression was used as a measure of differentiation efficiency. All cells in culture were maintained at 37°C in incubators with 5% CO2.

value: naah

value: iPSC-iCM

value: WT

value: cardiomyocyte differentiation


title: RNA-seq wy 8h 1

value: 10uM WY 1 8h


title: naah_line,rep2,d7


title: WT_3_DN

value: thymus

value: 10 weeks

value: Mettl3flox/wt; Cd4Cre


title: RNA-seq cort 8h 1

value: primary hepatocytes

value: wt


title: naah_line,rep1,d7


title: cardiac fibroblasts with TSP-4 overexpression, D

description:
THBS4plD
Mouse cardiac fibroblasts at passage 2 were cultured with TSP-4 plasmid.

value: cardiac fibroblasts

value: Cardiac fibroblasts were cultured in the presence of TSP-4 plasmid


title: H3K27ac ChIP-seq nt 8h 1

value: nt


title: cardiac fibroblasts with TSP-4 overexpression, B

description:
THBS4plB
Mouse cardiac fibroblasts at passage 2 were cultured with TSP-4 plasmid.


title: RNA-seq nt 8h 2


title: Mouse untreated activated PD1+ T cells from TDLNS VDJ

value: tumor draining lymph nodes

value: Activated (PD1+CD44+) and naive T cells

value: TRAMPC1-GP cell line


title: RNA-seq nt 8h 3


title: naah_line,rep2,d4


title: RNA-seq nt 8h 1


title: cardiac fibroblasts with TSP-4 overexpression, A

description:
THBS4plA
Mouse cardiac fibroblasts at passage 2 were cultured with TSP-4 plasmid.