title: UCB+OP9, non-adherent, scRNAseq

city: Nishinomiya

first: Yasunori

last: Yoshida

state: Hyogo

address: 1-1, Mukogawa-cho

country: Japan

institute: Hyogo college of medicine

description: 10x Genomics

data_processing:
The resulting raw reads were subjected to demultiplexing, alignment, barcode counting, UMI counting, and filtering using the Cell Ranger v.6.0.0 (10x Genomics). The human genome (GRCh38) was used as a reference to align reads.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: RBC depleted UCB

growth_protocol: RBC depletion of human UCB and PB was performed with EasySep RBC Depletion Reagent (Stem cell technologies, Vancouver, Canada) according to the manufacturer’s protocol, resuspended in DMEM/F12 (Gibco, cat.11330032; ThermoFisher Scientific) supplemented with EGF (Peproech, AF100-15-1mg; Thermo Fisher Scientific), FGF (Peprotech, 100-188-50ug), N-2(Gibco, 17502-001, Thermo Fisher Scientific) and antibiotic-antimycotic (Thermo Fisher Scientific, cat.15240096)

extract_protocol:
After 24 h culture, adherent(S2) and non-adherent cells(S3) were subjected to scRNA-seq. For the control, we used crude RBC depleted UCB(S1).
Single-cell suspension were processed through the 10x Genomics Chromium Controller following the protocol outlined in the Chromium Single Cell 3' Reagent Kits User Guide. Chromium Next GEM Single Cell 3' Kit v3.1 (Cat# PN-1000269), Chromium Next GEM Chip G Single Cell Kit (Cat# PN-1000127) and Dual Index Kit TT Set A (Cat# PN-1000215) were applied during the process.Briefly, UCB cells with/without OP9 pre-conditioning underwent single-cell capture procedure. Single-cell suspensions containing approximately 16,500 live cells per sample were loaded into Chromium controller to generate 10,000 single-cell gel-bead emulsions for library preparation and sequencing. Oil droplets of encapsulated single cells and barcoded beads (GEMs) were subsequently reverse-transcribed in a Veriti Thermal Cycler (Thermo Fisher Scientific), resulting in cDNA tagged with a cell barcode and unique molecular index (UMI). Then cDNA was amplified to generate single-cell libraries according to the manufacturer's protocol. Quantification was made with an Agilent Bioanalyzer High Sensitivity DNA assay (Agilent,High-Sensitivity DNA Kit, Cat# 5067-4626). Subsequently amplified cDNA was enzymatically fragmented, end-repaired, and polyA tagged. Cleanup/size selection was performed on amplified cDNA using SPRIselect magnetic beads (Beckman-Coulter, SPRIselect, Cat# B23317). Next, Illumina sequencing adapters were ligated to the size-selected fragments and cleaned up using SPRIselect magnetic beads. Finally, sample indices were selected and amplified, followed by a double-sided size selection using SPRIselect magnetic beads. Final library quality was assessed using an Agilent Bioanalyzer High Sensitivity DNA assay. Samples were then sequenced on an Illumina NovaSeq 6000 as paired-end mode (read1: 28bp; read2: 91bp).

treatment_protocol: RBC depleted UCB cells were plated on 5-cm Petri dishes at a density of 1x106 cells/mL with OP9 cells for 24hr

value: RBC depleted UCB

tag: treatment

value: OP9 pre-conditioning

tag: cell type

value: non-adherent UCB cells

value: total RNA


title: Normal control 6

status: Public on Jan 25 2023

type: SRA

city: Bergen

first: Oystein

last: Eikrem

address: Haukelandsveien 22

department: Department of Mecine

country: Norway

institute: Haukeland University Hospital

library_source: transcriptomic

data_processing:
Base calling was performed by RTA 1.17.21.3.
FASTQ files were generated using CASAVA 1.8.2 (Illumina, Inc. San Diego, CA, USA).
Assembly: GRCh38
Supplementary files format and content: MNd_ncounts_annot.txt
Supplementary files format and content: Abundance measurements

molecule: total RNA

organism: Homo sapiens

source_name: kidney FFPE

extract_protocol:
RNA was extracted with the High Pure FFPET RNA Isolation Kit (Roche Diagnostics).
RNA libraries were prepared for sequencing using the Illumina Exome (Access) capture protocol.

tag: tissue

value: kidney FFPE

value: glomeruli - LCM


title: ESC_H33KO_KLF5_rep2

city: Dallas

first: Laura

last: Banaszynski

state: TX

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology Sciences

country: USA

institute: UT Southwestern Medical Center

library_source: genomic

data_processing:
The CUT&Tag reads were aligned to the mm10 mouse reference genome using the BWA aligner (Li and Durbin, 2010) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks  (Quinlan et al, 2010).
The sequence length was 50 for R1 and 50 for R2 for paired-end data.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: ESCs were cultured under standard conditions (KO-DMEM, 2 mM Glutamax, 15% ES grade fetal bovine serum, 0.1 mM 2-mercaptoethanol, and leukemia inhibitory factor (LIF)). For early passages, cells were maintained on an irradiated feeder layer. To remove feeders, cells were passaged at least two passages off of feeders onto gelatin-coated plates.

extract_protocol:
Samples were prepared according to the Illumina Nextera protocol
Libraries were constructed according to the Illumina Nextera protocol.

tag: strain

tag: antibody

value: KLF5 (61099, Active Motif)


title: TI-0986-Relapse-AS2861

city: Valencia

first: Jaime

last: Font de Mora Sain

state: Valencia

address: Avenida Fernando Abril Martorell, 106

department: Oncology

country: Spain

institute: Instituto de Investigación Sanitaria La Fe

description: Liquidhope sample46

data_processing:
The libraries were sequenced on NovaSeq 6000 (Illumina) in paired-end with a read length of 2x151bp according to the manufacturer’s protocol for dual indexing. Image analysis, base calling and quality scoring of the run are processed using the manufacturer’s software Real Time Analysis (RTA 3.3.3) and followed by generation of FASTQ sequence files.  The EMSEQ reads were processed using the gemBS pipeline v4.03 using as reference GRCh38[23]. Reads with MAPQ scores < 20 and read pairs mapping to the same start and end points on the genome were filtered out after the alignment step. The first 5 bases from each read were trimmed before the variant and methylation calling step to avoid artifacts due to end repair. For each sample, CpG sites were selected where both bases were called with a Phred score of at least 20, corresponding to an estimated genotype error level of <=1%, and where the total number of reads informative for methylation from both strands combined was >=6. Sites with >500x coverage depth were excluded to avoid centromeric/telomeric repetitive regions. Sequencing depth for the analysis of copy number was calculated using samtools v1.15.
Assembly: hg38
Library strategy: Methyl-Seq

source_name: Blood-derived plasma circulating cell-free DNA

extract_protocol:
Around 1 ml of blood-derived plasma obtained at diagnosis was used to isolate cfcDNA with the QIAamp circulating nucleic acids kit (QIAGEN).
NEBNext Enzymatic Methyl-seq Kit (New England Biolabs, NEB), following manufacturer's recommendations
To prepare libraries for comprehensive methylome representation within a cfcDNA we used the NEBNext Enzymatic Methyl-seq Kit (New England Biolabs, NEB), following manufacturer's recommendations with minor modification that the cfcDNA was not sheared. The method utilizes 10 ng starting material of cfcDNA and relies on two step conversion of the cytosines. The first step uses TET2 oxidation of 5-methylcytosine that provides protection to the modified cytosines from conversion by APOBEC deamination, so only cytosines but not 5-methylcytosines are converted to uracil. Ultimately, cytosines are sequenced as thymines and 5-methylcytosines are sequenced as cytosines. The final 8 cycles of PCR library amplification were carried out using the NEB Unique dual index primer pairs (NEBNext multiplex oligos for Illumina).

tag: disease state

value: High-risk neuroblastoma

tag: gender

value: Female

tag: year to_diagnosis

tag: year to_last_follow-up

tag: age at_diagnosis_(months)

tag: relapse

value: Yes

tag: efs (months)

tag: exitus

tag: os (months)

tag: cfdna (inferred_status)

value: Tumor

tag: mycn amplification

tag: 11q deletion

value: No


title: Aged-58f-T21

city: Montreal

first: Vahab

last: Soleimani

state: QC

address: 3640 rue University

department: Human Genetics

country: Canada

institute: McGill University

data_processing:
Kallisto was used to map reads to the mouse reference genome (mm10) and to quantifying abundances of transcripts using default settings
Transcript-level abundances were imported into R and collapsed into gene counts using the tximport package
To estimate the effects of the experimental conditions, we used DESeq2 to fit the following model gene-wise model: count~ time + age + time:age, where the variable time denotes the effect of engraftment, the variable age denotes the effect of aging, and the interaction variable time:age represents the reprogramming effect on genes in the aged niche.
For the purposes of ranking and visualization, we use the apeglm shrinkage approach.
Assembly: mm10
Supplementary files format and content: *_abundance.tsv: reports abundances as “estimated counts” (est_counts) and in Transcripts Per Million (TPM).
Project’s Website (reproducible notebooks): https://csglab.github.io/transcriptional_reprogramming_muscle_cells/

source_name: satellite cells

extract_protocol:
1000 GFP positive satellite cells from the donor mice were sorted by Fluorescence-Activated Cell Sorting (FACS) by gating for the GFP+/DAPI- cell population.  These cells were sorted directly into the SMART-Seq (Takara) reaction buffer composed of lysis buffer, water and RNAse inhibitors, these cells act as the T0 time point.
Concurrently, 10,000-20,000 GFP positive cells were sorted from the same donor mouse and transplanted into the tibialis anterior of the host mouse.  After 21 days, these cells were then reisolated by FACS directly into the SMART-Seq reaction buffer.
Sequencing ready libraries were generated using SMART-Seq HT kit (Takara, cat. #624456) and illumine adapters were added using Nextera XT (Illumina, cat. #FC-131-1024, FC-131-1001).

tag: age of donor/age of host

value: 26 months/ NA

tag: tag

value: skeletal muscle


title: exp4re-induction2019_120 (RNAseq)

city: Pozzuoli

first: Margherita

last: Mutarelli

address: Via Campi Flegrei 34

department: ISASI

country: Italy

institute: CNR

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1
Genome_build: mm10
Supplementary_files_format_and_content: normalized counts matrix
Supplementary_files_format_and_content: counts

molecule: polyA RNA

source_name: Mouse Embryonic Stem cells blastocyst derived

growth_protocol: E14 mouse Embryonic Stem cells were routinely cultured on 0.2% gelatin coated multiwell plates in N2B27 medium (DMEM-F12 Neurobasal at 1:1 ratio (Life Technologies), 1X N2 Supplement (Life Technologies), 1X B27 Supplement (Life Technologies), 2mM L-Glutamine (Life Technologies), 0.1mM 2-mercaptoethanol with the addition of 2iL (3uM CHIR99021 (Axon), 1uM PD0325901 (Axon), 1uM LIF (Qkine)).

extract_protocol:
Cells were harvested at the appropriate time point and RNA was purified by using "Total RNA extraction kit, Norgen".
NEGEDIA Digital mRNAseq - research grade.
3' DGE RNA-seq

treatment_protocol: Cells were plated at single cell density on 0.2% Gelatin coated plates in N2B27 medium with 2iL. The next day 2iL was removed and replaced with N2B27 medium. Cells were collected after 12 24 36 48 60 72 84 or 96 hours of 2iL withdrawal. In parallel, cells after 48 and 96 hours of 2iL withdrawal were treated with 2iL and collected after 24 hours.

tag: cell line

tag: cell type

value: E14 mouse Embryonic Stem cells

tag: treatment

value: 2iL withdrawal for 120 hours


title: R3

city: Grand Forks

first: Marc

middle: D

last: Basson

state: ND

address: 1301 N Columbia Rd

institute: University of North Dakota

data_processing:
RNA-seq raw reads were stored in fastq format files containing the sequence data. We explored the fastq files to visualize preliminary results. In addition, we accessed the quality of reads using FastQC to check if any filtration of the raw reads was required16. The QC report of the datasets was assessed, and only qualified samples were included. Trimmomatic v.0.36 was used to eliminate potential adaptor sequences and low-quality nucleotides from sequencing reads. Using the STAR aligner v.2.5.2b, the trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL17. The STAR aligner is a spliced aligner that recognizes and includes splice junctions to aid in aligning whole read sequences. As a result of this procedure, BAM files were created18. Using feature Counts from the Subread package v.1.5.2, we computed the number of unique gene hits. The gene ID feature in the annotation file was used to summarize and provide the hit numbers. Special readings that fell within exon regions were counted19.
Single-cell analysis was performed in 10x Genomics Loupe Browser 4.1.0. Single-cell data were clustered by K-means into four groups, and cell types were identified using breast cancer cell types from Gambardella et al.29. The selection of four K-means clusters was based on minimizing the number of clusters to compare the intensity and number of cells in the clusters. Significant genes per cluster were found in Loupe Browser through globally distinguishing significant feature comparison including with log2 fold change as the displayed numeric value, features filtered by all significant genes per cluster and all gene expression exported. Genes with p < 0.05 were then selected. Violin plots corresponding to cluster expressions were produced in Loupe Browser.
Assembly: GRCh38

source_name: tumor xenograft

growth_protocol: MDA-MB-231 cells stably overexpressing SLFN12 and control cells were cultured in DMEM medium supplemented with 10% FBS at 37°C and 5% CO2 and allowed to passage twice and reach 70% confluency. Cell suspension of 350,000 cells per 100 µl of PBS was prepared in 5 ml sterile Eppendorf tubes. Mice were injected with Buprenorphine (1-2mg/kg) subcutaneously for pain control, anesthetized with 2% isoflurane A 2-4 mm incision was made lateral to the midline on the abdominal skin adjacent to the right fourth nipple. The fourth mammary fat pad was identified, retracted using forceps, and injected with 100 µl of cell suspension (350,000 cells) using a 25-gauge sterile syringe. The skin was sutured with silk suture and the mouse was allowed to recover from the anesthesia.

extract_protocol:
Xenograft tumors were then snap-frozen in liquid nitrogen and stored at -80°C prior to shipment on dry ice to GENEWIZ (South Plainfield, NJ) for sequencing.
Libraries were prepared using the Tecan Ovation SoLo RNA-Seq library preparation kit per manufacturer’s instructions. Libraries were quantified using Quant-iT PicoGreen dsDNA assay kit and read on BioTek FLx800 fluorescence microplate reader. Libraries were pooled equal molar and the sample pool was quantified using Biorad ddPCR. Libraries were sequenced using as stated below.
A Single-cell and Bulk-RNA sequencing dataset generated by Genewiz, Inc (South Plainfield, New Jersey). The Bulk-RNA sequencing dataset comprises six samples, of which three have normal expressions of SLFN12, and the remaining three have over-expression of SLFN12. Similarly, single-cell sequencing consists of two samples, of which one has normal expression, and the other has over-expression of SLFN12. After receiving the raw files (FASTQ) from Genewiz, pre-processing and normalization was performed in-house using the following approach.

tag: tissue

value: tumor xenograft

value: TNBC breast cancer

tag: genotype

value: SLFN12 Lentivirus


title: ETX embryoid Day 5 early

city: Rotterdam

first: Beatrice

last: Tan

address: Dr. Molewaterplein 40

department: Developmental Biology

country: Netherlands

institute: Erasmus MC

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cellranger mkref v6.0.0 was used to create a custom reference package containing the mm10 reference genome and the sequences of DSRED, GFP and EGP. The raw FASTQ files were processed using cellranger count based on the custom reference package. Cells with fewer than 500 counts, 250 detected genes and low complexity (log10 value of number of genes detected per count < 0.8) were removed. Genes with zero expression in all cells and that are expressed in less than 10 cells were removed.
Assembly: mm10
Supplementary files format and content: Tab-delimited file (tsv) with barcodes
Supplementary files format and content: Tab-delimited file (tsv) with genes
Supplementary files format and content: Matrix file (mtx) with expression values

source_name: Stem cell-derived ETX embryoid

extract_protocol:
ETX embryoids were collected on day 4, day 5 and day 6. ETX structures were selected on day 4 when they displayed a clear epiblast and a pro-amniotic cavity. Day-5 ETX embryoids were divided in a group displaying a morphology of early gastrulation and a group of ETX structures displaying signs of more advanced gastrulation. Selected day-6 ETX embryoids displayed a more developed phenotype with the apparent formation of an amnion, chorion and exocoelom. Per selected stage, 10 ETX structures were processed for 10x-sequencing as earlier described. Briefly, selected ETX embryoids were carefully removed from the wells and dissociated with TrypLE Express dissociation reagent (Life Technologies) at 37 °C for 5min and gently dissociated manually. Following inactivation with an equivalent amount of FBS, the single cells were filtered through a Flowmi Tip Strainer with 40 µm porosity (ThermoFisher Scientific, #136800040), washed and resuspended in PBS with 0.4% BSA.
Single cells were processed on the 10X Genomics Chromium Platform using the Chromium Next GEM Single Cell 3′ Reagent kit v3.1 with dual indexing (10X Genomics) following the manufacturer’s protocol. Briefly, 15,000 cells were loaded in each channel of a chip to be partitioned into gel beads in emulsion (GEMs). Within GEMs, cells were lysed followed by barcoded reverse transcription of RNA. Breaking of the GEMs was followed by amplification, fragmentation and addition of adapter and sample index. Libraries were pooled and sequenced 28-10-10-90 cycles on an Illumina NovaSeq6000 instrument aiming for a minimum coverage of 25,000 raw reads per cell.

value: Stem cell-derived ETX embryoid

tag: strain

value: Mixed

value: Fgfr2-Gata6 transgenic PrE ESCs, Actin-GFP ESCs, X-GFP TS cells

tag: day


title: TI-0986-Diagnosis-AS2860

description: Liquidhope sample45

value: Blood-derived plasma circulating cell-free DNA

tag: disease state

tag: gender

tag: year to_diagnosis

tag: year to_last_follow-up

tag: age at_diagnosis_(months)

value: Normal

value: not evaluable


title: TI-0961-Diagnosis-AS2897

description: Liquidhope sample39

value: High-risk neuroblastoma

value: Male

tag: relapse

tag: efs (months)

tag: exitus

tag: os (months)

tag: cfdna (inferred_status)


title: UCB+OP9, adherent, scRNAseq

description: 10x Genomics

value: RBC depleted UCB

value: OP9 pre-conditioning

value: adherent UCB cells

value: total RNA


title: exp4re-induction2019_96_24 (RNAseq)

tag: cell line

value: E14 mouse Embryonic Stem cells

value: 2iL withdrawal for 96 hours, followed by 2iL treatment for 24 hours


title: TI-0934-Diagnosis-AS2851

description: Liquidhope sample35

value: Yes

value: No

value: Tumor

tag: mycn amplification

tag: 11q deletion


title: LV-SLFN12

tag: tissue

value: tumor xenograft

tag: cell type

value: TNBC breast cancer

value: SLFN12 Lentivirus

tag: treatment


title: ESC_H33KO_KLF5_rep1

tag: strain

tag: antibody

value: KLF5 (61099, Active Motif)


title: TI-0977-Diagnosis-AS2858

description: Liquidhope sample43

value: Blood-derived plasma circulating cell-free DNA

tag: disease state

tag: gender

value: Female


title: ESC_H33WT_KLF5_rep3


title: ETX embryoid Day 6

description: 10x Genomics

value: Stem cell-derived ETX embryoid

value: Mixed

tag: genotype

value: Fgfr2-Gata6 transgenic PrE ESCs, Actin-GFP ESCs, X-GFP TS cells

tag: day


title: ETX embryoid Day 4

description: 10x Genomics


title: TI-0956-Relapse-AS2853

description: Liquidhope sample37

value: High-risk neuroblastoma

value: Male

tag: year to_diagnosis

tag: year to_last_follow-up

tag: age at_diagnosis_(months)

tag: relapse


title: TI-0985-Diagnosis-AS2859

description: Liquidhope sample44

tag: efs (months)

tag: exitus

tag: os (months)

tag: cfdna (inferred_status)


title: exp4re-induction2019_96 (RNAseq)

tag: cell line

value: 2iL withdrawal for 96 hours


title: ESC_H33WT_KLF5_rep1


title: TI-0913-Relapse-AS2850

description: Liquidhope sample34

tag: tissue

tag: mycn amplification

tag: 11q deletion


title: C2

tag: cell type

value: Control Lentivirus

tag: treatment


title: R2


title: C1


title: IFNAR2-delta7_hIFNb_24h rep2

city: 北京

first: Linnan

last: Zhang

state: 北京

address: 15,Datun Road, Chaoyang, Beijing

country: China

institute: IBP

data_processing:
quantify abundances of transcripts from RNA-Seq data using kallisto (0.43.0) with parameter --rf-stranded. transcript sequences were downloaded form gencode (Release 25)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include estimated counts and TPM values for each sample

extract_protocol:
After extracting the total RNA from samples, mRNA and non-coding RNAs are enriched by removing rRNA form the total RNA with kit.
By using the fragmentation buffer, the mRNA and non-coding RNAs are fragmented into short fragments (about 200~700 bp), then the first-strand cDNA is synthesized by random hexamer-primer using the fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand cDNA. The double strand cDNA is purified with QiaQuick PCR extraction kit and then used for end-polishing. Sequencing adapters are ligated to the fragments , then the second strand is degraded using UNG(Uracil-N-Glyosylase)finally. The fragments are purified by Agarose gel electrophoresis and enriched by PCR amplification.
lncRNA (including mRNA)

value: monocyte cell line

value: delta-7bp IFNAR2 mutant

value: ml IFNβ, 24 hours


title: exp4re-induction2019_2iL (RNAseq)

value: E14 mouse Embryonic Stem cells

value: untreated (2iL)


title: Chondrocytes miR-26a KO

city: Hiroshima

first: Shigeru

last: Miyaki

state: Hiroshima

address: 1-2-3, kasumi Minami-ku

department: Medical Center for Translational and Clinical Research

institute: Hiroshima University

data_processing:
Convert the fastq file to a fasta file. After checking the quality of the reads, it was determined that filtering of low quality reads was not necessary.
Map the converted fasta file to the mouse reference genome (mm10). The reads that are mapped to only one location are counted for each gene.
Transcript length data was retrieved from GRCm38.p6 (mm10). Transcripts Per Million (TPM) for each gene was calculated using raw counts and transcript length.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for all samples

source_name: Articular chondrocyte

growth_protocol: Articular chondrocytes from the femoral heads of mice at 3 weeks of age were isolated by digestion with 3.5 mg/ml collagenase Type 2 (Worthington, Lakewood, NJ, USA) in Dulbecco’s modified Eagle’s medium (DMEM) (FUJIFILM Wako, Osaka, Japan) for 1.5 hours at 37°C. Isolated chondrocytes were cultured in DMEM with 10 % fetal bovine serum.

extract_protocol:
Cultured chondrocytes were lysed using TRIZOL reagents. 1) Add 1 mL of TRIZOL to each tube and lyse the cells by pipetting. 2) Leave the tube at room temperature for 5 minutes. 3) Transfer the sample to a 1.5 mL tube and leave it at room temperature for 5 minutes. 4) Add 200 μL chloroform, stir by vortexing, and leave it at room temperature for 3 minutes. 5) Centrifuge at 12,000 g for 10 minutes at 4°C. 6) Transfer the aqueous layer to a new tube; (6) Collect the aqueous layer in a new tube and add 1 µL of 20 mg/mL Glycogen; (7) Add 500 µL 2-propanol, stir, and leave at room temperature for 10 minutes; (8) Centrifuge at 12,000g, 4°C, for 10 minutes (9) Discard the supernatant and add 1 mL of 75% ethanol; (10) Centrifuge at 7,500g, 4°C, for 5 minutes; (11) Discard the supernatant and leave the pellet to dry at room temperature for 5 minutes (12) Suspend in 10 μL of nuclease free water.RNA quality check using Agilent 2100 Bioanalyzer G2939A (Agilent Technologies) and Agilent RNA6000 Nano kit 5067-1511 (Agilent Technologies)
QuantSeq 3'mRNA-Seq Library Prep Kit for Illumina (FWD) <015.384> (LEXOGEN) was used. (1) Total of 500 ng RNA was used for each sample; (2) Synthesize cDNA using oligo (dT) primers; (3) Remove template mRNA; (4) Double-stranded cDNA synthesis using random primers; (5) 12-cycle PCR using indexed adapters; (6) Purification using the beads;

treatment_protocol: Double-stranded RNA oligonucleotides representing mature sequences that miR-26a mimic (sense: 5’-UUCAAGUAAUCCAGGAUAGGCU-3’ and anti-sense: 5’-CCUAUUCUUGGUUCCUUGCACG-3’) or Silencer Negative Control siRNA#1 (Themo Fisher Scientific) were transfected into miR-26a KO chondrocyte using Lipofectamine RNAiMax Reagent (Themo Fisher Scientific) according to the manufacturers’ instructions.

value: Articular chondrocyte

tag: strain

tag: age

value: 3 week


title: EV-SLFN12

value: tumor xenograft

value: TNBC breast cancer

tag: genotype


title: R1

value: SLFN12 Lentivirus


title: Chondrocytes miR-26a KO + 26a TF

data_processing:
Convert the fastq file to a fasta file. After checking the quality of the reads, it was determined that filtering of low quality reads was not necessary.
Map the converted fasta file to the mouse reference genome (mm10). The reads that are mapped to only one location are counted for each gene.
Transcript length data was retrieved from GRCm38.p6 (mm10). Transcripts Per Million (TPM) for each gene was calculated using raw counts and transcript length.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for all samples

value: 3 weeks

value: miR-26a mimic transfection


title: WT_hIFNb_24h rep2

value: wild type


title: ESC_H33WT_H3K4me3

data_processing:
The ChIP-seq reads were aligned to the mm10 mouse reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks  (Quinlan et al, 2010).
The seqeunce length was 33 for R1 and 33 for R2 for paired-end data.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

extract_protocol:
Native ChIP was performed as described (Goldberg et al. 2010). Briefly, cell were harvested treated with Mnase to produce fragments of 200-700 bp. Chromatin was isolated and used for ChIP according to standard procedures.
Libraries were constructed according to the Illumina Tru-seq protocol.

tag: strain background

tag: cell line/genotype

tag: antibody

value: H3K4me3 (AM39159, Active Motif)

tag: ChIP

value: Native


title: exp4re-induction2019_48 (RNAseq)

value: 2iL withdrawal for 48 hours


title: TI-0879-Diagnosis-AS2845

description: Liquidhope sample29

value: Blood-derived plasma circulating cell-free DNA

tag: disease state

value: High-risk neuroblastoma

tag: gender

value: Female

tag: year to_diagnosis

tag: year to_last_follow-up

tag: age at_diagnosis_(months)

tag: relapse

value: Yes

tag: efs (months)

value: No

value: Tumor


title: Chondrocytes WT

description: WT

value: Articular chondrocyte

value: Wild type


title: crude UCB, scRNAseq

description: 10x Genomics

tag: tissue

value: RBC depleted UCB

value: control

value: crude UCB

value: total RNA


title: TI-0895-Relapse-AS2847

description: Liquidhope sample31

value: Male

tag: exitus

tag: os (months)

tag: cfdna (inferred_status)

tag: mycn amplification

tag: 11q deletion


title: exp4re-induction2019_24 (RNAseq)

tag: cell line

tag: cell type

value: E14 mouse Embryonic Stem cells

tag: treatment

value: 2iL withdrawal for 24 hours


title: TI-0956-Diagnosis-AS2852

description: Liquidhope sample36


title: C3

value: tumor xenograft

value: TNBC breast cancer

tag: genotype

value: Control Lentivirus


title: exp4re-induction2019_48_24 (RNAseq)

value: 2iL withdrawal for 48 hours, followed by 2iL treatment for 24 hours


title: TI-0895-Diagnosis-AS2846

description: Liquidhope sample30

value: Blood-derived plasma circulating cell-free DNA

tag: disease state

value: High-risk neuroblastoma


title: ESC_H33KO_GRO-Seq_rep2

data_processing:
library strategy: GRO-seq
The GRO-seq reads were aligned to the mm10 mouse reference genome using the Bowtie aligner (Langmead, 2009) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks  (Quinlan et al, 2010).
The seqeunce length was 33 for R1.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

tag: strain background

tag: genotype/variation

tag: tissue/cell type

value: Embryonic stem cells


title: ESC_H33KO_H3K4me3

tag: cell line/genotype

tag: antibody

value: H3K4me3 (AM39159, Active Motif)

tag: ChIP

value: Native


title: TI-0905-Diagnosis-AS2848

description: Liquidhope sample32

tag: tissue

tag: gender

tag: year to_diagnosis

tag: year to_last_follow-up

tag: age at_diagnosis_(months)

tag: relapse

value: Yes

tag: efs (months)

value: Tumor

value: No


title: TI-0913-Diagnosis-AS2849

description: Liquidhope sample33

tag: exitus

tag: os (months)

tag: cfdna (inferred_status)

tag: mycn amplification

tag: 11q deletion


title: IFNAR1-KO_hIFNb_24h rep2

tag: cell line

tag: cell type

value: monocyte cell line

tag: genotype

value: IFNAR1 KO

tag: treatment

value: ml IFNβ, 24 hours


title: ESC_H33KO_GRO-Seq_rep1

tag: strain background

tag: genotype/variation

tag: tissue/cell type


title: IFNAR2-delta7_hIFNb_24h rep1

value: delta-7bp IFNAR2 mutant


title: exp3re-induction2019_96_24 (RNAseq)

value: E14 mouse Embryonic Stem cells

value: 2iL withdrawal for 96 hours, followed by 2iL treatment for 24 hours


title: Chondrocytes Cart-miR-23-KO

value: Articular chondrocyte

tag: strain

value: Col2a1-cre;miR-23a/b clusters flox/flox

tag: age

value: 3 week


title: IFNAR1-KO_hIFNb_24h rep1


title: exp3re-induction2019_96 (RNAseq)

value: 2iL withdrawal for 96 hours


title: ESC_H33WT_GRO-Seq_rep2


title: TI-0871-Diagnosis-AS2844

description: Liquidhope sample28

tag: tissue

value: Blood-derived plasma circulating cell-free DNA

tag: disease state

value: High-risk neuroblastoma

tag: gender

value: Female

tag: year to_diagnosis

tag: year to_last_follow-up

tag: age at_diagnosis_(months)


title: exp3re-induction2019_48_24 (RNAseq)

value: 2iL withdrawal for 48 hours, followed by 2iL treatment for 24 hours


title: TI-0867-Relapse-AS2843

description: Liquidhope sample27

tag: relapse

value: Yes

tag: efs (months)

tag: exitus

tag: os (months)

tag: cfdna (inferred_status)

value: Normal

tag: mycn amplification

value: not evaluable


title: WT_hIFNb_24h rep1

tag: cell line

tag: cell type

value: monocyte cell line

tag: genotype

value: wild type

tag: treatment


title: exp3re-induction2019_48 (RNAseq)

value: 2iL withdrawal for 48 hours


title: ESC_H33KO_Input_Brd4

extract_protocol:
Crosslinking ChIP was performed as described (Goldberg et al. 2010). Briefly, cell were harvested and crosslinked in 1% PFA. Chromatin was then sheared to 200-700 bp. For both procedures, chromatin was isolated and used for ChIP according to standard procedures.
Libraries were constructed according to the Illumina Tru-seq protocol.

tag: strain background

tag: genotype/variation

tag: tissue/cell type

value: Embryonic stem cells

tag: antibody

value: no antibody

tag: ChIP

value: Cross-link


title: WT_sIFN(I:C)_3h

value: 1000U sIFN(I:C), 3 hours


title: ESC_H33WT_GRO-Seq_rep1


title: exp3re-induction2019_2iL (RNAseq)

value: E14 mouse Embryonic Stem cells

value: untreated (2iL)


title: WT_hIFNa2a_3h

value: ml IFNα2a, 3 hours


title: IFNAR2-delta7_hIFNb_3h rep2

value: delta-7bp IFNAR2 mutant

value: ml IFNβ, 3 hours


title: exp3re-induction2019_120 (RNAseq)

value: 2iL withdrawal for 120 hours


title: TI-0836-Diagnosis-AS2838

description: Liquidhope sample22

tag: tissue

value: Blood-derived plasma circulating cell-free DNA

tag: disease state

value: High-risk neuroblastoma

tag: gender

value: Male

tag: year to_diagnosis

tag: year to_last_follow-up

value: Tumor

value: No

tag: 11q deletion


title: exp3re-induction2019_24 (RNAseq)

value: 2iL withdrawal for 24 hours


title: TI-0778-Relapse-AS2836

description: Liquidhope sample20

tag: age at_diagnosis_(months)

tag: relapse

value: Yes

tag: efs (months)

tag: exitus

tag: os (months)

tag: cfdna (inferred_status)

value: Normal

value: not evaluable


title: ESC_H33WT_Input_Brd4

tag: strain background

value: Embryonic stem cells

value: no antibody

value: Cross-link


title: EB_H33KO_ATAC-Seq_rep1

data_processing:
The ATAC-seq reads were aligned to the mm10 mouse reference genome using the BWA aligner (Li and Durbin, 2010) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks  (Quinlan et al, 2010).
The seqeunce length was 33 for R1 and 33 for R2 for paired-end data.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

growth_protocol: ESCs were cultured under standard conditions (KO-DMEM, 2 mM Glutamax, 15% ES grade fetal bovine serum, 0.1 mM 2-mercaptoethanol, and leukemia inhibitory factor (LIF)). For early passages, cells were maintained on an irradiated feeder layer. To remove feeders, cells were passaged at least two passages off of feeders onto gelatin-coated plates. EBs were differentiated for four days using the hanging drop method.

tag: genotype/variation

value: Embryoid bodies


title: IFNAR1-KO_control_3h rep2

tag: cell line

tag: cell type

value: monocyte cell line

tag: genotype

value: IFNAR1 KO

tag: treatment

value: -, 3 hours


title: TI-0778-Diagnosis-AS2835

description: Liquidhope sample19

tag: tissue

tag: disease state

tag: mycn amplification


title: exp2re-induction2019_48 (RNAseq)

value: E14 mouse Embryonic Stem cells

value: 2iL withdrawal for 48 hours


title: TI-0853-Diagnosis-AS2840

description: Liquidhope sample24

value: Blood-derived plasma circulating cell-free DNA

value: High-risk neuroblastoma

tag: gender

tag: year to_diagnosis

tag: year to_last_follow-up


title: exp2re-induction2019_96_24 (RNAseq)

value: 2iL withdrawal for 96 hours, followed by 2iL treatment for 24 hours


title: TI-0774-Diagnosis-AS2834

description: Liquidhope sample18

value: Male

tag: age at_diagnosis_(months)

tag: relapse

value: No

value: Tumor

tag: 11q deletion


title: exp2re-induction2019_120 (RNAseq)

value: 2iL withdrawal for 120 hours


title: EB_H33WT_ATAC-Seq_rep1

tag: tissue/cell type


title: IFNAR2-delta7_hIFNb_3h rep1

value: delta-7bp IFNAR2 mutant

value: ml IFNβ, 3 hours


title: TI-0771-Diagnosis-AS2833

description: Liquidhope sample17

value: Yes

tag: efs (months)

tag: exitus

tag: os (months)

tag: cfdna (inferred_status)


title: WT_control_3h rep2

tag: cell line

tag: cell type

value: wild type


title: TI-0867-Diagnosis-AS2842

description: Liquidhope sample26

value: Female


title: TI-0756-Relapse-AS2832

description: Liquidhope sample16


title: TI-0836-Relapse-AS2839

description: Liquidhope sample23


title: exp2re-induction2019_96 (RNAseq)

tag: treatment

value: 2iL withdrawal for 96 hours


title: ESC_H33WT_Brd4

tag: strain background

tag: genotype/variation

value: Embryonic stem cells

tag: antibody

tag: ChIP

value: Cross-link


title: exp1re-induction2019_120 (RNAseq)

value: E14 mouse Embryonic Stem cells


title: ESC_H33WT_ATAC-Seq rep2


title: ESC_H33KO_Brd4


title: IFNAR2-delta7_control_3h rep2

value: monocyte cell line

tag: genotype

value: -, 3 hours


title: IFNAR1-KO_hIFNb_3h rep2

value: IFNAR1 KO


title: TI-0861-Diagnosis-AS2841

description: Liquidhope sample25

tag: tissue

value: Blood-derived plasma circulating cell-free DNA

tag: disease state

value: High-risk neuroblastoma

tag: gender

tag: year to_diagnosis

tag: year to_last_follow-up

tag: mycn amplification


title: exp1re-induction2019_96_24 (RNAseq)

value: 2iL withdrawal for 96 hours, followed by 2iL treatment for 24 hours


title: exp2re-induction2019_48_24 (RNAseq)

value: 2iL withdrawal for 48 hours, followed by 2iL treatment for 24 hours


title: EB_H33KO_ATAC-Seq_rep2

tag: tissue/cell type

value: Embryoid bodies


title: ESC_H33KO_ATAC-Seq rep2


title: TI-0787-Diagnosis-AS2837

description: Liquidhope sample21

tag: age at_diagnosis_(months)

tag: relapse

tag: efs (months)

tag: exitus

tag: os (months)

value: Tumor

value: No

tag: 11q deletion


title: TI-0745-Relapse-AS2830

description: Liquidhope sample14

value: Yes

tag: cfdna (inferred_status)

value: Normal

value: not evaluable


title: TI-0745-Diagnosis-AS2829

description: Liquidhope sample13

value: Female


title: EB_H33WT_ATAC-Seq_rep2

tag: strain background

tag: genotype/variation


title: WT_hIFNb_3h rep2

tag: cell line

tag: cell type

tag: genotype

value: wild type

tag: treatment

value: ml IFNβ, 3 hours


title: exp1re-induction2019_96 (RNAseq)

value: E14 mouse Embryonic Stem cells

value: 2iL withdrawal for 96 hours


title: exp2re-induction2019_2iL (RNAseq)

value: untreated (2iL)


title: exp2re-induction2019_24 (RNAseq)

value: 2iL withdrawal for 24 hours


title: exp1re-induction2019_48_24 (RNAseq)


title: IFNAR1-KO_hIFNb_3h rep1

value: monocyte cell line

value: IFNAR1 KO


title: P180 Dot1l-Het3

city: Amsterdam

first: Marten P.

middle: Piet

last: Smidt

address: Sciencepark 904

department: SILS

institute: UvA

data_processing:
Illumina data analysis pipeline RTAv 2.4.11 and Bcl2fastq v2.17
adapter trimming (trimmomatic v0.30)
Burrows-wheeler transform mapping to Mus_musculus.GRCm38.p4
Frequency counting and DESEQ2 (v1.10.1)

source_name: dissected midbrain DA neurons

extract_protocol:
Tissue dissections at P180 and from these samples total RNAwas isolated.
NEBNext Utra directional RNA library prep kit for illumina was used according to the manufactures protocol.

treatment_protocol: WT vs Het vs KO

tag: tissue

value: midbrain dopamine neurons


title: exp1re-induction2019_24 (RNAseq)


title: P180 Dot1l-Het2


title: WT_control_3h rep1

value: -, 3 hours


title: IFNAR2-delta7_control_3h rep1

value: delta-7bp IFNAR2 mutant


title: IFNAR1-KO_control_3h rep1


title: WT_hIFNb_3h rep1


title: TI-0717-Diagnosis-AS2826

description: Liquidhope sample10

value: Blood-derived plasma circulating cell-free DNA

tag: disease state

value: High-risk neuroblastoma

tag: gender

value: Male

tag: year to_diagnosis

tag: year to_last_follow-up

value: Tumor


title: TI-0690-Diagnosis-AS2824

description: Liquidhope sample8

tag: age at_diagnosis_(months)

tag: relapse

value: No

tag: mycn amplification

value: Yes


title: TI-0729-Diagnosis-AS2828

description: Liquidhope sample12

tag: efs (months)

tag: exitus

tag: os (months)


title: exp1_DOX_96_2 (RNAseq)

growth_protocol: E14 mouse Embryonic Stem cells, stably transfected with a DOX-inducible Esrrb construct, were routinely cultured on 0.2% gelatin coated multiwell plates in N2B27 medium (DMEM-F12 Neurobasal at 1:1 ratio (Life Technologies), 1X N2 Supplement (Life Technologies), 1X B27 Supplement (Life Technologies), 2mM L-Glutamine (Life Technologies), 0.1mM 2-mercaptoethanol with the addition of 2iL (3uM CHIR99021 (Axon), 1uM PD0325901 (Axon), 1uM LIF (Qkine)).

treatment_protocol: Cells were plated at single cell density on 0.2% Gelatin coated plates in N2B27 medium with 2iL. The next day 2iL was removed and replaced with N2B27 medium either with or without Doxycycline. Cells were collected after 96 hours.

value: transfected with DOX-inducible Esrrb

value: 2iL withdrawal and Doxycycline treatment for 96 hours


title: Sperm, Hodgkin disease, 12month [HD15-2]

first: Jacquetta

last: Trasler

state: Quebec

address: 1001 Decarie Boul, Block E, ES1.4380

department: Pharmacology & Therapeutics; Human Genetics

data_processing:
library strategy: Customized 5-methyl-cytosine capture sequencing (MCC-Seq)
Raw fastq files were trimmed of adaporter sequences with trimmoatic (version 0.36)
Trimmed reads were aligned to the hg19 genome using bismark aligner (version 0.18.1)
Duplicate aligned reads (if they have the same 5' alignment positions for bother paired in paired-end reads) are removed with picard tools (version 2.9.0).  All duplicated reads are remvoed and only the best pairs, based on alignment score) is kepit
Methylation information was extracted from the bisulfite read aligment files for indivudial cytosines using bismark (version 0.18.1)
Assembly: hg19
Supplementary files format and content: CpG methylation profiles for individual samples as a txt file.  Files contains the following columns: chr, start, stop, number C on forward (fw), number of total fw, methylation fw, numer of C on reverse (rv), number total rv, methylation rv, total C, total reads, total methylation

source_name: Sperm

extract_protocol:
Frozen sperm was thawed on ice and genomic DNA isolation was performed using Qiagen DNeasy Blood & Tissue Kits (Qiagen, Canada) according to the manufacturer’s guide, with modifications. For sample  were incubated overnight at 37oC in a buffer containing EDTA, Tris , sarkosyl , dithiothreitol (DTT) and proteinase K (Invitrogen, Canada). The following day, Buffer AL was added to the buffer, and incubated at 70oC for 10min and the manufacturer’s guide was continued.
Using 1ug of DNA from each sample, whole genome bisulfite sequencing (WGBS) library preparation and targeting bisulfite sequencing was libraries were performed as described previously. Briefly, DNA was sonicated to obtain 300-400bp fragments, proceeded by DNA-end repair, 3’-end adenylation, adaptor ligation and clean up, according to the KAPA High Throughput Library Preparation kit protocol (Roche/KAPA Biosystems). Samples were then bisulfite converted using the EpiTect Fast DNA bisulfite kit (Qiagen) followed by 9-12 cycles of PCR amplification. The final WGBS libraries were purified using Agencourt AMPure Beads (Beckman Coulter) and were then enriched using our human sperm specific panel, using the SeqCap Epi Enrichment System protocol developed and optimized by Roche NimbleGen. Equal amounts of the multiplexed WGBS libraries (84ng each) were combined and hybridized to the human sperm specific capture panel at 47C for 72h. The captured libraries were washed, recovered and PCR amplified before final purification was conducted. The final capture libraries were sequenced one a single lane of the Illumina HiSeq4000 system using 100-bp paired end sequencing.

value: Sperm

value: Hodgkin Disease

tag: time

value: 12 months


title: exp2_DOX_96h_1 (RNAseq)

value: E14 mouse Embryonic Stem cells


title: P180 Dot1l-KO3

tag: genotype/variation


title: TI-0719-Diagnosis-AS2827

description: Liquidhope sample11

value: Female

tag: cfdna (inferred_status)

tag: 11q deletion


title: exp1re-induction2019_2iL (RNAseq)

tag: cell line

tag: cell type

value: untreated (2iL)


title: TI-0756-Diagnosis-AS2831

description: Liquidhope sample15

tag: tissue


title: Sperm, Hodgkin disease, 18month [HD15-3]

tag: treatment

value: 18 months


title: P180 Dot1l-KO2

value: midbrain dopamine neurons


title: Sperm, Testicular Cancer, 18month [TC29-3]

value: Testicular Cancer


title: exp1re-induction2019_48 (RNAseq)

value: 2iL withdrawal for 48 hours


title: Sperm, Testicular Cancer, 12month [TC29-2]


title: exp1_DOX_96h_1 (RNAseq)


title: TI-0688-Relapse-AS2823

description: Liquidhope sample7

value: Blood-derived plasma circulating cell-free DNA

tag: disease state

value: High-risk neuroblastoma

tag: gender

value: Normal

value: not evaluable


title: P180 Dot1l-wt1


title: P180 Dot1l-wt2


title: Sperm, Control2, 12month [CC40-2]

value: Control


title: TI-0702-Diagnosis-AS2825

description: Liquidhope sample9

value: Male

tag: year to_diagnosis

tag: year to_last_follow-up

value: No

value: Tumor

value: Yes


title: P180 Dot1l-Het1


title: P180 Dot1l-wt3


title: Sperm, Control2, 18month [CC40-3]

value: Sperm


title: P180 Dot1l-KO1


title: Sperm, Control1, 18month [CC33-3]


title: TI-0679-Relapse-AS2821

description: Liquidhope sample5

tag: age at_diagnosis_(months)

tag: relapse


title: exp2_noDOX_96h_2 (RNAseq)

value: E14 mouse Embryonic Stem cells

value: transfected with DOX-inducible Esrrb

value: 2iL withdrawal for 96 hours


title: TI-0679-Diagnosis-AS2820

description: Liquidhope sample4

tag: efs (months)

tag: mycn amplification


title: TI-0688-Diagnosis-AS2822

description: Liquidhope sample6

tag: exitus

tag: os (months)


title: Dot1l-KO3

data_processing:
Illumina data analysis pipeline RTAv 2.4.11 and Bcl2fastq v2.17
adapter trimming (trimmomatic v0.30)
Burrows-wheeler transform mapping to Mus_musculus.GRCm38.p4
Fequency counting and DESEQ2 (v1.10.1)

source_name: FACS sorted midbrain DA neurons

extract_protocol:
Tissue dissections and preparation for FACS sorting ( FACS ARIA3), from these samples total RNAwas isolated.
NEBNext Utra directional RNA library prep kit for illumina was used according to the manufactures protocol.

treatment_protocol: WT vs het vs KO

tag: strain

tag: genotype/variation


title: Dot1l-KO2


title: Dot1l-KO1


title: exp1_noDOX_96h_2 (RNAseq)


title: Dot1l-Het2


title: Sperm, Control1, 12month [CC33-2]

tag: time

value: 12 months


title: TI-0576-Diagnosis-AS2819

description: Liquidhope sample3

tag: cfdna (inferred_status)

tag: 11q deletion


title: exp1_noDOX_96h_1 (RNAseq)

tag: cell line

tag: cell type


title: 8939: D8 ttntv CM D150 3

city: SOUTH SAN FRANCISCO

first: Tracy

last: Yamawaki

state: California

address: 1120 VETERANS BLVD.

institute: AMGEN, INC.

data_processing:
read trimming and alignment performed with Oshell  v 10.0.1.111
Genome_build: hg38
Supplementary_files_format_and_content: Read count and quantile normalized fpkm (fpkq) in TSV files.

source_name: hiPSC cardiomyocyte

growth_protocol: cells  were  maintained  in “RPMI/1640+  B27 medium”at the density of 3.6 x 105cells/cm2with medium change every 3 days until use

extract_protocol:
RNeasy kit (Qiagen)
0.1-1μg of RNA was used as input for a modified Illumina TruSeq Stranded mRNA protocol.Reverse transcription was performed with RNaseOut (Invitrogen) and actinomycin-D (MP Biomedicals) and the product was cleaned using AMPure RNAClean beads (Beckman Coulter). Second-strand synthesis was performed substituting dUTP for dTTP. After size selection, UTP containing strands were cleaved using USER (New England Biolabs)

tag: genotype

value: TTNtv/+

tag: timepoint

value: hiPSC cardiomyocyte


title: 8937: D8 ttntv CM D150 1


title: exp2_noDOX_2iL_2 (RNAseq)

tag: treatment

value: untreated


title: exp2_noDOX_2iL_1 (RNAseq)


title: TI-572-Diagnosis-AS2817

description: Liquidhope sample1

tag: tissue

value: Blood-derived plasma circulating cell-free DNA

tag: disease state

tag: gender

value: Female

tag: year to_diagnosis

tag: year to_last_follow-up


title: Dot1l-wt3

value: midbrain dopamine neurons


title: SE1_NS_2

city: Isehara-shi

first: Atsushi

last: Fukuda

institute: Tokai University

data_processing:
RNA sample prepared stranded library with polyA selection for DNBSEQ.
Sequencing were performed on the DNBSEQ platform, in a 2x150bp, paired-end (PE) configuration, per lane, ~350M pair-end read/lane, per lane.
Assembly: hg38

source_name: human embryonic stem cells

growth_protocol: The hPSCs were cultured in StemFlex (Thermo Fisher Scientific) on a plate coated with Matrigel (Corning  ). For passaging hPSCs, 1mM EDTA and 10 mM Y-27632 (StemCell Technologies) were added to the culture  medium and maintained 24 h.

extract_protocol:
Total RNA is extracted using Rneasy plus micro kit (Qiagen) with manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols by Genewiz.

treatment_protocol: Gene manupulated cell lines were generated by CRISPR-Cas9 system.

value: female

value: human embryonic stem cells

value: NS coated


title: SE1_NS_1


title: 8936: wt CM D150 3

value: wt


title: exp1_noDOX_2iL_2 (RNAseq)


title: 8935: wt CM D150 2


title: 8934: wt CM D150 1


title: SE1_1

value: WT


title: TI-572-Relapse-AS2818

description: Liquidhope sample2

value: High-risk neuroblastoma

tag: age at_diagnosis_(months)

tag: relapse

value: Yes

tag: efs (months)

tag: exitus

value: Normal

tag: mycn amplification

value: not evaluable


title: SE1_2


title: Esrrb_96h_WCE_205 (ChIPseq)

data_processing:
Basecalls performed using bcl2fastq v2.20.0.422
Paired sequencing reads were aligned on mouse mm10 reference genome using BWA
Reads were filtered with samtools to remove unmapped read pairs, not primary alignment, reads failing platform quality, with mapping quality score below 30 and duplicate reads were then removed using picard MarkDuplicates.
Each sample was equally split in two pseudoreplicates and peaks were called with MACS2 with p < 0.1 on both samples and pseudoreplicates and filtered after Irreproducible Discovery Rate analysis with a threshold of 0.05
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak files
Supplementary_files_format_and_content: Normalized fold enrichment signal tracks were generated by using MACS2 callpeak with the -SPMR flag and then passing the bedgraph outputs into the bdgcmp function.

growth_protocol: E14 mouse Embryonic Stem cells were routinely cultured on 0.2% gelatin coated multiwell plates in N2B27 medium (DMEM-F12 Neurobasal at 1:1 ratio (Life Technologies), 1X N2 Supplement (Life Technologies), 1X B27 Supplement (Life Technologies), 2mM L-Glutamine (Life Technologies), 0.1mM 2-mercaptoethanol) with the addition of 2iL (3uM CHIR99021 (Axon), 1uM PD0325901 (Axon), 1uM LIF (Qkine)).

extract_protocol:
1x10^7 cells were fixed with 1% formaldehyde, chromatin was sonicated and ESRRB-DNA complexes were isolated with antibody
Libraries were prepared from 10 ng of DNA using the NEBNext® Ultra™ II DNA Library Prep Kit following the manufacturer protocol

treatment_protocol: Cells were plated at single cell density on 0.2% Gelatin coated plates in N2B27 medium with 2iL. The next day 2iL was removed and replaced with N2B27 medium. Cells were collected after 48 or 96 hours of 2iL withdrawal.

value: E14 mouse Embryonic Stem cells

tag: chip antibody

value: 2iL withdrawal for 96 hours


title: Esrrb_48h_WCE_204 (ChIPseq)

value: 2iL withdrawal for 48 hours


title: 8938: D8 ttntv CM D150 2

value: TTNtv/+

value: hiPSC cardiomyocyte


title: Dot1l-wt2

tag: strain

tag: genotype/variation


title: Dot1l-Het3


title: ADSC_NS_2

tag: cell type


title: 8931: D8 ttntv CM D90 1

tag: genotype


title: GM_84h_2i_1 (RNAseq)

growth_protocol: E14 mouse Embryonic Stem cells were routinely cultured on 0.2% gelatin coated multiwell plates in N2B27 medium (DMEM-F12 Neurobasal at 1:1 ratio (Life Technologies), 1X N2 Supplement (Life Technologies), 1X B27 Supplement (Life Technologies), 2mM L-Glutamine (Life Technologies), 0.1mM 2-mercaptoethanol with the addition of 2i or 2iL (3uM CHIR99021 (Axon), 1uM PD0325901 (Axon), 1uM LIF (Qkine)).

treatment_protocol: Cells were plated at single cell density on 0.2% Gelatin coated plates in N2B27 medium with 2i or 2iL. The next day 2i or 2iL were removed and replaced with N2B27 medium. Cells were collected after 12 24 36 48 60 72 84 or 96 hours of 2i or 2iL withdrawal.

tag: cell line

value: 2i withdrawal for 84 hours


title: Esrrb_48h_IP_201 (ChIPseq)

value: Mouse monoclonal anti-Esrrb, Perseus Proteomics Cat# PP-H6705-00; RRID:AB_2100412

tag: treatment


title: Esrrb_2iL_WCE_203 (ChIPseq)

value: untreated (2iL)


title: Dot1l-wt1

tag: tissue

value: midbrain dopamine neurons


title: GM_84h_2i_2 (RNAseq)


title: Dot1l-Het1


title: 8929: wt CM D90 2

tag: timepoint


title: GM_72h_2i_1 (RNAseq)

value: 2i withdrawal for 72 hours


title: 8930: wt CM D90 3


title: Esrrb_96h_IP_202 (ChIPseq)


title: GM_72h_2i_2 (RNAseq)


title: 8932: D8 ttntv CM D90 2


title: exp1_noDOX_2iL_1 (RNAseq)

value: transfected with DOX-inducible Esrrb

value: untreated


title: ADSC_NS_1

tag: gender

value: female

value: human embryonic stem cells

value: NS coated


title: Esrrb_2iL_IP_200 (ChIPseq)


title: mES_96h_A (ATACseq)

description:
ATAC_96h.pooled.fc.signal.bw
ATAC_96h.sort.optimal_peak.narrowPeak

data_processing:
Basecalls performed using bcl2fastq v2.20.0.422
Paired sequencing reads were aligned on mouse mm10 reference genome using BWA
Reads were filtered with samtools to remove unmapped read pairs, not primary alignment, reads failing platform quality, with mapping quality score below 30 and duplicate reads were then removed using picard MarkDuplicates
Peaks were called using the ENCODE ATAC-seq pipeline using an IDR threshold of 0.05
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak files contaning peaks of pooled replicates were generated with the ENCODE ATAC-seq pipeline
Supplementary_files_format_and_content: Normalized fold enrichment signal tracks of pooled replicates were generated with the ENCODE ATAC-seq pipeline

extract_protocol:
Nuclei from 100,000 live cells for each sample were extracted according to Coerces et al. protocol.
Ten PCR cycles were performed for each library using a SimplyAmp (Applied Biosystems, #A24811) thermal cycler. Finally, the libraries were run on a 2% agarose gel using the E-gel electrophoresis system (Thermofisher, #G6400EU) for size selection. Fragments ranging from 200 bp to 700 bp were then purified using the Zymoclean Gel DNA Recovery Kit (Zymo Research, #D4007).


title: ADSC_2

value: WT


title: NT2 cells, piR-36249 scramble, control, rep3

city: Hefei

first: xiaoyuan

last: song

address: Huangshan Road

institute: University of Science & Technology of China

data_processing:
The RNA-Seq reads were initially subject to adapter removal and filtered using Trimmomatic  (version 0.39)
Clean reads were mapped using HISAT2 (version 2.1.0) to the GRCh38 by default parameters
The mapped reads were then counted using featureCounts (version 2.0.1)
DEGs were determined using R package DESeq2 (version 1.26.0) with a P-value < 0.05 and an absolute value of log2FC > 1
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: tab-delimited text files include DEGs

source_name: NTera-2 (NT2)

extract_protocol:
Total RNA was extracted from cells using TRIzol™ Reagent following the manufacturer’s instructions.
RNA library construction and sequencing were performed by Berry Genomics (Beijing) following manufacturer's protocols.

value: NTera-2 (NT2)

value: Embryonal carcinoma

value: control

value: overexpress piR-36249 scramble


title: GM_48h_2i_2 (RNAseq)

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1
Genome_build: mm10
Supplementary_files_format_and_content: normalized counts matrix
Supplementary_files_format_and_content: counts

value: E14 mouse Embryonic Stem cells

value: 2i withdrawal for 48 hours


title: mES_48h_B (ATACseq)

description:
ATAC_48h.pooled.fc.signal.bw
ATAC_48h.sort.optimal_peak.narrowPeak

value: 2iL withdrawal for 48 hours


title: mES_96h_B (ATACseq)

value: 2iL withdrawal for 96 hours


title: NT2 cells, piR-36249 scramble, control, rep1


title: mES_48h_A (ATACseq)


title: GM_48h_2i_1 (RNAseq)


title: 8928: wt CM D90 1

value: wt

value: hiPSC cardiomyocyte


title: 8927: D8 ttntv CM D30 3

value: TTNtv/+


title: GM_60h_2i_2 (RNAseq)

value: 2i withdrawal for 60 hours


title: mES_2iL_B (ATACseq)

description:
ATAC_2iL.pooled.fc.signal.bw
ATAC_2iL.sort.optimal_peak.narrowPeak

value: untreated (2iL)


title: GM_60h_2i_1 (RNAseq)


title: 8926: D8 ttntv CM D30 2


title: 8933: D8 ttntv CM D90 3


title: GM_36h_2i_1 (RNAseq)

value: 2i withdrawal for 36 hours


title: NT2 cells, piR-36249 scramble, control, rep2


title: 8924: wt CM D30 3


title: 8923: wt CM D30 2


title: NT2 cells, piR-36249 mimics, rep1

value: piR-36249 knockdown

value: overexpress piR-36249 mimics


title: NT2 cells, piR-36249 mimics, rep2


title: NT2 cells, piR-36249 mimics, rep3


title: ADSC_1

value: female

value: human embryonic stem cells

value: WT


title: 8922: wt CM D30 1


title: GM_24h_2i_2 (RNAseq)

value: 2i withdrawal for 24 hours


title: MDA-MB-231 cells pre-treated with hAd-CM mixed with DMEM (1:1) for 3 days_rep 2

city: Taipei

first: Yong-Han

last: Su

address: No.1, Chang-Te St., Taipei, Taiwan

country: Taiwan

institute: National Taiwan University

data_processing:
The obtained raw FASTQ files were trimmed by Trimmomatic software (v0.38); parameters: LEADING:3, TRAILING:3, SLIDINGWINDOW:4:20, MINLEN:36.
Trimmed reads were aligned by HISAT2 software (v2.1.0); reference genome: GRCh38, Homo sapiens. Reads counts of aligned reads to each genes were assessed by FeatureCounts software. Version: v2.0.0.
Gene expression normalization was assessed by 2 approaches:   - edgeR (v3.28.1): Mean of M-values (TMM) normalization without biological duplicate  - DESeq2 (v1.26.0): Relative Log Expression (RLE) normalization with biological duplicate
Differentially expressed genes analysis was performed in R followed by 2 strategies:   - DEGseq (v1.40.0) (without biological replicate); statistic method: Poisson distribution  - DESeq2 (with biological replicate); statistic method:  negative binomial distribution  p-values were adjusted using the Benjamini and Hochberg’s approach.
Assembly: GRCh38
Supplementary files format and content: Reads counts and statistic results of DEGs between each two groups were included in a tab-delimited text file

source_name: breast cancer

extract_protocol:
Cells were lysed by TRIzol reagent, and total RNA was extracted according to the manufacturer's instructions. 1 µg of total RNA per sample was used to generate a sequencing library using KAPA mRNA HyperPrep Kit. mRNA was purified from the total RNA using magnetic oligo-dT beads and fragmented under high-temperature incubation. Double-stranded cDNA was then synthesized with the additional dAMPs on 3' ends, and the adapters with 3' dTMPs were applied to generate the final library fragments.
Library fragments ranging from 300-400 bp were purified with the KAPA Pure Beads system, and the library was amplified using KAPA HiFi HotStart ReadyMix. The library PCR products were purified using the KAPA Pure Beads system and the quality was assessed by the Qsep 100 platform.

treatment_protocol: Human whtie adipocytes (hAd) were  cultured in nutrition medium (PromoCell, C-27438). hAd-conditioned medium (hAd-CM) was collected every 3 days. Cellular debris were removed by centrifugation, and supernatant was stored at -80 °C until used. After serial collection from day 15 to day 45 of hAd culture, hAd-CM was pooled. For pre-treatment of cancer cells, hAd-CM was mixed with DMEM at 1:1 ratio to co-culture with cancer cells for 3 days. Nutrition medium mixed with DMEM (1:1) was used as a control.

value: breast cancer

value: TNBC

value: Pre-treated with hAd-CM mixed with DMEM (1:1) for 3 days


title: GM_24h_2i_1 (RNAseq)

value: E14 mouse Embryonic Stem cells


title: 8925: D8 ttntv CM D30 1


title: GM_36h_2i_2 (RNAseq)


title: Mll3KOMll4KI27_Neural_D16_RNA

city: Bethesda

first: Kai

last: Ge

state: MD

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

data_processing:
Basecalls performed using Bcl2fastq.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2.
Peaks were called using SICER with following configuration - For ChIP-Seq of histone modifications: Windows (200), Gaps (200), FDR (1e-3); for ChIP-Seq of MLL4: Windows (50), Gaps (50), FDR (1e-10)
Single-end reads of RNA-seq are aligned to the mm9 genome assembly using STAR.
SICER v1.1 was used to calculate the reads per kilo base per million (RPKM) on exonic regions as expression measurements for each gene.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using in-house script and the scores represent RPKM; tab-delimited text files include FPKM values for each gene.

source_name: Neurons

growth_protocol: Mouse ES cells were maintained on 0.1% gelatin and cultured in 2i+LIF medium (47.75% Advanced DMEM/F-12, 47.75%  Neurobasal, 0.5% N-2 supplement, 1% B-27 supplement minus Vitamin A, 1% GlutaMax, 1% Penicillin-Streptomycin, 1% EmbryoMax 2-mercaptoethanol supplemented with 1 µM MEK inhibitor PD0325901, 3 µM GSK3 inhibitor CHIR99021 HCl and 1,000 units/mL mouse LIF protein).

extract_protocol:
1 μg total RNA was subjected to mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490).
Isolated mRNAs were reverse-transcribed into double stranded cDNA and subjected to sequencing library construction using the NEBNext Ultra™ II RNA Library Prep Kit for Illumina (NEB, E7770) according to the manufacturer’s instructions.

treatment_protocol:
For embryoid body (EB) differentiation, ESCs were suspended into 2,000 cells / 20 µL drop on the lid of tissue culture dishes. EBs were harvested 2 days later and then were transferred into ultra-low-attached dishes. EBs were cultured in suspension in medium without LIF but supplemented with 2% qualified ESC FBS to the indicated time points. Meidum was changed every other day.
For neural differentiation, aggregates were generated following EB differentiation protocol from day 0 to day 8 except that after day 4, 5 µM retinoic acid was added. At day 8, aggregates were dissociated and neural progentor cells (NPCs) were plated on PDL/laminin-coated dishes in N-2 medium. The N-2 medium was changed after 2 hours and again after 1 day. After 2 days, the medium was replaced by the B-27 medium to induce neurogenesis. Medium was changed every other day.

value: ES-derived neurons

tag: stage of differentiation


title: mES_2iL_A (ATACseq)


title: Mll3KOMll4KI48_Neural_D8_RNA

source_name: Neural progenitor cells (NPCs)

value: ES-derived neural progenitor cells


title: Mll3KOMll4KI48_Neural_D16_RNA


title: M4LV

city: Hei Long Jiang Province

first: ji

middle: xuan

last: rui

address: Harbin

institute: the First Affiliated Hospital of Harbin Medical University

description:
Model
M4LV

data_processing:
hisat2 for sequence alignment
stringtie tools for transcript assembly, transcript abundance estimation, gene structure optimization
samtools tools for related file processing
Assembly: mRatBN7.2
Supplementary files format and content: Comma-separated csv files include count values for each Sample

organism: Rattus norvegicus

source_name: Left ventricle

extract_protocol:
After the total RNA extraction,RNA degradation and contamination was detected by 1% agarose gels; RNA purity and concentration was checked by Nanodrop2000（Thermo Fisher Scientific，MA，USA）；RNA concentration was checked using the Qubit® 3.0 Flurometer（Thermo Fisher Scientific，MA，USA）；RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Left ventricle


title: MDA-MB-231 cells pre-treated with hAd-CM mixed with DMEM (1:1) for 3 days_rep 1


title: Mll3KOMll4KI27_Neural_D8_RNA


title: OT_Capture_K9

city: Oxford

first: James

middle: Oliver Joshua

last: Davies

state: Oxon

address: Weatherall Institute of Molecular Medicine, John Radcliffe Hospital

department: Molecular Haematology Unit

country: United Kingdom

institute: Weatherall Institute of Molecular Medicine, Oxford University

description:
Off-target capture
Targetted oligonucleotide capture at off-target sites

data_processing:
CIRCLE-seq data were analysed using the standard pipeling (https://github.com/tsailabSJ/circleseq)
Targetted capture NGS data were analysed with bowtie2 and samtools mpileup followed by custom scripts
Base editing data were analysed with CRISPRESSO
Assembly: Hg19
Supplementary files format and content: Processed data files are included in the manuscript

source_name: Blood cells

growth_protocol: CD34+ cells were resuspended in Phase I medium for a three-phase differentiation adapted from that used for the BEL-A cell line (Trakarnsanga, Nat Comms 2017). Briefly, for differentiation 3x105 cells were resuspended on day 0 in Phase I media at 2x105 cells ml-1. Cell counts were performed on days 3 and 5 with additional Phase I media added to return the concentration to 105 cells ml-1. On day 7, cells were counted and pelleted (300 rcf, 5 min, RT) and resuspended in Phase II media at 2x105 cells ml-1. Cells were counted on day 9 and diluted to 2x105 cells ml-1 Phase II media. HUDEP-2 cells were cultured in expansion phase as previously described Canver, M. C. et al.,2015.

extract_protocol:
DNA was extracted using the PureLink Genomic DNA Mini Kit (Thermofisher) following the manufacturer's protocol with no modifications
For sequencing of base edited sites, modified 2-PCR version of the NEBnext Ultra (NEB) library preparation protocol was followed. In the first PCR primer pairs with NEB adaptor sequences 5’ to the HBB exon 1-specific primer sequence were used for amplification using the Herculase II PCR kit (Agilent) in a 50μl reaction, ensuring the products had the adaptor sequences added by the end of the PCR. 5μl of this was used directly without clean-up for the indexing PCR. This added either single or dual end indices taken from a NEBNext Multiplex Oligos for Illumina kit (NEB).

value: Blood cells

value: Differentiated erythroid cells

value: HbE/beta thalassaemia

value: Control


title: Mll3KOMll4flox2_Neural_D8_RNA


title: Mll3KOMll4flox1_Neural_D16_RNA


title: M5LV

description:
Model
M5LV


title: GM_12h_2i_2 (RNAseq)

extract_protocol:
Cells were harvested at the appropriate time point and RNA was purified by using "Total RNA extraction kit, Norgen".
NEGEDIA Digital mRNAseq - research grade.
3' DGE RNA-seq

value: 2i withdrawal for 12 hours


title: GM_96h_2iL_2 (RNAseq)

value: 2iL withdrawal for 96 hours


title: MDA-MB-231 cells pre-treated with nutrition medium mixed with DMEM (1:1) for 3 days_rep 2

value: Pre-treated with nutrition medium mixed with DMEM (1:1) for 3 days


title: M3LV

description:
Model
M3LV


title: Mll3KOMll4flox1_Neural_D8_RNA


title: M2LV

description:
Model
M2LV


title: GM_2i_1 (RNAseq)

value: untreated (2i)


title: OT_Capture_K8

value: HbE gRNA NGABE8e


title: OT_Capture_K7


title: GM_2i_2 (RNAseq)


title: M1LV

description:
Model
M1LV


title: RS_03

city: Sunway

first: Nurul

middle: Arneida

last: Husin

state: Selangor

address: Jalan Lagoon Selatan

country: Malaysia

institute: Monash University

description:
Durio zibethinus Murr.
ripeningstage03_1

data_processing:
The sequencing was run by using the Illumina Hiseq 150 PE Run. The expected data output was 16.7 million reads or equivalent to 5 GB per sample. For the total of 9 samples, the amount of the total data was 150.3 M or 45 GB. The total output of data on the sequencer is 58.0 G, and the filtered data (clean data) is 50.0 G. FastQC was run to check the quality of the raw data and the quality of the trimmed data. Comparison was made before and after (twice for each sample) to ensure only the cleaned reads were used for downstream analysis.
Trimmomatic is applied to performs a  trimming the Illumina FastQC of paired end  data.  It is used to remove the adapters that are added during the sequencing process. Perform alignment of  RNA-Seq reads to D. zibethinus reference genome sequence (accession number: GCF_00230385.1) using the ultra-high-throughput short read aligner Bowtie (2), and then analyzes the mapping results to identify splice junctions between exons.
Parameter TopHat: Type of data: Paired-end data. Input: RNA-Seq FASTQ file, forward and reverse reads, Mean inner distance between mate pairs: 300, STD. DEV for distance between mate pairs: 20, Report discordant pair alignments: Yes, use built-in reference genome from history,
TopHat setting to use: by default value (20 for maximum number of alignments to be allowed, 2 for final read mismatches and yes to output of unmapped reads in BAM format).
Output: junctions (BED track of junction), insertions, deletions, accepted_hits (BAM format of alignment files) and align summary.
Genome_build: NCBI Durio zibethinus Annotation Release 100. Accession number: GCF_00230385.1.
Supplementary_files_format_and_content: Tab-delimited text files include gene abundance analysis for all samples.

organism: Durio zibethinus

source_name: Durian Var. D24 fruit

extract_protocol:
RNA extraction kit namely GeneAll RibospinTM Seed/Fruit RNA mini kit was used to isolate the RNA. RNA samples were extracted according to the manufacturer’s protocols with the minor modifications to increase the yileds and purity. The assesment of RNA quality was carried out using implen nanodrop spectrophotometer, qubit fluorometer, 1% gel agarose electrophoresis, agilent bioanalyzer and agilent tapestation.
Poly-A mRNAs were purified from 1 ug of total RNA using the NEB Next Poly(A) mRNA magnetic isolation module. The first and second strand of cDNA synthesis was performed with purified mRNA using the NEB Next Ultra RNA Library Prep Kit (Ilumina). The index primers 1-9 were used for each of the samples to ensure every samples were having different barcode for pool method of sequencing. To obtain the final library, the cDNA fragments were amplified by PCR as per outlined in the NEB protocol. The purification of PCR reaction were carried out using AmPure XP beads. Nine pre-prepared cDNA libraries were send to NGS service provider (Novogene). The libraries were sequenced with HiSeq Ilumina Platform using 2x 150 bp paired end protocol.

tag: age

value: 127 days

tag: cultivar


title: M5brain

description:
Model
M5brain

source_name: brain

value: brain


title: GM_96h_2iL_1 (RNAseq)

source_name: Mouse Embryonic Stem cells blastocyst derived


title: M4brain

description:
Model
M4brain


title: RS_02

description:
Durio zibethinus Murr.
ripeningstage02_1


title: M1brain

description:
Model
M1brain


title: MDA-MB-231 cells pre-treated with nutrition medium mixed with DMEM (1:1) for 3 days_rep 1

value: breast cancer

value: TNBC


title: OT_Capture_K5

value: HbE gRNA V106W


title: RS_01

description:
Durio zibethinus Murr.
ripeningstage01_1


title: OT_Capture_K6


title: GM_84h_2iL_2 (RNAseq)

value: E14 mouse Embryonic Stem cells

value: 2iL withdrawal for 84 hours


title: GM_84h_2iL_1 (RNAseq)


title: M3brain

description:
Model
M3brain


title: OT_Capture_K2

value: HbE gRNA ABE813


title: P2_CIRCLE-seq_control

value: Blood cells

value: Peripheral blood mononuclear cells


title: C5LV

description:
Control
C5LV

value: Left ventricle


title: C4LV

description:
Control
C4LV


title: MS_02

description:
Durio zibethinus Murr.
maturestage02_1

value: 120 days


title: OT_Capture_K4

value: Differentiated erythroid cells

value: HbE/beta thalassaemia


title: MS_03

description:
Durio zibethinus Murr.
maturestage03_1


title: Mll3KOMll4flox2_Neural_D16_RNA

value: ES-derived neurons


title: M2brain

description:
Model
M2brain


title: GM_12h_2i_1 (RNAseq)

value: 2i withdrawal for 12 hours


title: GM_72h_2iL_2 (RNAseq)

value: 2iL withdrawal for 72 hours


title: OT_Capture_K3


title: C3LV

description:
Control
C3LV


title: P2_CIRCLE-seq

value: HbE gRNA


title: MS_01

description:
Durio zibethinus Murr.
maturestage01_1


title: GM_48h_2iL_2 (RNAseq)

value: 2iL withdrawal for 48 hours


title: YS_03

description:
Durio zibethinus Murr.
youngstage03_1

value: 90 days


title: GM_60h_2iL_2 (RNAseq)

value: 2iL withdrawal for 60 hours


title: GM_72h_2iL_1 (RNAseq)


title: YS_01

description:
Durio zibethinus Murr.
youngstage01_1


title: HUDEP_CIRCLE-seq

description: HUDEP CIRCLE-seq

value: Human erythroid cell line

value: HbE engineered


title: GM_36h_2iL_2 (RNAseq)

value: E14 mouse Embryonic Stem cells

value: 2iL withdrawal for 36 hours


title: TU3401, rpia-1 embryonic KD, Day 0, rep 2

city: HsinChu

first: Wen-Chi

last: Shen

state: East district

address: No. 101, Section 2, Kuang-Fu Road

department: Biology

institute: National Tsing Hua University, Taiwan

data_processing:
Signalling processin and base-calling is conducted by NovaSeq 6000 software (Illumina)
Data quality assessment is assessed by FastQC (V0.11.9) and MultiQC (V1.12).
Sequence triming is and filtering is conducted by Trimmomatic (V0.36).
Sequence alignment to nematode reference genome (Ce11) is conducted by HISAT2 (v2.2.1) in paired.
Read count extraction and normalization were performed using StrigTie (V.2.2.1), and reads summarization is counducted by FeatureCounts (V1.6.2)
Assembly: Ce11
Supplementary files format and content: tab-delimited text files include TPM/FPKM for each Sample

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: All C. elegans strains were cultivated under standard conditions, that is, the worms were grown at 20 °C on solid nematode growth medium  (NGM) agar seeded with Escherichia coli (OP50).

extract_protocol:
Samples were collected independently in triplicates, and each sample contained at least 500 worms, which were transferred to new plates every day until day-5-adult stage. RNA was extracted using RNeasy Kit (Qiagen, #74004).
RNA libraries for RNA-seq were prepared for sequencing using Illumina Stranded mRNA Prep protocols.

treatment_protocol: Worms were exposed to dsRNA producing E. coli HT115 (DE3) strain, which can be induced by isopropyl β-d-1-thiogalactopyranoside (IPTG), starting at the embryonic stage (whole life treatment) or post-developmental stage (adult-only treatment) on solid RNAi plates. The RNAi plates contained 100 μg/ml ampicillin, 10 μg/ml tetracycline, and 1 mM IPTG.

value: whole worm

value: uIs69 [pCFJ90 (myo-2p::mCherry) + unc-119p::sid-1]

value: rpia-1 knockdown

tag: time

value: Day 0


title: TU3401, rpia-1 embryonic KD, Day 0, rep 1


title: C1LV

description:
Control
C1LV

value: Left ventricle


title: TET2 siRNA3

city: Shanghai

first: Yefei

last: Shi

address: 301 Middle Yanchang Road

institute: Shanghai Tenth People’s Hospital

data_processing:
The paired-end RNA-sequencing data were generated from Illumina NovaSeq 6000 platform
The reads were mapped to GRCh37 by STAR aligner (v2.7.5b)
The gene counts for fragments mapped into exonic regions were called for GRCh37 ensembl genes by featureCounts in subread package (v2.0.0)

source_name: Human Umbilical Vein Endothelial Cells

growth_protocol: HUVECs were cultured in ECM (Cat# 1001, Sciencell) with 5% FBS, 1% ECGS, 1% P/S

extract_protocol:
Total RNA was isolated using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HUVECs were exposed to an atmosphere of 1% oxygen, 5% CO2 and 94% N2 for 48 h

value: Human Umbilical Vein Endothelial Cells

value: TET2 knockdown

value: hypoxia


title: TU3401, EV, Day 0, rep 3

value: control


title: YS_02

description:
Durio zibethinus Murr.
youngstage02_1


title: P1_CIRCLE-seq

value: Blood cells

value: Peripheral blood mononuclear cells

value: HbE/beta thalassaemia

value: HbE gRNA


title: GM_24h_2iL_2 (RNAseq)

first: Margherita

last: Mutarelli

value: 2iL withdrawal for 24 hours


title: TU3401, rpia-1 embryonic KD, Day 0, rep 3


title: P1_CIRCLE-seq_control

value: Control


title: C2LV

description:
Control
C2LV


title: GM_24h_2iL_1 (RNAseq)

value: E14 mouse Embryonic Stem cells


title: GM_2iL_1 (RNAseq)

value: untreated (2iL)


title: TET2 siRNA2


title: TU3401, EV, Day 0, rep 2

value: whole worm


title: GM_60h_2iL_1 (RNAseq)

value: 2iL withdrawal for 60 hours


title: GM_48h_2iL_1 (RNAseq)

value: 2iL withdrawal for 48 hours


title: C3brain

description:
Control
C3brain

value: brain


title: C1brain

description:
Control
C1brain


title: C4brain

description:
Control
C4brain


title: C5brain

description:
Control
C5brain


title: TU3401, EV, Day 0, rep 1

value: uIs69 [pCFJ90 (myo-2p::mCherry) + unc-119p::sid-1]

value: Day 0


title: GM_36h_2iL_1 (RNAseq)

value: 2iL withdrawal for 36 hours


title: leaf tissue, pGLCT2 knock out, permanent light, biol rep 4

city: Kaiserslautern

first: Benjamin

last: Pommerrenig

address: Paul-Ehrlich-Str. 22

country: Germany

institute: University of Kaiserslautern

data_processing:
The data processing steps are according to Novogene methods: Quality control: Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Alignment: Algorithm for mapping sequences: HISAT2 is selected to map the filtered sequenced reads to the reference genome. In general, HISAT2 supports genomes of any size, including those larger than 4 billion bases and most of the parameters are set to default. Spliced reads of RNA Seq data can be effictively aligned using HISAT2. HISAT2 v2.0.5 was run using the --dta --phred33 parameters.
Novel gene prediction was performed with StringTie v.1.3.3 and GffCompare v0.10.6 using default parameters
Assembly: ensemblplants_arabidopsis_thaliana_tair10_gca_000001735_1
Supplementary files format and content: tab-delimited xls files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: leaf tissue

extract_protocol:
RNA was extracted from leaves or leaf discs using the NucleoSpin® RNA Plant Kit (Macherey-Nagel) according to the manufacturer's instructions. 50 mg of fresh plant material was used for this purpose. The RNA was eluted from the column with 40 μl of RNase-free ddH2O
Directional library construction was perfomed by Novogene Sequencing Service. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: To apply an artificial continuous light condition, 24 -day-old plants grown under short day were transferred to a specific growth chamber (percival) with a continous light intensity of 100-120 µmol quanta m-2 s-1 for 10-12 days.

value: leaf tissue

tag: ecotype

value: pGLCT2 knock out

value: permament light


title: HUDEP CIRCLE-seq_control

description: HUDEP CIRCLE-seq control

value: Blood cells

value: Human erythroid cell line

value: HbE engineered


title: leaf tissue, pGLCT2 knock out, permanent light, biol rep 1


title: N2, rpia-1 adult only KD, Day 5, rep 1

value: WT

value: rpia-1 knockdown

value: Day 5


title: Young T21-1

city: Montreal

first: Vahab

last: Soleimani

address: 3640 rue University

institute: McGill University

data_processing:
Kallisto was used to map reads to the mouse reference genome (mm10) and to quantifying abundances of transcripts using default settings
Transcript-level abundances were imported into R and collapsed into gene counts using the tximport package
To estimate the effects of the experimental conditions, we used DESeq2 to fit the following model gene-wise model: count~ time + age + time:age, where the variable time denotes the effect of engraftment, the variable age denotes the effect of aging, and the interaction variable time:age represents the reprogramming effect on genes in the aged niche.
For the purposes of ranking and visualization, we use the apeglm shrinkage approach.
Assembly: mm10
Supplementary files format and content: *_abundance.tsv: reports abundances as “estimated counts” (est_counts) and in Transcripts Per Million (TPM).
Project’s Website (reproducible notebooks): https://csglab.github.io/transcriptional_reprogramming_muscle_cells/

source_name: satellite cells

extract_protocol:
1000 GFP positive satellite cells from the donor mice were sorted by Fluorescence-Activated Cell Sorting (FACS) by gating for the GFP+/DAPI- cell population.  These cells were sorted directly into the SMART-Seq (Takara) reaction buffer composed of lysis buffer, water and RNAse inhibitors, these cells act as the T0 time point.
Concurrently, 10,000-20,000 GFP positive cells were sorted from the same donor mouse and transplanted into the tibialis anterior of the host mouse.  After 21 days, these cells were then reisolated by FACS directly into the SMART-Seq reaction buffer.
Sequencing ready libraries were generated using SMART-Seq HT kit (Takara, cat. #624456) and illumine adapters were added using Nextera XT (Illumina, cat. #FC-131-1024, FC-131-1001).

tag: age of donor/age of host

value: 6 weeks/ 5 weeks

value: skeletal muscle


title: N2, EV, Day 5, rep 3

value: whole worm

value: control


title: TET2 siRNA1

value: Human Umbilical Vein Endothelial Cells

value: TET2 knockdown

value: hypoxia


title: leaf tissue, pGLCT2 overexpressor, permanent light, biol rep 4

value: pGLCT2 overexpressor


title: C2brain

description:
Control
C2brain

value: brain


title: Young T0-3

value: 5 weeks/ NA


title: Young T0-2


title: Aged T21-2

value: 24 months/ 6 weeks


title: GM_2iL_2 (RNAseq)

city: Pozzuoli

address: Via Campi Flegrei 34

institute: CNR

value: E14 mouse Embryonic Stem cells

value: untreated (2iL)


title: Ctrl siRNA1


title: N2, rpia-1 adult only KD, Day 5, rep 3


title: Ctrl siRNA3


title: Ctrl siRNA2

data_processing:
The paired-end RNA-sequencing data were generated from Illumina NovaSeq 6000 platform
The reads were mapped to GRCh37 by STAR aligner (v2.7.5b)
The gene counts for fragments mapped into exonic regions were called for GRCh37 ensembl genes by featureCounts in subread package (v2.0.0)
RNA counts


title: leaf tissue, pGLCT2 knock out, permanent light, biol rep 3

value: leaf tissue

value: pGLCT2 knock out

value: permament light


title: 293T_t4_control_3

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

data_processing:
FastQC 0.11.8 used for quality control
Fastp 0.19.6 used for adapter trimming and quality-filtering
STAR 2.6.1d used for alignment against the GRCh38 genome assembly and quantified according to the Gencode v26 annotation
Genome_build: GRCh38
Supplementary_files_format_and_content: Text tables with raw gene counts for each sample

source_name: 293T cells

growth_protocol: 293T cell were seeded at a dencity of 8*104 cell/well at 24well plates.

extract_protocol:
At time 0h, 2h, or 4h, post miR-1-3p or control RNA sequence overexpression (OE), total RNA was extracted from cells using TRIzol reagent (Thermo Fisher Scientific, USA), according to the manufacturer’s instructions. Final RNA concentration and purity were measured using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, USA).
TruSeq RNA Sample Preparation v2 Guide, Part # 15026495 Rev. F

treatment_protocol: Twenty-four hours later, at ~60% confluence, the cells were transfected with 15ng of synthetic miR-1-3por control RNA oligo, using Lipofectamine 2000 transfection reagent (Thermo Fisher Scientific, USA) for 0h,2h or 4h according to the manufacturer’s instructions.

value: human embryonic kidney

value: 4h control seq' OE

tag: repeat

value: 3rd biological repeat


title: N2, EV, Day 5, rep 1

value: whole worm

value: WT

value: Day 5


title: Young T0-1

value: 6 weeks/ NA

value: skeletal muscle


title: KSHV_replicate_2

city: Gainesville

first: Bernadett

last: Papp

state: FL

address: 1395 Center Drive D5-18

department: Oral Biology

institute: University of Florida

data_processing:
Sequencing of libraries were done on Illumina HiSeq3000 with base read length of 50. Facilty provided subsequent data extraction, processing such as demultiplexing with Illumina Bcl2fastq2 v 2.17 program.
Derived RNA-seq raw datasets were processed using FLOW software build version 10.0.22.1005 (Partek Inc., St. Louis, MO) using mainly default settings as recommended.
Analysis in FLOW included alignment to the hg38 version human genome build with STAR aligner (STAR-2.5.3a build), followed by Partek E/M Quantification to RefSeq Transcripts 101 - 2002-02-01 human transcript annotation model, generation of normalized gene counts, for gene and transcripts as indicated.
Assembly: hg38 human genome build
Supplementary files format and content: MatrixTable_Transcriptome_gene_counts.txt is a tab limited text files contain output of the Partek E/M Quantification to RefSeq transcript annotation model, indicating gene count tables as indicated for the specific genes, for the triplicate mock or KSHV infected samples, and output includes feature names and chromosomal coordinates.
Supplementary files format and content: MatrixTable_Transcriptome_transcript_counts.txt is a tab limited text files contain output of the Partek E/M Quantification to RefSeq transcript annotation model, indicating gene count tables as indicated for each specific transcript, for the triplicate mock or KSHV infected samples, and output includes feature names and chromosomal coordinates.

source_name: commercially derived cells originating from human gingiva of unknown pooled people

growth_protocol: Human gingival epithelial (HGEP) cells (Zen-Bio) were maintained in CnT Prime epithelial culture medium (Zen-Bio) according to manufacturer’s instructions.  Cells were maintained at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Cells were resuspended in TRIzol (Invitrogen). RNA preparation on RNeasy kit (Qiagen) columns as recommended..
Core facility produced the strand-specific RNA-seq libraries with their  Illumina protocol. RNA-Seq libraries by KAPA Stranded RNA-Seq Kit using standard workflow, includng unique adaptor ligations for multiplexing samples, strand selection, amplification.

treatment_protocol: For infections, KSHV stock was used which was previously produced from iSLKBAC16 KSHV producing cells as standard. For mock and KSHV-infected cells medium was changed at 2hpi and cells were harvested at 8hours post-infection timepoint. Cells were routinely cultured antibiotics free medium as recommended. Penicillin-streptomycin (P/S) was included in medium from 2hours post-treatment (at 2hours post-infection) via medium change on all samples.

value: human gingival epithelial cell

value: epithelial cell

value: unknown

value: KSHVinfected


title: Young T21-3

value: 5 weeks/ 5 weeks


title: leaf tissue, wild-type, permanent light, biol rep 3

value: wild-type


title: 293T_t4_mir1_2

value: 4h miR-1-3p OE

value: 2nd biological repeat


title: Aged T0-1

value: 24 months/ NA


title: leaf tissue, pGLCT2 overexpressor, permanent light, biol rep 2

value: leaf tissue

value: pGLCT2 overexpressor

value: permament light


title: 48hrAPF_Female_rep 2

city: Tallahassee

first: Michelle

middle: N

last: Arbeitman

state: Florida

address: 1115 W. Call Street

department: Department of Biomedical Sciences

institute: Florida State University

data_processing:
Raw reads were processed using the CellRanger software pipeline (v.3.0.2) “cellranger count” command to align reads to the Drosophila melanogaster (BDGP6.92) STAR reference genome, customized to contain the sequence for the mCD8-GFP cDNA and generate a multidimensional feature-barcode matrix for each replicate.
Genome_build: Drosophila melanogaster (BDGP6.92)
Supplementary_files_format_and_content: feature-barcode matrix

organism: Drosophila melanogaster

source_name: Central nervous system

growth_protocol: Pupae were sex-sorted at white pre-pupal stage and aged to 48hr after Puparium formation (APF) on Bromophenol blue agar plates at 25˚C on a 12 hour light and 12 hour dark cycle.

extract_protocol:
The tissue was dissected and dissociated as previously described in Brovero et al. 2020. GFP positive cells (fru P1-expressing cells) were separated using fluorescent activated cell sorting (FACS) with a FACSAria SORP with BD FACSDiva software.
Libraries were prepared following the 10x Chromium Single Cell 3’ Reagent Kits v3 User Guide using 12 PCR cycles for cDNA amplification and 16 PCR cycles for sample indexing.

treatment_protocol: Twenty 48hr after pupal formation (APF, +/- 1hr) sex-sorted flies were collected for fru P1 single cell experiments for each replicate Flies were collected and sex sorted at the white prepupal stage for appropriate aging to 48hr APF.

tag: Sex

value: Female


title: N2, rpia-1 adult only KD, Day 5, rep 2

value: whole worm

value: WT

value: rpia-1 knockdown


title: leaf tissue, wild-type, permanent light, biol rep 2


title: Aged T21-1

value: 24 months/ 6 weeks

value: skeletal muscle


title: 293T_t2_mir1_2

value: human embryonic kidney

value: 2h miR-1-3p OE


title: leaf tissue, pGLCT2 knock out, permanent light, biol rep 2

value: pGLCT2 knock out


title: Mock_replicate_2

value: commercially derived cells originating from human gingiva of unknown pooled people

value: human gingival epithelial cell

value: epithelial cell

value: unknown

value: Mock


title: leaf tissue, wild-type, permanent light, biol rep 1

value: leaf tissue

value: wild-type


title: leaf tissue, pGLCT2 overexpressor, permanent light, biol rep 1

value: pGLCT2 overexpressor

value: permament light


title: Mock_replicate_1


title: 48hrAPF_Male_rep 1

value: Male


title: 293T_t2_mir1_3

value: 3rd biological repeat


title: leaf tissue, wild-type, permanent light, biol rep 4


title: 293T_t2_control_2

value: 2h control seq' OE

value: 2nd biological repeat


title: 293T_t2_control_3


title: 293T_t4_mir1_3

value: 4h miR-1-3p OE


title: 293T_t0_3

value: human embryonic kidney

value: untreated


title: N2, EV, Day 5, rep 2

value: whole worm

value: WT

value: control

value: Day 5


title: Aged T0-2

value: 24 months/ NA

value: skeletal muscle


title: 293T_t0_2


title: KSHV_replicate_3

value: commercially derived cells originating from human gingiva of unknown pooled people

value: human gingival epithelial cell

value: epithelial cell

value: unknown

value: KSHVinfected


title: leaf tissue, pGLCT2 overexpressor, permanent light, biol rep 3

value: leaf tissue

value: pGLCT2 overexpressor

value: permament light


title: 293T_t4_control_1

value: 4h control seq' OE

value: 1st biological repeat


title: KSHV_replicate_1


title: 293T_t2_mir1_1

value: human embryonic kidney

value: 2h miR-1-3p OE


title: 293T_t4_control_2

value: 2nd biological repeat


title: 48hrAPF_Male_rep 2

value: Male


title: WT_20D_bio rep3

city: beijing

first: xiaojiao

last: Hu

address: No.12 Zhongguancun South Main Street, Haidian District

institute: Institute of crop science, Chinese academy of agricultural science

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and   the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the maize reference genome RefGen_V4 (ftp://ftp.ensemblgenomes.org/pub/plants/release-32/gff3/zea_mays/) using HISAT2
The gene expression levels were estimated using the fragments per kilobase of the transcript per million fragments (FPKM) mapped
Supplementary files format and content: FPKM value of expressed genes for all samples

organism: Zea mays

source_name: maize kernels

extract_protocol:
The total ribonucleic acid (RNA) was isolated from the kernels of WT and smk7a collected at 12 and 20 DAP using a RNA Easy Fast Extraction Kit (DP452, Tiangen, Beijing, China)
RNA libraries for RNA-seq were prepared using a TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions

value: maize kernels

value: WT

tag: development stages

value: kernels 20 days after polination

value: 20 DAP


title: Radiation 3

city: Belfast

first: Thomas

last: Cahill

address: 19 Chlorine Gardens

institute: Queens university Belfast

data_processing:
Sequence quality was assessed with FastQC to identify over-represented sequences and low quality reads
Low quality reads and over-represented sequences were removed with Cutadapt
The STAR aligner was utilised to align the RNA-Seq reads to the zebrafish genome (GRCz11)
HTSeq was used to determine the number of reads per transcript
DESeq2 was used for determination of differentially expressed genes
Assembly: zebrafish genome (GRCz11)
Supplementary files format and content: TXT file

organism: Danio rerio

source_name: Liver

extract_protocol:
Total mRNA was extracted from liver tissue of the zebrafish using Qiagen’s miRNeasy Mini kit (Qiagen, Hilden, Germany).
To prepare mRNA-Seq libraries the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA, USA) was utilized; 100ng of total input Liver RNA was used in accordance with the manufacturer’s protocol.
High through-put RNA sequencing (RNAseq) was performed at the Queens University Belfast, Genomics Core Technology Unit on an Illumina Next SEQ 500 instruments with the mRNA library sequenced to a minimum depth of 50 million reads.

treatment_protocol: A melatonin group (28.5- melatonin) received melatonin daily for 10 days at a concentration of 24 µM for 10 days to reduce locomotion and arousal. A reduced temperature group (18.5-Ctrl) received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group (18.5-mel) was established with a 10°C reduction in ambient temperature and the addition of 24 µM melatonin. A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.

tag: radiation (cgy)

tag: temperature (c)

tag: melatonin (um)


title: WT_12D_bio rep3

tag: genotype

value: kernels 12 days after polination

value: 12 DAP


title: Mock_replicate_3

value: commercially derived cells originating from human gingiva of unknown pooled people

tag: cell line

value: human gingival epithelial cell

tag: cell type

value: epithelial cell

value: unknown

tag: treatment

value: Mock


title: D8_CK138: D8 TTNtv/+ AMG2591713 treated CMW

city: SOUTH SAN FRANCISCO

first: Tracy

last: Yamawaki

address: 1120 VETERANS BLVD.

institute: AMGEN, INC.

data_processing:
reads were aligned and count tables generated using cellranger v 4.0.0
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: barcode tsv files include cellbarcodes, features tsv files include gene identifiers, matrix files are the cell by gene count table encoded as a sparse matrix in the Market Exchange Format (MEX)

source_name: cardiac microwire culture

growth_protocol: 300  μl  of  CMW  maintenance mediumcontaining DMEM/F12, 2% fetal bovine serum, 10 μg/ml insulin and 1xantibiotic/antimycotic (all from ThermoFisher)was gently added to each well for continuous culturing. Medium is changed every 2-3 days by very slowly removing halfof medium from the side of the well at half-way heightand through the drop-wise addition of halfof fresh CMW maintenance medium.

extract_protocol:
cardiac microwires were dissociated into a single cell suspension and encapsulated with the 10x Chromium
Samples were processed using the 10x Genomics 3'v3 kit

treatment_protocol: 14 days

tag: tissue

value: cardiac microwire culture

value: TTNtv/+


title: Radiation 2


title: 293T_t0_1

value: human embryonic kidney

value: untreated

value: 1st biological repeat


title: glkd-4

city: Seoul

first: Zeeshan

last: Nasim

address: Anam-ro 145, Seongbuk-Gu

department: School of Life Sciences and Biotechnology

country: South Korea

institute: Korea University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and differentially expressed genes were identified using TopHat2-Cufflinks pipeline
Genome_build: TAIR 10
Supplementary_files_format_and_content: TPM values for each sample, in excel file

source_name: seedlings

growth_protocol: Plant were grown  at 16°C under long day conditions on 1/2 strength MS

extract_protocol:
Total RNA was extracted using trizol reagent
Library were prepared by BGI for DNA nanoball (DNB) sequencing

treatment_protocol: Growth temperature of 16°C

tag: developmenta stage

value: glk1 glk2 double mutants

tag: protocol

value: 16°C grown

tag: tag


title: WT-2

value: WT


title: glkd-1


title: Torpor+radiation 4


title: glkd-3


title: WT_20D_bio rep2

value: maize kernels

value: kernels 20 days after polination

tag: time


title: WT_12D_bio rep2

value: kernels 12 days after polination


title: smk7a_20D_bio rep2

value: 20 DAP


title: 293T_t2_control_1

value: 2h control seq' OE


title: 293T_t4_mir1_1

value: 4h miR-1-3p OE


title: Torpor 2


title: smk7a_20D_bio rep1


title: Torpor+radiation 3


title: Torpor 1


title: LT_2: wt CMW

value: wt


title: WT_20D_bio rep1


title: glkd-2

tag: ecotype


title: D10_CK138: D10 TTNtv/+ AMG2591713 treated CMW