title: Hypome2 WT replicate 6

city: Geneva

first: Athanasia

last: Tzika

address: Quai Ernest-Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

description: Library name: EM_U6_1100_2024_6

data_processing:
Fastq files were mapped to the reference genome using STAR v2.7.10b and raw gene counts were extracted using featureCounts from Subread v2.0.6
Assembly: GCA_050574515.1
Supplementary files format and content: Table of raw counts (tsv format)

organism: Eublepharis macularius

source_name: Dorsal skin

extract_protocol:
RNA was extracted from dorsal skin of embryos at embryonic day 40 using the Direct-zol RNA MiniPrep kit (Zymo Research, R2050)
Libraries were prepared using the TruSeq Stranded mRNA Library kit

value: Dorsal skin

value: Hypome2 WT


title: c-mycORF_6h, rep2

status: Public on Oct 23 2025

type: SRA

city: Copenhagen N

first: Nils

last: Krietenstein

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

description:
Library name: c-mycORF_6h
Processed file derives from the merged of the three sequencing runs of two biological replicates

library_source: genomic

data_processing:
RCMC paired-end reads were downloaded as .fastq files and processed with Distiller pipeline (https://github.com/mirnylab/distiller-nf). Briefly, read pairs were aligned against the human reference assembly hg38. Aligned reads were parsed, PCR duplicates were removed, and pairs files were generated. Pairs files obtained from the Distiller pipeline were used in further analyses.
Pairs files were shifted by 73 bp relative to the read orientation, and read pairs separated by less than 500 bp were discarded to remove undigested di-nucleosome contaminants. The nucleosomal shift represents the approximate locations of the nucleosome dyad axes.
To retain only those reads that both mates align on the region of interest, the awk bash function was used. A 10-bp bin file of the human reference assembly hg38 was used to convert filtered reads into .cool files using cooler cload pairs of the cooler package (https://github.com/open2c/cooler).
Cool files were then converted into multiresolution cooler files using the cooler zoomify option of the cooler package (https://github.com/open2c/cooler).
RCMC data were visualized with cooltools package (https://github.com/open2c/cooltools) in python.
Assembly: Hg38
Supplementary files format and content: mcool files.  For CTCF and ORF c-Myc samples 500 bp, 1 kb, 2 kb, 5 kb, 10 kb resolutions were generated, for all the other cuts an additional 20 kb resolution was included.

molecule: genomic DNA

organism: Homo sapiens

source_name: HeLa Kyoto

growth_protocol: DMEM, 10% heat-inactivated FBS and penicillin-streptomycin antibiotics. Cells were cultured at 37 C, 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min at RT. The reaction was quenched with 0.25 M of glycine (final concentration) for 5 min at RT. Cells were then washed and crosslinked for the second time with ethylene glycol bis(succinimidyl succinate) EGS at a final concentration of 3 mM, the reaction was quenched with 0.4 M glycine (final concentration) for 5 min RT. Micro-C libraries were built and a tiled array of probes was used to enrich for the region of interest.
Region Capture Micro-C libraries were prepared using NEBNext UltraII DNA Library Prep Kit for Illumina with NEBNext Multiplex Oligos for Illumina from New England Biolabs (NEB). After library amplification, DNA libraries were size selected at 100-1000 bp in length using SPRIselect size selection beads from Beckman Coulter.

treatment_protocol: To generate site-specific DNA double-strand breaks, cells were transfected with sgRNA–Cas9 ribonucleoprotein complexes (RNPs) using Lipofectamine CRISPRMAX Cas9.

tag: cell line

value: HeLa Kyoto

tag: cell type

value: immortal human epithelial cell

tag: genotype

tag: treatment

value: Cas9 cleavage


title: KO 12hr 1

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

country: USA

institute: University of Pittsburgh

description:
Library name: Sample 22
KO 12hr 1

library_source: transcriptomic

data_processing:
Adapter sequences and low quality reads were filtered by Trimmoatic
Surviving reads were aligned to reference genome using STAR aligner
Assembly: mm39
Supplementary files format and content: TAB file for gene count

molecule: polyA RNA

organism: Mus musculus

source_name: liver

extract_protocol:
RNA was isolated from individual WT and EGFR-KO mice liver samples at 0, 1,3, 6, 12, and 24hr (n=3) using the TRIzol method.
Following AVITI library prep and RNA-seq protocols.

tag: tissue

value: liver

value: KO 12hr 1


title: WT 12hr 3

description:
Library name: Sample 21
WT 12hr 3

value: WT 12hr 3


title: pLG001-SP15-1

city: Shinjuku-ku

first: Aa

middle: Haeruman

last: Azam

state: Tokyo

address: Toyama 1-23-1

department: Research Center for Therapeutic Drugs and Vaccines Development

country: Japan

institute: The National Institute of Infectious Diseases

description: Library name: Sample 7

data_processing:
Sequencing quality was assessed using FastQC. Adapter sequences at the 5’ and 3’ ends were trimmed from raw reads using Cutadapt.
The processed reads were aligned, allowing for one mismatch, to mature tRNA sequences. Reads that did not align to mature tRNAs were subsequently aligned to precursor tRNA sequences using Bowtie. Unmapped reads were further aligned to miRNA reference sequences using miRDeep2.
Unmapped reads were further aligned to miRNA reference sequences using miRDeep2. The expression profiles of tRFs, tiRNAs, and miRNAs were determined based on the counts of mapped reads.
Differentially expressed tRFs, tiRNAs, and miRNAs were identified using the R package edgeR.
Assembly: mature and imature tRNA of E. coli DH10B
Supplementary files format and content: Differentially expressed tRFs, tiRNAs, and miRNAs (XLSX format)

molecule: total RNA

organism: Escherichia coli str. K-12 substr. DH10B

source_name: Prokaryotic cell

growth_protocol: Overnight cultures of E. coli (DH10B) cells containing either the plasmid pBAD-PtuA–PtuB or the full set of retron-Eco7 (pLG008) were grown in 10 mL of LB medium until reaching an OD₆₀₀ of 0.3.

extract_protocol:
Total RNA was extracted using miRNA isolation kit (QIAGEN, catalog number 217004), according to the manufacturer’s recommendation. Over 2g total RNA was resolved on Urea-PAGE and recovered within a size window of 60-100 nt for tRNA. Thereafter, purified tRNA was demethylated, alkaline-hydrolyzed by carbonate buffer, dephosphorylated by calf intestinal phosphatase (CIP), and re-phosphorylated by T4 polynucleotide kinase (T4 PNK).
Total RNA sample integrity was initially assessed using agarose electrophoresis, and RNA concentrations were measured using the NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, USA). Total RNA samples underwent pretreatment to remove RNA modifications that could interfere with small RNA sequencing library preparation. Specifically, pretreatment steps included: deacylation of 3’-aminoacyl (charged) RNA to 3’-OH for 3’-adapter ligation, removal of 3’-cP (2’,3’-cyclic phosphate) to generate 3’-OH for 3’-adapter ligation, phosphorylation of 5’-OH (hydroxyl group) to 5’-P for 5’-adapter ligation, and demethylation of m1A and m3C for efficient reverse transcription.  Following pretreatment, the total RNA was utilized for the preparation of tRF and tiRNA sequencing libraries. Library preparation involved a sequential workflow: (1) 3’-adapter ligation, (2) 5’-adapter ligation, (3) cDNA synthesis, (4) PCR amplification, and (5) size selection of PCR products between 134–160 bp, corresponding to 14–40 nt small RNAs. The libraries were analyzed and quantified using the Agilent 2100 Bioanalyzer (Agilent, USA). Equal amounts of each library, based on the quantification results, were pooled for sequencing. Sequencing was performed using an Illumina sequencer. Pooled libraries were denatured with 0.1 M NaOH to produce single-stranded DNA molecules and diluted to a final concentration of 1.8 pM. The libraries were loaded onto the sequencing reagent cartridge, and sequencing runs were conducted following the manufacturer’s protocols.
The NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (New England Biolabs, USA, Catalog number# E7300L) was used for library construction.

treatment_protocol: The bacteria carrying pBAD-PtuA–PtuB were induced with 0.2% arabinose to promote PtuAB expression, whereas those containing pLG008 were infected with phage SP15 and cultured at 37°C with shaking at 200 rpm for either 1 hour or 20 minutes, respectively. Following incubation, the cultures were centrifuged at 6,000 × g for 5 minutes, and the pellets were washed twice with PBS buffer.

value: Prokaryotic cell

tag: strain

tag: condition

value: early stationary (OD600 = 1.0)

value: Infected with phage SP17


title: virus and drug-3

city: Guangzhou

first: liu

last: lifu

state: Guangdong

address: Panyu xinzao NO.1 Road

country: China

institute: Guangzhou Medical University

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Gallus gallus reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 1.5 or fold change <2/3.
Assembly: hg38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: Lung

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: Lung

value: tumor pericytes

value: H1N1 virus infection + FDE intervention


title: pLG008-SP15-2

description: Library name: Sample 6

value: Infected with phage SP16


title: Hypome2 Homozygous replicate 2

description: Library name: EM_U6_1100_2024_5

value: Hypome2 Homozygous


title: KO 3hr 2

description:
Library name: Sample 17
KO 3hr 2

value: KO 3hr 2


title: Hypome2 WT replicate 3

description: Library name: EM_U6_1100_2023_2

value: Dorsal skin


title: pLG008-SP15-1

description: Library name: Sample 5

value: Infected with phage SP15


title: pLG001-SP15-2

description: Library name: Sample 8

value: Infected with phage SP18


title: c-mycORF_24h, rep2

description:
Library name: c-mycORF_24h
Processed file derives from the merged of the three sequencing runs of two biological replicates

value: HeLa Kyoto

value: immortal human epithelial cell


title: WT 3hr 1

description:
Library name: Sample 13
WT 3hr 1

value: liver

value: WT 3hr 1


title: virus and drug-1


title: KO 3hr 1

description:
Library name: Sample 16
KO 3hr 1

value: KO 3hr 1


title: Hypome2 Homozygous replicate 1

description: Library name: EM_U4_1127_2024_10


title: 23AB-Ara1

description: Library name: Sample 3

value: Prokaryotic cell

value: treated with 0.2% arabinoese


title: Hypome2 WT replicate 5

description: Library name: EM_U6_1100_2024_2

value: Hypome2 WT


title: WT 3hr 3

description:
Library name: Sample 15
WT 3hr 3

value: WT 3hr 3


title: virus-2

value: Lung

value: tumor pericytes

value: H1N1 virus infection


title: KO 1hr 1

description:
Library name: Sample 10
KO 1hr 1

value: KO 1hr 1


title: Hypome2 WT replicate 4

description: Library name: EM_U6_1100_2024_1


title: Hypome3 Homozygous replicate 3

description: Library name: Hypome3_Hom3

data_processing:
Fastq files were mapped to the reference genome using STAR v2.7.10b and raw gene counts were extracted using featureCounts from Subread v2.0.6
Assembly: JBLQZT000000000
Supplementary files format and content: Tables of raw counts (tsv format)

value: Homozygous Hypome3


title: WT 3hr 2

description:
Library name: Sample 14
WT 3hr 2

value: WT 3hr 2


title: virus and drug-2

value: H1N1 virus infection + FDE intervention


title: Hypome3 Homozygous replicate 2

description: Library name: Hypome3_Hom2

value: Dorsal skin


title: NPC-NI-Act

city: Cold Spring Harbor

first: Gayan

middle: Indhu

last: Balasooriya

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

data_processing:
We used the MEA pipeline. In silico diploid C57BL/6J / CAST/EiJ genome was reconstructed using the SHAPEIT2 pipeline as the mm10 reference geneome
We then aligned sequencing read files (.fastq) to the constructed in silico genome using Bowtie2 aligner  (version 2.3.4.3)
Peaks were called using contig caller embedded in Seqmonk software package with flowing parameters: readcount=>10, fragment length=500 bp, using input as the control
Assembly: mm10
Supplementary files format and content: .bw

source_name: mNPCs

growth_protocol: mESCs: 2i, mNPCs: 10% FBS, 1X L-Glutamine, 1X Non-Essential AA, 0.15 mM 2-Mercaptoethanol, 100 U/ml Penicilline-Streptomycin, 2.5 ug/ul murine EGF, 2.5 ug/ul murine Fgf2 in Knockout DMEM.

extract_protocol:
Crosslinking was carried out incubating 1% Formaldehyde. After quenching cell lysates, sonication was carried out using a Bioruptor® Pico sonication device (diagenode).
Illumina TruSeq ChIP libraray Preperation kit, 5 ng of ChIP-DNA per libraray, NextSeq500, PE-150, mid output

value: mNPCs

tag: antibody

value: RNA Pol II pSer2

value: C57BL/6J x CAST/EiJ


title: WT_Untreated_8h_rep1_steady_state

city: State College

first: Shardul

last: Kulkarni

address: 463 North Frear Laboratory

institute: Penn State University

data_processing:
For libraries to caluculate changes in steadystate and RNA halflife  (Triptolide libraries), FASTQ files were further processed as per the Bulk RNA-seq Data Standards and Processing Pipeline (https://www.encodeproject.org/), using STAR [(Dobin et al. 2013), version - STAR_2.5.1b_modified] and RSEM (RNA-Seq by Expectation-Maximization) tool. The reads were mapped to hg38 (GRCh38) using Gencode-v29 comprehensive gene set, predicted tRNA genes, and the ERCC spike-in controls. Read-counts for each gene generated by RSEM were used for differential expression analysis using DESeq2 (Love et al., 2014, PMID: 25516281). Genes with a sum of ≥ 8 across both replicates and conditions were used in DESeq2. The expression data were normalized to ERCC spike in controls using estimateSizeFactors function in DESeq2.
TT-seq data was mapped to a human and S pombe concatenated genome reference sequence using STAR aligner. The alignments were filtered using samtools where alignments with a mapping quality < 7 were skipped and only proper pairs were selected. TT-Seq raw read counts were obtained for gene including exon and intron regions using featureCounts, Differential expression analysis was performed with DESeq2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file with raw counts of each sample.

growth_protocol: Cells were maintained in complete media [Dulbecco's Modified Eagle Medium (DMEM) with 10% Fetal Bovine Serum, 1X glutamax and 1X Penicillin and Streptomycin] in 5% CO2 atmosphere at 37 °C in a humidified incubator.

extract_protocol:
To calculate changes in nascent RNA synthesis (TTseq): Parental (untagged), CNOT1AID and CNOT4AID cells were pretreated with 1mM auxin for 2 h, follwed by pulse labelling with 4-thiouridine (4SU) for 15 minutes, followed by total RNA extraction.
Total RNA was extracted from the cells using Trizol (Invitrogen#15596026) and cleaned up using PureLink RNA Mini kit (Invitrogen#12183018A)
For libraries to caluculate changes in steadystate and RNA halflife (Triptolide libraries), 500 ng of Turbo DNase digested RNA was mixed with 2 µl of 1:200 diluted ERCC Spike-in mix (Invitrogen#4456740) which was subjected to library preparation. TT-seq. libraries were prepared as described by Gregersen et al., 2020 (PMID: 31915390). Briefly, following depletion of desired protein, cells were treated with 4-thiouridine (4SU) for 15 minutes. The total RNA was extracted using Trizol and PureLink RNA Mini kit. RNA was mixed with that from S. pombe labelled with 4TU (as a spike in control). The labelled RNA was biotinylated using methanethiosulfonate (MTS)-biotin (Biotium#90065) and enriched using Dynabeads™ MyOne™ Streptavidin C1 (Invitrogen#65001). 300 ng of RNA was subjected to library preparation. All the sequencing libraries were prepared using Illumina Stranded Total RNA Prep with Ribo-Zero Plus (Illumina#20040525) according to manufacturer’s instructions. Sequencing was carried out at Genomics Research Incubator, Penn State University, USA using NextSeq™1000/2000 P2 Reagents(100Cycles) on NextSeq 2000.

treatment_protocol:
To calculate changes in steadystate RNA: Parental (untagged), CNOT1AID and CNOT4AID cells were treated with ± 1mM auxin for 8 h and 24 h, followed by total RNA extraction.
To calculate changes in RNA hallives: Parental (untagged), CNOT1AID and CNOT4AID cells were pretreated with 1mM auxin for 2 h, follwed by treatment with 1µM Triptlide for 0, 3, 6 and 12 h, followed by total RNA extraction.

value: Parental

value: Cells were left untreated for 8h


title: WT 1hr 2

description:
Library name: Sample 8
WT 1hr 2

value: liver

value: WT 1hr 2


title: Hypome2 WT replicate 2

description: Library name: EM_U4_1127_2024_12

value: Hypome2 WT


title: Hypome3 Homozygous replicate 1

description: Library name: Hypome3_Hom1


title: Control__CTCFsite_c-mycORF, rep2

description:
Library name: Control__CTCFsite_c-mycORF
Processed file derives from the merged of the three sequencing runs of two biological replicates

value: HeLa Kyoto

value: immortal human epithelial cell


title: WT 1hr 1

description:
Library name: Sample 7
WT 1hr 1

value: WT 1hr 1


title: control-1

value: Lung

value: tumor pericytes

value: control


title: KO 1hr 3

description:
Library name: Sample 12
KO 1hr 3

value: KO 1hr 3


title: NPC-IgM

value: IgM


title: virus-3

value: H1N1 virus infection


title: KO 0hr 3

description:
Library name: Sample 6
KO 0hr 3

value: KO 0hr 3


title: 23AB-Ara2

description: Library name: Sample 4

value: Prokaryotic cell

value: early stationary (OD600 = 1.0)

value: treated with 0.2% arabinoese


title: Hypome2 WT replicate 1

description: Library name: EM_U4_1127_2024_1

value: Dorsal skin


title: KO 1hr 2

description:
Library name: Sample 11
KO 1hr 2

value: liver

value: KO 1hr 2


title: 23-Ara2

description: Library name: Sample 2


title: Hypome3 Heterozygous replicate 1

description: Library name: Hypome3_Het1

value: Heterozygus Hypome3


title: 23-Ara1

description: Library name: Sample 1


title: control-3


title: KO 0hr 1

description:
Library name: Sample 4
KO 0hr 1

value: KO 0hr 1


title: virus-1


title: Hypome1 WT replicate 2

description: Library name: Hypome1_WT2

value: WT Hypome 1


title: Hypome1 WT replicate 1

description: Library name: Hypome1_WT1


title: NPC-LB1-Act

value: mNPCs

value: C57BL/6J x CAST/EiJ


title: H1299, DMSO RNA-seq, rep4

city: Hong Kong

first: Sha

address: Pokfulam Road, Hong Kong

department: Department of Chemistry

institute: The University of Hong Kong

data_processing:
For ChIP-seq data, raw reads were filtered using Trimmomatic (version 0.39). Clean reads were mapped to the human genome (GRCh38) using Bowtie2 (version 2.5.1).  The clean reads were also separately mapped to the drosophila genome (BDGP6). BigWig files for profile with deepTools (version 3.5.3).
For RNA-seq, raw reads were mapped to the human genome (GRCh38) using HISAT2 (version 2.1.0). Read counts were computed using featureCounts (version 2.0.1).
Assembly: hg38
Supplementary files format and content: bigWig ChIP-seq signal
Supplementary files format and content: RNA-Seq expression matrix

growth_protocol: H1299 cells were cultured in DMEM supplemented with 10% FBS, 100 U/ml penicillin, and 100 mg/ml streptomycin and  grown in a 37 °C humid incubator with 5% CO2

extract_protocol:
In ChIP-Seq,H1299 cells that stably expressed N-terminal Flag-YEATS2 were cultured in a 150 mm dish before treating with DMSO or 20 μM inhibitor for 4 hours. Cells were cross-linked by adding formaldehyde (37% v/v) to a final concentration of 1% (v/v) for 10 min at room temperature. After quenching and cell lysis, chromatin was sonicated to 150~500 bp fragment using sonicator. And 100 μg chromatin was diluted to 500 μL using sonication buffer and incubated with 10 μg antibody (anti-FLAG M2 MS) overnight at 4 °C. In RNA-Seq, Total RNA was isolated by Total RNA Isolation Mini Kit (Vazyme). The size distribution and quantity of the DNA library were detected by a bioanalyzer and Qubit.
In ChIP-Seq,DNA was purified and then ligated with Illumina adapters. The final DNA library was obtained by size selection and PCR amplification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. In RNA-Seq, the RNA library was prepared by end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.The quantified library was then pooled and sequenced on the Illumina platform NovaSeq PE150.

value: human non-small cell lung carcinoma cell line

value: DMSO


title: Hypome3 Heterozygous replicate 2

description: Library name: Hypome3_Het2


title: control-2

value: Lung

value: tumor pericytes

value: control


title: Hypome1 Homozygous replicate 4

description: Library name: Hypome1_Hom4

value: Homozygous Hypome1


title: WT 1hr 3

description:
Library name: Sample 9
WT 1hr 3

value: WT 1hr 3


title: Hypome3 Heterozygous replicate 3

description: Library name: Hypome3_Het3


title: H1299, LS-170 RNA-seq, rep3

value: Inhibitor


title: ESC-NI-Act

source_name: mESCs

value: mESCs

value: RNA Pol II pSer2


title: Hypome1 Homozygous replicate 3

description: Library name: Hypome1_Hom3

value: Dorsal skin


title: KO 0hr 2

description:
Library name: Sample 5
KO 0hr 2

value: liver

value: KO 0hr 2


title: H1299, DMSO RNA-seq, rep2


title: H1299, LS-170 RNA-seq, rep1


title: H1299, LS-170 RNA-seq, rep2


title: ESC-LB1-Act


title: WT 0hr 3

description:
Library name: Sample 3
WT 0hr 3

value: WT 0hr 3


title: ESC-IgM

value: IgM


title: WT_DMM_cartilage_M04

city: Suita

first: Yoshifumi

last: Takahata

state: Osaka

department: Dentistry

institute: Osaka University

description:
Library name: Sample1
Superficial-zone cartilage from the DMM-operated knee of mouse M04; paired sham from the same animal is available.

data_processing:
Base calling produced FASTQ files; adapters and low-quality bases were trimmed, and read quality was assessed
Assembly: Mus musculus GRCm39 (mm39)
Supplementary files format and content: BioSample (SAMN)

source_name: knee articular cartilage, superficial zone

growth_protocol: C57BL/6J mice were housed under SPF conditions (12-h light/dark cycle) with ad libitum access to food and water.

extract_protocol:
Total RNA was purified from tissue or cells using a column-based or phenol-chloroform method following the manufacturer’s instructions, including DNase treatment to remove genomic DNA
Poly(A)+ RNA was enriched from total RNA, and Illumina-compatible libraries were prepared according to the kit instructions.Libraries were sequenced on an Illumina HiSeq 2500 as ［single-end 100 bp］.

treatment_protocol: For in vivo samples, mice underwent destabilization of the medial meniscus (DMM) or sham surgery; superficial-zone cartilage from the medial femoral condyle was collected 8 weeks post-operation.

value: not provided

value: wild type

value: DMM surgery, 8 weeks post-surgery

tag: batch


title: WT_Sham_cartilage_M05

description:
Library name: Sample4
Superficial-zone cartilage from the DMM-operated knee of mouse M05; paired sham from the same animal is available.

value: knee articular cartilage, superficial zone

value: Sham surgery, 8 weeks post-surgery


title: WT_Sham_cartilage_M04

description:
Library name: Sample3
Superficial-zone cartilage from the DMM-operated knee of mouse M04; paired sham from the same animal is available.


title: Hypome1 Homozygous replicate 1

description: Library name: Hypome1_Hom1


title: WT 0hr 1

description:
Library name: Sample 1
WT 0hr 1

value: WT 0hr 1


title: WT 0hr 2

description:
Library name: Sample 2
WT 0hr 2

value: WT 0hr 2


title: H1299, DMSO RNA-seq, rep3

value: human non-small cell lung carcinoma cell line

value: DMSO


title: ZnO OVAL nanoparticles 10 Embryo day 5th rep4

type: RNA

city: Warszawa

first: Alicja

last: Majewska

address: Nowoursynowska 159

department: Department of Physiology Sciences

country: Poland

institute: Warsaw University of Life Sciences-SGGW Faculty of Veterinary Medicine

description: Gene expression in embryo after 5 days of incubation of eggs treated with ZnO OVAL

hyb_protocol: 1.65 µg of Cy3-labelled cRNA  was prepared for hybridization using Gene Expression Hybridization Kit (Agilent, USA) and following the manufacturers protocol. Hybridization was performed at 65°C for 17 h in a rotating Agilent hybridization oven. After hybridization, microarrays were washed with Wash Buffers (Agilent, USA) according to the manufacturers protocol.

scan_protocol: Acquisition and analysis of hybridization intensities were performed using Agilent DNA Microarray Scanner G2505C.

data_processing: The scanned images were analyzed with Feature Extraction Software (version 10.7.3.1) using default parameters (protocol GE_107_Sep09 and Grid: 026441_D_F_20160309) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Gallus gallus

source_name: embryo treated with nanoparticles ZnO OVAL for 5 days of incubation

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen, Hilden, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: As an experimental model, the in ovo model was used with the administration of the nanoparticle suspensions (100 µl per egg) to the air chamber of fertilised Ross 308 eggs. The nanoparticles were administered in  doses of 10  µg/ml, suspended in PBS. The control group (CTRL) received 100 µl of PBS. The incubation process was carried out at a temperature of 39°C and a humidity of 60%. The collection of embryos  samples was performed for  4, 5th days of incubation

extract_protocol: Total RNA was extracted from 4 and 5 day old chicken embryos using the RNeasy Mini Kit (Qiagen, Hilden, Germany). During RNA isolation, DNase (RNase-Free DNase Set, Qiagen, Hilden, Germany) was used to purify the isolated RNA from DNA contamination. The entire procedure was performed according to the manufacturer's instructions.  The NanoDrop™ 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) was used to assessment of RNA purity and concentration. RNA integrity was verified using the Agilent Bioanalyzer 2100 with the Agilent RNA 6000 Nano Kit (Agilent Technologies, Palo Alto, CA, USA). Samples showed  revealing high integrity (RIN =10).

tag: developmental stage

value: fertilised Ross 308 eggs

tag: agent

value: 100 µl suspension of ZnO OVAL nanoparticles in PBS, in concentration 10  µg/ml


title: H1299, LS-170 Input, rep2

value: Inhibitor


title: Hypome1 Homozygous replicate 2

description: Library name: Hypome1_Hom2

value: Dorsal skin

value: Homozygous Hypome1


title: NHEK59, C. acnes training, Pam3CSK4 induction

city: Szeged

first: Fanni

last: Balogh

address: Temesvári krt. 62

country: Hungary

institute: Biological Research Centre

description: Library name: NHEK59-19

data_processing:
Raw sequenced reads were aligned to GRCh38 reference genome using HISAT2 aligner, then StrandNGS program was used for downstream data analysis. For the normalization step the integrated DESeq algorithm of StrandNGS was used.
Assembly: GRCh38
Supplementary files format and content: xlsx file includes raw and normalized counts for each sample

source_name: normal human epidermal keratinocyte

growth_protocol: The experiments were conducted using normal human epidermal keratinocytes (NHEKs). Cells were cultured in complete keratinocyte serum-free medium (KSFM, Life Technologies, Carlsbad, CA, US) containing 1% antibiotic/antimycotic (AB/AM, Sigma Aldrich, St. Louis, MO, US) solution and supplemented with epidermal growth factor (EGF), brain pituitary extract (BPE), and 1% L-glutamine (GE Healthcare, Chicago, IL, USA), under standard laboratory conditions (37°C in a humidified atmosphere containing 5% v/v CO2).

extract_protocol:
Total RNA was isolated using TRI-Reagent (Molecular Research Center, Cincinnati, OH, USA).
To obtain global transcriptome data, high-throughput mRNA sequencing analysis was 21 performed on the Illumina (San Diego, CA, USA) sequencing platform. The total RNA sample 22 quality was checked on an Agilent BioAnalyzer (Agilent, Santa Clara, CA, USA) using a 23 Eukaryotic Total RNA Nano Kit according to the manufacturer’s protocol. Samples with RNA 24 integrity number > 7 were accepted for the library preparation process. RNA-Seq libraries were 25 prepared from total RNA using the Ultra II RNA Sample Prep kit (New England Biolabs, 26 Ipswich, MA, USA) according to the manufacturer’s protocol. Briefly, poly(A) RNAs were 27 captured by oligo dT-conjugated magnetic beads, and then the mRNAs were eluted and 28 fragmented at 94°C. First-strand cDNA was generated by random priming reverse transcription, 29 and after the second-strand synthesis step, double-stranded cDNA was generated. After end 30 repair, A-tailing, and adapter ligation, the adapter-ligated fragments were amplified by 31 enrichment PCR, and finally, sequencing libraries were generated. Sequencing runs were 32 executed on a NextSeq 500 instrument (Illumina) using single-end 75-cycle sequencing. mRNA 33 sequencing (from library preparation to the generation of fastq files) was performed at the 34 Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and 35 Molecular Biology, Faculty of Medicine, University of Debrecen (Debrecen, Hungary).

treatment_protocol: Cells were cultured in KSFM supplemented with EGF and BPE (+EGF/BPE) in the absence of AB/AM solution (−AB/AM). In the course of our experiments, 150,000 cells were seeded into each well of a 12-well plate in a total volume of 1 mL of culture medium. Primary training was conducted on the second day. The keratinocytes were incubated with C. acnes [multiplicity of infection (MOI) = 1:100] for 24 h. Following a wash step with PBS, the cells were maintained in 1 mL of KSFM (+EGF/BPE, +AB/AM) for 5 days, with medium replacement on day 3. Subsequently, the cells were stimulated with 5 μg/mL Pam3CSK4 (InvivoGen, San Diego, CA, USA) for 3 h in 0.5 mL of KSFM (+EGF/BPE, −AB/AM), in accordance with the previously established in vitro model of human monocyte training.

tag: origin

value: abdomen

value: normal human epidermal keratinocyte

value: NHEK-A

value: C. acnes + Pam3CSK4


title: Hypome1 Heterozygous replicate 3

description: Library name: Hypome1_Het3

value: Heterozygous Hypome1


title: NHEK59, Pam3CSK4 induction

description: Library name: NHEK59-13

value: Pam3CSK4 induction


title: H1299, DMSO RNA-seq, rep1


title: H1299, DMSO Input, rep2


title: WT_DMM_cartilage_M05

description:
Library name: Sample2
Superficial-zone cartilage from the DMM-operated knee of mouse M05; paired sham from the same animal is available.

value: knee articular cartilage, superficial zone

value: not provided

value: wild type

value: DMM surgery, 8 weeks post-surgery


title: H1299, DMSO Input, rep1

value: human non-small cell lung carcinoma cell line


title: H1299, LS-170 Input, rep1


title: Hypome1 Heterozygous replicate 2

description: Library name: Hypome1_Het2


title: osimertinib 5

city: Fukuoka

first: Kazuya

last: Tsubouchi

state: Fukuoka

address: 3-1-1, Maidashi, Higashi-ku

department: Respiratory Medicine

institute: Kyushu University

data_processing:
MGI DNBseq-G400 FAST was used to perform the amplicons deep sequencing following the standard operation protocol. The sequence format was 150bp pair read for all samples.
All sequencing reads were trimmed low-quality bases and adapters with Trimmomatic (v.0.38) .
Raw counts for each gene were estimated in each sample using RSEM version 1.3.0 and Bowtie 2. Calculation of the log fold-change (log FC) and p-value were performed using edgeR.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with GeneSymbol index.

source_name: osimertinib

extract_protocol:
The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using MGIEasy rRNA Depletion Kit and MGIEasy RNA Directional Library Prep Set  according protocols

tag: group name

value: osimertinib

value: lung


title: NHEK59, C. acnes training

description: Library name: NHEK59-7

value: C. acnes training


title: Hypome1 Heterozygous replicate 1

description: Library name: Hypome1_Het1


title: osimertinib 2


title: ZnO OVAL nanoparticles 10 Embryo day 5th rep2

value: fertilised Ross 308 eggs

value: 100 µl suspension of ZnO OVAL nanoparticles in PBS, in concentration 10  µg/ml


title: ZnO OVAL nanoparticles 10 Embryo day 5th rep3


title: osimertinib 1


title: NHEK59, Control

description: Library name: NHEK59-2

value: Control


title: ZnO OVAL nanoparticles 10 Embryo day 5th rep1


title: NHEK22, C. acnes training, Pam3CSK4 induction

description: Library name: NHEK22-43

value: abdomen


title: H1299, LS-170 YEATS2 ChIP-seq, rep2

value: Inhibitor


title: ZnO LONG nanoparticles 10 Embryo day 5th rep4

description: Gene expression in embryo after 5 days of incubation of eggs treated with ZnO LONG

source_name: embryo treated with nanoparticles ZnO LONG for  5 days of incubation

value: 100 µl suspension of ZnO LONG nanoparticles in PBS, in concentration 10  µg/ml


title: NHEK23, C. acnes training, Pam3CSK4 induction

description: Library name: NHEK23-44

value: normal human epidermal keratinocyte

value: NHEK-A

value: C. acnes + Pam3CSK4


title: ZnO LONG nanoparticles 10 Embryo day 5th rep1


title: ZnO LONG nanoparticles 10 Embryo day 5th rep3


title: osimertinib 4


title: H1299, LS-170 YEATS2 ChIP-seq, rep1


title: naphthalene 2

source_name: naphthalene

value: naphthalene


title: CTRL Embryo day 5th rep2

description: Gene expression in embryo after 5 days incubation of eggs

source_name: embryo not treated with nanoparticles

value: 100 µl PBS per egg


title: NHEK22, C. acnes training

description: Library name: NHEK22-19


title: NHEK23, Pam3CSK4 induction

description: Library name: NHEK23-31

value: Pam3CSK4 induction


title: ZnO LONG nanoparticles 10 Embryo day 5th rep2


title: NHEK22, Control

description: Library name: NHEK22-8


title: osimertinib 3


title: control 3

source_name: control

value: control


title: H1299, DMSO YEATS2 ChIP-seq, rep2

value: human non-small cell lung carcinoma cell line

value: DMSO


title: CTRL Embryo day 5th rep1


title: NHEK22, Pam3CSK4 induction

description: Library name: NHEK22-33


title: RS-TD2_L001-ds

city: Adelaide

first: Feargal

middle: J

last: Ryan

state: Adelaide

address: North Terrace

country: Australia

institute: SAHMRI

description: Total RNA of Human retinal mueller glial cells infected with T. gondii

data_processing:
Trimmomatic-0.38
Cutadapt-1-9-1
Hisat2 v2.1.0
samtools 1.3.1
FeatureCounts 1.5.0-p2
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited gene count matrix output from FeatureCounts

source_name: Retina

growth_protocol: Retinal Mueller glial cells were isolated from human cadaveric donor eyes using enzymatic digestion of tissue, followed by culture in DMEM with Non-Essential Amino Acids Solution (1x), GlutaMAX Supplement (1x), 1 mM sodium pyruvate (Thermo Fisher Scientific), 10% FBS and 100 U/mL penicillin-100 μg/mL streptomycin.

extract_protocol:
Total RNA was extracted using Thermo Fisher Scientific TRIzol Reagent, following the manufacturer’s instructions.
TruSeq Stranded Total RNA Sample Preparation kit, following the manufacturer’s instructions. The small RNA library was constructed using the IlluminaTruSeqSmall RNA Library Prep kit, following the manufacturer’s instructions, with the exception that purification steps were supplemented with 3% Pippin Prep gels.
Total RNA NovaSeq 2x150bp. Small RNA NextSeq 1x75bp

treatment_protocol: Cells were infected with one strain of Toxoplasma gondii (GT1 or GPHT, MOI 5) or mock-infected for 4 hours and held for a total of 24 hours before RNA extraction.

value: Human retinal Mueller glial cell

tag: infection


title: control 2

value: lung


title: H1299, DMSO YEATS2 ChIP-seq, rep1


title: NHEK23, Control

description: Library name: NHEK23-9


title: ZnO OVAL nanoparticles 10 Embryo day 4th rep2

description: Gene expression in embryo after 4 days of incubation of eggs treated with ZnO OVAL

source_name: embryo treated with nanoparticles ZnO OVAL for  4 day of incubation

value: fertilised Ross 308 eggs


title: RS-GT1D6_L001-ds


title: RS-TD6_L001-ds


title: RS-GT1D5_L001-ds


title: CTRL Embryo day 5th rep4


title: naphthalene 3


title: CTRL Embryo day 5th rep3


title: RS-TD5_L001-ds


title: NHEK23, C. acnes training

description: Library name: NHEK23-19

value: C. acnes training


title: NHEK21, C. acnes training, Pam3CSK4 induction

description: Library name: NHEK21-45

value: mammary

value: NHEK-B


title: RS-TD4_L001-ds


title: RS-TD3_L001-ds


title: naphthalene 1


title: NHEK79, C. acnes training, Pam3CSK4 induction

description: Library name: NHEK79_25


title: CDK8CDK19KO_2

city: Boston

first: Chen

last: Chu

state: MA

address: 450 Brookline Ave, Smith 914

institute: Dana-Farber Cancer Institute

description:
Library name: DKO_2
2 x 150 bp

data_processing:
The data were aligned to mm10 using Salmon 1.4.0 (using the default parameters)
The DEGs were calculated using DESeq2.
Assembly: mm10
Supplementary files format and content: csv files containing normalized counts

source_name: bone marrow

growth_protocol: BMDMs were differentiated according to Liu, et al PMID: 37074910

extract_protocol:
Total RNAs were extracted using RNAeasy Kit from Qiagen
Library preparation (Roche, Kapa mRNAseq Hyper prep) and sequencing analysis (Illumina NovaSeq X Paired-end 2 x 150 bp) were performed at the Molecular Biology Core facility in Dana-Farber Cancer Institute.

value: bone marrow

value: bone marrow-derived marcrophages (BMDM)

value: no treatment


title: NHEK21, Pam3CSK4 induction

description: Library name: NHEK21-32

value: normal human epidermal keratinocyte


title: RS-TD1_L001-ds


title: ZnO OVAL nanoparticles 10 Embryo day 4th rep4

value: 100 µl suspension of ZnO OVAL nanoparticles in PBS, in concentration 10  µg/ml


title: control 1


title: NHEK79, Pam3CSK4 induction

description: Library name: NHEK79_22


title: RS-GT1D2_L001-ds


title: CDK8CDK19KO_1

description:
Library name: DKO_1
2 x 150 bp


title: NHEK79, C. acnes training

description: Library name: NHEK79_13


title: RS-GT1D1_L001-ds


title: CDK8CDK19KO_4

description:
Library name: DKO_4
2 x 150 bp


title: NHEK79, Control

description: Library name: NHEK79_8

value: Control


title: CDK8CDK19KO_3

description:
Library name: DKO_3
2 x 150 bp


title: NHEK21, Control

description: Library name: NHEK21-7


title: ZnO LONG nanoparticles 10 Embryo day 4th rep4

description: Gene expression in embryo after 4 days of incubation of eggs treated with ZnO LONG

source_name: embryo treated with nanoparticles ZnO LONG for  4 days of incubation

value: 100 µl suspension of ZnO LONG nanoparticles in PBS, in concentration 10  µg/ml


title: ZnO OVAL nanoparticles 10 Embryo day 4th rep3


title: RS-GT1D4_L001-ds


title: NHEK11, C. acnes training, Pam3CSK4 induction

description: Library name: NHEK11-26

value: C. acnes + Pam3CSK4


title: RS-GT1D3_L001-ds


title: ZnO OVAL nanoparticles 10 Embryo day 4th rep1

source_name: embryo treated with nanoparticles ZnO OVAL for  4 days of incubation


title: NHEK11, Pam3CSK4 induction

description: Library name: NHEK11-21

value: Pam3CSK4 induction


title: NHEK21, C. acnes training

description: Library name: NHEK21-20


title: VAV-cre_4

description:
Library name: VAV_4
2 x 150 bp

value: VAV-cre


title: CTRL Embryo day 4th rep3

description: Gene expression in embryo after 4 days incubation of eggs

value: 100 µl PBS per egg


title: ZnO LONG nanoparticles 10 Embryo day 4th rep3


title: VAV-cre_3

description:
Library name: VAV_3
2 x 150 bp


title: ZnO LONG nanoparticles 10 Embryo day 4th rep1


title: VAV-cre_2

description:
Library name: VAV_2
2 x 150 bp


title: RS-GHPTD4_L001-ds

value: Human retinal Mueller glial cell


title: CTRL Embryo day 4th rep4


title: NHEK11, C. acnes training

description: Library name: NHEK11-17


title: DKO_4

description:
Library name: DKO_4
2 x 150 bp

extract_protocol:
Total RNAs were extracted using Trizol with the standard protocol
Library preparation (Roche, Kapa mRNAseq Hyper prep) and sequencing analysis (Illumina NovaSeq X Paired-end 2 x 150 bp) were performed at the Molecular Biology Core facility in Dana-Farber Cancer Institute.

value: tissue

value: DKO

value: No treatment


title: EnrichedNeuron_Scrambled_shRNA_8

city: Sha Tin

first: Jacquelyne

last: Sun

state: New Territories

address: Room 612A, Mong Man Wai Building,

department: School of Life Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Library name: Scrambled_shRNA_EN8

data_processing:
The FASTQ files were first checked for quality using FastQC - as samples all passed our benchmarks, the clean raw data files were subsequently aligned using the STAR alignment software to the mouse genome provided by Gencode M34. featureCounts was then used to quantify the sequencing data, which is the raw counts file provided in this GEO accession. Assembly: mm39 Supplementary files format and content: Tab delimited text file containing the raw counts for each samples.
Assembly: mm39
Supplementary files format and content: RawCounts.txt.gz

source_name: Enriched cortical neurons from cerebral cortex

extract_protocol:
After termination with carbon dioxide, each mouse was perfused with chilled PBS for 3 minutes. The brain tissue was harvested carefully and dissected into 8-10 sagittal slices with the help of a murine brain matrix (Ted Pella). Prefrontal cortex tissues where stereotaxic injection of Esrra shRNA was conducted of one mouse was polled in a petri dish filled with D-PBS (Dulbecco’s Phosphate Buffered Saline with calcium and magnesium, supplemented with 1 g/L glucose and 36 mg/L sodium pyruvate). The dishes were placed on ice until further downstream processing. Tissue dissociation was performed with the Adult Brain Dissociation Kit for mouse (Miltenyi Biotec), following the manufacturer’s instructions. Prefrontal cortex tissues of each mouse was transferred to a gentleMACS C Tube (Miltenyi Biotec) containing both enzyme mixes from the kit for enzymatic digestion. Mechanical enzymatic tissue dissociation was performed using program 37C_ABDK_01 of the gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec). After dissociation, each brain tissue homogenate was applied to one 70 µm cell strainer (Corning, Corning, MA, USA). For detailed protocol, please see the methods section of the publication.
Frozen whole cortex tissues from the test subjects of the AOF/VCD model, laser microdissection enriched GTP-positive cortex and hippocampal tissues from the AAV-study model or enriched neuronal populations were sent to the Novogene for total RNA extraction and RNA sequencing with the Illumina HiSeq X Ten platform. FASTQ files obtained were subsequently analysed by the FastQC (V. 0.11.9) of Babraham Bioinformatics, serving as a quality control assessment tool for these data. After assuring the quality of the data files, genome indexes were generated using the STAR software using. These indexes were generated with the mouse annotation and mouse genome assembly provided by the Gencode Release 28 (GRCm39, released in May 2021). The cleaned dataset was then aligned with the genome indexes using the STAR alignment software. FeatureCounts was then used to quantify the sequencing data. Data extraction, matrix construction and differential gene expression analysis was then performed using the DESeq2 package with standard procedures on R.


title: RS-GHPTD3_L001-ds


title: DKO_3

description:
Library name: DKO_3
2 x 150 bp


title: T_D6_R1_001

description: Small RNA-Seq of Human retinal mueller glial cells infected with T. gondii


title: NHEK11, Control

description: Library name: NHEK11-10

value: mammary


title: DKO_2

description:
Library name: DKO_2
2 x 150 bp


title: EnrichedNeuron_Scrambled_shRNA_7

description: Library name: Scrambled_shRNA_EN7

value: Enriched cortical neurons from cerebral cortex


title: EnrichedNeuron_Scrambled_shRNA_6

description: Library name: Scrambled_shRNA_EN6


title: RS-GHPTD1_L001-ds


title: RS-GHPTD2_L001-ds


title: T_D5_R1_001


title: EnrichedNeuron_Scrambled_shRNA_5

description: Library name: Scrambled_shRNA_EN5


title: DKO_1

description:
Library name: DKO_1
2 x 150 bp

value: bone marrow


title: CTRL Embryo day 4th rep1

value: fertilised Ross 308 eggs


title: RS-GHPTD6_L001-ds


title: VAV-cre_1

description:
Library name: VAV_1
2 x 150 bp

value: bone marrow-derived marcrophages (BMDM)

value: no treatment


title: CDK19KO_4

description:
Library name: CDK19KO_4
2 x 150 bp


title: ZnO LONG nanoparticles 10 Embryo day 4th rep2


title: RS-GHPTD5_L001-ds


title: CDK19KO_3

description:
Library name: CDK19KO_3
2 x 150 bp


title: CDK19KO_2

description:
Library name: CDK19KO_2
2 x 150 bp


title: EnrichedNeuron_Scrambled_shRNA_2

description: Library name: Scrambled_shRNA_EN2


title: T_D2_R1_001


title: T_D1_R1_001


title: CDK19KO_1

description:
Library name: CDK19KO_1
2 x 150 bp


title: CDK8KO_4

description:
Library name: CDK8KO_4
2 x 150 bp


title: GT1_D5_R1_001


title: CTRL Embryo day 4th rep2


title: T_D4_R1_001


title: EnrichedNeuron_Esrra_shRNA_7

description: Library name: Esrra_shRNA_EN7


title: EnrichedNeuron_Esrra_shRNA_8

description: Library name: Esrra_shRNA_EN8


title: GT1_D6_R1_001


title: EnrichedNeuron_Scrambled_shRNA_1

description: Library name: Scrambled_shRNA_EN1


title: EnrichedNeuron_Scrambled_shRNA_4

description: Library name: Scrambled_shRNA_EN4


title: EnrichedNeuron_Esrra_shRNA_6

description: Library name: Esrra_shRNA_EN6


title: T_D3_R1_001


title: CDK8KO_3

description:
Library name: CDK8KO_3
2 x 150 bp


title: GT1_D4_R1_001


title: EnrichedNeuron_Scrambled_shRNA_3

description: Library name: Scrambled_shRNA_EN3


title: GT1_D3_R1_001


title: CDK8KO_2

description:
Library name: CDK8KO_2
2 x 150 bp


title: GT1_D2_R1_001


title: CDK8KO_1

description:
Library name: CDK8KO_1
2 x 150 bp


title: EnrichedNeuron_Esrra_shRNA_4

description: Library name: Esrra_shRNA_EN4


title: GT1_D1_R1_001


title: EnrichedNeuron_Esrra_shRNA_3

description: Library name: Esrra_shRNA_EN3


title: WT corn snake replicate 3

description: Library name: C_Hypo_WT3

data_processing:
Fastq files were mapped to the reference genome using STAR v2.7.10b and raw gene counts were extracted using featureCounts from Subread v2.0.6
Assembly: GCF_029531705.1
Supplementary files format and content: Table of raw counts (tsv format)

organism: Pantherophis guttatus

source_name: Dorsal skin

value: Dorsal skin

value: WT


title: EnrichedNeuron_Esrra_shRNA_2

description: Library name: Esrra_shRNA_EN2


title: WT corn snake replicate 2

description: Library name: C_Hypo_WT2


title: VAV_3

description:
Library name: VAV_3
2 x 150 bp


title: GHPT_D6_R1_001


title: GHPT_D4_R1_001


title: C3H10T1-2-Parental_sgCtrl_WGBS

city: Montreal

first: Jacek

last: Majewski

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

country: Canada

institute: McGill University

data_processing:
Raw WGBS reads were processed and analyzed as previously described (Chen et al., 2022), where they were mapped and methylation calling was performed using Bismark v0.22.3 against the mouse assembly mm10, ENCODE blacklisted regions were removed and only CpGs covered by ≥5× in all samples were retained for the computation of DNA methylation levels.
Assembly: mm10
Supplementary files format and content: bigWig

growth_protocol: C3H10T1/2 mouse mesenchymal stem cells (ATCC) were cultured in DMEM with 10% fetal bovine serum (FBS,) and supplemented with 1% GlutaMax.

extract_protocol:
1000 ng of genomic DNA extracted from approximately 4 million cells and fragmented to 300-400 bp using the Covaris focused-ultrasonicator E210.
The NxSeq AmpFREE Low DNA Library Kit (Lucigen - CA10837-144) was used. End repair, A-tailing, adapter ligation, and clean-up steps were performed as per the manufacturer’s recommendations. Bisulfite conversion was performed using the EZ-96 DNA Methylation-Gold™ MagPrep Kit (Zymo Research) according to the manufacturer’s protocol. Bisulfite-converted DNA was amplified by PCR using the KAPA Hifi HotStart Uracil+ Kit (Roche) according to the manufacturer’s protocol. The amplified libraries were then purified using AMPure XP Beads (Beckman Coulter). 150-bp paired-end sequencing of the WGBS libraries was performed using the Illumina HiSeqX system.

value: fibroblast


title: EnrichedNeuron_Esrra_shRNA_5

description: Library name: Esrra_shRNA_EN5


title: VAV_2

description:
Library name: VAV_2
2 x 150 bp


title: GHPT_D5_R1_001


title: EnrichedNeuron_Esrra_shRNA_1

description: Library name: Esrra_shRNA_EN1


title: Hypomelanistic corn snake replicate 3

description: Library name: C_Hypo_Homo3

extract_protocol:
RNA was extracted from dorsal skin of embryos at embryonic day 40 using the Direct-zol RNA MiniPrep kit (Zymo Research, R2050)
Libraries were prepared using the TruSeq Stranded mRNA Library kit

value: Homozygous Hypomelanistic


title: WT corn snake replicate 1

description: Library name: C_Hypo_WT1


title: GHPT_D3_R1_001


title: C3H10T1-2_NSD1-2-SETD2-TKO_WGBS


title: WT_2

description:
Library name: WT_2
2 x 150 bp


title: Hypomelanistic corn snake replicate 2

description: Library name: C_Hypo_Homo2


title: GHPT_D2_R1_001


title: WT_3

description:
Library name: WT_3
2 x 150 bp


title: WT_1

description:
Library name: WT_1
2 x 150 bp


title: VAV_4

description:
Library name: VAV_4
2 x 150 bp


title: VAV_1

description:
Library name: VAV_1
2 x 150 bp


title: C3H10T1-2_NSD1-2-3-SETD2-QKO_WGBS


title: AP1-AP1_R0

status: Public on Oct 22 2025

city: Berlin

first: Jose

middle: M.

last: Muino

address: Max-Dohrn-Str. 8-10

country: Germany

institute: German Federal Institute for Risk Assessment

description: Control

data_processing:
Basecalling was done using NovaSeq Control Software 1.7.5, RTA v3.4.4, and bcl2fastq2.20 v2.20.0.422
Sequence correction: As both reads of the pair-end reads represent the same 20bp DNA sequence. Any nucleotide called N was substituted by the nucleotide of the other read. When pair-end reads represented different sequences, they were eliminated.
Selex analysis was done with the R package SELEX_1.26.0. Using kmer length = 12 , markov chain order set to 6, and minCount =10
Supplementary files format and content: CSV file, with 4 columns: kmer sequence, Observed number of counts, Probability, Expected number of read counts, Affinity, SE

organism: synthetic construct

source_name: in vitro generated 20bp dsDNA sequences

extract_protocol: SELEX-seq dsDNA libraries were generated from ssDNA sequences which contain 20 random nucleotides in the middle by a single-cycle PCR amplification round with complementary primers essentially as described by Jolma et al. (2010). The coding sequence of AP1 was cloned into the pTNTTM vector (Promega) which was fused by 3X FLAG-tag, and then the AP1 proteins with 3XFLAG tags were synthesized using TNT® SP6 High-Yield Wheat Germ Protein Expression System (Promega) according to manufacturers’ instructions in a total volume of 20 µl. The protein-DNA binding reaction mix was prepared as studied before with a total volume of 120 µl (Smaczniak et al., 2012b, Chen et al., 2023), the mix contained 20 µl in vitro synthesized protein and 50 ng dsDNA. The binding mix was incubated on ice for one hour, followed by immunoprecipitation using 10 µl Anti-FLAG® M2 magnetic beads (Sigma-Aldrich) in a thermomixer at 4ºC at 800 rpm for one hour. After immunoprecipitation, magnetic beads were washed 5 times with 150 µl binding buffer without salmon-sperm DNA and briefly rinsed with 500 µl 1XTE buffer. Bound DNA was elucidated in 50 µl 1X TE in a 90ºC thermomixer at full speed for 20 min. Next, magnetic beads were immobilized and the supernatant was transferred to a new tube. To allow a subsequent round of SELEX, the eluate DNA was amplified by PCR with a qPCR-selected cycle with SELEX PCR primers (Chen et al., 2023). The quality and concentration of the amplicon were checked by TapeStation (Agilent) and Qubit® Fluorometer (Thermo). 50 ng of the amplicon was used for the subsequent round of SELEX. For high throughput sequencing, round-specific adaptor pairs that contain all features needed for direct sequencing were used for library amplification by PCR, and the PCR cycle number used here was also selected by qPCR. All the SELEX sequencing libraries were mixed in equimolar amounts, sequencing was performed on NovaSeq 6000 (Illumina).

value: in vitro generated 20bp dsDNA sequences

tag: protein complex interrogated

tag: round of selex enrichment

value: Round 0


title: C3H10T1-2_NSD1-2-3-SETD2-ASH1L-QuiKO_WGBS


title: Hypomelanistic corn snake replicate 1

city: Geneva

first: Athanasia

institute: University of Geneva

description: Library name: C_Hypo_Homo1


title: AP1-AP1_R3S1

description: Sample

value: Round 4


title: Scere, lib697, control, CMC, TGIRT, rep1

city: Rehovot

first: Miguel

middle: A.

last: Garcia-Campos

state: Center District

address: Herzl 234, Meyer Bldg., Room 1410

department: Molecular Genetics

country: Israel

institute: Weizmann Insitute of Science

description: Library name: Sample 29

data_processing:
Reads were aligned using STAR v2.7.5c (Dobin et al., 2013), alignments sorted using SAMtools v1.9 (Danecek et al., 2021), and processed to compute count data per nucleotide position using txtools 1.0.5 (Garcia-Campos et al., 2024)
Assembly: GCF_000146045.2
Supplementary files format and content: tab delimited file with count data for read-ends, read-starts, coverage, and nucleotide frequency per transcriptomic position

organism: Saccharomyces cerevisiae

source_name: Cell culture

growth_protocol: grown at 30°C overnight in YPD 2% medium, diluted in fresh YPD and grown to log phase. The cells were spun down in a chilled centrifuge and flash frozen in liquid nitrogen

extract_protocol:
RNA was extracted using the MasterPure Yeast RNA purification kit (Biosearch Technologies), by the manufacturer’s instructions
Remaining primers left in the reaction were digested by addition of 3 μL ExoSAP-IT (Applied Biosystems, 78205) to the 20 μL reverse transcription reaction, and incubation at 37°C for 12 min. RNA was degraded by adding 2.5 μL of NaOH 1M and 1 μL of 0.5M EDTA, and incubation at 70°C for 12 min. The base was neutralized with the addition of 1M HCl, cDNA was cleaned using MyOne silane beads. An adapter was added to the 3’ end of the cDNA by ligating 50 pmoles 5iLL-22 DNA adapter using T4 RNA Ligase 1, High concentration (NEB, M0437M), DMSO 4%, ATP 1mM and PEG8000 25% at 23°C for 3 h. After clean-up with MyOne silane beads, we amplified the cDNA library for 12 cycles using Illumina Library PCR primers F and R and KAPA HiFi HotStart ReadyMix (Roche, KK2601). Amplified libraries were cleaned with Kapa pure beads (Roche, KK8002), quantified using Qubit (Life Technologies) and the distribution of library size was determined using TapeStation (Agilent Technologies).

value: Yeast culture

value: control


title: Scere, lib697, control, NaCNBH3, TGIRT, rep1

description: Library name: Sample 27


title: Scere, lib697, control, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 31


title: Scere, lib697, control, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 30


title: Scere, lib697, control, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 34


title: Scere, lib697, control, Mock, TGIRT, rep1

description: Library name: Sample 33


title: Scere, lib697, control, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 26


title: Scere, lib697, control, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 23


title: Scere, lib697, control, AlkBmix, TGIRT, rep1

description: Library name: Sample 28


title: Scere, lib697, control, Mock, SSIII, rep1

description: Library name: Sample 25


title: Scere, lib697, control, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 24


title: Scere, lib697, control, Bisulfite, TGIRT, rep1

description: Library name: Sample 32


title: Scere, lib697, control, CMC, SSIII, rep1

description: Library name: Sample 22


title: Scere, lib697, control, NaCNBH3, SSIII, rep1

description: Library name: Sample 21


title: Scere, lib697, control, Mock, RTHIV, rep1

description: Library name: Sample 19


title: Scere, lib524, control, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 17


title: Scere, lib524, control, Mock, TGIRT, rep1

description: Library name: Sample 16


title: Scere, lib524, control, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 13


title: Scere, lib524, control, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 14


title: Scere, lib524, control, AlkBmix, TGIRT, rep1

description: Library name: Sample 11


title: Scere, lib524, control, Bisulfite+MgCl2+Heat, SSIII, rep1

description: Library name: Sample 9


title: Scere, lib524, control, NaCNBH3, TGIRT, rep1

description: Library name: Sample 10


title: Scere, lib524, control, CMC, TGIRT, rep1

description: Library name: Sample 12


title: Scere, lib524, control, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 8


title: Coronary artery endothelial cells with 2 Gy of ionizing radiation

type: genomic

city: Cheonan

first: Jihye

last: Park

address: Cheonan Campus 119 Dan-daero

country: South Korea

institute: Dankook university

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing:
Each methylation data point is represented by fluorescent signals from the M (methylated) and U (unmethylated) alleles.
Background intensity computed from a set of negative controls was subtracted from each analytical data point.
The ratio of fluorescent signals was then computed from the two alleles ß = (max(M, 0))/(|U| + |M| + 100).
The ß-value reflects the methylation level of each CpG site.
A ß-value of 0~1 was reported signifying percent methylation, from 0% to 100%, respectively, for each CpG site.

label: Cy5 and Cy3

source_name: coronary artery endothelial cells irradiated with 2 Gy

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from human aortic or coronary artery endothelial samples using Qiagen DNeasy Kit according to standard instructions.

treatment_protocol: Irradiation with ionizing radiation with 0.1, 0.5, 2, and 6 Gy.

value: coronary artery endothelial cells

value: treated with 2 Gy (2 Gy/min) of ionizing radiation


title: Scere, lib524, control, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 5


title: Scere, lib524, control, Bisulfite, TGIRT, rep1

description: Library name: Sample 15


title: Scere, lib524, control, CMC, SSIII, rep1

description: Library name: Sample 4


title: Scere, lib524, control, Mock, SSIII, rep1

description: Library name: Sample 7


title: Coronary artery endothelial cells with 6 Gy of ionizing radiation

source_name: coronary artery endothelial cells irradiated with 6 Gy

value: treated with 6 Gy (2 Gy/min) of ionizing radiation


title: GHPT_D1_R1_001

value: Human retinal Mueller glial cell


title: Scere, lib697, control, NaBH4HydBiotin, RTHIV, rep1

description: Library name: Sample 20


title: Scere, lib524, control, NaBH4HydBiotin, RTHIV, rep1

description: Library name: Sample 2


title: Scere, lib524, control, Mock, RTHIV, rep1

description: Library name: Sample 1


title: Aortic endothelial cells treated with 0.1 Gy of ionizing radiation

source_name: aortic endothelial cells irradiated with 0.1 Gy

value: aortic endothelial cells

value: treated with 0.1 Gy (0.1 mGy/min) of ionizing radiation


title: TER94_2HEAD

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description: Library name: SJDMNORM018103_G1-FD_TER94_2HEAD

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to dm3 whole genome using an internal pipeline that employs bwa and STAR
Htseq was used to extract raw counts
Assembly: dm3
Supplementary files format and content: SJDM_dm3_raw_count_36.txt,  matrix raw counts with gene names and FlyBase ID

organism: Drosophila melanogaster

source_name: head

extract_protocol:
trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: head

value: TER94/VCP RNAi


title: Aortic endothelial cells treated with 6 Gy of ionizing radiation

source_name: aortic endothelial cells irradiated with 6 Gy


title: Tropo_3HEAD

description: Library name: SJDMNORM018101_G1-FD_Tropo_3HEAD

value: Tropomyosin 1 (Tm1) RNAi


title: Tropo_2HEAD

description: Library name: SJDMNORM018100_G1-FD_Tropo_2HEAD


title: TER94_1HEAD

description: Library name: SJDMNORM018102_G1-FD_TER94_1HEAD


title: Tropo_1HEAD

description: Library name: SJDMNORM018099_G1-FD_Tropo_1HEAD


title: Scere, lib524, control, NaCNBH3, SSIII, rep1

description: Library name: Sample 3

value: WT


title: ND75_2HEAD

description: Library name: SJDMNORM018094_G1-FD_ND75_2HEAD

value: ND-75 RNAi


title: Aortic endothelial cells treated with 0.5 Gy of ionizing radiation

source_name: aortic endothelial cells irradiated with 0.5 Gy

value: treated with 0.5 Gy (0.1 mGy/min) of ionizing radiation


title: ND75_1HEAD

description: Library name: SJDMNORM018093_G1-FD_ND75_1HEAD


title: ProsB5_2HEAD

description: Library name: SJDMNORM018079_G1-FD_ProsB5_2HEAD

value: prosb5 RNAi


title: ND75_3HEAD

description: Library name: SJDMNORM018095_G1-FD_ND75_3HEAD


title: Coronary artery endothelial cells with 0.5 Gy of ionizing radiation

source_name: coronary artery endothelial cells irradiated with 0.5 Gy


title: white_3HEAD

description: Library name: SJDMNORM018074_G1-FD_white_3HEAD

value: white RNAi


title: white_2HEAD

description: Library name: SJDMNORM018073_G1-FD_white_2HEAD


title: Coronary artery endothelial cells with 0.1 Gy of ionizing radiation

source_name: coronary artery endothelial cells irradiated with 0.1 Gy


title: ProsB5_1HEAD

description: Library name: SJDMNORM018078_G1-FD_ProsB5_1HEAD


title: white_1HEAD

description: Library name: SJDMNORM018072_G1-FD_white_1HEAD


title: GFP_3HEAD

description: Library name: SJDMNORM018071_G1-FD_GFP_3HEAD

value: GFP RNAi


title: Coronary artery endothelial cells not treated with ionizing radiation

source_name: coronary artery endothelial cells

value: not treated


title: Aortic endothelial cells treated with 2 Gy of ionizing radiation

source_name: aortic endothelial cells irradiated with 2 Gy


title: GFP_1HEAD

description: Library name: SJDMNORM018069_G1-FD_GFP_1HEAD


title: TER94_3TH

description: Library name: SJDMNORM018056_G1-FD_TER94_3TH

source_name: thorax

value: thorax


title: TER94_2TH

description: Library name: SJDMNORM018055_G1-FD_TER94_2TH


title: TER94_1TH

description: Library name: SJDMNORM018054_G1-FD_TER94_1TH


title: ND75_1TH

description: Library name: SJDMNORM018045_G1-FD_ND75_1TH


title: ND75_2TH

description: Library name: SJDMNORM018046_G1-FD_ND75_2TH


title: ProsB5_3TH

description: Library name: SJDMNORM018032_G1-FD_ProsB5_3TH


title: Tropo_3TH

description: Library name: SJDMNORM018053_G1-FD_Tropo_3TH


title: ProsB5_1TH

description: Library name: SJDMNORM018030_G1-FD_ProsB5_1TH


title: Tropo_1TH

description: Library name: SJDMNORM018051_G1-FD_Tropo_1TH


title: white_2TH

description: Library name: SJDMNORM018025_G1-FD_white_2TH


title: GFP_3TH

description: Library name: SJDMNORM018023_G1-FD_GFP_3TH


title: white_3TH

description: Library name: SJDMNORM018026_G1-FD_white_3TH


title: GFP_2TH

description: Library name: SJDMNORM018022_G1-FD_GFP_2TH


title: white_1TH

description: Library name: SJDMNORM018024_G1-FD_white_1TH


title: Ischemic cardiomyopathy patient rep22

city: Valencia

first: Estefanía

last: Tarazón

address: Avenida Fernando Abril Martorell 106

country: Spain

institute: Instituto de investigación Sanitaria La Fe

description: Library name: ISQ23

data_processing:
The quality control of the raw data was performed using the FastQC tool. For the adapter and quality filler of the raw data, trim_galore was applied [http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/] (accessed on 15 May 2020). Then, the insufficient quality reads (phred score < 20) were subsequently eliminated using Picard Tools software. RNA predictions were estimated using HT Seq software (version 0.6.0).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts  for each sample

source_name: Heart

extract_protocol:
Myocardial samples were homogenized using a TissueLyser LT (Qiagen, Hilden, Germany). RNA extraction for ncRNA-seq analysis was performed using a Quick-RNATM Miniprep Plus Kit (Zymo Research, CA, USA). RNA quantification was conducted using NanoDrop 1000 spectrophotometer and a Qubit 3.0 fluorometer (Thermo Fisher Scientific, Horsham, UK). RNA purity and integrity were assessed using a 0.8% agarose gel electrophoresis and Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip Kit (Agilent Technologies, CA, USA). All the samples presented a 260/280 absorbance ratio > 2.0 and an RNA integrity number ≥ 9.0.
For the ncRNA-seq analysis, cDNA libraries were prepared according to Illumina´s recommendations. Briefly, 3’ and 5’ adaptors were sequentially ligated to the RNA before reverse transcription and cDNA synthesis. The resulting cDNA was amplified using PCR to generate an indexed double-stranded cDNA library, followed by size selection with a 6% polyacrylamide gel. Library quality and concentration were assessed using a 4200 TapeStation (Agilent Technologies; Madrid, Spain) with the D1000 High-Sensitivity assay. The cDNA libraries were then pooled and sequenced using paired-end sequencing (100 × 2) on an Illumina HiSeq 2500 sequencer (Illumina, CA, USA).

value: Heart

tag: Sex

value: male

tag: disease state

value: Hert failure patient


title: Scere, lib524, control, Bisulfite+MgCl2+Heat, TGIRT, rep1

description: Library name: Sample 18

value: Yeast culture

value: control


title: Ischemic cardiomyopathy patient rep21

description: Library name: ISQ_33


title: Ischemic cardiomyopathy patient rep20

description: Library name: ISQ48


title: Ischemic cardiomyopathy patient rep18

description: Library name: ISQ128


title: Ischemic cardiomyopathy patient rep17

description: Library name: ISQ64


title: Ischemic cardiomyopathy patient rep19

description: Library name: ISQ53


title: Scere, lib524, control, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 6


title: Ischemic cardiomyopathy patient rep16

description: Library name: ISQ5


title: Ischemic cardiomyopathy patient rep15

description: Library name: ISQ19


title: ProsB5_2TH

description: Library name: SJDMNORM018031_G1-FD_ProsB5_2TH


title: Tropo_2TH

description: Library name: SJDMNORM018052_G1-FD_Tropo_2TH


title: ND75_3TH

description: Library name: SJDMNORM018047_G1-FD_ND75_3TH


title: Ischemic cardiomyopathy patient rep14

description: Library name: ISQ12


title: Ischemic cardiomyopathy patient rep11

description: Library name: ISQ51


title: Ischemic cardiomyopathy patient rep12

description: Library name: ISQ49


title: Ischemic cardiomyopathy patient rep13

description: Library name: ISQ13


title: Aortic endothelial cells not treated with ionizing radiation

source_name: aortic endothelial cells

tag: cell type

value: aortic endothelial cells


title: Ischemic cardiomyopathy patient rep8

description: Library name: ISQ61


title: Ischemic cardiomyopathy patient rep7

description: Library name: ISQ60


title: Ischemic cardiomyopathy patient rep10

description: Library name: ISQ1


title: Ischemic cardiomyopathy patient rep4

description: Library name: ISQ110


title: GFP_1TH

description: Library name: SJDMNORM018021_G1-FD_GFP_1TH

tag: genotype


title: Ischemic cardiomyopathy patient rep5

description: Library name: ISQ30


title: Ischemic cardiomyopathy patient rep9

description: Library name: ISQ58


title: Ischemic cardiomyopathy patient rep3

description: Library name: ISQ36


title: Ischemic cardiomyopathy patient rep6

description: Library name: ISQ31


title: Ischemic cardiomyopathy patient rep2

description: Library name: ISQ165


title: Ischemic cardiomyopathy patient rep1

description: Library name: ISQ14


title: Idiopathic dilated cardiomyopathy patient rep19

description: Library name: DIL59


title: Idiopathic dilated cardiomyopathy patient rep20

description: Library name: DIL6


title: Idiopathic dilated cardiomyopathy patient rep18

description: Library name: DIL21


title: Idiopathic dilated cardiomyopathy patient rep16

description: Library name: DIL119


title: Idiopathic dilated cardiomyopathy patient rep17

description: Library name: DIL68


title: Idiopathic dilated cardiomyopathy patient rep15

description: Library name: DIL96


title: Idiopathic dilated cardiomyopathy patient rep14

description: Library name: DIL106

value: female


title: Idiopathic dilated cardiomyopathy patient rep13

description: Library name: DIL20


title: Idiopathic dilated cardiomyopathy patient rep12

description: Library name: DIL39


title: Idiopathic dilated cardiomyopathy patient rep10

description: Library name: DIL69


title: Idiopathic dilated cardiomyopathy patient rep9

description: Library name: DIL54


title: Idiopathic dilated cardiomyopathy patient rep8

description: Library name: DIL80


title: Idiopathic dilated cardiomyopathy patient rep11

description: Library name: DIL28


title: Idiopathic dilated cardiomyopathy patient rep5

description: Library name: DIL105


title: Idiopathic dilated cardiomyopathy patient rep7

description: Library name: DIL62


title: Idiopathic dilated cardiomyopathy patient rep6

description: Library name: DIL24


title: Idiopathic dilated cardiomyopathy patient rep4

description: Library name: DIL_184


title: Idiopathic dilated cardiomyopathy patient rep2

description: Library name: DIL117


title: Control rep8

description: Library name: CNT156

value: Healthy control


title: Idiopathic dilated cardiomyopathy patient rep1

description: Library name: DIL63


title: Control rep6

description: Library name: CNT161


title: Control rep4

description: Library name: CNT200


title: Idiopathic dilated cardiomyopathy patient rep3

description: Library name: DIL8


title: Control rep3

description: Library name: CNT38


title: Control rep5

description: Library name: CNT66


title: Control rep2

description: Library name: CNT115


title: 20-somite stage, wildtype, rep 1

first: Yunxia

last: Wang

address: 300 Longwood Ave

institute: Boston Children's Hospital

description: Library name: Sample 3

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were converted to FASTQ files using bcl2fastq. 25 bases were trimmed from the 3’ end of read 1 using cutadapt.  Next, the zUMIs pipeline was used to demultiplex the sequencing data, remove reads with low-quality cell barcodes or UMIs, map the filtered reads to the zebrafish genome (version danRer11) plus ZsYellow, and generate count matrices, which were processed by the Seurat package (version 4.3.0). Cells with less than 500 genes detected, more than 3000 genes detected, or more than 20% mitochondrial reads were filtered from the analysis. In addition, transcripts encoding ribosomal subunits were also removed before log normalization, data scaling, principal component analysis, cell clustering, and UMAP visualization. Datasets from each developmental timepoint were integrated using canonical correlation analysis (CCA). Integrated data were then used for data scaling, PCA, cell clustering, and UMAP visualization. Differentially expressed genes between cell clusters were identified by the FindAllMarkers function using the default Wilcoxon test method. The heatmap showing the top 10 most highly expressed genes in each cluster was generated with the DoHeatmap function. Cell types were annotated based on the top differentially expressed genes. The LPM cluster was further divided into subclusters. The expression of selected marker genes for each LPM subcluster were visualized using the VlnPlot function. Gene Ontology (GO) enrichment analysis was performed for marker genes in each LPM subcluster using the clusterProfiler package (version 4.6.2).
Assembly: zebrafish genome (version danRer11)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: embryos

extract_protocol:
14- and 20-ss wildtype (TU) and Tg(nkx2.5:ZsYellow) embryos were dissociated to single cells. Briefly, 750 – 1000 embryos were collected and their chorions removed by incubation in 1mg/ml Pronase for 3–4 min followed by washing in 0.5X Danieau Buffer.  Yolks were removed in deyolking buffer followed by embryo dissociation in FACSmax Cell Dissociation solution. After passage through a 40 μm strainer, single cells were resuspended in fresh FACSmax Cell Dissociation solution and passed through a fluorescent activated cell sorter (BD FACSMelodyTM Cell Sorter) to separate the ZsYellow positive fraction. Sorted cells were collected in 0.1% BSA D-PBS.
The library prep protocol was based on SMART-Seq protocols with modifications. The workflow of the library preparation can be summarized as follows: Reverse transcription with Maxima H Minus RTase at 50°C for 60 min, followed by enzyme inactivation at 85°C for 3min -> post droplet breaking cleanup with MyOne SILANE beads -> Template switching using  Maxima H Minus RTase (incubate for 30’ at 25°C, 90’ at 42°C and hold at 4°C; with lid set to 50°C.) -> 1X SPRI purification -> cDNA amplification with PCRI Fwd Primer V2 and PCRI Rev Primer -> 0.6X SPRI purification. The gene expression libraries were made by subjecting the amplified cDNA to Fragmentation, end repair and A-tailing, followed by ligation using NEBNext UltraII FS DNA Library Prep kit for Illumina -> 0.8X SPRI cleanup -> sample indexing by PCR -> double-sided SPRI cleanup.

value: embryos

tag: cell line

value: nkx2.5:ZsYellow cells


title: 20-somite stage, wildtype, rep 2

description: Library name: Sample 4

tag: tissue


title: 14-somite stage, wildtype, rep 2

description: Library name: Sample 2


title: 14-somite stage, wildtype, rep 1

description: Library name: Sample 1


title: HSC_D13_2

city: Chongqing

first: Huang

last: Wu

state: Chongqing

address: 10 Changjiang Access Road

department: Department of Blood Transfusion

institute: Daping Hospital, Army Medical University

data_processing:
Index of the reference genome was built using bowtie2 v2.2.8 and paired-end clean reads were aligned.
CircRNAs were detected and identified by using find_circ and CIRI2 programs with default parameters.
The raw counts were first normalized using TPM.
Differential expression analysis was performed using the DEGseq (2010) R package.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: umbilical cord blood CD34+ cells

growth_protocol: CD34+ cells cultured in StemSpan™ SFEM II Medium with antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNAs were extracted using Trizol Reagent. Ribosomal RNA was removed by Epicentre Ribozero™ rRNA Removal Kit or linear RNA was digested by RNaseR(Epicentre).
RNA-Seq libraries preparation with NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®  according to the manufacturer's instructions.

treatment_protocol: megakaryocyte differentiation was induced by treatment  25 ng/ml stem cell factor (SCF) and 20 ng/ml thrombopoietin (TPO). Media was changed on days 3, 6 and 9; days 6 and 9 had no SCF and TPO was increased to 50 ng/mL.

value: umbilical cord blood CD34+ cells

value: hematopoietic stem cell

tag: treatment

value: megakaryocyte differentiation

tag: time

value: Day 13


title: Control rep1

description: Library name: CNT3


title: HSC_D6_1

value: Negative control (scr)


title: HSC_D6_3


title: HSC_D6_2


title: Control rep7

description: Library name: CNT67


title: SIHY003_7

city: Wako city

first: Taisei

last: Wakigawa

state: Saitama prefecture

address: 2-1, Hirosawa

institute: RIKEN

description: MitoIP-Ribo-Seq

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: The human or mouse nuclear genomes (human, hg38; mouse, mm10) and custom-made mitochondrial transcript sequences
Supplementary files format and content: Fpcount text files contain three columns:  1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts. Fpframing text files contain nine columns:  1. the length of mitoribosome footprint; 2. the fraction of mitoribosome footprint; 3~5. the number of mitoribosome footprint at each frames;  6~8,the fraction of mitoribosome footprint at each frames; 9. the relative entropy of mitoribosome footprint.
Library strategy: MitoIP-Ribo-Seq

extract_protocol:
MitoIP-Ribo-Seq, MitoIP-Thor-Ribo-Seq, and MitoIP-Thor-Disome-Seq: Cells were cultured in 15-cm dishes, washed with ice-cold PBS, and lysed with 1200 µl of hypotonic buffer (10 mM HEPES-KOH pH 7.5, 10 mM KCl, 1.5 mM MgCl2, 1 mM DTT, 100 µg/ml cycloheximide, and 100 µg/ml chloramphenicol). The lysate was incubated with anti-TOM22 antibody-conjugated beads from Mitochondria Isolation Kit, Human (Miltenyi Biotec) for 60 min at 4°C. The subsequent wash and elution steps were performed with wash buffer (10 mM HEPES-KOH pH 7.5, 10 mM KCl, 15 mM MgCl2, 1 mM DTT, 100 µg/ml cycloheximide, and 100 µg/ml chloramphenicol), according to the manufacturer’s instructions. The eluted mitochondrial fraction was pelleted by centrifugation at 7,000 × g for 10 min at 4°C and resuspended in modified lysis buffer (20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 15 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 µg/ml cycloheximide, 100 µg/ml chloramphenicol, and 2.5 U/ml TURBO DNase). After clarification by centrifugation at 20,000 × g for 10 min at 4°C, the supernatant was used for library preparation. For the mitoribosome run-off assay, HEK293 cells were pre-treated with 100 µg/ml retapamulin for 30, 60, 90, 120 s, or 30 min and then incubated with 100 µg/ml chloramphenicol and 100 µg/ml cycloheximide to arrest translation elongation. Subsequently, cell lysis and mitochondrial purification were performed as described above, adding 100 µg/ml retapamulin to all the solutions. For the mouse cardiac muscle, the frozen tissues were pulverized with 600 µl of liquid nitrogen-frozen hypotonic buffer using the Multi-beads Shocker at 3000 rpm for 30 sec for 2 cycles (Yasui Kikai). The lysate was clarified by an EASYstrainer (Greiner Bio-One), and mitochondria isolation was conducted as described above. Ribo-Seq and RNA-Seq: Cells in a 10-cm dish were lysed with 600 µl of lysis buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1% Triton X-100, 1 mM DTT, 100 µg/ml cycloheximide, and 100 µg/ml chloramphenicol) and treated with 25 U/ml TURBO DNase (Thermo Fisher Scientific). Then, the lysate was clarified by centrifugation at 20,000 × g for 10 min at 4°C.
Ribo-seq and MitoIP-Ribo-Seq: RNase treatment, ribosome pelleting, Ribo-FilterOut, size selection, preadenylated linker ligation, rRNA depletion, reverse transcription, cDNA circularization, and PCR amplification. MitoIP-Thor-Ribo-Seq and MitoIP-Thor-Disome-Seq: preadenylated linkers with the antisense sequence of T7 promoter were ligated and footprints were amplified by in vitro transcription. RNA-seq: the libraries were prepared by a SEQuoia Express Standard RNA Library Prep Kit (Bio-Rad).

tag: condition

value: naive


title: SIHY003_8

description: MitoIP-Ribo-Seq


title: SIHY003_5

description: MitoIP-Ribo-Seq


title: SIHY003_6

description: MitoIP-Ribo-Seq


title: SIHY003_1

description: MitoIP-Ribo-Seq


title: SIHY003_2

description: MitoIP-Ribo-Seq


title: SIHY002_8

description: MitoIP-Ribo-Seq


title: SIHY003_4

description: MitoIP-Ribo-Seq


title: SIHY002_5

description: MitoIP-Ribo-Seq


title: SIHY003_3

description: MitoIP-Ribo-Seq


title: SIHY002_7

description: MitoIP-Ribo-Seq


title: SIHY002_6

description: MitoIP-Ribo-Seq


title: SIHY002_3

description: MitoIP-Ribo-Seq


title: SIHY002_4

description: MitoIP-Ribo-Seq


title: HSC_D13_3


title: SIHY002_2

description: MitoIP-Ribo-Seq


title: SIHY002_1

description: MitoIP-Ribo-Seq


title: SIHY004_4

description: Ribo-Seq

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: The human or mouse nuclear genomes (human, hg38; mouse, mm10) and custom-made mitochondrial transcript sequences
Supplementary files format and content: Fpcount text files contain three columns:  1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts. Fpframing text files contain nine columns:  1. the length of mitoribosome footprint; 2. the fraction of mitoribosome footprint; 3~5. the number of mitoribosome footprint at each frames;  6~8,the fraction of mitoribosome footprint at each frames; 9. the relative entropy of mitoribosome footprint.
Library strategy: Ribo-Seq


title: SIHY004_3

description: Ribo-Seq


title: SIHY004_2

description: Ribo-Seq


title: HSC_D13_1


title: SIHY004_1

description: Ribo-Seq


title: Bsubt, lib524, control, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 17

data_processing:
Reads were aligned using STAR v2.7.5c (Dobin et al., 2013), alignments sorted using SAMtools v1.9 (Danecek et al., 2021), and processed to compute count data per nucleotide position using txtools 1.0.5 (Garcia-Campos et al., 2024)
Assembly: GCF_000009045.1
Supplementary files format and content: tab delimited file with count data for read-ends, read-starts, coverage, and nucleotide frequency per transcriptomic position

organism: Bacillus subtilis

source_name: bacterial culture

growth_protocol: Were grown in LB medium to late-exponential phase (OD600  ~2) at 37°C

extract_protocol:
Extraction was carried out using the FastRNA Pro Blue kit (MP Biomedicals) by the manufacturer’s instructions
Remaining primers left in the reaction were digested by addition of 3 μL ExoSAP-IT (Applied Biosystems, 78205) to the 20 μL reverse transcription reaction, and incubation at 37°C for 12 min. RNA was degraded by adding 2.5 μL of NaOH 1M and 1 μL of 0.5M EDTA, and incubation at 70°C for 12 min. The base was neutralized with the addition of 1M HCl, cDNA was cleaned using MyOne silane beads. An adapter was added to the 3’ end of the cDNA by ligating 50 pmoles 5iLL-22 DNA adapter using T4 RNA Ligase 1, High concentration (NEB, M0437M), DMSO 4%, ATP 1mM and PEG8000 25% at 23°C for 3 h. After clean-up with MyOne silane beads, we amplified the cDNA library for 12 cycles using Illumina Library PCR primers F and R and KAPA HiFi HotStart ReadyMix (Roche, KK2601). Amplified libraries were cleaned with Kapa pure beads (Roche, KK8002), quantified using Qubit (Life Technologies) and the distribution of library size was determined using TapeStation (Agilent Technologies).

value: bacterial culture

tag: strain

value: WT

tag: batch


title: Bsubt, lib524, control, CMC, TGIRT, rep1

description: Library name: Sample 12


title: Bsubt, lib524, control, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 14


title: Bsubt, lib524, control, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 13


title: Bsubt, lib524, control, Mock, TGIRT, rep1

description: Library name: Sample 16


title: Bsubt, lib524, control, AlkBmix, TGIRT, rep1

description: Library name: Sample 11


title: Bsubt, lib524, control, NaCNBH3, TGIRT, rep1

description: Library name: Sample 10


title: Bsubt, lib524, control, Bisulfite, TGIRT, rep1

description: Library name: Sample 15


title: Bsubt, lib524, control, Bisulfite+MgCl2+Heat, SSIII, rep1

description: Library name: Sample 9


title: Bsubt, lib524, control, MocklowdNTPs, SSIII, rep1

description: Library name: Sample 8


title: Bsubt, lib524, control, NaHCO3+NaCNBH3, SSIII, rep1

description: Library name: Sample 5


title: Bsubt, lib524, control, NaBH4HydBiotin, RTHIV, rep1

description: Library name: Sample 2


title: Bsubt, lib524, control, Mock, SSIII, rep1

description: Library name: Sample 7


title: Bsubt, lib524, control, NaHCO3+Heat, SSIII, rep1

description: Library name: Sample 6


title: Bsubt, lib524, control, NaCNBH3, SSIII, rep1

description: Library name: Sample 3


title: Hvolc, lib553, pH4_42C, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 169

data_processing:
Reads were aligned using STAR v2.7.5c (Dobin et al., 2013), alignments sorted using SAMtools v1.9 (Danecek et al., 2021), and processed to compute count data per nucleotide position using txtools 1.0.5 (Garcia-Campos et al., 2024)
Assembly: GCF_000025685.1
Supplementary files format and content: tab delimited file with count data for read-ends, read-starts, coverage, and nucleotide frequency per transcriptomic position

organism: Haloferax volcanii

source_name: Bacterial culture

growth_protocol: Were grown in duplicates in YPC medium containing  1.4M, 2.4M (optimum) and 4M salt at 42°C (optimum), as well as at low temperature (30°C) and high temperature (50°C) in YPC containing  2.4M salt

extract_protocol:
The aqueous phase was collected after centrifugation and mixed with an equal volume of ethanol. RNA was processed with the NEB Monarch Total RNA Miniprep Kit. DNase digestion to eliminate genomic DNA.
Remaining primers left in the reaction were digested by addition of 3 μL ExoSAP-IT (Applied Biosystems, 78205) to the 20 μL reverse transcription reaction, and incubation at 37°C for 12 min. RNA was degraded by adding 2.5 μL of NaOH 1M and 1 μL of 0.5M EDTA, and incubation at 70°C for 12 min. The base was neutralized with the addition of 1M HCl, cDNA was cleaned using MyOne silane beads. An adapter was added to the 3’ end of the cDNA by ligating 50 pmoles 5iLL-22 DNA adapter using T4 RNA Ligase 1, High concentration (NEB, M0437M), DMSO 4%, ATP 1mM and PEG8000 25% at 23°C for 3 h. After clean-up with MyOne silane beads, we amplified the cDNA library for 12 cycles using Illumina Library PCR primers F and R and KAPA HiFi HotStart ReadyMix (Roche, KK2601). Amplified libraries were cleaned with Kapa pure beads (Roche, KK8002), quantified using Qubit (Life Technologies) and the distribution of library size was determined using TapeStation (Agilent Technologies).

value: Bacterial culture


title: Hvolc, lib553, pH4_42C, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 170


title: Hvolc, lib553, pH2p4_42C, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 165


title: Bsubt, lib524, control, Bisulfite+MgCl2+Heat, TGIRT, rep1

description: Library name: Sample 18


title: Hvolc, lib553, pH2p4_50C, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 168


title: Hvolc, lib553, pH2p4_30C, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 163


title: Hvolc, lib553, pH1p4_42C, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 162


title: Hvolc, lib553, pH2p4_30C, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 164


title: TER94_3HEAD

description: Library name: SJDMNORM018104_G1-FD_TER94_3HEAD

value: head

value: TER94/VCP RNAi


title: Hvolc, lib553, pH2p4_30C, Mock, TGIRT, rep2

description: Library name: Sample 154


title: Hvolc, lib553, pH4_42C, Mock, TGIRT, rep1

description: Library name: Sample 159


title: Hvolc, lib553, pH2p4_50C, Mock, TGIRT, rep1

description: Library name: Sample 157


title: Hvolc, lib553, pH2p4_50C, Mock, TGIRT, rep2

description: Library name: Sample 158


title: Hvolc, lib553, pH2p4_42C, Mock, TGIRT, rep1

description: Library name: Sample 155


title: Bsubt, lib524, control, Mock, RTHIV, rep1

description: Library name: Sample 1

value: control


title: Hvolc, lib553, pH2p4_30C, Mock, TGIRT, rep1

description: Library name: Sample 153


title: Hvolc, lib553, pH1p4_42C, Mock, TGIRT, rep2

description: Library name: Sample 152


title: Bsubt, lib524, control, CMC, SSIII, rep1

description: Library name: Sample 4


title: Hvolc, lib553, pH2p4_50C, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 167


title: Hvolc, lib553, pH4_42C, Bisulfite, TGIRT, rep2

description: Library name: Sample 150


title: Hvolc, lib553, pH2p4_50C, Bisulfite, TGIRT, rep2

description: Library name: Sample 148


title: GFP_2HEAD

description: Library name: SJDMNORM018070_G1-FD_GFP_2HEAD

value: GFP RNAi


title: Hvolc, lib553, pH2p4_42C, Bisulfite, TGIRT, rep1

description: Library name: Sample 145


title: Hvolc, lib553, pH2p4_30C, Bisulfite, TGIRT, rep2

description: Library name: Sample 144


title: Hvolc, lib553, pH2p4_42C, Bisulfite, TGIRT, rep2

description: Library name: Sample 146


title: Hvolc, lib553, pH2p4_30C, Bisulfite, TGIRT, rep1

description: Library name: Sample 143


title: Hvolc, lib553, pH1p4_42C, Bisulfite, TGIRT, rep2

description: Library name: Sample 142


title: Hvolc, lib553, pH4_42C, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 139


title: Hvolc, lib553, pH1p4_42C, Bisulfite, TGIRT, rep1

description: Library name: Sample 141


title: Hvolc, lib553, pH4_42C, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 140


title: Hvolc, lib553, pH1p4_42C, NaBH4HydBiotin, TGIRT, rep1

description: Library name: Sample 161


title: Hvolc, lib553, pH4_42C, Mock, TGIRT, rep2

description: Library name: Sample 160


title: Hvolc, lib553, pH2p4_42C, Mock, TGIRT, rep2

description: Library name: Sample 156


title: Hvolc, lib553, pH2p4_50C, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 138


title: Hvolc, lib553, pH2p4_50C, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 137


title: Hvolc, lib553, pH2p4_30C, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 134


title: Hvolc, lib553, pH2p4_30C, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 133


title: Hvolc, lib553, pH1p4_42C, Mock, TGIRT, rep1

description: Library name: Sample 151


title: Hvolc, lib553, pH1p4_42C, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 132


title: Hvolc, lib553, pH1p4_42C, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 131


title: Hvolc, lib553, pH2p4_42C, NaHCO3+Heat, TGIRT, rep1

description: Library name: Sample 135


title: Hvolc, lib553, pH4_42C, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 130


title: Hvolc, lib553, pH2p4_50C, Bisulfite, TGIRT, rep1

description: Library name: Sample 147


title: Hvolc, lib553, pH2p4_42C, NaBH4HydBiotin, TGIRT, rep2

description: Library name: Sample 166


title: Hvolc, lib553, pH4_42C, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 129


title: Hvolc, lib553, pH2p4_50C, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 128


title: Hvolc, lib553, pH4_42C, Bisulfite, TGIRT, rep1

description: Library name: Sample 149


title: Hvolc, lib553, pH2p4_42C, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 125


title: Hvolc, lib553, pH2p4_42C, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 126


title: Hvolc, lib553, pH2p4_30C, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 123


title: Hvolc, lib553, pH2p4_30C, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 124


title: Hvolc, lib553, pH1p4_42C, NaHCO3+NaCNBH3, TGIRT, rep2

description: Library name: Sample 122


title: Hvolc, lib553, pH1p4_42C, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 121


title: Hvolc, lib553, pH4_42C, CMC, TGIRT, rep2

description: Library name: Sample 120


title: Hvolc, lib553, pH4_42C, CMC, TGIRT, rep1

description: Library name: Sample 119


title: Hvolc, lib553, pH2p4_42C, CMC, TGIRT, rep2

description: Library name: Sample 116


title: Hvolc, lib553, pH2p4_50C, CMC, TGIRT, rep2

description: Library name: Sample 118


title: TG_2mon_6

city: Ithaca

first: Praveen

last: Sethupathy

state: New York

address: 618 Tower Road, T7006

institute: Cornell University

data_processing:
The sequencing reads were aligned to the mouse genome (mm10). RNA-sequencing reads were mapped to genome release using STAR (v2.5.3a)
Transcript quantification was performed using Salmon (v0.6.0)
Normalization, sex and batch corrections and differential expression analysis were performed using DESeq2. The Benjamini-Hochberg method was used for multiple testing corrections.
Assembly: mm10
Supplementary files format and content: Normalized counts files are comma separated value matrices containing DESeq2 normalized counts for each of the samples.

source_name: liver

extract_protocol:
NEBNext Ultra II Directional Library Prep Kit
Total RNA was isolated from mouse liver tissues using the Total RNA Purification Kit (Norgen Biotek). RNA was quantified with the Nanodrop 2000 (ThermoFisher), and RNA integrity was assessed by the Agilent 4200 Tapestation (Agilent Technologies).
Batch_A: Libraries were prepared using Illumina TruSeq polyA + Sample Prep Kit and sequenced on the NextSeq2000 platform at the UNC High Throughput Sequencing Core Facility. Batch_B: Libraries were prepared using NEBNext Ultra II Directional Library Prep Kit and sequenced on the NextSeq2000 (Illumina) at the Biotechnology Research Center at the Cornell University.

value: TG

tag: age

value: Male

value: liver


title: Hvolc, lib553, pH2p4_42C, CMC, TGIRT, rep1

description: Library name: Sample 115


title: TG_2mon_5


title: Hvolc, lib553, pH2p4_50C, NaHCO3+NaCNBH3, TGIRT, rep1

description: Library name: Sample 127


title: Hvolc, lib553, pH2p4_30C, CMC, TGIRT, rep2

description: Library name: Sample 114


title: TG_2mon_4


title: Hvolc, lib553, pH1p4_42C, CMC, TGIRT, rep2

description: Library name: Sample 112


title: Hvolc, lib553, pH2p4_30C, CMC, TGIRT, rep1

description: Library name: Sample 113


title: WT_2mon_6


title: WT_2mon_5


title: Hvolc, lib553, pH1p4_42C, CMC, TGIRT, rep1

description: Library name: Sample 111


title: Hvolc, lib553, pH4_42C, AlkBmix, TGIRT, rep2

description: Library name: Sample 110


title: WT_2year_4


title: Hvolc, lib553, pH2p4_50C, AlkBmix, TGIRT, rep2

description: Library name: Sample 108


title: TG_2mon_3

extract_protocol:
Illumina TruSeq polyA + Sample Prep Kit
Total RNA was isolated from mouse liver tissues using the Total RNA Purification Kit (Norgen Biotek). RNA was quantified with the Nanodrop 2000 (ThermoFisher), and RNA integrity was assessed by the Agilent 4200 Tapestation (Agilent Technologies).
Batch_A: Libraries were prepared using Illumina TruSeq polyA + Sample Prep Kit and sequenced on the NextSeq2000 platform at the UNC High Throughput Sequencing Core Facility. Batch_B: Libraries were prepared using NEBNext Ultra II Directional Library Prep Kit and sequenced on the NextSeq2000 (Illumina) at the Biotechnology Research Center at the Cornell University.

value: Female


title: TG_2mon_2


title: Hvolc, lib553, pH4_42C, AlkBmix, TGIRT, rep1

description: Library name: Sample 109


title: Hvolc, lib553, pH2p4_50C, AlkBmix, TGIRT, rep1

description: Library name: Sample 107


title: WT_2mon_4


title: Hvolc, lib553, pH2p4_42C, AlkBmix, TGIRT, rep1

description: Library name: Sample 105


title: Hvolc, lib553, pH2p4_42C, AlkBmix, TGIRT, rep2

description: Library name: Sample 106


title: Hvolc, lib553, pH2p4_42C, NaHCO3+Heat, TGIRT, rep2

description: Library name: Sample 136


title: Hvolc, lib553, pH2p4_50C, CMC, TGIRT, rep1

description: Library name: Sample 117


title: WT_2mon_3


title: ProsB5_3HEAD

description: Library name: SJDMNORM018080_G1-FD_ProsB5_3HEAD

value: prosb5 RNAi


title: WT_2mon_2


title: WT_2mon_1


title: Hvolc, lib553, pH2p4_30C, AlkBmix, TGIRT, rep1

description: Library name: Sample 103


title: Hvolc, lib553, pH1p4_42C, AlkBmix, TGIRT, rep2

description: Library name: Sample 102


title: WT_2year_3