title: Fat body, dsMock, rep4

city: Barcelona

first: Jose Luis

last: Maestro

state: Catalonia

address: Passeig Marítim de la Barceloneta, 37-49

department: Complexity of Life

institute: Institute of Evolutionary Biology

data_processing:
Quality control of libraries with FastQC
Read filtering and trimming with Trimmomatic
Read alignment with HISAT2
Transcript assembly with StringTie
Assembly: GenBank genome assembly: GCA_003018175.1
Supplementary files format and content: Excel spreadsheet containing raw gene counts and normalized counts (FPKM and TPM) for each sample

organism: Blattella germanica

source_name: Fat body

growth_protocol: Blattella germanica specimens used for RNA-seq analysis were obtained from a population reared at the Institut de Biologia Evolutiva (CSIC-UPF). Conditions were 70% humidity at 30 ºC and a commercial dog food diet.

extract_protocol:
RNA was isolated using the GenElute Mammalian Total RNAKit (Sigma, Madrid, Spain).
mRNA libraries from fat body were prepared using the TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: We sequenced four replicates for each of the 4 mRNA-seq libraries. Specimens were injected dsRNA according to their treatment (dsInR1, dsInR2, dsInR3 or dsMock) twice, 12 and 5 days prior to extraction.

value: Fat body

tag: agent

value: dsMock


title: BC796_CD14_pos

status: Public on Jan 28 2025

type: SRA

city: Manchester

first: Kiran

last: Batta

address: Paterson Building

department: Division of cancer Sciences

country: United Kingdom

institute: The University of Manchester

description: Library name: KB13_07_796_CD14_pos

library_source: genomic

data_processing:
Quality control of fastq files was performed using FastQC and multiQC. BBDuk was used to trim low quality reads.  Y-chromosomal and mitochondrial reads were removed from ATAC-seq data using Samtools
For differential accessibility analysis, DiffBind16 (v2.14; R v3.6.2) was used. DiffBind was also used to calculate fractions of reads in peaks. To annotate differentially accessible regions as identified by DiffBind to genes, Homer (v 4.10) annotatePeaks.pl was used, again with the hg38 assembly of the human reference genome. Normalisation was done by fraction of reads in peaks.
Assembly: HG38
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Homo sapiens

source_name: PBMNCs

growth_protocol: CD14+ monocytes were enriched from cryopreserved PBMNC samples by MACS for use in fast-ATAC-seq. 5000 cells were used per reaction.

extract_protocol:
Fast-ATAC preparation was done based on Croces et al. Nature methods 2017
Library preparation was performed as per Buenrostro et al. Curr. Protoc. Mol. Biol. 2015

tag: tissue

value: PBMNCs

tag: cell type

value: Monocytes

tag: individual

value: CMML Patient


title: 760199_PBMC_unstim_HC

city: Tel Aviv

first: Rachel

last: Brandes Leibovitz

address: Ramat Aviv

country: Israel

institute: Tel Aviv University

library_source: transcriptomic

data_processing:
MMSEQ package was used to infer gene expression levels
we mapped clean reads to reference transcripts using Bowtie2 software
we calculated the gene  expression level (FPKM) for each sample with the RSEM software
Assembly: hg19
Supplementary files format and content: FPKM normalized reads

molecule: total RNA

source_name: PBMC

extract_protocol: RNA was extracted using the RNEasy mini kit.

tag: disease state

value: Healthy control

value: PBMC


title: 760198_PBMC_unstim_HC


title: BC786_CD14_pos

description: Library name: KB13_06_786_CD14_pos


title: Mouse T cell_control_tox_1

city: Wuhan

first: Canhui

last: Cao

state: China

address: Jiefang Road 1095

country: China

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Tec

data_processing:
Basecalls were performed using bcl2fastaV217 for Novaseg output.
ChlP-seq reads were trimmed from 3' end until the final base had a quality score>30, using Trimmomatic v0.33, discarding reads left with <20bp
ChlP-seq reads were aligned to the hg38/GRCm38.p6  genome usina Bowtie version 1.1.2.
To create ChlP-seq coverage plots, the locations of the mapped ChlP-seg reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.0
Assembly: hg38/GRCm38.p6
Supplementary files format and content: none

organism: Mus musculus

source_name: Spleen

growth_protocol: Jurkat cells were cultured in Roswell Park Memorial Institute (RPMI)-1640 medium (Gibco, Cat. No. 11875093). U14, TC-1 and ID8 were grown in Dulbecco’s Modification of Eagle’s Medium (DMEM) medium (Gibco, Cat. No. 11966025).  All mediums contain 10% fetal bovine serum (FBS, Thermo Fisher Scientific, Cat. No. A4766801) and 1% Penicillin/streptomycin (Servicebio, Cat. No. G4003). Cells were kept at 5% CO2 and at 37 ℃. T cells were cultured in RPMI 1640 Medium (Gibco, Cat. No. 11875093) supplementing with 10% FBS (Thermo Fisher Scientific, Cat. No. A4766801), 1% penicillin/streptomycin (Servicebio, Cat. No. G4003), interleukin-2 (IL-2) at a concentration of 150 U/mL (Thermo Fisher Scientific, Cat. No. PMC0025), 50 mmol/L of β-mercaptoethanol (Gibco, Cat. No.21985023), and 2 mmol/L of GlutaMAXTM (Gibco, Cat. No. 35050061). T cells were maintained in a controlled environment with 20% O2, 5% CO2, and a temperature of 37 °C.

extract_protocol:
The Chromatin immunoprecipitation (ChIP) assay was performed according to manufacturer instructions with SimpleChip Plus sonication chromatin IP kit (Cell Signaling Technology (CST), Cat. No. 56383) in Jurkat T cells or mouse T cells after treatment with DMSO or plerixafor for 48h, and T cells isolated from the spleens of tumor-bearing mice as described above. For each ChIP, 5106 cells were used. Briefly, cells were cross-linked with 1% methanol-free formaldehyde and quenched by 125mM glycine, and then the chromatin was sonicated to generate 500-800bp DNA fragments. The DNA-protein supernatant was used for immunoprecipitation by incubating with TOX (CST, Cat. No. 5638336778) or p-STAT3 (CST, Cat. No. 9145). Subsequently, the chromatin was eluted and the cross-link was reversed
The DNA libraries were prepared using TruSeq ChIP library preparation kit (Illumina) and sequenced on NovaSeq 6000

value: Spleen

tag: cell line

value: Mouse T cell

value: Mouse spleen T cell

tag: treatment

value: Control


title: Fat body, dsMock, rep2

country: Spain

molecule: polyA RNA


title: BC665_CD14_pos

description: Library name: KB13_05_665_CD14_pos


title: Mouse T cell_plerixafor_input

value: Plerixafor


title: Fat body, dsMock, rep1


title: 760197_PBMC_unstim_HC


title: BC932_CD14_pos

description: Library name: KB13_04_932_CD14_pos


title: Fat body, dsInR3, rep4


title: 760196_PBMC_unstim_HC


title: Mouse T cell_control_input


title: 760195_PBMC_unstim_HC


title: HV4_CD14_pos

description: Library name: KB13_03_HV4_CD14_pos

value: Healthy volunteer


title: Fat body, dsInR3, rep3


title: 760193_PBMC_unstim_HC


title: Fat body, dsInR3, rep2


title: attf-6 binding peak2 deletion smRNA sequencing rep. 1

city: Columbus

first: Yi-Hui

last: Wang

state: OH

address: 1060 Carmack Road

department: Biological Chemistry and Pharmacology

country: USA

institute: The Ohio State University

description: small RNA

data_processing:
Raw reads weer trimmed of adapters and removed of poor quality sequences using TrimGalore. Sequences were then collapsed and transformed into fasta files using cutsom shell scripts.
Reads were aligned to contaminating RNAs (rRNAs, tRNAs, snRNAs…) using Bowtie. Reads that failed to align were aligned to the genome using Bowtie.
Aligned reads were normalized and assigned to genomic features using custom shell scripts. Alignments were converted to BigWig files using UCSC Tools.
Downstream analysis was preformed using R/Python/IGV.
Assembly: WormBase WS279
Supplementary files format and content: Tab Delimmited Counts Matrix
Supplementary files format and content: Unique fasta file of collapsed reads

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Synchronized L1 were platted and maintained at 20 celcius on NGM median supplemented with OP50 E. coli . Animals were then harvested when the population reached adulthood.

extract_protocol:
Synchronized adult worms were collected, washed three times with the M9 buffer and once in ddH2O, and resuspended suspended in TRI Reagent (Sigma). Worms were lysed using the Bead Mill 24 homogenizer (Thermo Fisher Scientific) and the lysate was transferred to a clean tube. 0.1 volumes of bromochloropropane (Sigma) were added to the lysis to perform RNA extraction. Isopropanol (Sigma) was then used to precipitate RNA from the aqueous phase. Small RNAs were enriched using MirVana miRNA Isolation Kit (Thermo Fisher Scientific), according to the manufacturer’s instructions.
Small RNA-sequencing libraries were prepared using a previously established small RNA cloning protocol(Li, et al. 2020; Pastore, et al. 2021a; Pastore, et al. 2024). To sequence all types of small RNA species, small RNA samples were treated with the polyphosphatase PIR-1 to remove γ and β phosphates from 5’-triphosphorylated RNAs(Li, et al. 2020). To clone csRNAs, small RNA samples were sequentially treated with intestinal alkaline phosphatase (NEB) and Tobacco acid pyrophosphatase(Gu, et al. 2012). The monophosphorylated RNAs were ligated to a 3’ adapter (IDT, Supplementary Table S2) using T4 RNA ligase 2 (NEB) at 15 °C overnight. T4 RNA ligase 1 (NEB) was used to ligate the 5’ adapter (IDT, Supplementary Table S2). The ligated products were reverse-transcribed into cDNA using SuperScript IV Reverse Transcriptase (Thermo Fisher Scientific). The resulting cDNAs were amplified by PCR. Libraries with unique barcodes were pooled and sequenced on the NovaSeq platform (SP 2×50 bp, Illumina).

treatment_protocol: Synchronized L1 were platted and maintained at 20 celcius on NGM median supplemented with OP50 E. coli . After reaching L4s stage, all worms were transferred to NGM containing 4 mM Auxin plate with OP50 E. coli . Animals were then harvested when the population reached adulthood.

value: whole animal

tag: genotype

value: attf-6::3xflag (I)/ ATTF-6 binding site deletion_peak2 delta (IV:14387943 -IV:14388536)


title: HV3_CD14_pos

description: Library name: KB13_02_HV3_CD14_pos


title: attf-6 binding peak1 deletion smRNA sequencing rep. 2

description: small RNA

value: attf-6::3xflag (I) / ATTF-6 binding site deletion_peak1 delta (IV:13709294 -IV:13709476)


title: 760122_PBMC_unstim_HC


title: Fat body, dsInR3, rep1


title: Fat body, dsMock, rep3


title: 760121_PBMC_unstim_HC


title: APECED patient, Gingival biopsy, post-ruxolitinib (15 mg dosing)

city: Bethesda

first: Behdad (Ben)

last: Afzali

state: MD

address: 10 Center Drive, Building 10

department: NIDDK

institute: National Institutes of Health

description: Gingival  biopsy optained from an APECED patient with AIRE mutation after tratment with JAK/STAT inhibitor, ruxolitinib.

data_processing:
Sequence reads were assessed for quality on fastqc and mapped to NCBI/GRCh38  using bowtie2 (--sensitive-local --no-unal)
Read count was calculated using Rsubread (with default parameter) tools while using the GTF file (gencode.v39.annotation.gtf.gz) obtained from https://www.gencodegenes.org/human/
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file contain RPKM values for each Sample

source_name: Gingival biopsy

extract_protocol:
Total RNA was extracted from whole tissue using TruSeq Stranded Total RNA Kit following manufacturer’s recommendations (Illumina, San Diego, CA).
Sequencing libraries were prepared by the Illumina Nextera XT method following manufacturer’s recommendations (Illumina, San Diego, CA).
Paired-end RNA-seq on NextSeq500 sequencer (Illumina)

treatment_protocol: Standardized 4mm long x 2mm wide gingival collar biopsies and/or 4mm buccal punch biopsies were obtained  from APECED patients (N = 3) and healthy donors (N = 3) under local anesthesia. APECED patients and healthy donors had no signs of mucosal candidiasis, inflammation, or infection at the time of tissue harvesting. Oral tissue was homogenized using Miltenyi Gentlemacs M tube (cat# 130-093-236).

value: Gingival biopsy

value: AIRE mutation

value: APECED patient

value: post-ruxolitinib (15 mg dosing)


title: Fat body, dsInR2, rep4

value: Fat body


title: attf-6 binding peak1 deletion smRNA sequencing rep. 1

description: small RNA


title: control for peak deletion smRNA sequencing rep. 2

description: small RNA

value: attf-6::3xflag (I)


title: APECED patient, Gingival biopsy, post-ruxolitinib (10 mg dosing)

value: post-ruxolitinib (10 mg dosing)


title: 760096_PBMC_unstim_HC

value: Healthy control

value: PBMC


title: attf-6 binding peak2 deletion smRNA sequencing rep. 2

description: small RNA


title: Fat body, dsInR2, rep3


title: 760095_PBMC_unstim_HC


title: control for peak deletion smRNA sequencing rep. 1

description: small RNA


title: APECED patient, Gingival biopsy, pre-ruxolitinib

description: Gingival  biopsy optained from an APECED patient with AIRE mutation.

value: pre-ruxolitinib


title: Fat body, dsInR2, rep2


title: 760094_PBMC_unstim_HC


title: APECED patient, Buccal biopsy, AIRE.30

description: Buccal biopsy optained from an APECED patient with AIRE mutation.

source_name: Buccal biopsy

value: Buccal biopsy

value: Baseline


title: 760093_PBMC_unstim_HC


title: APECED patient, Buccal biopsy, AIRE.23c


title: Fat body, dsInR2, rep1


title: HV2_CD14_pos

description: Library name: KB13_01_HV2_CD14_pos

value: PBMNCs

value: Monocytes


title: attf-6 depletion CIPTAP sequencing rep. 1

description: capped small RNA

value: whole animal

value: GFP::tev::aid::attf-6 (I)/ wrdSi51 [mex-5p::TIR1::F2A::mTagBFP2::AID*::NLS::tbb-2 3'UTR] II

value: 4mM Auxin


title: 760091_PBMC_unstim_HC


title: Healthy donor, Buccal biopsy, HV079

description: Health buccal biopsy was obtained from an individual that met criteria for oral health.

value: wild-type

value: Healthy donor


title: Healthy donor, Buccal biopsy, HV077


title: Fat body, dsInR1, rep3


title: 760089_PBMC_unstim_HC


title: control smRNA sequencing rep. 2

description: small RNA

value: wrdSi51 [mex-5p::TIR1::F2A::mTagBFP2::AID*::NLS::tbb-2 3'UTR] (II)


title: Fat body, dsInR1, rep2


title: 760086_PBMC_unstim_HC


title: Healthy donor, Buccal biopsy, HV076


title: Fat body, dsInR1, rep1


title: control smRNA sequencing rep. 1

description: small RNA


title: a211 e1

status: Public on Jan 27 2025

city: Philadelphia

first: Sydney

last: Shaffer

state: PA

address: 421 Curie Boulevard

department: Penn Medicine

institute: University of Pennsylvania

description:
Library name: a211_e1
MAESTER

data_processing:
MAESTER raw sequencing data was demultiplexed and converted to FASTQ files using bcl2fastq (v2.20.0.422). Reads were trimmed of sequences that dropped below a quality threshold using a custom Python script: reads were broken up into 10-bp segments whose average quality (Q) score was calculated; the entire sequence following and including the first 10-bp segment with an average Q score lower than 25 was removed from the read. Reads that contained barcodes not present in the corresponding filtered 10x data for each sample were removed, and remaining Read 2 FASTQ files had the library barcode, 10x cell barcode (CB), and UMI added to the read identifier. Reads were then aligned to the 10x reference genome used above with STAR58.
Mitochondrial mutations were called using maegatk, which was developed specifically for this protocol22. Before running maegatk, the CB and UMI were transferred from the Read 2 identifiers to the MAESTER BAM files as SAM tags, and the BAM files were merged with 10x mitochondrial reads. maegatk was run with the following arguments: -g rCRS-mb 100-mr 1.
Allele frequencies of mitochondrial variants in single cells were calculated in R from the maegatk output and combined with accompanying variant information including mean coverage, mean Q score, and allele frequency quantiles within specified cell subsets. This information was used to select for variants within each sample that had a mean coverage of >5, mean quality of >27, and AF of >25% in at least 1% of epithelial cells; such filtering identified germline and significant tissue-specific variants. The above filtering steps were based on previously published scripts (https://github.com/petervangalen/MAESTER-2021). Additionally, variants of interest were further filtered to exclude any that were found in multiple patients, since these were more likely to be artifacts.
In order to confirm somatic mitochondrial variants, we developed a zero-inflated beta binomial model to capture the background noise from contamination and technical artifacts within cells for those variants. P-values could then be calculated for the variant in question in each cell to determine whether it was improbable (and therefore true) given the modeled background noise using a zero-inflated binomial test. Finally, significant cells for a given variant were identified by calculating a false discovery rate using an empirical null distribution (based on the signal in non-epithelial cells) that accounted for differences in sequencing coverage between cells. A full description of the statistical method is provided in the supplementary information. Variants containing at least three significant cells from the ZIBB analysis after accounting for expected false positives were plotted as allele frequency heatmaps or in gene expression-derived UMAPs. Allele frequency UMAPs included cells with a minimum coverage of five for the variant of interest.
Assembly: GRCh38-2020-A53
Supplementary files format and content: *maegatk.rds

source_name: Esophagus

extract_protocol:
Fresh pinch biopsies were washed twice in DPBS before being coarsely chopped with a scalpel and transferred into 0.5 mL DPBS solution containing 0.1 WU ml-1 Liberase TH (Roche, 5401151001) and 0.5 U ml-1 RQ1 DNase I (Promega, M6101). The samples were incubated at 37 °C in successive 10-minute rounds with gentle vortexing every 2 minutes and trituration every 5 minutes. At the end of each round of incubation, large tissue pieces were spun down in a microcentrifuge and the supernatant containing single cells was passed through a 70-um cell strainer fitted onto a 50-mL conical tube containing 8 mL DPBS + 1% bovine serum albumin (BSA; Sigma-Aldrich, A7906) in DPBS on ice. 0.5 mL fresh dissociation solution was added to the tissue at the beginning of each incubation step. The samples were further filtered through the 0.35 um cell-strainer cap of a FACS tube and single cells were pelleted by centrifugation at 400g for 4 minutes at 4 °C. Samples were washed twice in 1 mL DPBS + 0.04% BSA and finally resuspended in 50 uL DPBS + 0.04% BSA, at which point they were counted in 0.2% trypan blue (Gibco, 15250061) in preparation for 10x Genomics Chromium Next GEM Single Cell 3’ v3.1 library preparation. For the frozen BE biopsy from Patient 2, the tissue was quickly thawed at 37 °C and rinsed three times in DPBS + 10% fetal bovine serum (GE, SH30396.03) before being dissociated and filtered as described above. After the final filtering step, dead cells were removed with the Dead Cell Removal Kit (Miltenyi Biotec, 130-090-101) following the manufacturer’s protocol.
Mitochondrial transcripts were enriched from the intermediate 10x cDNA libraries following the MAESTER protocol22. Briefly, previously amplified full-length cDNA was further amplified over six cycles in 12 separate PCR reactions containing primers that together spanned the mitochondrial transcriptome; 5-20 ng input cDNA was used in each reaction. PCR products for each sample were pooled and purified using Ampure XP (Beckman Coulter, A63881). Sequencing primer binding sites, adapters, and dual indices were added to the resulting cDNA over another six cycles of PCR and again purified using Ampure XP. Final MAESTER libraries were in the expected range of 2-100 ng ul-1 for concentration and fragment sizes of 300-1,500 bp. Libraries were sequenced on an Illumina NextSeq 550 with a v2.5 300 cycle kit, allocating 28 cycles for Read 1 and 270 cycles for Read 2, as well as eight cycles for both indices; a custom index 2 primer was used (10x-Ci5P).

value: Esophagus


title: a199 s10

description:
Library name: a199_s10
MAESTER


title: a199 s8

description:
Library name: a199_s8
MAESTER


title: a211 c11

description:
Library name: a211_c11
MAESTER

source_name: Stomach

value: Stomach


title: a199 s5

description:
Library name: a199_s5
MAESTER


title: a211 be7

description:
Library name: a211_be7
MAESTER

source_name: Barrett's Esophagus

value: Barrett's Esophagus


title: control CIPTAP smRNA sequencing

description: capped small RNA


title: a199 s6

description:
Library name: a199_s6
MAESTER


title: a211 be4

description:
Library name: a211_be4
MAESTER


title: Fat body, dsInR1, rep4

value: Fat body


title: attf-6 depletion smRNA sequencing rep. 2

description: small RNA


title: EFlib-1_AEZ023

city: Cleveland

first: Kenneth

last: Matreyek

address: 2103 Cornell Rd

department: Pathology

institute: Case Western Reserve University

description:
Library name: Sample3
plasmid DNA

library_source: other

data_processing:
The DNA was sequenced with a NextSeq 550 using a NextSeq 550 Mid output 150 cycle kit (Illumina).
Following sequencing, the reads were converted to fastq format and de-multiplexed with bcl2fastq. Reads were paired using PEAR or fastqjoin. To process the paired reads, we created a custom Python script that extracted the nucleotide sequence and compared it to the wildtype DNA sequence. If there was no difference between nucleotide sequence and wildtype sequence, the script classified the sequence as "WT". If there was a difference, the script converted the nucleotide sequence to its protein sequence. The protein sequence was compared to the wildtype  protein sequence and any differences were read out as variants at that position. Any reads that had mulitple variants and frameshifts were discarded to retain single variant changes. For each read, raw counts were outputted into a tsv file, and total variant counts were tallied inito a summary.tsv file. For Samples56-73 and 76-77, a custom Python file was created to extract the first 10 nucleotides and quality scores from read1 fastq file, the reverse complement of the first 10 nucleotides and quality scores from read2 fastq file, and only retained reads that had sequences that matched the known sequences used in the barcoding procedure. Reads that passed this step were output into tsv file where two sets of 10 nucleotides were concatenated as a 20 nt barcode. These barcodes were counted and these corresponded to counts of the variants.
Sequencing counts were imported into R, where custom code was used to convert counts into frequencies, and survival scores were calculated as the log transformed ratio of the variant frequency in cells to the variant frequency in the plasmid library
Assembly: GCGACAGGAACCAGCTCGGGGGCCAACTCTGAGGAGTCCACTGCAGCAGAGTTTTGCCGAATTGACAAGCCCCTGTGTCACAGTGAGGATGAGAAACTCAGCTTCGAGGCAGTCCGTAACATCCACAAACTGATGGACGATGATGCCAATGGTGATGTGGATGTGGAAGAAAGTGATGAGTTCCTGAGGGAAGACCTCAATTACCATGACCCAACAGTGAAACACAGCACCTTCCATGGTGAGGATAAGCTCATCAGCGTGGAGGACCTGTGGAAGGCATGGAAGTCATCAGAAGTATACAATTGGACCGTGGATGAGGTGGTA
Supplementary files format and content: "survival_scores.csv" is a comma separated value table containing survival scores of all variants averaged across replicates. Columns are survival ratios in the following cells/bacteria: endo_ratio and endo_ssv_ratio - standard LP cells, sko_ratio and sko_ssv_ratio - knockout LP cells, bac_ratio - DH10b E.coli, lb_10b - DH10b in LB, lb_dh5a - DH5a in LB, lb_bl21 - BL21 in LB, mm_10b - DH10b in M9 minimal media, mm_dh5a - DH5a in M9 minimal media, mm_bl21 - BL21 in M9 minimal media, ca_10b - DH10b in M9+calcium chloride, ca_dh5a - DH5a in M9+calcium chloride, ca_bl21 - BL21 in M9+calcium chloride
Supplementary files format and content: "dbc_score.csv" is a comma separated value table containing survival scores for variants counted using double barcodes. Columns are survival scores in: endo_dbc_score - standard LP cells, sko_dbc_score - knockout LP cells

molecule: other

organism: synthetic construct

growth_protocol: For cultured cells, growth media is DMEM with 10% FBS, 1% Penicillin/Streptomycin and 2 ug/mL doxycycline. For bacteria, Sample1-4, 37, 74-81, 84, 87, 90, 93, 96, 99, and 102 were grown in Luria Broth, Sample79, 82, 85, 88, 91, 94, 97, 100, 103 were grown in M9 minimal media, Sample80, 83, 86, 89, 92, 95, 98, 101, 104 were grown in M9 minimal media with additional 100uM calcium chloride

extract_protocol:
Plasmid DNA was extracted from bacteria using GeneJET Plasmid Miniprep Kit (Thermo Fisher Scientific, K0503). Genomic DNA was extracted from thawed cell pellets using DNeasy Blood and Tissue Kit (Qiagen, 69506)
Plasmid DNA was used as template material for PCR amplification of a 360bp segment corresponding to the cEFhand of STIM1. The extracted genomic DNA was used as the template material for PCR amplification of a 568bp segment corresponding to the cEFhand of STIM1. To avoid sequencing any lingering unintegrated plasmid DNA, a forward primer hybridizing to the Bxb1 integrase coding region encoded in the landing pad was directly 5-prime of the region of interest, so that only integrated plasmids would be amplified. Each sample was amplified with a single 40 μL reaction containing 2 μg of genomic DNA (as assessed by spectrophotometry at A260), 0.25uM forward primer containing an i7 index and p7 cluster generator sequence, 0.25uM reverse primer containing i5 index barcode and p5 cluster generator sequence, and 20 μL of Phusion plus high-fidelity PCR mix (Thermo Scientific, F631S). The amplicons were created with an initial 95°C incubation for 3 mins, and 28 total cycles of 95°C for 15 secs, 60°C for 15 secs, 72°C for 30 secs, followed by a final extension step of 72°C for 1 min. The PCR reaction contents were mixed with 6x DNA loading dye (New England Biolabs, B7024S) and separated on 1% agarose gel prepared in Tris-acetate-EDTA buffer, and electrophoresed. Double stranded DNA bands migrating at 568 nt for genomic and 360nt for plasmid were observed with SYBR Safe DNA Gel Stain (Thermo Scientific, S33102) were excised and extracted with GeneJET Gel Extraction and DNA Cleanup Micro Kit (Thermo Fisher Scientific, K0832). The concentrations of the final DNA were quantified with a Qubit dsDNA BR assay kit (Life technologies, Q32853). Amplicons from all the experimental conditions were pooled together in equimolar ratios, subject to a final quality control step for homogeneity with an Agilent Fragment Analyzer and cluster estimation with quantitative PCR.

value: E.coli bacteria

value: Transformation into bacteria for plasmid DNA library


title: EFlib-2_AEZ019

description:
Library name: Sample2
plasmid DNA


title: a198 s10

description:
Library name: a198_s10
MAESTER


title: attf-6 depletion smRNA sequencing rep. 1

description: small RNA


title: EFlib-1_AEZ019

description:
Library name: Sample1
plasmid DNA


title: EFlib-2_AEZ023

description:
Library name: Sample4
plasmid DNA


title: a198 s8

description:
Library name: a198_s8
MAESTER


title: a198  s6

description:
Library name: a198_s6
MAESTER


title: I0661

description:
Library name: Sample104
plasmid DNA


title: a198 s5

description:
Library name: a198_s5
MAESTER


title: a198 s1

description:
Library name: a198_s1
MAESTER


title: I0660

description:
Library name: Sample103
plasmid DNA


title: a198 s4

description:
Library name: a198_s4
MAESTER


title: I0658

description:
Library name: Sample101
plasmid DNA


title: a196 scj 2

description:
Library name: a196scj2
MAESTER

source_name: Squamocolumnar Junction

value: Squamocolumnar Junction


title: a199 s4

description:
Library name: a199_s4
MAESTER


title: a199 s3

description:
Library name: a199_s3
MAESTER


title: a196 scj 1

description:
Library name: a196scj1
MAESTER


title: I0656

description:
Library name: Sample99
plasmid DNA


title: I0655

description:
Library name: Sample98
plasmid DNA


title: I0654

description:
Library name: Sample97
plasmid DNA


title: a195 scj 2

description:
Library name: a195scj2
MAESTER


title: a196 be

description:
Library name: a196be
MAESTER


title: a195 be

description:
Library name: a195be
MAESTER


title: I0653

description:
Library name: Sample96
plasmid DNA


title: I0652

description:
Library name: Sample95
plasmid DNA


title: I0651

description:
Library name: Sample94
plasmid DNA


title: I0650

description:
Library name: Sample93
plasmid DNA


title: a195 scj 1

description:
Library name: a195scj1
MAESTER


title: a199 s1

description:
Library name: a199_s1
MAESTER


title: I0649

description:
Library name: Sample92
plasmid DNA


title: a194 es S6

description:
Library name: a194_es_S6
MAESTER


title: I0659

description:
Library name: Sample102
plasmid DNA


title: I0648

description:
Library name: Sample91
plasmid DNA


title: a193 es

description:
Library name: a193_es
MAESTER


title: I0647

description:
Library name: Sample90
plasmid DNA


title: a194 st

description:
Library name: a194_st
MAESTER


title: I0657

description:
Library name: Sample100
plasmid DNA


title: a194 be

description:
Library name: a194_be
MAESTER


title: I0646

description:
Library name: Sample89
plasmid DNA


title: I0645

description:
Library name: Sample88
plasmid DNA


title: a193 be 1

description:
Library name: a193_be_1
MAESTER


title: a193 be 2

description:
Library name: a193_be_2
MAESTER


title: I0644

description:
Library name: Sample87
plasmid DNA


title: a192 be 2 S2

description:
Library name: a192_be_2_S2
MAESTER


title: I0642

description:
Library name: Sample85
plasmid DNA


title: a192 be 1 S1

description:
Library name: a192_be_1_S1
MAESTER


title: I0641

description:
Library name: Sample84
plasmid DNA


title: I0640

description:
Library name: Sample83
plasmid DNA


title: a188 st

description:
Library name: a188_st
MAESTER


title: a193 st

description:
Library name: a193_st
MAESTER


title: a188 be S1

description:
Library name: a188_be_S1
MAESTER


title: I0638

description:
Library name: Sample81
plasmid DNA


title: a187 es

description:
Library name: a187_es
MAESTER


title: I0639

description:
Library name: Sample82
plasmid DNA


title: a187 st

description:
Library name: a187_st
MAESTER


title: I0637

description:
Library name: Sample80
plasmid DNA


title: I0636

description:
Library name: Sample79
plasmid DNA


title: a187 be S2

description:
Library name: a187_be_S2
MAESTER


title: a186 be S2

description:
Library name: a186_be_S2
MAESTER


title: I0635

description:
Library name: Sample78
plasmid DNA


title: Plasma, post acute, Female 5

city: University Place

first: WILLIAM

last: CONKRIGHT

state: WA

address: 2938 73rd Avenue Ct W

institute: US Army

data_processing:
Quality control completed with bcl2fastq.gz from Illumina, no trimming required
Reads were mapped to the designated reference genome (miRbase_v22) using Ensembl release 101 primary assembly with STAR version 2.5.1a
Differential gene expression analysis was performed using the edgeR workflow
Assembly: miRbase_v22
Supplementary files format and content: Excel spreadsheets that include the raw counts for each sample and differential expression data.

source_name: Blood Plasma

extract_protocol:
RNA extraction using Plasma/Serum Exosome Purification and RNA Isolation Mini Kit (Norgen Biotek Corp., 55000; Thorold, ON, Canada), according to manufacturer's instructions
Single-end libraries constructed from EV RNA using TruSeq Small RNA library kit from Illumina according to manufacturer's recommendations for low yield sampels.

value: Blood Plasma

tag: Sex

value: female

tag: time point

value: Post

tag: condition

value: Acute resistance exercise

value: Post-acute resistance exercise


title: I0522-2

description:
Library name: Sample77
plasmid DNA


title: Plasma, post acute, Female 4


title: Plasma, pre acute, Female 5

value: Pre

value: Pre-acute resistance exercise


title: I0522

description:
Library name: Sample76
plasmid DNA


title: I0521

description:
Library name: Sample74
plasmid DNA


title: Plasma, pre acute, Female 4


title: I0521-2

description:
Library name: Sample75
plasmid DNA


title: I0643

description:
Library name: Sample86
plasmid DNA


title: I0520

description:
Library name: Sample73
library strategy is amplicon sequencing of DNA recombined into cells

source_name: HEK 293T

value: HEK 293T

value: Cultured cells, knockout LP cells

value: Recombination into genomic landing pad


title: a191 be S1

description:
Library name: a191_be_S1
MAESTER


title: Plasma, pre acute, Female 3


title: a188 es

description:
Library name: a188_es
MAESTER

value: Esophagus


title: I0519

description:
Library name: Sample72
library strategy is amplicon sequencing of DNA recombined into cells


title: Plasma, post acute, Female 2


title: I0518

description:
Library name: Sample71
library strategy is amplicon sequencing of DNA recombined into cells


title: Plasma, pre acute, Female 2


title: I0516

description:
Library name: Sample69
library strategy is amplicon sequencing of DNA recombined into cells


title: I0517

description:
Library name: Sample70
library strategy is amplicon sequencing of DNA recombined into cells


title: Plasma, post acute, Female 1


title: Plasma, pre acute, Female 1


title: I0514

description:
Library name: Sample67
library strategy is amplicon sequencing of DNA recombined into cells


title: Plasma, post acute, Male 5

value: male


title: Plasma, pre acute, Male 5


title: I0513

description:
Library name: Sample66
library strategy is amplicon sequencing of DNA recombined into cells


title: I0512

description:
Library name: Sample65
library strategy is amplicon sequencing of DNA recombined into cells


title: Plasma, post acute, Male 4


title: Plasma, pre acute, Male 4


title: Plasma, post acute, Female 3


title: I0510

description:
Library name: Sample63
library strategy is amplicon sequencing of DNA recombined into cells

value: Cultured cells, standard LP cells


title: I0511

description:
Library name: Sample64
library strategy is amplicon sequencing of DNA recombined into cells


title: I0509

description:
Library name: Sample62
library strategy is amplicon sequencing of DNA recombined into cells


title: Plasma, post acute, Male 2


title: Plasma, post acute, Male 3


title: Plasma, pre acute, Male 2


title: Plasma, pre acute, Male 3


title: I0508-2

description:
Library name: Sample61
library strategy is amplicon sequencing of DNA recombined into cells


title: I0507-2

description:
Library name: Sample60
library strategy is amplicon sequencing of DNA recombined into cells


title: Plasma, pre acute, Male 1


title: I0506-2

description:
Library name: Sample59
library strategy is amplicon sequencing of DNA recombined into cells


title: Plasma, post acute, Male 1


title: I0505-2

description:
Library name: Sample58
library strategy is amplicon sequencing of DNA recombined into cells


title: I0503-2

description:
Library name: Sample56
library strategy is amplicon sequencing of DNA recombined into cells


title: I0504-2

description:
Library name: Sample57
library strategy is amplicon sequencing of DNA recombined into cells


title: SCP derived Cardiomyocytes (dd17) 3

city: Carpi

first: Emiliano

last: Bolesani

state: Modena

address: Via Giuliano Benassi, 7

department: Process Development & Cell Therapy

country: Italy

institute: Evotec SE

description:
Cardiomyocytes derived after removal of IQ-1/CHIR and 7 days in culture
N1012_R1_trimmed.fq_SCP-CMs (dd17)_3

data_processing:
Raw data processing was conducted by use of nfcore/rnaseq (version 1.5dev) which is a bioinformatics best-practice analysis pipeline used for RNA sequencing data at the National Genomics Infrastructure at SciLifeLab Stockholm, Sweden. The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.
Genome_build: The genome reference and annotation data were taken from GENCODE.org (Homo sapiens; GRCh38; release 28).
Supplementary_files_format_and_content: Normalization and differential expression analysis were performed with DESeq2 (Galaxy Tool Version 2.11.40.2) with default settings except for “Output normalized counts table” which was set to “Yes”. DESeq2 normalization was performed with all eighteen samples, additionally, six unrelated samples were contained during normalization. These additional samples are not relevant nor comprised in this project or manuscript, nor do compromise the gene expression analysis

source_name: human Pluripotent Stem Cells (hPSCs)

extract_protocol:
Single Cell suspension was obtained with the STEMdiff Cardiomyocyte Dissociation Kit (Stemcell Technologies).
500 ng of total RNA per sample were utilized as input for mRNA enrichment procedure with ‘NEBNext® Poly(A) mRNA Magnetic Isolation Module’ (E7490L; New England Biolabs) followed by stranded cDNA library generation using ‘NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina’ (E7760L; New England Biolabs). All steps were performed as recommended in the User Manual E7760 (Version 1.0_02-2017; NEB) except that all reactions were downscaled to 2/3 of initial volumes. Furthermore, one additional purification step was introduced at the end of the standard procedure, using 1x ‘Agencourt® AMPure® XP Beads’ (#A63881; Beckman Coulter, Inc.). cDNA libraries were barcoded by single indexing approach, using ‘NEBNext Multiplex Oligos for Illumina – Set 1’ (Index Primer 1-12). All generated cDNA libraries were amplified by 6 cycles of final PCR. Fragment length distribution of individual libraries was monitored using ‘Bioanalyzer High Sensitivity DNA Assay’ (5067-4626; Agilent Technologies). Quantification of libraries was performed by use of the ‘Qubit® dsDNA HS Assay Kit’ (Q32854; ThermoFisher Scientific).

value: Cardiomyocytes derived from IQ-1/CHIR SCPs

tag: cell line / strain

value: hESC3 NKX2-5 wt/GFP


title: SCP derived Cardiomyocytes (dd17) 2

description:
Cardiomyocytes derived after removal of IQ-1/CHIR and 7 days in culture
N1005_R1_trimmed.fq_SCP-CMs (dd17)_2


title: SCP derived Cardiomyocytes (dd17) 1

description:
Cardiomyocytes derived after removal of IQ-1/CHIR and 7 days in culture
N0997_R1_trimmed.fq_SCP-CMs (dd17)_1


title: I0508

description:
Library name: Sample55
library strategy is amplicon sequencing of DNA recombined into cells


title: Cardiomyocytes (dd17) 3

description:
Cardiomyocytes following biphasic Wnt pathway modulation (7 days in culture)
N1011_R1_trimmed.fq_CMs (dd17)_3

value: Cardiomyocytes (7 days in culture)


title: I0515

description:
Library name: Sample68
library strategy is amplicon sequencing of DNA recombined into cells


title: Cardiomyocytes (dd17) 1

description:
Cardiomyocytes following biphasic Wnt pathway modulation (7 days in culture)
N0996_R1_trimmed.fq_CMs (dd17)_1


title: I0506

description:
Library name: Sample53
library strategy is amplicon sequencing of DNA recombined into cells


title: I0507

description:
Library name: Sample54
library strategy is amplicon sequencing of DNA recombined into cells


title: Stabilized Cardiac Progenitors (dd10) 3

description:
IQ-1/CHIR treated cells from dd4 until dd12
N1009_R1_trimmed.fq_SCPs (dd10)_3

value: IQ-1/CHIR Stabilized cardiac progenitors


title: I0503

description:
Library name: Sample50
library strategy is amplicon sequencing of DNA recombined into cells


title: I0505

description:
Library name: Sample52
library strategy is amplicon sequencing of DNA recombined into cells


title: Stabilized Cardiac Progenitors (dd10) 2

description:
IQ-1/CHIR treated cells from dd4 until dd11
N1001_R1_trimmed.fq_SCPs (dd10)_2


title: Cardiomyocytes (dd10) 3

description:
Cardiomyocytes following biphasic Wnt pathway modulation
N1008_R1_trimmed.fq_CMs (dd10)_3

value: Cardiomyocytes


title: Stabilized Cardiac Progenitors (dd10) 1

description:
IQ-1/CHIR treated cells from dd4 until dd10
N0994_R1_trimmed.fq_SCPs (dd10)_1


title: Cardiomyocytes (dd10) 2

description:
Cardiomyocytes following biphasic Wnt pathway modulation
N1000_R1_trimmed.fq_CMs (dd10)_2


title: I0501

description:
Library name: Sample48
library strategy is amplicon sequencing of DNA recombined into cells


title: I0502

description:
Library name: Sample49
library strategy is amplicon sequencing of DNA recombined into cells


title: I0500

description:
Library name: Sample47
library strategy is amplicon sequencing of DNA recombined into cells


title: I0499

description:
Library name: Sample46
library strategy is amplicon sequencing of DNA recombined into cells


title: Cardiomyocytes (dd10) 1

description:
Cardiomyocytes following biphasic Wnt pathway modulation
N0993_R1_trimmed.fq_CMs (dd10)_1


title: I0498

description:
Library name: Sample45
library strategy is amplicon sequencing of DNA recombined into cells


title: Mesodermal Progenies (dd4) 3

description:
Cells collected on dd4 of differentiation (after Wntc-59 addition on dd3)
N1007_R1_trimmed.fq_dd4_3

value: Cardiac Mesoderm Progenitors (dd4) ISL1


title: I0497

description:
Library name: Sample44
library strategy is amplicon sequencing of DNA recombined into cells


title: Mesodermal Progenies (dd4) 2

description:
Cells collected on dd4 of differentiation (after Wntc-59 addition on dd3)
N0999_R1_trimmed.fq_dd4_2


title: Mesodermal Progenies (dd4) 1

description:
Cells collected on dd4 of differentiation (after Wntc-59 addition on dd3)
N0992_R1_trimmed.fq_dd4_1


title: I0496

description:
Library name: Sample43
library strategy is amplicon sequencing of DNA recombined into cells


title: human Pluripotent Stem Cells (dd0) 3

description:
Cells collected on dd0 of differentiation (3 days of preculture
N1015_R1_trimmed.fq_dd0_3

value: Pluripotent Cells (dd0)


title: human Pluripotent Stem Cells (dd0) 2

description:
Cells collected on dd0 of differentiation (3 days of preculture
N1014_R1_trimmed.fq_dd0_2


title: I0493

description:
Library name: Sample40
library strategy is amplicon sequencing of DNA recombined into cells


title: Cardiomyocytes (dd17) 2

description:
Cardiomyocytes following biphasic Wnt pathway modulation (7 days in culture)
N1004_R1_trimmed.fq_CMs (dd17)_2


title: human Pluripotent Stem Cells (dd0) 1

description:
Cells collected on dd0 of differentiation (3 days of preculture
N1003_R1_trimmed.fq_dd0_1


title: I0495

description:
Library name: Sample42
library strategy is amplicon sequencing of DNA recombined into cells


title: I0492

description:
Library name: Sample39
library strategy is amplicon sequencing of DNA recombined into cells


title: I0504

description:
Library name: Sample51
library strategy is amplicon sequencing of DNA recombined into cells


title: Input_35_16c_S10_R1.dd10 (ICG)_2_Igg_fastq.gz

description: Biphasic Wnt pathway modulation, treatment (dd4-dd10), IgG

data_processing:
QC was performed using FastQC v.0.10.0
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2 version 2.2.6.2 with default configurations.
peaks were called using MACS2 version 2.1.1.20160309.0. with the following settings: min. FDR-value (0.5), "Do not build shifting model", Arbitrary extension size (125bp).
noise peaks were filtered using mm9-blacklist from ENCODE.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph and files were generated using MACS2. Narrowpeaks and Broadpeaks were called on H3K27ac bound regions respectively. RPKM normalized bigwigs were generated using bamCoverage in Galaxy deepTools platform with default settings.

growth_protocol: Cells were seeded at 7.5x104 cells/cm2 in E8 medium on d-4 (day -4), 48h (from seeding) medium was changed every 24h, then every day after that. On dd0, the confluent layer of pluripotent cells was induced with 7.5μM CHIR99021 in RPMI with B27 supplement in absence of insulin for 24h. On dd3, the media change was done in presence of the PORCN inhibitor Wnt-C59 at 2μM. On dd4 different modulators were added in RPMI medium with B27 supplement (RB[+]).

extract_protocol:
Cells were fixed with freshly prepared 4% PFA for 15 min at RT. Approximately 4x106 cells were used per immunoprecipitation (IP) reaction. Cell samples were sonicated using a Bioruptor Next Gen (Diagenode) for 20 cycles, 30 sec ON/30 sec OFF
ChIP-seq library preparation was performed using NEBNext Ultra DNA library prep kit for Illumina (E7370) as per manual’s instructions

treatment_protocol: IQ-1 (Tocris; Cat.No. 4713) at 10μM was added in combination with 1μM CHIR; ICG-001 (Tocris; Cat.No. 4505) at 5μM, and on Control cells a simple media change. Media change was performed every other day, namely dd6, dd8, dd10 in the presence of the molecules

value: hPSC-derived cardiac progenies

tag: chip-seq antibody

value: anti-IgG (17–10109, Millipore)- 2µg/IP


title: I0491

description:
Library name: Sample38
library strategy is amplicon sequencing of DNA recombined into cells


title: Input_33_16c_S7_R1.dd10 (SCPs)_3_Igg_fastq.gz

value: hPSC-stabilized cardiac progenies (SCPs)


title: I0453

description:
Library name: Sample36
library strategy is amplicon sequencing of DNA recombined into cells


title: I0466

description:
Library name: Sample37
plasmid DNA

value: E.coli bacteria

value: Transformation into bacteria for plasmid DNA library


title: Input_32_16c_S7_R1.dd10 (SCPs)_2_Igg_fastq.gz


title: Input_34_16c_S10_R1.dd10 (ICG)_1_Igg_fastq.gz

tag: biological replicates


title: Input_29_16c_S4_R1.dd10 (CMs)_c2_fastq.gz

description: Biphasic Wnt pathway modulation, input

value: anti-H3K27ac (C15410196, Diagenode)- 2µg/IP


title: Input_31_16c_S7_R1.dd10 (SCPs)_1_Igg_fastq.gz


title: I0449

description:
Library name: Sample32
library strategy is amplicon sequencing of DNA recombined into cells

value: HEK 293T

value: Cultured cells, knockout LP cells

value: Recombination into genomic landing pad


title: Input_30_16c_S4_R1.dd10 (CMs)_c3_fastq.gz

description: Biphasic Wnt pathway modulation, input


title: Input_27_16c_S1_R1.dd4_c3_fastq.gz

description: Biphasic Wnt pathway modulation, input


title: I0451

description:
Library name: Sample34
library strategy is amplicon sequencing of DNA recombined into cells


title: I0447

description:
Library name: Sample30
library strategy is amplicon sequencing of DNA recombined into cells


title: I0445

description:
Library name: Sample28
library strategy is amplicon sequencing of DNA recombined into cells


title: Input_28_16c_S4_R1.dd10 (CMs)_c1_fastq.gz

description: Biphasic Wnt pathway modulation, input


title: I0448

description:
Library name: Sample31
library strategy is amplicon sequencing of DNA recombined into cells


title: I0444

description:
Library name: Sample27
library strategy is amplicon sequencing of DNA recombined into cells


title: Chip23_16c_S22_R1.dd10 (ICG)_2_H3K_fastq.gz

description: Biphasic Wnt pathway modulation, treatment (dd4-dd10)

value: hPSC-CBP inhibition in cardiac progenies


title: Chip24_16c_S22_R1.dd10 (ICG)_3_H3K_fastq.gz


title: I0442

description:
Library name: Sample25
library strategy is amplicon sequencing of DNA recombined into cells


title: I0494

description:
Library name: Sample41
library strategy is amplicon sequencing of DNA recombined into cells

value: Cultured cells, standard LP cells


title: I0446

description:
Library name: Sample29
library strategy is amplicon sequencing of DNA recombined into cells


title: Input_25_16c_S1_R1.dd4_c1_fastq.gz

description: Biphasic Wnt pathway modulation, input

value: hESC3 NKX2-5 wt/GFP


title: Chip22_16c_S22_R1.dd10 (ICG)_1_H3K_fastq.gz


title: I0452

description:
Library name: Sample35
library strategy is amplicon sequencing of DNA recombined into cells


title: Chip21_16c_S19_R1.dd10 (SCPs)_3_H3K_fastq.gz


title: I0441

description:
Library name: Sample24
library strategy is amplicon sequencing of DNA recombined into cells


title: I0450

description:
Library name: Sample33
library strategy is amplicon sequencing of DNA recombined into cells


title: Chip20_16c_S19_R1.dd10 (SCPs)_2_H3K_fastq.gz


title: I0440

description:
Library name: Sample23
library strategy is amplicon sequencing of DNA recombined into cells


title: Chip18_16c_S16_R1.dd10 (CMs)_c3_H3K_fastq.gz

description: Biphasic Wnt pathway modulation

value: hPSC-derived cardiomyocytes


title: Chip19_16c_S19_R1.dd10 (SCPs)_1_H3K_fastq.gz


title: I0438

description:
Library name: Sample21
library strategy is amplicon sequencing of DNA recombined into cells


title: Chip17_16c_S16_R1.dd10 (CMs)_c2_H3K_fastq.gz

description: Biphasic Wnt pathway modulation


title: I0437

description:
Library name: Sample20
library strategy is amplicon sequencing of DNA recombined into cells


title: I0439

description:
Library name: Sample22
library strategy is amplicon sequencing of DNA recombined into cells


title: I0330

description:
Library name: Sample19
library strategy is amplicon sequencing of DNA recombined into cells


title: Chip15_16c_S13_R1.dd4_c3_H3K_fastq.gz

description: Biphasic Wnt pathway modulation


title: I0443

description:
Library name: Sample26
library strategy is amplicon sequencing of DNA recombined into cells


title: I0329

description:
Library name: Sample18
library strategy is amplicon sequencing of DNA recombined into cells


title: I0328

description:
Library name: Sample17
library strategy is amplicon sequencing of DNA recombined into cells


title: Chip14_16c_S13_R1.dd4_c2_H3K_fastq.gz

description: Biphasic Wnt pathway modulation


title: Chip13_16c_S13_R1.dd4_c1_H3K_fastq.gz

description: Biphasic Wnt pathway modulation


title: I0327

description:
Library name: Sample16
library strategy is amplicon sequencing of DNA recombined into cells


title: I0326

description:
Library name: Sample15
library strategy is amplicon sequencing of DNA recombined into cells


title: Lymph node sample of CLL patient 1323

first: Vicente

last: Chapaprieta

address: C/Rosselló 149-153

institute: IDIBAPS

description: Library name: CLL1323

data_processing:
Sequence reads were trimmed for adaptor sequence using trimmomatic v0.39.
Ribosomic RNA from trimmed sequence reads were filtered out using Sort-MeRNA v4.3.2.
Transcript-level counts with respect to reference genome GRCh38.p13 were calculated using kallisto v0.46.1.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include transcripts Ensembl identifier (ENST), length, effective length, estimated counts and transcripts per million (tpm) for each Sample

source_name: Lymph node

extract_protocol:
RNA was extracted from frozen lymph nodes using the AllPrep DNA/RNA Mini Kit (Qiagen, cat. no 80204).
Libraries for RNA-seq were prepared using the Stranded mRNA Library Prep, Ligation kit (Illumina, cat. no. 20040534).

value: Lymph node

value: chronic lymphocytic leukemia


title: Lymph node sample of CLL patient 758

description: Library name: CLL758


title: Lymph node sample of CLL patient 64

description: Library name: CLL64


title: I0324

description:
Library name: Sample13
library strategy is amplicon sequencing of DNA recombined into cells


title: I0325

description:
Library name: Sample14
library strategy is amplicon sequencing of DNA recombined into cells


title: I0323

description:
Library name: Sample12
library strategy is amplicon sequencing of DNA recombined into cells


title: Lymph node sample of CLL patient 63

description: Library name: CLL63


title: Lymph node sample of CLL patient 45

description: Library name: CLL45


title: I0322

description:
Library name: Sample11
library strategy is amplicon sequencing of DNA recombined into cells


title: phr2, NP, replicate 3

city: Yangzhou

first: Mingnan

last: Qu

state: Jiangsu

address: Pazhou Dadao Rd, 17-19

institute: Yangzhou Univerisity

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100.
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9.
Perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: msu7.0
Supplementary files format and content: FPKM values for each Sample.

organism: Oryza sativa

source_name: leaf

growth_protocol: All the plant materials  were grown in 1/2MS medium under normal conditions.

extract_protocol:
Total RNA was extracted from rice leaves using a Trelief® RNApre Pure Plant Kit (tsingke, code: TSP411) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 3-week-old rice plants were transfered to 1/2MS without Phosphorus (Pi), rice leaves were collected at day 3 after the treatment.

value: leaf

value: PHR2 knockout

value: Non-Pi stress of day 3


title: I0320

description:
Library name: Sample9
library strategy is amplicon sequencing of DNA recombined into cells


title: phr2, NP, replicate 1


title: I0321

description:
Library name: Sample10
library strategy is amplicon sequencing of DNA recombined into cells


title: I0318

description:
Library name: Sample7
library strategy is amplicon sequencing of DNA recombined into cells


title: phr2, CK, replicate 2

value: No treatment


title: I0317

description:
Library name: Sample6
library strategy is amplicon sequencing of DNA recombined into cells


title: phr2, CK, replicate 1


title: ZH11, NP, replicate 3

value: WT


title: I0316

description:
Library name: Sample5
library strategy is amplicon sequencing of DNA recombined into cells


title: Input_36_16c_S10_R1.dd10 (ICG)_3_Igg_fastq.gz

description: Biphasic Wnt pathway modulation, treatment (dd4-dd10), IgG

value: hPSC-derived cardiac progenies

value: anti-IgG (17–10109, Millipore)- 2µg/IP


title: ZH11, NP, replicate 2


title: ZH11, NP, replicate 1


title: ZH11, CK, replicate 3


title: Buccal_P41019091109837

city: Los Angeles

first: Jonathan

last: Chan

state: CA

address: 610 Charles E. Young Drive South

department: Molecular, Cellular, Developmental Biology

institute: University of California, Los Angeles

description: Library name: P41019091109837

data_processing:
Reads were aligned to the human genome using BSBolt Align, which generated compressed binary alignment files (BAM) in the SAM format. For each of these loci we extracted the reads from each sample using the samtools view function (samtools 1.14). We then used the multialign algorithm on MATLAB R2023a to align the reads to the template sequence with the GapOpen parameter set to 50 and terminalGapAdjust set to true,
Assembly: hg38
Supplementary files format and content: Comma-delimited .txt files where each row corresponds to a locus and each column corresponds to a sample. Entries are the computed value of the average methylation (buccalswab_avgmeth.txt), cellular heterogeneity-adjusted average methylation (buccalswab_chalm.txt), or methylation entropy (buccalswab_entropy.txt).

source_name: Endothelial

extract_protocol:
Buccal swabs were collected from human subjects and incubated overnight at 50º C before DNA extraction.
Fragmented DNA was subject to end repair, dA-tailing and adapter ligation using the NEBNext Ultra II Library prep kit using custom pre-methylated adapters (IDT). Pools of 16 purified libraries were hybridized to the biotinylated probes according to the manufacturer’s protocol. Captured DNA was treated with bisulfite prior to PCR amplification using KAPA HiFi Uracil+(Roche) with the following conditions: 2 min at 98°C; 14 cycles of (98°C for 20 sec; 60°C for 30 sec; 72°C for 30 sec); 72°C for 5 minutes; hold at 4°C. Library QC was performed using the High-Sensitivity D1000 Assay on a 2200 Agilent TapeStation. Pools of 96 libraries were sequenced on a NovaSeq6000 (S1 lane) as paired-end 150 bases.

value: Endothelial

tag: age

tag: height (in)

tag: weight (lbs)


title: Buccal_P41019091109831

description: Library name: P41019091109831


title: Buccal_P41019091109817

description: Library name: P41019091109817


title: Buccal_P41019091109813

description: Library name: P41019091109813


title: ZH11, CK, replicate 2


title: phr2, NP, replicate 2


title: ZH11, CK, replicate 1


title: Buccal_P41019091109805

description: Library name: P41019091109805


title: E7

city: Chongqing

first: Zhiwei

last: Chen

address: The Second Affiliated Hospital of Chongqing Medical University, 74  Linjiang Road, Yuzhong District, Chongqing

description:
Library name: samples18
Column name in raw_counts_Human.txt: G66NCA

data_processing:
Raw data(raw reads) of fastq format were firstly processed through in-house perl scripts
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Assembly: hg38,GRCm39
Supplementary files format and content: Human_FPKMs.csv
Supplementary files format and content: Mouse_FPKMs.csv
Supplementary files format and content: raw_counts_Human.txt
Supplementary files format and content: raw_counts_Mouse.txt

source_name: liver

extract_protocol:
RNA was harvested using  RNA Nano 6000 Assay Kit of the Bioanalyz 2100 system (Agilent Technologies,CA,USA). 1.3 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seq Library Prep Kifollowing manufacturer's protocols

value: liver

tag: subject status

value: ENEG patient

value: Treatment naïve

tag: batch


title: I0319

description:
Library name: Sample8
library strategy is amplicon sequencing of DNA recombined into cells

value: HEK 293T

tag: cell type

value: Recombination into genomic landing pad


title: Buccal_P41019091104753

description: Library name: P41019091104753

tag: tissue


title: phr2, CK, replicate 3


title: Buccal_P41019091104756

description: Library name: P41019091104756


title: Buccal_P41019091104751

description: Library name: P41019091104751


title: SOG1-FLAG-OE1, input, 40 Gy, replicate 2

description: Library name: SOG1-FLAG-OE1_input_40 Gy2

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp software(version 0.20.1). Clean data were obtained for downstream analyses by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
The clean reads were mapped to the genome using bowtie2 (version 2.4.2). MACS2 (version 2.2.7.1) was used to call peaks.
Called peaks were then annotated using R package ChIPseeker.
HOMER (http://homer.ucsd.edu/homer/download.html,v4.11.1) were used to find de novo and known motif.
Differential peaks analysis was performed using R package  Diffbind for experimental design with replication.
Assembly: msu7.0
Supplementary files format and content: bigWig

source_name: Leaf

extract_protocol:
Rice leaf samples (5 g) were crosslinked in buffer containing 4% (w/v) formaldehyde. Nuclei were isolated and chromatin was sheared by sonication into 200- to 600-bp fragments. Sonicated chromatin was precleared with 100 µl protein A agarose for 1.5 h and immunoprecipitated into three fractions: with anti-GLK1 for the GLK1-bound chromatin, with anti-GLK2 for the GLK2-bound chromatin, and the anti-Histone H3 (AHO1432, Invitrogen, 1.5–2 mg) as a nonspecific chromatin-binding protein. Chromatin-bound DNA fragments were eluted after reverse cross-linking by incubation overnight with proteinase K at 37°C. The incubation was repeated again at 65°C overnight and subsequently the DNA was purified following the manufacturer’s instructions.
The ChIP-seq of the immunoprecipitated chromatin DNA from combined GLK1 and GLK2 were generated with varied index label by NEBNext® UltraTM DNA Library Prep Kit for Illumina (NEB, USA, cat. E7645L). Add End Repair Reaction Buffer (10X) and End Prep Enzyme Mix for end repair by the following condition: 20°C for 30min, 65°C for 30min. And then NEBNext Adaptor and Blunt/TA Ligase Master Mix was added to ligate adaptor at 20°C for 15 min. USER Enzyme was added to remove base U of adaptor at 37°C for 5 min. After purification with beads, products are amplified with PCR by the following conditions: initial denaturation at 98℃ for 10 sec; denaturation at 98℃ for 10 sec, annealing at 65℃ for 30 sec, and extension at 72℃ for 30 sec. The library size was selected and then purified with AMPure XP Beads. Qubit was used for library quantification and High-sensitivity DNA chip was used for test of library insert size. The libraries were sequenced on an Illumina NovaSeq 6000 platform and 150 bp paired-end reads were generated.

treatment_protocol: 3-week-old rice plants were expoture to γ-irradiation of 40 Gy, rice leaves were collected at 20 h after the treatment.

value: Leaf

value: γ-irradiation of 40 Gy


title: SOG1-FLAG-OE1, input, 40 Gy, replicate 1

description: Library name: SOG1-FLAG-OE1_input_40 Gy1


title: E6

institute: The Second Affiliated Hospital of Chongqing Medical University

description:
Library name: samples17
Column name in raw_counts_Human.txt: G19NCA


title: E5

description:
Library name: samples16
Column name in raw_counts_Human.txt: W21


title: Buccal_P41019091104731

description: Library name: P41019091104731


title: Buccal_P41019091109844

description: Library name: P41019091109844


title: Chip16_16c_S16_R1.dd10 (CMs)_c1_H3K_fastq.gz

description: Biphasic Wnt pathway modulation

value: hPSC-derived cardiomyocytes

value: hESC3 NKX2-5 wt/GFP

value: anti-H3K27ac (C15410196, Diagenode)- 2µg/IP


title: SOG1-FLAG-OE1, FLAG IP, 40 Gy, replicate 2

description: Library name: SOG1-FLAG-OE1_FLAG_40 Gy2


title: E4

description:
Library name: samples15
Column name in raw_counts_Human.txt: W3


title: Buccal_P41019091104730

description: Library name: P41019091104730


title: Buccal_P41019091104727

description: Library name: P41019091104727


title: Buccal_P41019091104677

description: Library name: P41019091104677


title: SOG1-FLAG-OE1, FLAG IP, 40 Gy, replicate 1

description: Library name: SOG1-FLAG-OE1_FLAG_40 Gy1


title: E3

description:
Library name: samples14
Column name in raw_counts_Human.txt: W20


title: Buccal_P41019091104671

description: Library name: P41019091104671


title: Buccal_P41019081706836

description: Library name: P41019081706836


title: phr2, input, NP, replicate 2

value: leaf

value: PHR2 knockout

tag: fraction

value: input


title: Buccal_P41019081706790

description: Library name: P41019081706790


title: E1

description:
Library name: samples12
Column name in raw_counts_Human.txt: W5


title: E2

description:
Library name: samples13
Column name in raw_counts_Human.txt: W23


title: Buccal_P41019081706814

description: Library name: P41019081706814


title: Buccal_P41019081706783

description: Library name: P41019081706783


title: phr2, input, NP, replicate 1

value: Non-Pi stress of day 3


title: Buccal_P41019081706785

description: Library name: P41019081706785


title: EM11

description:
Library name: samples11
Column name in raw_counts_Human.txt: W9

value: ENEG patients with MASLD


title: Buccal_P41019081706782

description: Library name: P41019081706782


title: Buccal_P41019081706759

description: Library name: P41019081706759


title: phr2, input, CK, replicate 1

value: No treatment


title: Buccal_P41019091104746

description: Library name: P41019091104746

value: Endothelial


title: phr2, input, CK, replicate 2


title: EM10

description:
Library name: samples10
Column name in raw_counts_Human.txt: W16

value: liver


title: Buccal_P41019081706746

description: Library name: P41019081706746


title: Buccal_P41019081706745

description: Library name: P41019081706745


title: phr2, GLK IP, NP, replicate 2

value: IP


title: EM9

description:
Library name: samples9
Column name in raw_counts_Human.txt: W15

value: Treatment naïve


title: EM8

description:
Library name: samples8
Column name in raw_counts_Human.txt: W12


title: Buccal_P41019081706743

description: Library name: P41019081706743


title: Buccal_P41019081706739

description: Library name: P41019081706739


title: phr2, GLK IP, CK, replicate 2


title: EM7

description:
Library name: samples7
Column name in raw_counts_Human.txt: W10


title: Buccal_P41019081706707

description: Library name: P41019081706707


title: Buccal_P41019081706685

description: Library name: P41019081706685


title: phr2, GLK IP, CK, replicate 1


title: Buccal_P41019081706684

description: Library name: P41019081706684


title: EM6

description:
Library name: samples6
Column name in raw_counts_Human.txt: W17


title: Buccal_P41019081704275

description: Library name: P41019081704275


title: Buccal_P41019081704253

description: Library name: P41019081704253


title: Buccal_P41019081704248

description: Library name: P41019081704248


title: EM5

description:
Library name: samples5
Column name in raw_counts_Human.txt: W13


title: Buccal_P41019081704246

description: Library name: P41019081704246


title: EM4

description:
Library name: samples4
Column name in raw_counts_Human.txt: W11


title: Buccal_P41019081704250

description: Library name: P41019081704250


title: EM3

description:
Library name: samples3
Column name in raw_counts_Human.txt: W8


title: normalized log2 ratio (Res A/HL60)

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: Ratio of radiation-resistant HL60/wild type HL60

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: HL60 cells were mainteined RPMI1640 medium supplemented 10% heat-inactivated fetal bovine serum and 1% penicillin/streptomycin. The cultures were incubated in a 5% CO2 incubator at 37℃.

extract_protocol: The total RNAs in cultured cell of radiation-resistant type and wild type were extracted using  Rneasy plusmini kit (QIAGEN Inc.) according to the manufacturer's instructions.

treatment_protocol: HL60 cells were exposed from higher dose rate of X-irradiation (4 times per 4 weeks, total dose is 16 Gy) and the after samples were incubated at least 7 days in the condition of RPMI1640 medium with 10%FBS.

value: female

value: leukemia cell line

source_name: Res HL60


title: Buccal_P41019081704235

description: Library name: P41019081704235


title: phr2, GLK IP, NP, replicate 1


title: EM2

description:
Library name: samples2
Column name in raw_counts_Human.txt: W7


title: Buccal_P41019081706687

description: Library name: P41019081706687


title: EM1

description:
Library name: samples1
Column name in raw_counts_Human.txt: W4


title: PV_5L_ZT10_M_MCC3804A292_S146

city: Pittsburgh

first: Colleen

middle: A.

last: McClung

address: 450 Technology Drive

institute: University of Pittsburgh

description: Library name: PV_5L_ZT10_M_MCC3804A292_S146

data_processing:
FASTQC
HTSeq
DESeq2 normalization (median of ratios)
Cosinor modeling
Assembly: Mus musculus Ensembl GRCm38
Supplementary files format and content: .csv

source_name: Brain

extract_protocol:
A co-immunoprecipitation protocol was used as previously described in (Chandra et al., 2015; Becker-Krail et al., 2022; DePoy et al., 2024), with minor modifications. Briefly, tissue was homogenized and incubated overnight with an anti-hemagglutinin A (HA) antibody (Abcam, Cambridge, UK). HA-tagged ribosomes, conjugated to an anti-HA antibody, were then isolated using Dynabeads (Invitrogen, Waltham, MA, USA). RNA was extracted and purified using an EZNA RNA Isolation Kit (Omega Bio-Tek Total RNA Miniprep kit) with ENZA RNase-Free DNAase (Omega Bio-Tek, Norcross, GA, USA).
cDNA synthesis: SMART-seq HT kit; Library prep: Nextera Flex

value: Brain

value: Pyramidal neurons

value: Ribo-tag mice


title: normalized log2 ratio (Res B/HL60)


title: normalized log2 ratio (Res HL60/HL60)


title: PV_5M_ZT22_F_MCC3804A288_S177

description: Library name: PV_5M_ZT22_F_MCC3804A288_S177


title: Buccal_P41019081704241

description: Library name: P41019081704241


title: Buccal_P41019081704177

description: Library name: P41019081704177


title: Buccal_P41019081704247

description: Library name: P41019081704247


title: Buccal_P41019081704185

description: Library name: P41019081704185


title: Buccal_P41019081704149

description: Library name: P41019081704149


title: PV_5J_ZT18_F_MCC3804A183_S215

description: Library name: PV_5J_ZT18_F_MCC3804A183_S215


title: ATAC_Caco-2_rep1

city: BREST

first: Clara

last: Blotas

address: 22 rue Camille Desmoulins

country: France

institute: INSERM 1078

description: Library name: ATAC, Caco-2, replicate 1

data_processing:
ATAC-seq : base-calling, alignment, filtering, peak-calling, ouput files are generated with atacseq pipeline v0.12 (iwc worflow)
Assembly: hg19
Supplementary files format and content: bigwig

source_name: Colon

growth_protocol: DMEM + 10% FBS

extract_protocol:
For ATAC-seq, cells are resuspended in cold lysis buffer and transposition is performed with buffer containing tagment DNA enzyme (Illumina). DNA is purified using the MinElute PCR purification kit (Qiagen).
For ATAC-seq, libraries are amplified using NEBNext High-Fidelity 2 × PCR Master Mix (New England Biolabs). PCR products are purified using QIAquick PCR purification kit (Qiagen). Libraries are paired-end sequenced using Illumina sequencing (NextSeq500 Illumina).

value: Colon

tag: cell line


title: ATAC_Caco-2_rep2

description: Library name: ATAC, Caco-2, replicate 2


title: Buccal_P41019081704242

description: Library name: P41019081704242


title: PV_5I_ZT22_M_MCC3804A291_S198

description: Library name: PV_5I_ZT22_M_MCC3804A291_S198


title: Buccal_P41019081704123

description: Library name: P41019081704123


title: PV_5H_ZT14_F1_MCC3804A266_S188

description: Library name: PV_5H_ZT14_F1_MCC3804A266_S188


title: Buccal_P41019081704118

description: Library name: P41019081704118


title: ATAC_Capan-1_rep2

description: Library name: ATAC, Capan-1, replicate 2

source_name: Pancreas

value: Pancreas


title: ATAC_Capan-1_rep1

description: Library name: ATAC, Capan-1, replicate 1


title: Buccal_P41019081704206

description: Library name: P41019081704206


title: PV_5K_ZT_14_M1_MCC3804A304_S179

description: Library name: PV_5K_ZT_14_M1_MCC3804A304_S179


title: Buccal_P41019081704111

description: Library name: P41019081704111


title: PV_5G_ZT6_F1_MCC3804A290_S191

description: Library name: PV_5G_ZT6_F1_MCC3804A290_S191


title: Buccal_P41019081704090

description: Library name: P41019081704090


title: Buccal_P41019081704106

description: Library name: P41019081704106


title: H3K27me3_Caco-2_rep2

description: Library name: H3K27me3, Caco-2, replicate 2

data_processing:
CUT&RUN-seq : base-calling, alignment, filtering, peak-calling, ouput files are generated with cutandrun v0.8 (iwc worflow)
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: CUT&Run

extract_protocol:
For CUT&RUN-seq, cells are incubated with activated concanavalin A beads and resuspended with buffer containing 0,06 % digitonin.
For CUT&RUN-seq, specific antibodies are added, H3K27ac (Ab4729), CTCF (Active Motif 61311) and incubated at 4°C for 2 hours. pAG-MNase is activated for 30 minutes on ice.  Stop buffer is added and samples are incubated at 37°C for 30 minutes to release DNA fragments. End-repair and A-tailing are then performed using the KAPA HyperPrep kit (Roche). Size selection is performed using AMPure XP beads (Beckman Coulter) with double purification by addition of HXP buffer (20% PEG 8000, 2.5 M NaCl). Amplified libraries are then obtained by adding HotStar ReadyMix 2X and primer mix 10X. Libraries are amplified using NEBNext High-Fidelity 2 × PCR Master Mix (New England Biolabs). PCR products are purified using QIAquick PCR purification kit (Qiagen). Libraries are paired-end sequenced using Illumina sequencing (NextSeq500 Illumina).


title: PV_5F_ZT10_F1_MCC3804A262_S158

description: Library name: PV_5F_ZT10_F1_MCC3804A262_S158


title: Buccal_P41019081703575

description: Library name: P41019081703575


title: Buccal_P41019081703576

description: Library name: P41019081703576


title: Buccal_P41019081703557

description: Library name: P41019081703557


title: Buccal_P41019081704126

description: Library name: P41019081704126


title: H3K27me3_Caco-2_rep1

description: Library name: H3K27me3, Caco-2, replicate 1


title: Buccal_P41019081703571

description: Library name: P41019081703571


title: Buccal_P41019081703556

description: Library name: P41019081703556


title: PV_5D_ZT18_F_MCC3804A305_S186

description: Library name: PV_5D_ZT18_F_MCC3804A305_S186


title: PV_5C_ZT6_M_MCC3804A315_S201

description: Library name: PV_5C_ZT6_M_MCC3804A315_S201


title: Buccal_P41019081703527

description: Library name: P41019081703527


title: Buccal_P41019081703539

description: Library name: P41019081703539


title: H3K27ac_Caco-2_rep1

description: Library name: H3K27ac, Caco-2, replicate 1


title: Buccal_P41019081704121

description: Library name: P41019081704121


title: CTCF_Caco-2_rep2

description: Library name: CTCF, Caco-2, replicate 2


title: PV_5B_ZT2_M_MCC3804A286_S161

description: Library name: PV_5B_ZT2_M_MCC3804A286_S161


title: Buccal_P41019081703523

description: Library name: P41019081703523


title: Buccal_P41019081703526

description: Library name: P41019081703526


title: Buccal_P41019081703517

description: Library name: P41019081703517


title: PV_5A_ZT18_M_MCC3804A313_S187

description: Library name: PV_5A_ZT18_M_MCC3804A313_S187


title: Buccal_P41019081703512

description: Library name: P41019081703512


title: PV_5E_ZT2_F1_MCC3804A308_S148

description: Library name: PV_5E_ZT2_F1_MCC3804A308_S148


title: H3K27ac_Caco-2_rep2

description: Library name: H3K27ac, Caco-2, replicate 2


title: H3K27ac_Capan-1

description: Library name: H3K27ac, Capan-1


title: Buccal_P41019081703500

description: Library name: P41019081703500


title: Buccal_P41019081703479

description: Library name: P41019081703479


title: Input_26_16c_S1_R1.dd4_c2_fastq.gz

description: Biphasic Wnt pathway modulation, input

value: hPSC-derived cardiac progenies

value: hESC3 NKX2-5 wt/GFP

value: anti-H3K27ac (C15410196, Diagenode)- 2µg/IP


title: scATAC-seq_Multiome_Atrial_EB_day8

city: Nijmegen

first: Rebecca

middle: Regina

last: Snabel

state: Gelderland

address: Geert Grooteplein 26-28

department: Molecular Developmental Biology

country: Netherlands

institute: RIMLS

description:
barcode_colnames.tsv
metadata.csv
genomicregions_rownamesATAC.csv
seurat_ATAC_counts.mtx

library_source: transcriptomic single cell

data_processing:
Mapping was performed with the CellRanger-ARC software as provided by 10X for Multiome datasets.
One combined dataset was build using Seurat (PMID: 31178118) and Signac (PMID: 34725479) and the count assays from this object were saved here as separate RNA and ATAC matrices.
Assembly: GRCh38
Supplementary files format and content: Matrices of scRNA and scATAC modalities are saved as .mtx files, which need to be combined with the barcodes_colnames.tsv and genes_rownamesRNA.csv or genomicregions_rownamesATAC.csv, respectively, files to create column- and row-names for the matrix.

source_name: hESC-derived cardiac progenitor cells

growth_protocol: Embryoid Body (EB) cardiomyocyte differentiation cultures.

extract_protocol:
Wnt-modulating protocols culturing the cells for a max of 8 days, either with or without RA treatment at day 4.
10X Genomics Single Cell Multiome ATAC + Gene Expression
scRNA-seq and scATAC-seq from the same nucleus (10X Multiome)

treatment_protocol: Ventricular or atrial conditions were cultured, with atrial treated with Retinoic Acid (RA) at Day 4.

value: hESC-derived cardiac progenitor cells

value: cardiomyocyte

tag: cell population

value: AM

tag: treatment

value: Cmdifferentiation


title: Buccal_P41019081703465

description: Library name: P41019081703465

value: Endothelial


title: scATAC-seq_Multiome_Ventricular_EB_day8

value: VM

tag: genotype


title: Buccal_P41019081703462

description: Library name: P41019081703462


title: PV_4J_ZT18_F3_MCC3804A295_S170

description: Library name: PV_4J_ZT18_F3_MCC3804A295_S170


title: scRNA-seq_Multiome_Atrial_EB_day8

description:
barcode_colnames.tsv
metadata.csv
genes_rownamesRNA.csv
seurat_RNA_counts.mtx


title: Buccal_P41019081703456

description: Library name: P41019081703456


title: Buccal_P41019081703391

description: Library name: P41019081703391


title: Buccal_P41019081703384

description: Library name: P41019081703384


title: PV_4I_ZT14_F2_MCC3804A318_S165

description: Library name: PV_4I_ZT14_F2_MCC3804A318_S165


title: scRNA-seq_Multiome_Ventricular_EB_day8


title: PV_4H_ZT14_M2_MCC3804A281_S183

description: Library name: PV_4H_ZT14_M2_MCC3804A281_S183


title: CTCF_Caco-2_rep1

description: Library name: CTCF, Caco-2, replicate 1


title: Buccal_P41019061105737

description: Library name: P41019061105737


title: PV_4G_ZT22_F_MCC3804A297_S185

description: Library name: PV_4G_ZT22_F_MCC3804A297_S185


title: Buccal_P41019061105735

description: Library name: P41019061105735


title: VM_ZNF711_3

data_processing:
Using Seq2Science (PMID: 38025697) for filtering and mapping of the reads.
Assembly: GRCh38
Supplementary files format and content: GRCh38-counts.tsv contains the STAR (PMID: 23104886) mapped counts of all samples together.

source_name: hESC-derived cardiac cells

growth_protocol: Embryoid Body (EB) cardiomyocyte differentiation cultures of different KOs.

extract_protocol:
Wnt-modulating protocols culturing the KO cells for a max of 14 days, either with or without RA treatment at day 4.
RiboErase depletion KAPA, Roche

treatment_protocol: KOs were generated with CRISPR-Cas9 with TRAC targeting as control. Ventricular or atrial conditions were cultured, with atrial treated with Retinoic Acid (RA) at Day 4.

value: hESC-derived cardiac cells


title: PV_4L_ZT2_M2_MCC3804A317_S157

description: Library name: PV_4L_ZT2_M2_MCC3804A317_S157


title: Buccal_P41019061105701

description: Library name: P41019061105701


title: VM_ZNF711_2


title: Buccal_P41019081703471

description: Library name: P41019081703471


title: Buccal_P41019061105696

description: Library name: P41019061105696


title: PV_4F_ZT6_F2_MCC3804A270_S159

description: Library name: PV_4F_ZT6_F2_MCC3804A270_S159


title: Buccal_P41019061105688

description: Library name: P41019061105688


title: PV_4K_ZT10_M_MCC3804A319_S173

description: Library name: PV_4K_ZT10_M_MCC3804A319_S173


title: PV_4E_ZT6_M2_MCC3804A274_S189

description: Library name: PV_4E_ZT6_M2_MCC3804A274_S189


title: AM_ZNF711_3


title: VM_ZNF711_1


title: PV_4D_ZT10_F2_MCC3804A273_S182

description: Library name: PV_4D_ZT10_F2_MCC3804A273_S182


title: Buccal_P41019061105682

description: Library name: P41019061105682


title: Buccal_P41019081703461

description: Library name: P41019081703461


title: Buccal_P41019061105693

description: Library name: P41019061105693


title: Buccal_P41019061105656

description: Library name: P41019061105656


title: AM_ZNF711_2


title: AM_ZNF711_1


title: Buccal_P41019061105655

description: Library name: P41019061105655


title: Buccal_P41019061105657

description: Library name: P41019061105657


title: PV_4B_ZT18_M_MCC3804A263_S166

description: Library name: PV_4B_ZT18_M_MCC3804A263_S166


title: Buccal_P41019061105651

description: Library name: P41019061105651


title: Buccal_P41019061105653

description: Library name: P41019061105653


title: VM_TRAC_3


title: Buccal_P41019061105650

description: Library name: P41019061105650


title: PV_4A_ZT2_F3_MCC3804A314_S194

description: Library name: PV_4A_ZT2_F3_MCC3804A314_S194


title: Buccal_P41019061105647

description: Library name: P41019061105647


title: VM_TRAC_2


title: Buccal_P41019061105649

description: Library name: P41019061105649


title: Buccal_P41019061105686

description: Library name: P41019061105686


title: Buccal_P41019061105645

description: Library name: P41019061105645


title: PV_3K_ZT22_M_MCC3804A296_S178

description: Library name: PV_3K_ZT22_M_MCC3804A296_S178


title: Buccal_P41019061105642

description: Library name: P41019061105642


title: PV_3J_ZT6_F_MCC3804A300_S147

description: Library name: PV_3J_ZT6_F_MCC3804A300_S147


title: VM_TRAC_1


title: PV_3L_ZT18_F_MCC3804A298_S192

description: Library name: PV_3L_ZT18_F_MCC3804A298_S192


title: Buccal_P41019061105644

description: Library name: P41019061105644


title: AM_TRAC_3


title: AM_TRAC_2


title: Buccal_P41019061105638

description: Library name: P41019061105638


title: PV_4C_ZT22_M_MCC3804A303_S171

description: Library name: PV_4C_ZT22_M_MCC3804A303_S171


title: PV_3I_ZT2_M_MCC3804A277_S152

description: Library name: PV_3I_ZT2_M_MCC3804A277_S152


title: Buccal_P41019061105633

description: Library name: P41019061105633


title: Buccal_P41019061105632

description: Library name: P41019061105632


title: AM_TRAC_1


title: Buccal_P41019061105630

description: Library name: P41019061105630


title: PV_3G_ZT22_F_MCC3804A311_S172

description: Library name: PV_3G_ZT22_F_MCC3804A311_S172


title: Buccal_P41019061105624

description: Library name: P41019061105624


title: VM_ZNF503_3


title: Buccal_P41019061105623

description: Library name: P41019061105623


title: PV_3F_ZT18_M_MCC3804A146_S233

description: Library name: PV_3F_ZT18_M_MCC3804A146_S233


title: Buccal_P11111111111113

description: Library name: P11111111111113


title: VM_ZNF503_2


title: VM_ZNF503_1


title: PV_3E_ZT10_M_MCC3804A151_S211

description: Library name: PV_3E_ZT10_M_MCC3804A151_S211


title: AM_ZNF503_3


title: PV_3D_ZT14_M_MCC3804A170_S236

description: Library name: PV_3D_ZT14_M_MCC3804A170_S236


title: Buccal_P11111111111112

description: Library name: P11111111111112


title: Buccal_P41019061105634

description: Library name: P41019061105634


title: AM_ZNF503_2


title: PV_3B_ZT6_M_MCC3804A191_S216

description: Library name: PV_3B_ZT6_M_MCC3804A191_S216


title: SKMEL5-NT2

city: New York

first: Miranda

last: Hunter

state: NY

address: 418 E 68th St

institute: Memorial Sloan Kettering Cancer Center

description: Library name: SKMEL5-NT2

data_processing:
Image analysis and base calling were conducted by the NovaSeq Control Software (NCS). Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification.
FASTQC was used for quality control of raw sequencing reads.
Trimmomatic was used to remove sequencing adapters.
Reads were aligned to GRCh38 using STAR and alignment checked using SeQC.
Assembly: GRCh38
Supplementary files format and content: Counts matrix for each sample in .tab format.

source_name: Cell line

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Plus Universal Mini kit following manufacturer’s instructions. RNA samples were quantified using Qubit 2.0 Fluorometer and RNA integrity was checked using Agilent TapeStation 4200.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions. Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation, and quantified by using Qubit 2.0 Fluorometer as well as by quantitative PCR).

value: Cell line

value: Melanoma


title: Buccal_P11111111111111

description: Library name: P11111111111111


title: PV_3C_ZT2_F2_MCC3804A172_S250

description: Library name: PV_3C_ZT2_F2_MCC3804A172_S250

value: Brain


title: GBM1A patient-derived neurospheres, transgenic POU5F1 and SOX2 co-expression

city: Baltimore

first: Amanda

middle: Leigh

last: Johnson

address: 707 N Broadway St, Rm 408

institute: Johns Hopkins School Of Medicine

description:
Library name: GBM1A-OS
10X Genomics

data_processing:
Count matrices were generated using CellRanger software. Data processing was conducted using the Seurat v5 package in R Studio. Low quality cells, defined as number of features/counts < 500 and percentage of mitochondrial reads > 20%, were excluded and counts were normalized using the SCTransform Seurat function prior to downstream analyses.
Assembly: Human hg38
Supplementary files format and content: Comma-separated values file with log-normalized counts

source_name: GBM neurospheres

growth_protocol: GBM1A neurospheres were cultured in serum-free conditions using Stemline Neural Stem Cell Expansion Medium (Sigma-Aldrich, St. Louis, MO, USA) supplemented with 20ng/mL epidermal growth factor and 10ng/mL fibroblast growth factor.

extract_protocol:
GBM neurospheres were pelleted and resuspended in 200uL of medium containing EGF/bFGF. The neurospheres were then gently mixed using a wide-bore pipette tip to create a single-cell suspension. The single cell suspension was filtered using a 40um nylon mesh cell strainer to remove cell clumps and debris. Single-cell concentrations were determined using an automated cell counter.  Cells were centrifuged at 500 rcf for 5 min at room temperature and cell pellets were resuspended in PBS with 0.05% BSA according to the recommendations in the Chromium Next GEM Single Cell 5' Reagent Kits v2 protocol to achieve 10,000 cell recovery.
Library construction was performed using the 10X Genomics Chromium v2 platform according to standard protocol.

treatment_protocol: GBM1A-OS neurospheres are a transgenic cell line generated from parental GBM1A neurospheres with the second-generation lentiviral system according to Addgene protocols, using the psPAX2 packaging plasmid and pMD2.G envelope plasmid (Addgene, Watertown, MA, USA). The lentiviral packaging/envelope plasmids and the transgene vectors for POU5F1 (Oct4; pLM-vexGFP-Oct4, Addgene #22240) and SOX2 (pLM-mCitrine-Sox2, Addgene #23242) were co-transfected into HEK293FT cells using the Lipofectamine 3000 kit (Thermo Fisher, Waltham, MA, USA) according to the manufacturer's recommendations. After 48h, lentiviral particles in the supernatant were concentrated using Lenti-X concentrator solution (Takara Bio, San Jose, CA, USA) and resuspended in 1mL PBS to transduce GBM1A neurospheres. Cells were infected overnight with the lentivirus particles plus 1ug/mL polybrene. The next morning, cells were replated in fresh neurosphere media.

value: GBM neurospheres

value: Transgenic co-expression of POU5F1 and SOX2


title: SKMEL5-KO3

description: Library name: SKMEL5-KO3


title: SKMEL5-KO2

description: Library name: SKMEL5-KO2


title: AM_ZNF503_1


title: SKMEL5-KO1

description: Library name: SKMEL5-KO1


title: MM E2329 Immune-Age Old

city: Atlanta

first: Shivani

last: Kapadia

state: GA

address: 1365 Clifton Road NE

department: Hematology and Medical Oncology

institute: Emory University

description: Library name: E2329BM

data_processing:
Reads were aligned to human reference sequence GRCh38/hg38, filtered, deduplicated and converted into a feature barcode matrix using Cell Ranger 6.0
Samples with low fraction reads (<70%), high reads mapped to antisense strand (>10%) and with problematic barcode rank plot were excluded. Final samples with feature barcode matrix containing data for genes and 55 surface proteins were analyzed using Seurat V5.  Cells with fewer than 200 unique sequenced genes, more than 10% mitochondrial gene and more than 70,000 sequenced features were filtered to exclude dead cells and doublets. The data was batch corrected using Harmony method using Seurat V5 data integration pipeline.
Assembly: GRCh38/hg38
Supplementary files format and content: 10x Genomics output files: HDF5 and FASTQ
Library strategy: CITE-Seq

source_name: Bone Marrow

extract_protocol:
Cells were fixed, permeabilized and washed in accordance with the fluidigm`s cell surface and nuclear staining protocol as described.
Gene expression and cell surface libraries were prepared according to the protocol from 10X Genomics

value: Bone Marrow

tag: disease state

value: Multiple Myeloma

tag: age group

value: Immune-Age Old


title: PV_2L_ZT22_M_MCC3804A199_S217

description: Library name: PV_2L_ZT22_M_MCC3804A199_S217

value: Pyramidal neurons

value: Ribo-tag mice


title: PV_3A_ZT14_F2_MCC3804A167_S213

description: Library name: PV_3A_ZT14_F2_MCC3804A167_S213


title: PV_2K_ZT2_M_MCC3804A181_S258

description: Library name: PV_2K_ZT2_M_MCC3804A181_S258


title: MM E2324 Immune-Age  Old

description: Library name: E2324BM

value: Immune-Age  Old


title: MM E2328 Immune-Age Old

description: Library name: E2328BM


title: MM E2326 Immune-Age Young

description: Library name: E2326BM

value: Immune-Age Young


title: VM_LHX2_2

value: cardiomyocyte


title: MM E2263 Immune-Age Young

description: Library name: E2263BM


title: VM_LHX2_1

value: Cmdifferentiation


title: SKMEL5-NT1

description: Library name: SKMEL5-NT1


title: PV_2JZT6_F_MCC3804A153_S227

description: Library name: PV_2JZT6_F_MCC3804A153_S227


title: SKMEL5-NT3

description: Library name: SKMEL5-NT3


title: PV_2I_ZT18_F_MCC3804A160_S220

description: Library name: PV_2I_ZT18_F_MCC3804A160_S220


title: MM E2242 Immune-Age Young

description: Library name: E2242BM


title: GBM1A patient-derived neurospheres, parental

description:
Library name: GBM1A
10X Genomics


title: AM_LHX2_3

value: AM


title: MM E2228 Immune-Age Young

description: Library name: E2228BM


title: MM E2243 Immune-Age Old

description: Library name: E2243BM


title: AM_LHX2_2


title: PV_2H_ZT14_M_MCC3804A174_S206

description: Library name: PV_2H_ZT14_M_MCC3804A174_S206


title: MGUS R024 Immune-Age Old

description: Library name: R024BM

value: monoclonal gammopathy of uncertain significance


title: MM E2238 Immune-Age Old

description: Library name: E2238BM


title: PV_2G_ZT10_F_MCC3804A178_S237

description: Library name: PV_2G_ZT10_F_MCC3804A178_S237


title: AM_LHX2_1

value: hESC-derived cardiac cells


title: MGUS R020 Immune-Age Old

description: Library name: R020BM


title: MGUS R023 Immune-Age Young

description: Library name: R023BM


title: 18550_EB_Ventricular_d18

data_processing:
Using Seq2Science (PMID: 38025697) for filtering and mapping of the reads.
Mapping was performed with Kallisto | Bustools wrapper (PMID: 33795888), using the following setting: ‘--technology 1,8,16:1,0,8:0,0,0’.
One combined dataset was build using Seurat (PMID: 31178118) and the count assays from this object were saved here as separate spliced (sf) and unspliced (uf) matrices.
Assembly: GRCh38
Supplementary files format and content: Matrices of spliced (sf) and unspliced (uf) are saved as .mtx files, which need to be combined with the respective barcode.tsv and genes.tsv files to create column- and row-names for the matrix.

growth_protocol: Monolayer (Mon), Embryoid Body (EB) and Engineered Heart Tissue (EHT) cardiomyocyte differentiation cultures.

extract_protocol:
Wnt-modulating protocols culturing the cells for a max of 26 days, either with or without RA treatment at day 4.
SORT-seq/CEL-Seq2


title: Buccal_P41019081704127

description: Library name: P41019081704127

value: Endothelial


title: MGUS R015 Immune-Age Young

description: Library name: R015BM


title: PV_2F_ZT6_M2_MCC3804A159_S212

description: Library name: PV_2F_ZT6_M2_MCC3804A159_S212


title: VM_LHX2_3

value: VM


title: MGUS R016 Immune-Age Old

description: Library name: R016BM


title: MGUS R014 Immune-Age Old

description: Library name: R014BM


title: PV_2E_ZT22_F_MCC3804A171_S243

description: Library name: PV_2E_ZT22_F_MCC3804A171_S243

value: Brain


title: MGUS R013 Immune-Age Old

description: Library name: R013BM


title: PV_2D_ZT_14_F_MCC3804A189_S259

description: Library name: PV_2D_ZT_14_F_MCC3804A189_S259


title: 18551_EB_Ventricular_d14


title: MGUS R010 Immune-Age Young

description: Library name: R010BM


title: MGUS R009 Immune-Age Young

description: Library name: R009BM


title: MGUS R006 Immune-Age Old

description: Library name: R006BM


title: 18545_Mon_Ventricular_m11


title: PV_2C_ZT18_M_MCC3804A196_S253

description: Library name: PV_2C_ZT18_M_MCC3804A196_S253


title: MGUS R008 Immune-Age Young

description: Library name: R008BM


title: MGUS R001 Immune-Age Old

description: Library name: R001BM


title: PV_2B_ZT10_M_MCC3804A155_S241

description: Library name: PV_2B_ZT10_M_MCC3804A155_S241


title: SFTS_7，replicate 7, scRNAseq

city: Hefei

first: Yin

last: Zhang

state: Anhui

address: No. 218 Jixi Rd

institute: First Affiliated Hospital of Anhui Medical University

description:
Library name: sample 7
10x Genomics

data_processing:
10X Genomics Cell Ranger software (version 3.1.0) was used to convert raw BCL files to FASTQ files, alignment and counts quantification.
Assembly: Ensembl_release109
Supplementary files format and content: The format of the raw data files is "fastq.gz"; The format of the processed data files is "expression.xls".

source_name: Peripheral blood

extract_protocol:
Perform high-throughput sequencing on the final libraries using Illumina NovaSeq X Plus. A Single Cell 3’ Library comprised standard Illumina paired-end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI were encoded in Read 1, while Read 2 was used to sequence the cDNA fragment. Sample index sequences were incorporated as the i7 index read. Read 1 and Read 2 were standard Illumina® sequencing primer sites used in paired-end sequencing.
Cellular suspensions were loaded on a 10X Genomics GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs). Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. Upon dissolution of the Gel Bead in a GEM, primers containing (i) an Illumina® R1 sequence (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 10 nt Unique Molecular Identifier (UMI), and (iv) a poly-dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded, full-length cDNAs were then reverse-transcribed from poly-adenylated mRNA.

value: Peripheral blood

value: monocytes

tag: Sex

value: female


title: MGUS R003 Immune-Age  Young

description: Library name: R003BM

value: Bone Marrow

value: Immune-Age  Young


title: SFTS_6，replicate 6, scRNAseq

description:
Library name: sample 6
10x Genomics

value: male


title: 18556_Mon_Ventricular_d14


title: MGUS R005 Immune-Age  Young

description: Library name: R005BM

value: mmune-Age  Young


title: PV_1K_ZT10_F_MCC3804A154_S234

description: Library name: PV_1K_ZT10_F_MCC3804A154_S234

value: Pyramidal neurons

value: Ribo-tag mice


title: PV_2A_ZT2_F_MCC3804A194_S239

description: Library name: PV_2A_ZT2_F_MCC3804A194_S239


title: 18544_EHT_Ventricular_m11

value: cardiomyocyte


title: 18549_Mon_Ventricular_m5

value: Cmdifferentiation


title: PV_1J_ZT10_M_MCC3804A164_S249

description: Library name: PV_1J_ZT10_M_MCC3804A164_S249


title: SFTS_3，replicate 3, scRNAseq

description:
Library name: sample 3
10x Genomics


title: SFTS_4，replicate 4, scRNAseq

description:
Library name: sample 4
10x Genomics


title: PV_1I_ZT6_F_MCC3804A188_S252

description: Library name: PV_1I_ZT6_F_MCC3804A188_S252


title: 19783_EHT_Atrial_d12


title: SFTS_5，replicate 5, scRNAseq

description:
Library name: sample 5
10x Genomics


title: SFTS_2，replicate 2, scRNAseq

description:
Library name: sample 2
10x Genomics


title: 18548_EHT_Atrial_m12


title: 19782_EHT_Ventricular_d12


title: PV_1G_ZT14_M_MCC3804A144_S218

description: Library name: PV_1G_ZT14_M_MCC3804A144_S218


title: 19781_EHT_Atrial_d12


title: 18546_Mon_Atrial_m5


title: HAP1 cells, WT, mock, 6hpi, rep2

city: Freiburg

first: Florian

last: Full

address: Hermann-Herder-Str. 11

country: Germany

institute: institute of Virology, University Medical Center Freiburg

description: Library name: DUX4_wt_M2_6h

data_processing:
Sequence reads were mapping to hg38 by STAR
Assembly: hg38
Supplementary files format and content: counts files were generated by featurecounts

extract_protocol:
Cells were resuspended in Trizol (Invitrogen) and RNA extracted from Trizol.
RNA-sequencing libraries were constructed using commercial kits (New England Biolabs) total RNA-seq

value: HAP1 cells

value: WT

value: Mock


title: PV_1E_ZT22_M_MCC3804A148_S247

description: Library name: PV_1E_ZT22_M_MCC3804A148_S247


title: HAP1 cells, WT, mock, 4hpi, rep2

description: Library name: DUX4_wt_M2_4h


title: HAP1 cells, WT, mock, 10hpi, rep2

description: Library name: DUX4_wt_M2_10h


title: HAP1 cells, WT, mock, 6hpi, rep1

description: Library name: DUX4_wt_M1_6h


title: HAP1 cells, WT, mock, 8hpi, rep2

description: Library name: DUX4_wt_M2_8h


title: 19780_EHT_Ventricular_d12

value: hESC-derived cardiac cells


title: PV_1B_ZT22_F_MCC3804A147_S240

description: Library name: PV_1B_ZT22_F_MCC3804A147_S240


title: HAP1 cells, WT, mock, 10hpi, rep1

description: Library name: DUX4_wt_M1_10h


title: PV_1A_ZT14_F_MCC3804A193_S232

description: Library name: PV_1A_ZT14_F_MCC3804A193_S232