title: Nucleosome mapping in SNF2 depletion yeast cells

city: UNIVERSITY PARK

first: Lu

last: Bai

address: 406 South Frear

data_processing:
Pacbio subreads with at least 3 passes were converted to consensus sequences using the ccs command.
CCS reads were aligned using MATLAB scripts based on global and local alignment. GC and other C in each reference sequence were converted to GY and T, respectively. We removed reads if 1) alignment accuracy is lower than 90%, 2) there is more than one mismatch in the synthetic oligo region (430-540 bp in the reference sequence that contains NDF motifs), 3) there is a mismatch in NDF motifs, or 4) methylation level too low (< four methylated GC in total).
Aligned DNA sequences were converted to numeric arrays. Methylated GC (GC in read) was converted to 1, unmethylated GC (GT in read) was converted to -1. Other nucleotides were converted to 0. Arrays with less than four 1 were removed. Arrays were piled up to generate a matrix.
Methylation level of each biosample was normalized to one of the WT sample (SRR18404682, sample ID:17R) to account for the variantion of M.CviPI expression.
In nucleosome prediction step, we assumed that the DNA is fully protected towards the nucleosome dyad but has some flexibility near the entry/exit sites. We correlated this pattern with the methylation measurement in a 147 bp window from 5’ to 3’ to get a “nucleosome penalty score” and placed nucleosomes at the local minimums. In scenarios where a nucleosome covers NDF motifs, we calculated the total methylation level in the “NDR region” (from -958 bp to -405 bp). If it is higher than 90% of that in the background sequences, we assumed that the nucleosome-like protection was generated by other complexes, and this nucleosome was removed. We then further optimized the nucleosome positions to remove the bias generated by 5’ to 3’ scanning. When a protected region has a length between mono- and di-nucleosomes, the nucleosome was set as 160 bp and placed at the center of the protected region. If this lengthy protection was adjacent to an NDF motif, we placed the nucleosome at the edge of this region away from the motif assuming that part of the protection was generated by the NDF, or factors recruited by the NDF.
Supplementary files format and content: Normalized and combined DNA methylation matrixes were storaged in txt files. In methylation matrix, 1, -1, and 0 represent methylated GC, unmethylated GC, and other nucleotide, respectively. Each txt file contains 169 matrixes which aligned to the169 sythetic oligoes in the library. Nucleosome prediction matrixes were storaged in csv files. In nucleosome matrix, each number represent the nucleosome occupancy at each position . Each csv file contains 169 matrixes which aligned to the169 sythetic oligoes in the library. The title of each matrix contains the sample name, sequence index, and the NDF name. For example, methylation_matrix_INO80_1_ABF1 means this methylation matrix was from INO80 depletion strain; the index of the sequence was 1; and this sequence containing ABF1 motif.

source_name: Yeast cell

growth_protocol: Yeast was grown in SCD-Ura-Met medium to OD660 0.2

extract_protocol:
Yeast cells were digested by 100ug/ml of Zymolyase 100T at 37 degree and lysed by lysis buffer (0.28M EDTA pH8.0, 0.22M Tris-HCl pH8.0, and 2.2%SDS) at 65 degree. Genomics DNA was then extracted using phenol-cholorform-isoamly alcohol. Genomic DNA was treated with RNaseA, and cleaned up by Omega cycle pure kit.
EpiTect Fast DNA Bisulfite kit was used to bisulfite convert methylated genomic DNA. 1µg of DNA was used for each reaction; 2 cycles of 95degree for 5min and 60degree for 20min were used to convert DNA. Target synthetic libraries were then amplified by EpiMark Hot Start Taq DNA Polymerase and Turbo Cx Pfu. A 25ul PCR reaction contains 1ul of bisulfite-converted template, 0.5ul of each 10uM primer, 5ul of 5X EpiMark Taq buffer, 0.5ul of 10mM dNTPs, 0.125ul of EpiMark Hot Start Taq DNA Polymerase, and 0.05ul of Pfu Turbo Cx HotStart DNA polymerase. PCR thermal cycle is shown below: 1 cycle of 95 for 5min, 23cycles of 95degree for 25s, 55degree for 30s and 68degree for 90s, and 1cycle of 68degree for 5min. PCR reactions were concentrated using Amicon Ultra 30K filters and then cleaned up using SPRI beads.

treatment_protocol: Yeast cells were treated with 1ug/ml of Rapamycin for 2 hour followed by 10ug/ml Doxycycline for 2 hours.

value: MATa, can1, his3, leu2, ura2, hoprurs2 (nt-1298 to -272), tor1-1, fpr1::NAT, RPL13A-2XFKBP12::TRP1, SNF2:SNF2-FRB-TAP::kanMX, ho:CYC1corepr(7xtetO)-SV40NLS-M.CviPI:TDH3pr-TetR-SSN6:TDH3pr-rvTetR-VP16AD-Gal4AD::KlLEU2, CLN2:HOprurs2-swi5mut-NDFmotifs-GFP:CaURA3

value: 2hr 1ug/ml Rapamycin followed by 2hr 10ug/ml Doxycycline


title: DC907 cold treat 3 day rep2

status: Public on Apr 06 2022

type: SRA

city: Nanning

first: Zhichi Zeng

last: Zhichi Zeng

address: Nanning

country: China

institute: Guangxi University

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Use fastq software to evaluate the quality of the row data. Use NGS QC toolkit software to filter the row data.
Clean reads were compared to the reference genome of rice cultivar 9311 using hisat2
The genome mapping results of all sequenced reads data were put together, assembled with cufflinks, and then compared with known gene models with cuffcompare
Differential expression analysis was performed using DEseq  package in R. We define Padj < 0.05 as differential gene, where Padj is the p value corrected by multi hypothesis test
Genome_build: 9311
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Oryza sativa Indica Group

source_name: stems and leaves

growth_protocol: 9311 and DC07 were hydroponically cultured in plastic barrels with Hogland nutrient solution and grew to four leaf stage at room temperature

extract_protocol:
The aboveground samples of rice were collected, quenched in liquid nitrogen, and RNA was collected with Trizol reagent. Illumina truseq RNA sample preparation kit was used to construct sequencing library together with 1 ug total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In this study, rice seedlings were treated with cold stress at 8 ℃± 0.5 ℃ for 1 or 3 days, and then recovered at room temperature for 1 or 3 days

tag: developmental stage

value: four-leaf stage

tag: genotype

tag: treatment

value: cold stress treatment for 3 day


title: HF-cultured [H2c]

city: Clayton

first: Hieu

middle: Tri

last: Nim

state: VIC

address: Monash University Clayton Campus, Wellington Rd

department: Australian Regenerative Medicine Institute

country: Australia

institute: Monash University

description:
Control kept additional 3 days in culture
H2c-RNA_GT20-13848_CTGAAGCT-GCCTCTAT_S3
20-rosenthal-001_gene_counts.txt

data_processing:
Single-end reads were mapped to the UCSC mouse transcriptome by Bowtie, allowing up to two mismatches, and expression levels of all UCSC genes were estimated by RSEM with default parameters.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: 20-rosenthal-001_gene_counts.txt: Tab-delimited count matrix.

organism: Mus musculus

source_name: Murine adult heart fibroblasts

extract_protocol:
RNA concentration and quality were assessed using the Nanodrop 2000 spectrophotometer (Thermo Scientific) and the RNA 6000 Pico assay (Agilent Technologies). Libraries were constructed using the SMARTer Stranded Total RNA-Seq Kit v2-Pico (Takara), according to the manufacturer’s protocol. Libraries were pooled and sequenced 75 bp single-end on the NextSeq 500 (Illumina) using NextSeq High Output Kit v2.5 reagents (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Adult fibroblasts from heart, tail and kidney were isolated from 10 weeks old Rosa mT/mG male mice. After ten days cells were collected, counted and 4-5x10^5 cells were transferred in individual 1.5ml Eppendorf tubes (one per each kidney transplant), resuspended in 15-20ul of saline solution and kept on ice, until ready for the surgery. Fragments of fragments of sterile absorbable gelatin foam (Surgifoam, Ethicon), about 1mm long, were soaked in a drop of cell suspension and transplanted in the further end of a pocket created in the subcapsular space of the kidney of syngeneic 10-11 weeks old C57bl6/j mice. The full surgical procedure is described in the paper. The remaining cells were re-plated (5x10^4/well of a mw6 plate) for the cultured cells controls.

tag: cell type

value: primary heart fibroblasts

value: C57BL/6 background Rosa mT/mG

tag: age

value: adult

tag: condition

value: Cultured


title: HF-cultured [H3c]

description:
Control kept additional 3 days in culture
H3c-RNA_GT20-13849_TAATGCGC-GCCTCTAT_S2
20-rosenthal-001_gene_counts.txt


title: SJRHB013758_X2

city: Memphis

first: Michael

last: Dyer

state: TN

address: 262 Danny Thomas Pl MS 324

department: Developmental Neurobiology

country: USA

institute: St. Jude Children's Research Hospital

description: single cell RNA-sequence

data_processing:
Single cell or nucleus RNA-seq reads from tumors or O-PDXs were aligned using the 10x Genomics Cell ranger Pipeline (v3.0.2) to the hg19 reference data v3.0.0 (for tumors) or hg19-and-mm10 v3.0.0 (for O-PDXs). In the case of single-nucleus datasets, a custom pre-mRNA reference was used to include intronic reads into expression matrices
Genome_build: hg19 or hg19-and-mm10
Supplementary_files_format_and_content: Cell Ranger output

organism: Homo sapiens

source_name: Orthotopic patient-derived xenograft

extract_protocol:
single cell dissociation
Tumor and xenograft samples were dissociated using an enzymatic tumor dissociation with papain. A detailed protocol is available on protocols.io at https://dx.doi.org/10.17504/protocols.io.98ah9se
10x Genomics 3' single-cell gene expression kit

tag: tissue

value: xenograft

tag: protocol

value: 10x genomics 3' scRNA-seq


title: CS_seedling_pNET_seq_rep2

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

data_processing:
Library strategy: pNET-seq
Sequencing reads were cleaned with Trim Galore (version 0.6.4) and cutadapt (version 1.16) programs to remove sequencing adapters, low quality bases (< 20), short reads and the 4 bases in 5’end and 3’end of R1 and R2 which were randomly introduced.
Clean reads were aligned to the International Wheat Genome Sequencing Consortium (IWGSC) reference sequence (version 1.0) with the bowtie2 (version 2.3.5.1) program and only keep the reads with one best unique alignment. We also used SortMeRNA (version 2.1b) program to remove the reads originating from chloroplast, mitochondria and rRNA.
For GRO-seq, the 5′ coordinate of R1 reads was considered the position of the engaged polymerase for future analyses. Each site density of GRO-seq was then calculated in plus and minus strands and normalized by the count of unique mapped reads. For pNET-seq,  the 5′ coordinate of R2 reads with the directionality indicated by R1 reads was considered the position of the engaged polymerase.
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: GRO-seq and pNET-seq signal in each site were provided in bedgraph file.

organism: Triticum aestivum

source_name: Triticum aestivum 12-days-old seedlings

growth_protocol: The bread wheat (Triticum aestivum) cultivar “Chinese Spring” were grown under long day condition.

extract_protocol:
Leaf tissue of 12-day-old seedlings were collected by flash freezing with liquid nitrogen and followed by nuclei isolation.
For GRO-seq, nuclei were isolated by the Percoll gradient procedure as previously described except that the concentration of Triton X-100 was reduced to 0.5%. In vitro run-on, and nascent RNA purification were performed as previously reported20. The obtained nascent RNA was treated with T4 PNK (NEB), followed by TRIzol purification and subject to small RNA library construction using NEXTflex™ Small RNA-Seq Kit v3 (PerkinElmer) according to the manufacturer manual. The cDNA libraries were sequenced on the Illumina NovaSeq platform. For pNET-seq, nuclei were isolated by a lysis-and-wash procedure as previously described except that the concentration of Triton X-100 was reduced to 0.5%. The RNA Pol II associated RNA were immunoprecipitated using Pol II antibody (Abcam, ab817) and followed by small RNA cDNA library construction. The size selection of nascent RNA was omitted. The cDNA libraries were sequenced on the Illumina NovaSeq platform.

treatment_protocol: No treatment applied

value: 12-days-old seedlings

tag: cultivar

value: Chinses Spring


title: Nucleosome mapping in INO80 depletion yeast cells

state: PA

institute: Penn State University

library_source: genomic

molecule: genomic DNA

organism: Saccharomyces cerevisiae

treatment_protocol: Yeast cells were treated with 1ug/ml of Rapamycin for 1 hour followed by 100nM beta-estradiol for 2 hours.

value: MATa, can1, his3, leu2, ura2, hoprurs2 (nt-1298 to -272), tor1-1, fpr1::NAT, RPL13A-2XFKBP12::TRP1, INO80:INO80-FRB-GFP-TAP::kanMX, ADH1::M.CviPI:LexA-ERHBD-VP16::LEU2, MET25pr-TetR::HIS3, CLN2:HOprurs2-swi5mut-NDFmotifs-GFP:CaURA3

value: 1hr 1ug/ml Rapamycin followed by 2hr 100nM beta-estradiol


title: DC907 cold treat 3 day and recover 3 day rep1

value: recovered 3 day after cold treatment for 3 day


title: DC907 cold treat 1 day and recover 3 day rep3

value: recovered 3 day after cold treatment for 1 day


title: HF- transplanted [H3]

description:
Transplanted under the kidney capsule for 3 days
H3-RNA_GT20-13840_CTGAAGCT-GTCAGTAC_S7
20-rosenthal-001_gene_counts.txt

value: Transplanted


title: DC907 cold treat 3 day rep1


title: HF-cultured [H1c]

description:
Control kept additional 3 days in culture
H1c-RNA_GT20-13847_GAATTCGT-GCCTCTAT_S15
20-rosenthal-001_gene_counts.txt


title: SJRHB013758_X1

description: single cell RNA-sequence


title: DC907 cold treat 1 day and recover 3 day rep2


title: SJRHB012_Z

description: single cell RNA-sequence


title: HF- transplanted [H2]

description:
Transplanted under the kidney capsule for 3 days
H2-RNA_GT20-13839_GAATTCGT-GTCAGTAC_S17
20-rosenthal-001_gene_counts.txt


title: SJRHB012_Y

description: single cell RNA-sequence


title: Nucleosome mapping in ISW2 depletion yeast cells

value: MATa, can1, his3, leu2, ura2, hoprurs2 (nt-1298 to -272), tor1-1, fpr1::NAT, RPL13A-2XFKBP12::TRP1, ISW2:ISW2-FRB-GFP-TAP::kanMX, ADH1::2xlexO-GAL1corepr-SV40NLS-M.CviPI:LexA-ERHBD-VP16::LEU2, MET25pr-TetR::HIS3, CLN2:HOprurs2-swi5mut-NDFmotifs-GFP:CaURA3


title: SJRHB030680_X1

description: single cell RNA-sequence


title: Nucleosome mapping in WT yeast cells

value: MATa, can1, his3, leu2, ura2, hoprurs2 (nt-1298 to -272), tor1-1, fpr1::NAT, RPL13A-2XFKBP12::TRP1, ADH1::2xlexO-GAL1corepr-SV40NLS-M.CviPI:LexA-ERHBD-VP16AD::LEU2, CLN2:HOprurs2-swi5mut-NDFmotifs-GFP:CaURA3, Met25pr-TetR::HIS3


title: SJRHB012405_X1

description: single cell RNA-sequence


title: Nucleosome mapping in STH1 depletion yeast cells

value: MATa, can1, his3, leu2, ura2, hoprurs2 (nt-1298 to -272), tor1-1, fpr1::NAT, RPL13A-2XFKBP12::TRP1, ADH1::2xlexO-GAL1corepr-SV40NLS-M.CviPI:LexA-ERHBD-VP16AD::LEU2, STH1:STH1-FRB-TAP::kanMX, CLN2:HOprurs2-swi5mut-NDFmotifs-GFP:CaURA3

value: MATa, can1, his3, leu2, ura2, hoprurs2 (nt-1298 to -272), tor1-1, fpr1::NAT, RPL13A-2XFKBP12::TRP1, ADH1::2xlexO-GAL1corepr-SV40NLS-M.CviPI:LexA-ERHBD-VP16::LEU2, MET25pr-TetR::HIS3, CLN2:HOprurs2-swi5mut-NDFmotifs-GFP:CaURA3


title: DC907 cold treat 1 day and recover 1 day rep3

value: four-leaf stage

value: recovered 1 day after cold treatment for 1 day


title: DC907 cold treat 1 day and recover 3 day rep1


title: TFc-cultured [T3c]

description:
Control kept additional 3 days in culture
T3c-RNA_GT20-13855_GAATTCGT-AGGATAGG_S4
20-rosenthal-001_gene_counts.txt

source_name: Murine adult tail fibroblasts

value: primary tail fibroblasts

value: C57BL/6 background Rosa mT/mG

value: adult


title: HF- transplanted [H1]

description:
Transplanted under the kidney capsule for 3 days
H1-RNA_GT20-13838_ATTCAGAA-GTCAGTAC_S11
20-rosenthal-001_gene_counts.txt

value: primary heart fibroblasts


title: SJRHB011_X

description: single cell RNA-sequence

value: xenograft

value: 10x genomics 3' scRNA-seq


title: TFc-cultured [T2c]

description:
Control kept additional 3 days in culture
T2c-RNA_GT20-13854_ATTCAGAA-AGGATAGG_S16
20-rosenthal-001_gene_counts.txt

value: Cultured


title: KF- transplanted [K2]

description:
Transplanted under the kidney capsule for 3 days
K2-RNA_GT20-13842_CGGCTATG-ACGTCCTG_S10
20-rosenthal-001_gene_counts.txt

source_name: Murine adult kidney fibroblasts

value: primary kidney fibroblasts


title: WT_2

city: Shenyang

first: Xiaotong

last: Zhu

state: Liaoning

address: No. 77 Puhe Road Shenyang North NEW AREA

department: Department of Immunology

institute: China Medical University

description: integral membrane protein GPR180, putative

data_processing:
Illumina Csava 1.7 software was used for basecalling.
Raw reads in the fastq format were firstly processed through in-house Perl scripts to remove low-quality reads, reads containing adapter, and ploy-N. Meanwhile, the Q20, Q30 and GC content of the clean data were calculated.
The UMI (Unique Molecular Identifiers) was extracted by the UMI-tools (v2.0.4). Only clean UMI reads were kept for further analysis.
RNA-seq reads from each sample were mapped to the P. berghei ANKA genome obtained from the NCBI reference genome (PbANKA01) using the Hisat2 (v2.0.4).The UMI-tools (v1.0.0) were used to deduplicate reads based on the mapping coordinates and the UMI attached to the read.
Assembly: GCF_900002375.1
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

organism: Plasmodium berghei

source_name: parasite

extract_protocol:
Total RNA was extracted from the 48% Nycodenz purified activated gametocytes (incubation at 25℃ for 15 min ) of the WT and Δpbgpr180 K1 parasites using the Qiagen RNeasy kit (Qiagen, Dusseldorf, Germany). The purity of RNA was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total of 1 µg total RNA was used to purify the mRNAs using poly-T oligo-attached magnetic beads, followed by fragmentation using divalent cations under elevated temperature in the first-strand synthesis reaction buffer.
RNA libraries were prepared for sequencing using standard illumina protocols

value: wild type

value: activated gametocytes


title: SJRHB010928_X1

description: single cell RNA-sequence


title: DC907 cold treat 1 day and recover 1 day rep1


title: KO_2

value: delta pbgpr180


title: TFc-cultured [T1c]

description:
Control kept additional 3 days in culture
T1c-RNA_GT20-13853_AGCGATAG-GCCTCTAT_S12
20-rosenthal-001_gene_counts.txt


title: KO_1


title: SJRHB010927_X1

description: single cell RNA-sequence


title: DC907 cold treat 1 day rep3

value: cold stress treatment for 1 day


title: WT_1


title: SJRHB000026_X2

description: single cell RNA-sequence


title: TF- transplanted [T3]

description:
Transplanted under the kidney capsule for 3 days
T3-RNA_GT20-13846_ATTCAGAA-GCCTCTAT_S13
20-rosenthal-001_gene_counts.txt

value: Transplanted


title: DC907 cold treat 1 day rep2


title: SJRHB000026_X1

description: single cell RNA-sequence


title: TF- transplanted [T1]

description:
Transplanted under the kidney capsule for 3 days
T1-RNA_GT20-13844_TCTCGCGC-ACGTCCTG_S1
20-rosenthal-001_gene_counts.txt


title: TF- transplanted [T2]

description:
Transplanted under the kidney capsule for 3 days
T2-RNA_GT20-13845_AGCGATAG-AGGCTATA_S6
20-rosenthal-001_gene_counts.txt


title: SJRHB046156_A1

description: single nucleus RNA-sequence

source_name: Patient tumor

extract_protocol:
single nucleus extraction
Nuclei were isolated from frozen tissue samples using a combination of detergent and mechanical separation in TST buffer. A detailed protocol is available on protocols.io at https://dx.doi.org/10.17504/protocols.io.bhbcj2iw
10x Genomics 3' single-cell gene expression kit

value: tumor

value: 10x genomics 3' snRNA-seq


title: SJRHB031320_D1_sn

description: single nucleus RNA-sequence


title: DC907 cold treat 1 day rep1

value: four-leaf stage


title: DC907 control rep3

value: untreated


title: SJRHB013759_A2

description: single nucleus RNA-sequence


title: DC907 control rep2


title: SJRHB013759_A1

description: single nucleus RNA-sequence


title: DC907 control rep1


title: 9311 cold treat 3 day and recover 1 day rep3

value: WT

value: recovered 1 day after cold treatment for 3 day


title: polyA RNA-seq in NRVMs at pH 7.44, rep3

city: Oxford

first: Pawel

last: Swietach

address: Sherrington Building, Parks Road

department: Department of Physiology, Anatomy & Genetics

country: United Kingdom

institute: University of Oxford

data_processing:
RNA-seq reads were aligned to the rn6 genome using STAR
Duplicate reads were removed using samtools rmdup
Read counts were determined using featureCounts (Subread package)
Differential gene expression analysis was conducted using DESeq2
Genome_build: rn6
Supplementary_files_format_and_content: feature counts, contrast table

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Neonatal rat ventricular myocytes (NRVMs)

growth_protocol: Primary neonatal rat ventricular myocytes were isolated from P1/P2 hearts of 1-2 day old Sprague-Dawley rats by enzymatic digestion, and a ‘pre-plating’ step was introduced to reduce fibroblasts in the myocyte-containing supernatant. Cells were plated onto fibronectin-coated TC culture dishes and cultured in M2 medium (80% DMEM medium containing 24 mM NaHCO3 and 20% M199 medium with 26mM NaHCO3) and incubated in a 5% CO2 atmosphere.  Initially, medium was supplemented with 10% horse serum, 5% newborn calf serum and penicillin/streptomycin mixture. Next day, cells were serum-starved, followed by incubation in different concentrations of NaHCO3 for 48 h to adjust the pH as indicated.

extract_protocol:
Total RNA was extracted using Quick-RNA Miniprep Kit (Zymo Research) following manufacturer’s instructions and eluted into nuclease-free water.
PolyA RNA was purified using the NEBNext Poly(A) mRNA magnetic isolation module (E7490) and DNA libraries were prepared using the NEBNext Ultra II Directional RNA library preparation kit for Illumina (E7765).

treatment_protocol: Serum-starved cells were incubated in NaHCO3 at concentrations from 3.05 mM to 24.4 mM for 48 h to adjust the pH of the medium as indicated

tag: strain

value: Sprague-Dawley


title: polyA RNA-seq in NRVMs at pH 7.44, rep2

value: Neonatal rat ventricular myocytes (NRVMs)


title: 9311 cold treat 3 day and recover 1 day rep2


title: polyA RNA-seq in NRVMs at pH 7.44, rep1


title: polyA RNA-seq in NRVMs at pH 7.12, rep3


title: SJRHB030680_R1_sn

description: single nucleus RNA-sequence


title: SJRHB010468_D1

description: single nucleus RNA-sequence


title: SJRHB013757_D2

description: single nucleus RNA-sequence


title: SJRHB049189_D1

description: single nucleus RNA-sequence


title: 2B-sg4C CS_1

type: RNA

city: Taipei

first: Ching-Yu

last: Lin

address: R202, Institute of Biological Chemistry National Taiwan University, No. 1, Sec. 4, Roosevelt Rd.

department: Ph.D. Program for Cancer Molecular Biology and Drug Discovery

country: Taiwan

institute: Taipei Medical University

description: KDM4C gene knockout cell repeat 1, culture in RPMI 1640 medium with charcoal stripping 10% FBS

hyb_protocol: Samples were hybridized with Clariom™ S Assay, human Arrays (Affymetrix) and scanned at the NHRI Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: The data were analyzed using Transcriptome Analysis Console (TAC) Software default analysis settings. Expression values were processed with Signal Space Transformation (SST) and Robust Multichip Average method, which included log2 transformation and quantile normalization.

label: biotin

source_name: human prostate cell line

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Plus cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Control and CRISPR knockout gene KDM4C in Prostate cell line C4-2B after sequencing were seeding 1^10^6 in 10 cm2 dish and harvested cell afer 2 days incubation.

extract_protocol: C4-2B RNA was isolated by using the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: Empty All-in-one CRISPR-cas9 pasmid bought from RNAiCore as control group, CRISPR knockout KDM4C as experimental groups.

tag: cell line

value: immortalized human prostate epithelial cell line

tag: gender

value: male

tag: disease state

value: prostate cancer


title: 9311 cold treat 3 day rep3

value: cold stress treatment for 3 day


title: polyA RNA-seq in NRVMs at pH 7.12, rep2


title: 9311 cold treat 3 day rep2


title: 2B-sg4C CS_2

description: KDM4C gene knockout cell repeat 2, culture in RPMI 1640 medium with charcoal stripping 10% FBS


title: 2B-sgCon CS_2

description: control cell repeat 2, culture in RPMI 1640 medium with charcoal stripping 10% FBS

value: sgcontrol


title: 2B-sg4C CS_3

description: KDM4C gene knockout cell repeat 3, culture in RPMI 1640 medium with charcoal stripping 10% FBS


title: 2B-sgCon CS_1

description: control cell repeat 1, culture in RPMI 1640 medium with charcoal stripping 10% FBS


title: DC907 cold treat 1 day and recover 1 day rep2

value: recovered 1 day after cold treatment for 1 day


title: Aging-3

city: Beijing

first: Jinghua

last: Yang

address: 32 North Third Ring Road West, Haidian District, Beijing

institute: Beijing Zhiyun data technology co. LTD

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2565BA).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at The Agilent Feature Extraction Software (version 11.0.1.1) was used to analyze and extract array images. Quantile normalization and subsequent data processing were conducted in GeneSpring GX v12.1 software package (Agilent Technologies). Threshold defined as fold-change > 2.0 (Student’s t test, P < 0.05) was used as a volcano plot filtering for DE lncRNAs and mRNAs.

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Frozen meniscus tissue from Aging and Young patient were cryo pulverized using biopulverizer (Biospec) and homogenized with TRIzol (Invitrogen Life Technologies) by Mini-Bead-Beater-16 (Biospec). RNA was collected from each sample based on the manufacturer’s protocols.

treatment_protocol: The fresh meniscus tissues were snap-frozen in liquid nitrogen and then stored at -80 degrees Celsius.

value: Meniscus tissue

value: aged


title: polyA RNA-seq in NRVMs at pH 7.12, rep1


title: 2B-sgCon CS_3

description: control cell repeat 3, culture in RPMI 1640 medium with charcoal stripping 10% FBS


title: Young-4

value: young


title: Young-5


title: SJRHB013758_D1

description: single nucleus RNA-sequence

value: tumor


title: 9311 cold treat 3 day and recover 1 day rep1


title: Young-1


title: Aging-4


title: polyA RNA-seq in NRVMs at pH 6.98, rep3


title: 9311 cold treat 3 day rep1


title: Young-3


title: SJRHB012405_D1

description: single nucleus RNA-sequence

value: 10x genomics 3' snRNA-seq


title: 9311 cold treat 1 day and recover 1 day rep3

value: four-leaf stage


title: SJRHB012_S

description: single nucleus RNA-sequence


title: SJRHB013758_D2

description: single nucleus RNA-sequence


title: polyA RNA-seq in NRVMs at pH 6.98, rep2


title: 9311 cold treat 1 day and recover 1 day rep2


title: RNA-Seq HepG2 SAMD1 KO repl1

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

country: Germany

institute: Philipps University of Marburg

data_processing:
ChIP-Seq data were aligned to human genome hg19 or hg38 using Bowtie, allowing one mismatch.
SAM files were converted to bigwig files using SamTools, and deepTools/bamCoverage. Data were normalized to RPKM.
RNA-Seq data were aligned to human transcriptome GenCode.v34 using RNA Star. Counts per gene were determined using FeatureCounts. Differentially expressed genes and normalized reads were determined using DeSeq2.
Genome_build: hg19,hg38
Supplementary_files_format_and_content: bigwig
Supplementary_files_format_and_content: RNA-Seq DESeq2.txt, RNA-Seq Normalized-Counts.txt

growth_protocol: HepG2 cells were cultured with MEM, GlutaMAX™ (Thermo Fisher Scientific; 41090036) supplemented with 10% Fetal Bovine Serum (Merck; F7524), 1% Penicillin-Streptomycin (Thermo Fisher Scientific; 15140148), and 1x non-essential amino acids (Thermo Fisher Scientific; 11140050).

extract_protocol:
ChIP experiments were performed in accordance to the One Day ChIP kit protocol (Diagenode). Total RNA was extracted by using the RNeasy Mini system (Qiagen) including an on-column DNaseI digestion.
For ChIP-Seq library five nanograms of precipitated DNA were used for indexed sequencing library preparation using the Microplex library preparation kit v2 (Diagenode). RNA-Seq libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina).

value: SAMD1 KO


title: RNA-Seq HepG2 SAMD1 KO repl2


title: RNA-Seq HepG2 SAMD1 KO repl3


title: 9311 cold treat 1 day and recover 1 day rep1

value: WT


title: RNA-Seq HepG2 Control repl3

value: Control


title: polyA RNA-seq in NRVMs at pH 6.98, rep1

value: Sprague-Dawley


title: SJRHB011_D

description: single nucleus RNA-sequence


title: polyA RNA-seq in NRVMs at pH 6.79, rep3

value: Neonatal rat ventricular myocytes (NRVMs)


title: 9311 cold treat 1 day rep2

value: cold stress treatment for 1 day


title: polyA RNA-seq in NRVMs at pH 6.79, rep2


title: RNA-Seq HepG2 Control repl2


title: Aging-1


title: SJRHB010927_D1

description: single nucleus RNA-sequence


title: SJRHB010928_R1

description: single nucleus RNA-sequence


title: polyA RNA-seq in NRVMs at pH 6.4, rep3


title: SJRHB012_R

description: single nucleus RNA-sequence


title: Aging-5


title: 9311 cold treat 1 day rep1


title: SJRHB000026_R3

description: single nucleus RNA-sequence


title: polyA RNA-seq in NRVMs at pH 6.79, rep1


title: ChIP-Seq H3K4me2 HepG2 SAMD1 KO

tag: antibody

value: H3K4me2 (Diagenode; C15310035)


title: SJRHB000026_R2

description: single nucleus RNA-sequence


title: 9311 cold treat 1 day rep3


title: SJRHB031320_D1

description: single cell RNA-sequence

value: 10x genomics 3' scRNA-seq


title: 9311 control rep3

value: untreated


title: 9311 control rep2


title: ChIP-Seq H3K4me2 HepG2 Control


title: ChIP-Seq SAMD1 HepG2 Control

value: SAMD1 (self made)


title: ChIP-Seq SAMD1 HepG2 SAMD1 KO


title: polyA RNA-seq in NRVMs at pH 6.4, rep1


title: 9311 control rep1


title: SJRHB030680_R1

description: single cell RNA-sequence

data_processing:
Single cell or nucleus RNA-seq reads from tumors or O-PDXs were aligned using the 10x Genomics Cell ranger Pipeline (v3.0.2) to the hg19 reference data v3.0.0 (for tumors) or hg19-and-mm10 v3.0.0 (for O-PDXs). In the case of single-nucleus datasets, a custom pre-mRNA reference was used to include intronic reads into expression matrices
Genome_build: hg19
Genome_build: hg19-and-mm10
Supplementary_files_format_and_content: matrix

extract_protocol:
Tumor and xenograft samples were dissociated using an enzymatic tumor dissociation with papain. A detailed protocol is available on protocols.io at https://dx.doi.org/10.17504/protocols.io.98ah9se
10x genomics 3’ scRNA-seq gene expression kits were used to construct libraries
10x genomics 3’ scRNA-seq gene expression kits were used to construct libraries

treatment_protocol: Nuclei were isolated from frozen tissue samples using a combination of detergent and mechanical separation in TST buffer. A detailed protocol is available on protocols.io at https://dx.doi.org/10.17504/protocols.io.bhbcj2iw


title: RNA-Seq HepG2 Control repl1


title: InfectedGroup_T36

status: Public on Apr 05 2022

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

data_processing:
Procession of the 10× gene expression data, including barcode processing and single-cell gene counting, was performed using software CellRanger (version: 3.0.2) (http://10xgenomics.com/), and then the sequenced data were mapped into manually combined reference genome with merging Ensembl sus scrofa genome (Sus_scrofa.Sscrofa11.1.dna_sm.toplevel.fa) and virus ASFV genome (MH766894_2.fa). Unique molecular identifiers (UMIs) were quantified based on manually combined annotation file of Ensembl sus scrofa GTF file (Sus_scrofa.Sscrofa11.1.94.gtf) and virus ASFV GTF file (MH766894_2.gtf).
Genome_build: Sus scrofa
Supplementary_files_format_and_content: "barcodes.tsv" files include barcode information, "features.tsv" files include gene features and "matrix.mtx" files include gene expression.

organism: Sus scrofa

source_name: Alveolar lavage fluid

extract_protocol:
Primary porcine alveolar macrophages (PAMs) were collected from 3-week-old Specific Pathogen Free (SPF) pigs, and maintained in RPMI 1640 medium (GIBCO, USA) supplemented with 10% fetal bovine serum (FBS) (GIBCO, USA), 200 mg/mL streptomycin, and 200 IU/mL penicillin at 37℃. The ASFV Pig/SY18 strain was isolated and further propagated in PAMs for amplification culture. Viral titration was performed by hemadsorption (HAD) assays and expressed as HAD 50 /ml. All experiments with live virus were conducted in biosafety level 3 (BSL-3) facilities in Harbin Veterinary Research Institute (HVRI) of the Chinese Academy of Agricultural Science (CAAS).
5×105 PAM cells per well were seeded in 12-well plate and infections were carried out at a multiplicity of infection (moi) of 1. After 1 h of incubation, the viruses were removed and the cells were washed twice by PBS, then fresh medium was added. At the indicated times (0h, 2h, 6h, 10h, 15h, 24h and 36h), cells were washed gently and trypsinized. Single cell suspensions were washed with PBS + 0.04%BSA, resuspended in 200 μL PBS + 0.04%BSA, passed through a 30 μm filter, and placed on ice. Cells were counted using trypan blue exclusion on a LUNA-II™ Automated Cell Counter (Logos Biosystems). The appropriate numbers of cells to achieve a targeted cell input of 10,000 cells per condition were used to generate the GEMs (Gel Bead-In Emulsion). The Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1(10X Genomics, Pleasanton, CA, USA) was used for GEMs generation, cDNA synthesis and library preparation following the manufacturer’s instruction.

tag: source

value: Alveolar lavage fluid

tag: group

value: Infected group

tag: time point

value: 36 hpi

tag: sequence library

value: Sample index 1


title: InfectedGroup_T10

value: 10 hpi


title: InfectedGroup_T24

value: 24 hpi


title: InfectedGroup_T15

value: 15 hpi


title: InfectedGroup_T6

value: 6 hpi


title: InfectedGroup_T2

value: 2 hpi


title: UninfectedGroup_T36

value: Uninfected group


title: polyA RNA-seq in NRVMs at pH 6.4, rep2

value: Sprague-Dawley


title: UninfectedGroup_T15


title: UninfectedGroup_T10


title: UninfectedGroup_T6


title: UninfectedGroup_T0

value: 0 hpi


title: UninfectedGroup_T2


title: genome DMS(+)_rep2

city: Nanjing

first: Xiaorong

last: Fan

address: Nanjing city Wei Tong Road 6

department: 1State Key Laboratory of Crop Genetics and Germplasm Enhancement

institute: Nanjing Agricultural University

data_processing:
Library strategy: DMS-MaPseq
Adapters were trimmed by TrimGalore, clean reads over 70bp were retained.
Reads were aligned using Tophat allowing 10% mismatches. Next, uniquely mapped reads were extracted using the Linux command grep with NH:I:1 tag.
Mismatch count and coverage in each nuclotide were called, and mismatches located within 3nt of an insertions or deletion were masked for future analysis.
Genome_build: MSU Rice Genome Annotation Project Release 7
Supplementary_files_format_and_content: text files include mismatch count and coverage in each nucleotide for each Sample.

organism: Oryza sativa

source_name: rice leaves

extract_protocol:
DMS-treated or DMS-Untreated samples were pelleted and resuspended in 1 mL Trizol, RNA was extracted by phenol-chloroform extraction and isopropanol precipitation.rRNA was subtracted with Ribo-zero rRNA removal kit for plant (illumina).
For target-specific DMS-MaPseq, 6 µg of DMS-treated sample was mixed with gene-specific RT primers. The reverse transcription was proceeded with TGIRT-III (Ingex). Then specific gene cDNA were amplified using KOD hot start DNA polymerase with gene-specific primers. For genome-wide DMS, DMS-MaPseq library was constructed using Illumina TruSeq® Stranded Total RNA Sample Prep Plant kit (Illumina) and TGIRT enzyme (InGex).

treatment_protocol: Three-week-old rice seedlings were collected and immersed in 20ml of 1X DMS reaction buffer (40mM HEPES pH7.5, 100mM KCl and 0.5mM MgCl2).  200,  400, 500µl of DMS was added to the reaction buffer to give a final concentration of 1%, 2% and 2.5% , respectively.The same volume of DEPC-treated water was added into the reaction buffer for the mock treatment. DMS treatment was performed for 15 min at 30°C with shaking at 250rpm or under vacuum (approximately 12 psi) at room temperature without shaking. To quench the reaction, 6 ml β-Mercaptoethanol was added to a final concentration of 23%, and the mixture was incubated for 5 min under vacuum.

value: leaves

value: Three-week-old

tag: targeted gene

value: total RNA


title: genome DMS(+)_rep1


title: OsPHO2_5'UTR DMS(+)

value: PHO2 RNA


title: genome DMS(-)


title: OsPHO2_5'UTR DMS(-)


title: Os18SrRNA DMS(+)Vacuum2%


title: Os18SrRNA DMS(+)Vacuum1%


title: Os18SrRNA DMS(-)


title: Os18SrRNA DMS(+)Shaking2%


title: UninfectedGroup_T24


title: DNA-h3x2a-wt-HU150-x51

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

data_processing:
Library strategy: DNA-seq
demultiplexing with bcl2fastq
paired end alignment to S288_R64 with bowtie2 (-p8 --local --very-sensitive )
readfiltering based on fragment size (keep 0-700 bp)
genome coverage with bedtools (-pc -d)
Assembly: GCA_000146045.2, for samples ending with X39, S43, S44 and S47c ombined S. cerevisiae (GCA_000146045.2) and C. glabrata () genome
Supplementary files format and content: *.out.gz.gz file contains zipped genome coverage for all 12,157,105 bases in the S. cerevisiae genome (CHr 1-16+mitochondria); or 24,495,413 bases in the combined genome (first S.cerevisae then C. glabrata)

source_name: cells

growth_protocol: yeast cells were grown to saturation overnight in YPD and then dilute in fresh,pre-warmed YPD and incubated for at least 6 hours at 30deg before G1 arrest (alpha factor). After 3 hours in alpha facor, cells were released into HU and samples for DNA-seq taken in 10-20 minute intervals

extract_protocol:
DNA was extracted as described in Yaakov et al, Nature Eco and Evo (2017)
Sequencing libraries were preapred as described in Yaakov et al, Nature Eco and Evo (2017)

tag: genotype

value: MATa his3[delta]1 leu2[delta]0 LYS2 met15[delta]0 ura3[delta]0 HTB2-GGS-TEV  HHT1-GGS-HA-Fast-MYC HHT2-GGS-HA-Fast-MYC, bar1

tag: spike in

tag: sensor

tag: library type

value: DNA

tag: time point (async, 3 hrs alpha or min in hu)

value: wt


title: DNA-h3x2a-wt-alpha-x51

value: alpha


title: DNA-h3x2a-wt-HU165-x51


title: DNA-h3x2b-wt-HU165-x51


title: DNA-h3x2b-wt-HU180-x51


title: DNA-h3x2b-wt-alpha-x51


title: genome DMS(+)_rep3

tag: tissue

tag: age


title: DNA-h3x2a-wt-HU180-x51

tag: strain


title: DNA-h3x2b-wt-HU150-x51


title: DNA-h3x2b-wt-HU130-x51


title: DNA-h3x2a-wt-HU110-x51


title: DNA-h3x2b-wt-HU140-x51


title: DNA-h3x2a-wt-HU140-x51


title: DNA-h3x2b-wt-HU120-x51


title: Os18SrRNA DMS(+)Shaking1%


title: Os18SrRNA DMS(+)Vacuum2.5%


title: DNA-h3x2a-wt-HU120-x51


title: Os18SrRNA DMS(+)Shaking2.5%


title: DNA-h3x2a-wt-HU070-x51


title: DNA-h3x2b-wt-HU070-x51


title: DNA-h3x2b-wt-HU110-x51


title: DNA-h3x2a-wt-HU100-x51


title: DNA-h3x2a-wt-HU090-x51


title: DNA-h3x2a-wt-HU080-x51


title: DNA-h3x2b-wt-HU080-x51


title: DNA-h3x2a-wt-HU015-x51


title: DNA-h3x2b-wt-HU090-x51


title: DNA-h3x2a-wt-HU030-x51


title: DNA-h3x2a-wt-HU040-x51


title: DNA-h3x2b-wt-HU050-x51


title: DNA-h3x2a-wt-HU050-x51


title: DNA-h3x2a-vps75-alpha-x51

value: MATa his3[delta]1 leu2[delta]0 LYS2 met15[delta]0 ura3[delta]0 HTB2-TEV, HHT1-HA-TEVsite-MYC, HHT2-HA-TEVsite-MYC, bar1, vps75::HYG


title: DNA-h3x2b-vps75-HU165-x51


title: DNA-h3x2b-wt-HU040-x51


title: DNA-h3x2a-vps75-HU165-x51


title: DNA-h3x2a-wt-HU130-x51


title: DNA-h3x2b-wt-HU100-x51


title: DNA-h3x2b-wt-HU030-x51


title: DNA-h3x2a-vps75-HU180-x51


title: DNA-h3x2a-vps75-HU150-x51


title: DNA-h3x2b-vps75-HU150-x51


title: DNA-h3x2a-vps75-HU130-x51


title: DNA-h3x2b-vps75-HU110-x51


title: DNA-h3x2a-vps75-HU120-x51


title: DNA-h3x2b-vps75-HU140-x51


title: DNA-h3x2a-vps75-HU110-x51


title: DNA-h3x2b-vps75-HU120-x51


title: DNA-h3x2b-vps75-HU100-x51


title: DNA-h3x2a-vps75-HU090-x51


title: DNA-h3x2b-vps75-HU090-x51


title: DNA-h3x2b-vps75-HU130-x51


title: DNA-h3x2a-vps75-HU100-x51


title: DNA-h3x2a-vps75-HU140-x51


title: DNA-h3x2a-vps75-HU080-x51


title: DNA-h3x2b-vps75-HU080-x51


title: DNA-h3x2b-vps75-HU050-x51


title: DNA-h3x2b-vps75-HU030-x51


title: DNA-h3x2b-vps75-alpha-x51


title: DNA-h3x2b-vps75-HU015-x51


title: DNA-h3x2a-vps75-HU030-x51


title: DNA-h3x2a-vps75-HU050-x51


title: DNA-h3x2b-vps75-HU040-x51


title: DNA-h3x2a-rtt109-HU180-x51

value: MATa his3[delta]1 leu2[delta]0 LYS2 met15[delta]0 ura3[delta]0 HTB2-TEV, HHT1-HA-TEVsite-MYC, HHT2-HA-TEVsite-MYC, bar1, rtt109::NAT


title: DNA-h3x2a-rtt109-alpha-x51


title: DNA-h3x2a-rtt109-HU165-x51


title: DNA-h3x2b-rtt109-HU165-x51


title: DNA-h3x2b-rtt109-HU150-x51


title: DNA-h3x2a-vps75-HU040-x51


title: DNA-h3x2a-vps75-HU015-x51


title: DNA-h3x2b-vps75-HU180-x51


title: DNA-h3x2b-vps75-HU070-x51


title: DNA-h3x2a-rtt109-HU150-x51


title: DNA-h3x2a-vps75-HU070-x51


title: DNA-h3x2b-rtt109-alpha-x51


title: DNA-h3x2b-rtt109-HU140-x51


title: DNA-h3x2a-rtt109-HU140-x51


title: DNA-h3x2a-rtt109-HU090-x51


title: DNA-h3x2b-rtt109-HU090-x51


title: DNA-h3x2b-rtt109-HU130-x51


title: DNA-h3x2b-rtt109-HU180-x51


title: DNA-h3x2a-rtt109-HU100-x51


title: DNA-h3x2b-rtt109-HU110-x51


title: DNA-h3x2a-rtt109-HU120-x51


title: DNA-h3x2a-rtt109-HU110-x51


title: DNA-h3x2a-rtt109-HU040-x51


title: DNA-h3x2b-rtt109-HU030-x51


title: DNA-h3x2a-rtt109-HU130-x51


title: DNA-h3x2a-rtt109-HU015-x51


title: DNA-h3x2b-rtt109-HU015-x51


title: DNA-h3x2a-rtt109-HU030-x51


title: DNA-h3x2a-rtt109-HU080-x51


title: DNA-h3x2b-rtt109-HU080-x51


title: DNA-h3x2b-rtt109-HU070-x51


title: DNA-h3x2a-rtt109-HU050-x51


title: DNA-h3x2b-rtt109-HU050-x51


title: DNA-h3x2a-rtt109-HU070-x51


title: RNAseq (total RNA) of strain with 208 rDNA repeats [CGY28.49]

city: South San Francisco

first: Nathaniel

middle: H

last: Thayer

state: CA

address: 1130 Veteran's Blvd

institute: Calico Life Sciences LLC

data_processing:
Reads generated from the Illumina Nova-seq and were demultiplexed with bcl2fastq based on the barcode sequence of each sample. Reads were pseudo-aligned and then quantified using Salmon by deploying the mapping based mode using a Salmon generated index.
RNA-seq data was quantified  using Salmon-0.8.1 with two separate annotation indices:  •open-reading frames (ORFs) as defined by SGD‘complex transcriptome’ index created by aggregating ORFs,   their longest annotated UTRs + all non-canonical and non-  coding transcripts pulled from SGD.   Salmon was run using the ‘quant’ command with the following   settings:‘libType’: ‘ISR’, ‘useVBOpt’: [], ‘numBootstraps’: ‘30’, and 549  ‘incompatPrior’: ‘0’. 550  Salmon quantification was prepared and processed for differential  expression analysis using Tximport . Differential gene expression  analysis was performed with DESEQ2 using a Wald test and replicative lifespan as a numeric variable.
Genome_build: sacCer3
Supplementary_files_format_and_content: tab-delimited tables with TPMs values or normalized counts for each gene in all samples (polyA_TPMs.txt and noSelect_NORM_counts.txt)
Supplementary_files_format_and_content: tab-delimited text files with TPMs values or normalized counts for each gene (one file per sample)

source_name: culture

extract_protocol:
Frozen cell pellets (10 million cells) were resuspended in 200 µL of Lysis buffer (10 mM Tris [pH 8.0], 0.5 % SDS, 10 mM EDTA). Following the addition of 200 µL Acid Phenol [pH 4.3], samples were vortexed for 30 s. Samples were incubated at 65 C for 30 min in a Thermomixer with intermittent shaking (2000 RPM for 1 min every 15 min). 400 µL of ethanol were then added and the RNA was purified using the Direct-zol RNA Miniprep Plus kit (#R2071, Zymo research) according to the manufacturer’s protocol, including the optional DNase digestion step. RNA integrity was confirmed using an Agilent Bioanalyzer.
RNA-Seq total: No-selection libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit (#PNE7760L, Illumina) without the polyA selection step. Given the concentration of RNA is much higher for total unselected RNA,10 ng of total RNA was input and the fragmentation time was increased to 20 minutes (vs. 15 min standard) to ensure efficient fragmentation of rRNA and proceeded with the vendor’s protocol.
RNA -Seq polyA: Standard polyA selected RNA-seq libraries were generated using the NEBNext 538  Ultra II Directional RNA Library Prep Kit using 250 ng of input and   vendor’s protocol with polyA selection.

value: MATa his3d1 lyp1d0 can1d::STE2pr-spHIS5

tag: polya recovery

value: not applicable


title: RNAseq (total RNA) of strain with 224 rDNA repeats [CGY28.52]


title: RNAseq (total RNA) of strain with 197 rDNA repeats [CGY28.50]


title: DNA-h3x2b-rtt109-HU100-x51


title: RNAseq (total RNA) of strain with 237 rDNA repeats [CGY20.55]


title: DNA-h3x2b-rtt109-HU040-x51


title: DNA-h3x2b-rtt109-HU120-x51


title: RNAseq (total RNA) of strain with 129 rDNA repeats [CGY24.16]


title: RNAseq (total RNA) of strain with 118 rDNA repeats [CGY20.46]


title: RNAseq (total RNA) of strain with 147 rDNA repeats [CGY20.50]


title: RNAseq (total RNA) of strain with 156 rDNA repeats [CGY24.09]


title: RNAseq (total RNA) of strain with 72 rDNA repeats [CGY24.17]


title: RNAseq (polyA RNA) of strain with 237 rDNA repeats [CGY20.55]

value: norm


title: RNAseq (polyA RNA) of strain with 197 rDNA repeats [CGY28.50]


title: RNAseq (polyA RNA) of strain with 166 rDNA repeats [CGY28.53]

value: low


title: RNAseq (polyA RNA) of strain with 224 rDNA repeats [CGY28.52]


title: RNAseq (polyA RNA) of strain with 208 rDNA repeats [CGY28.49]


title: RNAseq (polyA RNA) of strain with 129 rDNA repeats [CGY24.16]


title: RNAseq (polyA RNA) of strain with 156 rDNA repeats [CGY24.09]


title: RNAseq (polyA RNA) of strain with 147 rDNA repeats [CGY20.50]


title: RNAseq (polyA RNA) of strain with 72 rDNA repeats [CGY24.17]


title: RNAseq (polyA RNA) of strain with 104 rDNA repeats [CGY24.21]


title: RNAseq (polyA RNA) of strain with 118 rDNA repeats [CGY20.46]


title: ATACseq profile from strain with 225 rDNA repeats [CLS_rDNAcn_ATAC_strain89]

data_processing:
Reads were trimmed: `sickle pe -t sanger -x \      -f $FASTQ_F_FILE -r $FASTQ_R_FILE \      -o $TRIMMED_FASTQ_F_FILE -p $TRIMMED_FASTQ_R_FILE \      -s $SINGLE_FILE;`
Reads were aligned with bowtie2: `bowtie2 -p 4 -x /home/adamw/seq_data/ref/SacCer3.fasta \      -1 $TRIMMED_FASTQ_F_FILE -2 $TRIMMED_FASTQ_R_FILE \      | samtools view -bS -@ 4 - > $BAM_FILE;`
Bedfiles were created mapping the insertion location (beginning/end) of each read: `samtools view -bf 0x2 $BAMFILE | bamToBed -i stdin -bedpe | cut -f1,2,6,7,8,9 > "${BAMFILE}.bed";`
Reads were shifted 4 or 5 bp depending on orientation to correct for offset of ATACseq read from actual insertion site.
Total number of insertions at each genomic position were calculated and bigwig files were generated.
Normalized insertion density was calculated by normalizing to the total number of intersertions per sample.
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files were generated using custom python scripts; scores represent the count of insertions at each genomic position.
Supplementary_files_format_and_content: hdf5 file contains a table with a total count of intersertions at each genomic position for each sample

growth_protocol: Cells were grown in synthetic complete medium (SC). SC contained 1x SC mix and 1x YNB with Ammonium Sulfate (Sunrise Science), 2 % Glucose, 2 % Methyl-alpha-D-Mannopyranoside (MMP, Sigma Aldrich) at pH 4.5. Cell cultures were kept at low density (optical density < 0.05) at all times, after an initial grow up to saturation.

extract_protocol:
For each sample, 5 million cells were spun down at 1200 g for 4 min and resuspended in 250 µL media. Cells were washed twice with SB buffer (1 M Sorbitol, 40 mM HEPES [pH 7.5], 10 mM MgCl2) and then resuspended in 190 µL SB Buffer. 10 µL of 10 mg/mL Zymolyase\-100T were added and cells were incubated at 30 C for 30 min while shaking (600 RPM) in a thermomixer (Eppendorf). Spheroplasts were spun down at 1500 g for 5 min, washed twice with SB Buffer, resuspended in 50 µL Tagmentation Mix (25 µL Nextera Tagment DNA Buffer, 22.5 µL nuclease-free water, 2.5 µL Nextera Tagment DNA Enzyme I) and incubated at 37 C for 30 min. DNA was purified over DNA Clean and Concentrator-5 kit columns (#D4013, Zymo Research) following the manufacturer’s protocol, eluted in 11 µL nuclease-free water and stored at -20 C until ready for PCR.
PCR reactions were set up using Nextera Index i5 and i7 series PCR primers (Illumina). 25 µL NEBNext Hi-Fidelity 2x PCR Master Mix, 7.5 µL water, 6.25 µL i5 primer (10 µM), 6.25 µL i7 primer (10 µM) and 5 µL tagmented DNA from above were mixed, such that each sample had a unique barcoded primer pair. PCR amplification was run (72 C for 5 min and 98 C for 30 s; 8 cycles: 98 C for 10 s, 63 C for 30 s, 72 C for 1 min; hold at 4 C). PCR reactions were cleaned up over DNA Clean and Concentrator-5 columns to eliminate primers (#D4013, Zymo Research), eluted in 22 µL water, analyzed on the BioAnalyzer and size selected for fragments between 150-600 base pairs using a Pippin Prep (Sage Science).

tag: rdna copy number estimate

tag: batch


title: RNAseq (polyA RNA) of strain with 84 rDNA repeats [CGY29.01]


title: ATACseq profile from strain with 156 rDNA repeats [CLS_rDNAcn_ATAC_strain42]


title: ATACseq profile from strain with 84 rDNA repeats [CLS_rDNAcn_ATAC_strain105]


title: ATACseq profile from strain with 237 rDNA repeats [CLS_rDNAcn_ATAC_strain34]


title: RNAseq (total RNA) of strain with 84 rDNA repeats [CGY29.01]


title: ATACseq profile from strain with 147 rDNA repeats [CLS_rDNAcn_ATAC_strain29]


title: ATACseq profile from strain with 104 rDNA repeats [CLS_rDNAcn_ATAC_strain50]


title: ATACseq profile from strain with 208 rDNA repeats [CLS_rDNAcn_ATAC_strain86]


title: ATACseq profile from strain with 118 rDNA repeats [CLS_rDNAcn_ATAC_strain25]


title: ATACseq profile from strain with 72 rDNA repeats [CLS_rDNAcn_ATAC_strain49]


title: ATACseq profile from strain with 197 rDNA repeats [CLS_rDNAcn_ATAC_strain87]


title: ATACseq profile from strain with 129 rDNA repeats [CLS_rDNAcn_ATAC_strain48]


title: ATACseq profile from strain with 162 rDNA repeats [CLS_rDNAcn_ATAC_strain90]


title: At18SrRNA DMS(-)

organism: Arabidopsis thaliana

source_name: Arabidopsis leaves


title: At18SrRNA DMS(+)Vacuum1%


title: HK-2cell_48h_vildagliptin2

city: Zhengzhou

first: Yi

last: Song

address: 1 Jianshe East Road

institute: The First Affiliated Hospital of Zhengzhou University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing:
Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Expression Profiling Data:Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 3 out of 15 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.
When comparing two groups of profile differences (such as disease versus control), the “fold change” (i.e. the ratio of the group averages) between the groups for each circRNA is computed. The statistical significance of the difference may be conveniently estimated by t-test. circRNAs having fold changes 1.5 and p-values  0.05 are selected as the significantly differentially expressed.

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: HK-2 cells were cultured in DMEM medium supplemented with 10% fetalfoetal bovine serum, and 100 U/mLU/ml penicillin, and 0.1 mg/mLl streptomycin at 37°C ℃ under humidified air with 5% CO2.

extract_protocol: Lyse cells directly in a culture dish by adding 1 ml of TRIzol Reagent to a 3.5 cm diameter dish, and passing the cell lysate several times through a pipette. The amount of TRIzol Reagent added is based on the area of the culture dish (1 ml per 10 cm2) and not on the number of cells present.2. Phase Separation  Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at 12,000 × g for 15 minutes at 4°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIzol Reagent used for homogenization.  RNA Precipitation  Transfer the aqueous phase to a fresh tube. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol Reagent used for the initial homogenization. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at 12,000 × g for 10 minutes at 4°C.   RNA Wash  Remove the supernatant. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIzol Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at 7,500 × g for 5 minutes at 4°C.  Redissolving the RNA  At the end of the procedure, air-dry the RNA pellet for 5-10 minutes. Dissolve RNA in 85ul or less RNase-free water by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60°C.

treatment_protocol: HK-2 cell were cultured with normal glucose and high glucose.After synchronized by culturing in DMEM for 24 h, the cells were treated with normal glucose (5.6mM), high glucose (30.0 mM) for 24 h, then treated with Dapagliflozin (2.5 μM), Metformin (5 mM), Vidagliptin (150 μM) for 48 h in 6-well plates.

tag: cell line

value: HK-2 cell


title: HK-2cell_48h_dapagliflozin3


title: HK-2cell_72h_highglocuse2

source_name: HK-2 cell,72h, high glucose


title: HK-2cell_72h_normalglocuse2

source_name: HK-2 cell,72h, normal glucose


title: HK-2cell_48h_metformin2


title: HK-2cell_48h_vildagliptin3


title: HK-2cell_72h_highglocuse1


title: HK-2cell_48h_vildagliptin1


title: HK-2cell_48h_metformin1


title: HK-2cell_48h_metformin3


title: P3_CA200_3h

city: Vienna

first: Anela

last: Tosevska

address: Waehringer Guertel 18-20

department: Division of Rheumatology

country: Austria

institute: Medical Univrsity of Vienna

data_processing:
Quality check using FastQC
Mapping using STAR v.2.4.1a
PCR duplicates were removed using UMItools
Feature count using HTSeq-count
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Plasma

extract_protocol:
QIAGEN miRNeasy serum/plasma kit was used according to the manufacturer's instructions.
RNA-seq libraries were prepared with the Ovation SoLo RNAseq kit (NuGEN, cat# 0500-32)

treatment_protocol: Study participants received 100/200mg of either APG-157 or Placebo

tag: disease

value: Head and Neck Cancer

tag: treatment

value: APG

tag: concentration

tag: patient


title: P3_CA200_pre


title: P3_CA200_pre_B


title: P3_CA200_3h_B


title: P3_CA200_24h


title: HK-2cell_48h_dapagliflozin1


title: HK-2cell_48h_dapagliflozin2


title: HK-2cell_72h_normalglocuse1


title: HK-2cell_72h_highglocuse3


title: T113_G3_M07_E2

city: Lausanne

first: Giovanna

last: Ambrosini

address: Station 19

country: Switzerland

institute: EPFL

data_processing:
Raw sequence data quality control performed using FastQC (v0.11.8)
Whole glands were sequenced, and mouse and human reads were separated computationally. Raw reads were aligned to the human (hg38) and mouse genome (mm9) using HISAT2 (v2.1.0) 45, the exact parameters are: hisat2 -k 5 -p 4 --seed 42 .
Gene counts were generated using FeatureCounts (v1.6.2). Data preprocessing was done using the limma package from Bioconductor (v3.8).
Genome_build: hg38
Supplementary_files_format_and_content: Gene counts

source_name: PDX Intraductal xenograft

growth_protocol: Eight to 12-week-old NSG females were injected into the cleaved teat with a blunt end Hamilton syringe with 100 000 cells. Growth was followed over 45 days through live imaging with Xenogen IVIS Imaging System 200.

extract_protocol:
PDXs treated with hormone pellets were dissociated to organoids. RNA extracted using TriZOL reagent (Invitrogen) total RNA was isolated with miRNeasy Mini Kit (Qiagen). PDX samples have been split in two batches for RNA sequencing (batch1 and batch2)
Illumina HiSeq, 2x150bp configuration

treatment_protocol: One week after injection the mice were implanted with subcutaneous hormone releasing pellets containing placebo, 0.3 mg E2, 20 mg P4 or the combination of the two (E2+P4).

tag: cell type

value: Human breast cancer tumor

value: Xenografted mammary gland


title: T113_G3_M10_CTRL

value: CTRL


title: T113_G3_M08_CTRL


title: T113_G3_M06L_P4


title: P3_CA200_24h_B


title: T113_G3_M06_P4


title: T113_G3_M04L_E2


title: HK-2cell_72h_normalglocuse3


title: T113_G3_M09_P4


title: T113_G3_M06R_P4


title: Human peripheral blood mononuclear cells (PBMCs)

city: Dallas

first: Allan-Hermann

last: Pool

state: TX

address: 6000 Harry Hines Blvd

department: Department of Neuroscience, Peter O'Donnell Brain Institute, Department of Anesthesia and Pain Management

institute: University of Texas Southwestern Medical Center

data_processing:
Gene-cell matrices were generated by mapping sequencing reads to standard exonic or optimized transcriptomic references (both based on either mouse GRCm38 primary sequence assembly and Ensembl 98 genome annotation for mouse data and GRCh38 primary sequence assembly and Ensembl 98 genome annotation for human data) with Cell Ranger 6.0.0.
Optimized mouse and human transcriptomic references are available at www.thepoollab.org/resources
Assembly: GRCm38 (mm10) for mouse data and GRCh38 for human data
Supplementary files format and content: Processed data files are simple gene-cell matrices (genes as rows, cell indexes as columns).

source_name: Human PBMCs (Hemacare)

extract_protocol:
Mice were anaesthetized with isoflurane. Brains were extracted and dissected in NMDG-ACSF. Tissue was digested with papain in trehalose-HEPES-ACSFand triturated to generate single cell suspensions. Human PBMC samples were commercially acquired from Hemacare.
Sequencing libraries were constructed following 10x Genomics 3' v2 standard protocols.
3' Single-cell RNA-Seq

value: PBMCs


title: T113_G3_M04R_E2


title: T109_G2_M17_P4


title: T109_G2_M20_E2


title: T109_G2_M02_E2


title: T109_G2_M19_CTRL


title: T109_G2_M05_P4


title: T109_G2_M13_CTRL


title: T109_G2_M10_E2


title: T109_G2_M15_P4


title: T109_G2_M08_P4


title: T105_G3_M20_CTRL


title: T113_G3_M01_CTRL


title: T109_G2_M16_E2


title: T105_G3_M14_P4


title: T105_G3_M04_E2


title: T105_G3_M17_CTRL


title: T105_G3_M13_P4


title: T109_G2_M01_CTRL


title: T105_G3_M18_CTRL


title: T105_G3_M19_CTRL


title: T105_G3_M15_P4


title: T105_G3_M02_E2


title: T105_G3_M01_E2


title: T109_G2_M07_CTRL


title: T105_G3_M03_E2


title: T111_G2_M14_P4


title: T111_G2_M15_P4


title: T105_G3_M16_CTRL


title: T111_G2_M13_E2+P4


title: T111_G2_M12_E2


title: T105_G3_M12_P4


title: T111_G2_M08_CTRL


title: T111_G2_M10_E2


title: T111_G2_M09_DHT

value: DHT


title: T111_G2_M03_E2


title: T111_G2_M04_E2+P4


title: T111_G2_M07_P4


title: T111_G2_M05_CTRL


title: T111_G2_M06_DHT


title: T110_G2_M14_E2+P4


title: T110_G2_M08_CTRL


title: T110_G2_M13_P4


title: T110_G2_M05_P4


title: T111_G2_M01_CTRL


title: T110_G2_M09_E2


title: T110_G2_M02_CTRL


title: T110_G2_M03_E2


title: T110_G2_M04_E2+P4


title: T110_G2_M06_CTRL


title: T110_G2_M10_E2+P4


title: T110_G2_M07_P4


title: PL015_G3_M39_E2


title: PL015_G3_M38_P4


title: PL015_G3_M36_CTRL


title: T110_G2_M12_P4


title: PL015_G3_M37_E2+P4


title: T110_G2_M01_CTRL


title: PL015_G3_M40_CTRL


title: T111_G2_M02_DHT


title: PL015_G3_M34_E2+P4


title: PL015_G3_M29_P4


title: PL015_G3_M31_CTRL


title: PL015_G3_M27_E2+P4


title: PL015_G3_M25_E2


title: PL015_G3_M26_E2


title: M15

data_processing:
Raw sequence data quality control performed using FastQC (v0.11.8)
Whole glands were sequenced, and mouse and human reads were separated computationally 44. Raw reads were aligned to the human (hg38) and mouse genome (mm9) using HISAT2 (v2.1.0) 45, the exact parameters are: hisat2 -k 5 -p 4 --seed 42 .
Gene counts were generated using FeatureCounts (v1.6.2). Data preprocessing was done using the limma package from Bioconductor (v3.8).

source_name: MCF7 Intraductal xenograft

extract_protocol:
MCF7 xenografts treated with hormone pellets were dissociated to single cells, mouse cells were depleted with immunomagnetic beads (Miltenyi, cat#130-104-694). RNA extracted using TriZOL reagent (Invitrogen) total RNA was isolated with miRNeasy Mini Kit (Qiagen).
Illumina HiSeq, 2x150bp configuration

value: Breast cancer cell line


title: PL015_G3_M33_E2


title: M13


title: M07


title: M06


title: M11


title: M09


title: M10


title: M14


title: PL015_G3_M35_P4


title: M12


title: A673 containing KO of UQCRFS1 treated with 500 nM SP-2509_Rep 2

city: Columbus

first: Jack

last: Tokarsky

state: OH

address: 700 Children's Drive

department: Center for Childhood Cancer and Blood Diseases

institute: Nationwide Children's Hospital

description:
UQCRFS1_2509_2
UQCRFS1 differential analysis table.xlsx

data_processing:
Quality control of reads were analyzed using FASTQC and Multiqc
Reads were trimmed using Trim_galore
Reads were aligned to the human genome using STAR version 2.5.2b
Reads were analyzed for differential analysis using DESeq2
Comparison of genesets were performed using GSEA version 4.0.3
Genome_build: hg19
Supplementary_files_format_and_content: Processed data consist of differential analysis between cell lines. These are Excel documents that have raw and normalized reads to determine changes in gene expression

source_name: Ewing sarcoma cells

growth_protocol: Cells were grown in A673 media (DMEM, Sodium Pyruvate, Penicilin-streptomycin, 10% FBS) and incubated at 37 dC with 5% CO2. Cells were seeded at 1x10^6 cells 24 hr before treatment.

extract_protocol:
Total cellular mRNA was collected using Qiagen RNeasy Plus mini kit following manufacturer's protocol. Samples were DNase treated and 2 µg of sample was submitted for sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were provided fresh media containing either 0.1% DMSO or 500 nM SP-2509 (as indicated) and treated for 48 hr before collection of cells.

value: Childhood Cancer Cell Line

value: Ewing sarcoma cells

tag: genetic modification

value: Ubiquinol-Cytochrome C Reductase, Rieske Iron-Sulfur Polypeptide 1 (UQCRFS1) KO


title: M04


title: M05


title: PL015_G3_M28_P4


title: A673 containing KO of UQCRFS1 treated with 500 nM SP-2509_Rep 1

description:
UQCRFS1_2509_1
UQCRFS1 differential analysis table.xlsx


title: A673 containing KO of UQCRFS1 treated with 0.1% DMSO_Rep 1

description:
UQCRFS1_DMSO_1
UQCRFS1 differential analysis table.xlsx

value: 0.1% dimethylsulfoxide (DMSO)


title: A673 containing KO of CYC1 treated with 500 nM SP-2509_Rep 2

description:
CYC1_2509_2
CYC1 differential analysis table.xlsx

value: Cytochrome C1 (CYC1) KO


title: spinal cord normal saline 7days rep4 Sup

city: Changsha

first: Manyu

last: Xing

state: Hunan

address: 87 Xiangya Road

institute: Xiangya hospital, Central South University

description: Biological replicate 4 of 4. spinal cords of normal rats

hyb_protocol: The labeled cRNAs were combined and hybridized to Arraystar Rat CircRNA Epitranscriptomic Arrays (8x15K, Arraystar) at 65 °C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: The arrays were scanned in two-color channels by an Agilent Scanner G2505C (Agilent, the USA) after washing.

data_processing: The raw RNA intensities of IP (Cy5-labelled) and Sup (Cy3-labelled) were analyzed by Agilent Feature Extraction software (version 11.0.1.1) and normalized with average of log2-scaled spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 4 out of 8 samples were retained for further “m6A methylation level”  analyses. “m6A methylation level” was calculated for the percentage of modification based on the IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities. Differentially m6A-methylated circRNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds.

source_name: spinal cord

label_protocol: The total RNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. The “IP” and “Sup” RNAs were treated with RNase R, and then labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar Super RNA Labeling Kit.

growth_protocol: The animals were housed in a specific pathogen-free and individually ventilated cages at a room with 12/12 light-dark cycle and temperature of 22 ± 1 °C.

extract_protocol: The total RNA of rat lumber spinal cords (L4 - L6) was extract following the standard protocol of TRI Reagent.

treatment_protocol: The adult male SD rats were randomly divided into normal saline group (NS group) and morphine tolerance group (MT group). Rats in the MT group were administrated morphine hydrochloride injection 10 μg/10 μl intrathecally through the tube inserted into the sheath at 8:00 a.m. and 20:00 p.m. for 7 consecutive days, the NS group was given 10 μl of normal saline at the same time point.

value: spinal cord

tag: group

value: saline

tag: antibody

value: input


title: A673 containing KO of CYC1 treated with 0.1% DMSO_Rep 2

description:
CYC1_DMSO_2
CYC1 differential analysis table.xlsx


title: A673 containing KO of CYC1 treated with 0.1% DMSO_Rep 1

description:
CYC1_DMSO_1
CYC1 differential analysis table.xlsx


title: A673 containing KO of CYC1 treated with 500 nM SP-2509_Rep 1

description:
CYC1_2509_1
CYC1 differential analysis table.xlsx


title: A673 containing KO of MRPL45 treated with 500 nM SP-2509_Rep 2

description:
MRPL45_2509_2
MRPL45 differential analysis table.xlsx

value: Mitochondrial Ribosome Protein L45 (MRPL45) KO


title: spinal cord morphine 7days rep3 Sup

description: Biological replicate 3 of 4. spinal cords of morphine tolerance rats

value: morphine tolerant


title: spinal cord morphine 7days rep2 Sup

description: Biological replicate 2 of 4. spinal cords of morphine tolerance rats


title: spinal cord morphine 7days rep1 Sup

description: Biological replicate 1 of 4. spinal cords of morphine tolerance rats


title: spinal cord morphine 7days rep4 Sup

description: Biological replicate 4 of 4. spinal cords of morphine tolerance rats


title: spinal cord normal saline 7days rep4 IP

value: anti-N6-methyadenosine (m6A)


title: spinal cord normal saline 7days rep3 Sup

description: Biological replicate 3 of 4. spinal cords of normal rats


title: spinal cord normal saline 7days rep2 Sup

description: Biological replicate 2 of 4. spinal cords of normal rats


title: spinal cord normal saline 7days rep1 Sup

description: Biological replicate 1 of 4. spinal cords of normal rats


title: A673 containing KO of MRPL45 treated with 0.1% DMSO_Rep 2

description:
MRPL45_DMSO_2
MRPL45 differential analysis table.xlsx


title: A673 containing KO of MRPL45 treated with 500 nM SP-2509_Rep 1

description:
MRPL45_2509_1
MRPL45 differential analysis table.xlsx


title: spinal cord normal saline 7days rep3 IP


title: A673 containing KO of UQCRFS1 treated with 0.1% DMSO_Rep 2

description:
UQCRFS1_DMSO_2
UQCRFS1 differential analysis table.xlsx


title: LowCariesRisk-4

city: San Francisco

first: Dawud

last: abduweli uyghurturk

state: California

address: 513 Parnassus Ave.

institute: UCSF

data_processing:
qiime2: DADA2, denoising, qiime2 version: 2021.4
qiime2: feature-table plugin, feature table generation
qiime2: phylogeny plugin, rooted-tree generation
R and phyloseq library, phyloseq object creation, R version: R version 4.1.2, Package Phyloseq versin: 1.38.0
Assembly: HOMD_16S_rRNA_RefSeq_V15.22
Supplementary files format and content: feature count in txt file

organism: human oral metagenome

source_name: Dental plaque and saliva

extract_protocol:
The samples were first lysed using bead-beating, and DNA was extracted in a class 1000 clean room by a guanidine thiocyanate silica column-based purification method using a liquid-handling robot. PCR amplification of the 16S rRNA genes was performed with primers containing universal primers amplifying the V4 variable region (515F: GTGCCAGCMGCCGCGGTAA and 806R: GGACTACHVGGGTWTCTAAT). The primers contained Illumina tags and barcodes. Samples were barcoded with a unique combination of forward and reverse indexes allowing for simultaneous processing of multiple samples. PCR products were pooled, column-purified, and size-selected through microfluidic DNA fractionation.
Consolidated libraries were quantified by quantitative real-time PCR using the Kapa Bio-Rad iCycler qPCR kit on a BioRad MyiQ
16S rRNA gene sequencing

value: Dental plaque and saliva

tag: sampleID

tag: subject

tag: caries risk

value: LowCariesRisk

tag: visit


title: HighCariesRisk-3

tag: tissue

value: HighCariesRisk


title: HighCariesRisk-4


title: A673 containing KO of MRPL45 treated with 0.1% DMSO_Rep 1

description:
MRPL45_DMSO_1
MRPL45 differential analysis table.xlsx


title: spinal cord normal saline 7days rep2 IP


title: LowCariesRisk-3


title: spinal cord morphine 7days rep3 IP


title: spinal cord normal saline 7days rep1 IP


title: spinal cord morphine 7days rep1 IP


title: spinal cord morphine 7days rep2 IP


title: HighCariesRisk-2


title: Ewing sarcoma cells - A673 treated with 0.1% DMSO_Rep 2

description:
A673_DMSO_2
A673 differential analysis table.xlsx

value: WT


title: HighCariesRisk-1


title: Ewing sarcoma cells - A673 treated with 500 nM SP-2509_Rep 1

description:
A673_2509_1
A673 differential analysis table.xlsx


title: spinal cord morphine 7days rep4 IP


title: Ewing sarcoma cells - A673 treated with 0.1% DMSO_Rep 1

description:
A673_DMSO_1
A673 differential analysis table.xlsx


title: P191217_Blood_1

first: Jiesheng

last: Li

state: 北京

address: Peking University

institute: Peking University

data_processing:
Single-cell RNA-seq was performed through the GemCode Single Cell Platform using the GemCode Gel Bead, Chip, and Library Kits (10x Genomics, Pleasanton) as per the manufacturer’s protocol.
Purified libraries were analyzed by an Illumina Hiseq 4000 sequencer with 150-bp paired-end reads.
The Cell Ranger toolkit (version 3.1.0) provided by 10x Genomics was applied to align reads and generate the gene-cell unique molecular identifier (UMI) matrix against the reference genome GRCh38 downloaded from 10x Genomics official website
Using Scanpy (v1.4.3), raw counts were normalized and were transformed into logarithmic scales.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include log-counts-per-ten-thousand values for each Sample

source_name: The Fifth Medical Center of Chinese PLA General Hospital

extract_protocol:
Single cells were extracted using standard 10X genomics protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Blood

tag: Stage

value: AR

tag: donor


title: P191127_Liver_1

value: Liver

value: AC


title: P191217_Liver_1


title: LowCariesRisk-2


title: in_Nutlin_pep_R2

city: Boulder

first: Taylor

middle: K

last: Jones

state: CO

address: 3415 Colorado Ave

institute: University of Colorado Boulder

data_processing:
The ChIP-seq data were mapped to hg38 and processed using Nextflow pipeline v1.0 (https://github.com/Dowell-Lab/ChIP-Flow).
Genome_build: hg38
Supplementary_files_format_and_content: Bed file with gene, raw and corrected count information.

source_name: Input DNA from HCT116 cells

growth_protocol: HCT116 cells were grown in McCoy's media (Gibco, 16600082) with Gibco 100x Antibiotic-Antimycotic (Fisher Sci, 15240062) penicillin-streptomycin and 10% fetal bovine serum (FBS) supplementation.

extract_protocol:
The cells were fixed with 1% formaldehyde for 10 min and quenched with 125mM glycine for 5 min before nuclei isolation in NRO buffer. Shearing was performed based on the Covaris truChIP Chromatin Shearing Kit and sheared in 1 mL of Covaris D3 buffer for 8 min, with a duty factor 5% and peak power of 75,200 cycles/burst with a Covaris M220 Focused-ultrasonicator. Protein G Dynabeads (6 µg antibody 25 µL beads per condition.) were loaded with the crosslinked chromatin and allowed to incubate with shaking at 4°C overnight (~18hr). The beads were then washed at 4°C with 2x IP Buffer, 2x RIPA Buffer, 2x LiCl Wash Buffer and 2x TE Salt Buffer. Samples were kept on ice throughout the wash steps, and all washes were completed in less than 30 minutes; each wash step was 1 min to reduce sample loss.  After washes, the sample was eluted from beads with PK buffer containing 100 µg of Proteinase K and incubated at 65oC for 2 hr with periodic vortexing. The eluted sample was removed from the magnetic beads and reverse-crosslinked for 16 hr at 65°C. DNA was purified by phenol chloroform extraction using Light-5PRIME Phase Lock Tubes based on the manufacturer’s instructions. To increase yield, samples were ethanol precipitated from glycogen (20µg/sample), sodium acetate (pH 5.2) and 10mM MgCl2 and kept at -20ºC overnight.
Libraries with approximately 1 ng of input DNA were prepared using the KAPA Hyper Prep Kit and sequenced on Illumina NextSeq V2 high output 75-cycle. Adapters were diluted 1:10 before use and amplified for 12-14 cycles before sequencing.
KAPA Hyper Prep Kit (KAPA Biosystems: KK8502)

treatment_protocol: Cells were then trypsinized, washed with PBS and resuspended in 250 µL Neon Buffer R at 2.2 million cells/100µL.  The cells were then drawn into a 100 µL Neon pipet tip and electroporated with or without the peptide at 10 µM. The electroporated cells were then split into 5 mL of McCoy’s 5A media without antibiotic either with 0.1% DMSO or 10 µM Nutlin3a.  For wells containing cells electroporated with peptide, an additional 200 nM peptide was added to allow for further peptide uptake.  The cells were then placed back at 37 °C for 3 hours.

value: Wild-type HCT116

value: colorectal carcinoma

value: 10uM Nutlin3a + 10uM bivalent peptide


title: P191210_Blood_1


title: P191210_Liver_1


title: KSHV

city: Little Rock

first: Yong-Chen

middle: William

last: Lu

address: 4301 W Markham St

department: Pathology

institute: University of Arkansas for Medical Sciences

data_processing:
QIIME2-2021.4
Genome_build: SILVA_132 reference database
Supplementary_files_format_and_content: tables in csv

organism: human saliva metagenome

source_name: saliva

extract_protocol:
Saliva DNA was obtained from HIV+/- patients
V4 region of the 16S rRNA was amplified at the Argonne National Laboratory

tag: target

value: 16S rRNA V4


title: P191126_Liver_1


title: LowCariesRisk-1


title: in_Nutlin_R2

tag: cell line

value: 10uM Nutlin3a + water


title: in_Nutlin_pep_R1


title: in_DMSO_pep_R2

value: 0.1% DMSO + 10uM bivalent peptide


title: P191127_Blood_1


title: in_DMSO_pep_R1


title: P191126_Blood_1


title: in_DMSO_R2

value: 0.1% DMSO + water


title: Ewing sarcoma cells - A673 treated with 500 nM SP-2509_Rep 2

description:
A673_2509_2
A673 differential analysis table.xlsx

value: Childhood Cancer Cell Line

value: Ewing sarcoma cells


title: P191008_Liver_1


title: in_DMSO_R1


title: Nutlin_pep_R2

source_name: Pol II Ser5 (3E8) ChIP-seq from HCT116 cells

tag: chip antibody

value: Pol II Ser5 (3E8)


title: P191008_Blood_1


title: P191112_Liver_1

value: IA


title: in_Nutlin_R1

tag: treatment


title: P191112_Blood_1


title: DMSO_pep_R2


title: P191028_Liver_1


title: DMSO_R2


title: DMSO_R1


title: Nutlin_R1


title: P190911_Blood_1


title: P190801_Liver_1


title: P190911_Liver_1


title: DDX3X-displaced tracer tRNA replicate 2

first: Schaefer

last: Matthias

state: AT

address: Schwarzspanierstrasse 17-I

department: Cell and Developmental Biology

institute: Medical University Vienna, Center for Anatomy & Cell Biology

data_processing:
basecalling was performed by VBCF sequencing facility
Reads (if libraries were pair-end sequenced, only R1 mate was further processed) were trimmed for adapter sequences and low quality bases with q score less than 10 were removed from the 3' end using the cutadapt software. Command line: cutadapt -q 10 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC input.fastq > output_trimmed.fastq
Reads were further mapped to the collapsed tRNA annotation originating from https://github.com/FlorianPichot/tRNA_reference_construction . Command line:  bowtie2 --no-unal --no-1mm-upfront -D 15 -R 2 -N 0  -L 10 -i S,1,1.15 -x index -U sample.fastq -S output.sam 2> sample_mapping_report.txt
Sam files were converted to bam file, sorted and indexed using samtools (samtools view -S -b; samtools sort; samtools index)
Number of reads mapping to individual tRNA cluster was extracted by samtools idxstats. Command line samtools idxstats sample_sorted.bam > sample_idxstats.txt
Genome_build: custom collapsed human tRNA space (PMID: 33435213). FASTA available on series record and at https://github.com/FlorianPichot/tRNA_reference_construction/blob/main/Available_references/Homo_sapiens/
Supplementary_files_format_and_content: tsv files containing number of reads mapping to individual tRNA clusters

growth_protocol: HEK293 cells cultured in a humidified incubator at 37°C, 5% CO2 in standard DMEM supplemented with antibiotic/antimycotics, 2 mM L-glutamine and 10% fetal bovine serum.

extract_protocol:
Cells were collected from culture dish and solubilized in Trizol. Total RNA was extracted, and separated using UREA-PAGE. tRNAs were excised, eluted from crushed gel pieces and precipitated by isopropanol. Refolded tRNAs were further treated with recombinant angiogenin endonuclease, radiolabeled using P32-gamma-ATP and used to monitor DDX3X helicase unwinding activity
Libraries were prepared according to NEBNext small RNA cloning protocol (E7580S)

tag: enzymatic treatment

value: Cleaved with recombinant Angiogenin and subjected to DDX3X unwinding assay

tag: biochemical separation

value: Separated by native PAGE prior to library cloning

tag: molecule subtype

value: tRNA


title: P190808_Liver_1

value: IT


title: P190910_Liver_1

value: Liver


title: kidney pdx1 heterozygous ko rep7

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
TPM abundance estimates, generated with kallisto quant 0.4.6
Genome_build: GRCz11
Supplementary_files_format_and_content: TPM abundance estimates and raw counts generated with kallisto.

organism: Danio rerio

source_name: total kidney

extract_protocol:
Kidneys were removed and stored at -20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

tag: genotype

value: kidney


title: P190910_Blood_1

value: Blood


title: P190902_Blood_1


title: P190808_Blood_2


title: P190902_Liver_1


title: kidney pdx1 heterozygous ko rep8


title: kidney pdx1 heterozygous ko rep6


title: kidney pdx1 heterozygous ko rep5


title: kidney pdx1 heterozygous ko rep9


title: P190808_Blood_1


title: kidney pdx1 heterozygous ko rep4


title: Nutlin_R2

value: Wild-type HCT116

tag: cell type

value: colorectal carcinoma


title: kidney pdx1 heterozygous ko rep3


title: D529409_Liver_1

value: NL


title: kidney pdx1 heterozygous ko rep2


title: kidney pdx1 heterozygous ko rep1


title: P191028_Blood_1


title: D529354_Liver_1


title: D529351_Liver_1


title: Heat denatured tracer tRNA replicate 2

value: Cleaved with recombinant Angiogenin and heat denatured


title: kidney wildtype rep2

value: WT


title: D528848_Liver_1


title: DHA+TGFβ-3

city: guangzhou

first: Shenglan

last: Yang

state: guangdong

address: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 South Xianlie Road, Guangzhou , People’s Republic of China

institute: zhongshan ophthalmic center

data_processing:
The cDNA libraries were sequenced on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated.
Raw reads in fastq format were first processed using Trimmomatic to remove low quality reads
The clean reads were mapped to the human genome (GRCh38; https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/) using HISAT2
FPKM values of each gene were calculated using Cufflinks and corresponding read counts were obtained by HTSeq-count.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table include FPKM values for each sample

source_name: orbital fibroblasts

extract_protocol:
Total RNA was extracted using a mirVana miRNA Isolation Kit (Ambion) according to the manufacturer’s protocol
RNA-Seq libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: orbital connective tissue

value: orbital fibroblasts

value: treated with DHA(20uM) and TGF-beta1(10ng/mL)


title: Dhc570_Liver_1

city: Beijing


title: D529409_Blood_1


title: DHA+TGFβ-2


title: TGFβ-2

value: treated with TGF-beta1(10ng/mL) for 48h


title: D529354_Blood_1


title: D528848_Blood_1


title: D529074_Blood_1


title: DHA+TGFβ-1


title: TGFβ-3


title: P190719_Liver_1

value: IA


title: P190719_Blood_1


title: TGFβ-1


title: control2

value: untreated


title: P190716_Liver_1

value: AR


title: control1


title: D529074_Liver_1


title: kidney wildtype rep3


title: kidney wildtype rep1


title: P190402_Liver_1


title: P190326_Liver_1


title: Liver_iD3

city: San Antonio

first: Masahiro

last: Morita

state: Texas

address: 4939 Charles Katz Drive

department: Department of Molecular Medicine

institute: University of Texas Health Science Center at San Antonio

data_processing:
NextSeq 500 (75bp single read).
The data was analyzed by RaNA-seq.

source_name: Liver

growth_protocol: Mice were maintained on a 12-hr light-dark cycle with access to food and water ad libitum.

extract_protocol:
Total RNAs were isolated from livers of mice using TRIzol reagent and purified with a RNeasy Kit according to the manufacturer’s instruction.
mRNA-seq libraries were prepared with TruSeq stranded mRNA-seq kit.

treatment_protocol: Mice were intraperitoneally administrated with a drug.

tag: strain

tag: gender

value: Male

value: Treated with iD1


title: Liver_iD2

value: Liver


title: Liver_iD1


title: P190326_Blood_1

value: IT


title: D529351_Blood_1

value: Blood


title: Liver_Veh3

value: Untreated


title: Liver_Veh2


title: control3


title: Liver_Veh1


title: Liver tissue of wild-type mouse 3

city: Tsu city

first: Naoto

last: Fujiwara

state: Mie

address: 2-174 Edobashi

country: Japan

institute: Mie University

data_processing:
Raw sequencing reads were aligned to mouse reference genome (mm10) by STAR 2-pass algorithm, and gene expression levels were calculated as count per million (CPM) normalized by relative log expression (RLE) method
Genome_build: mm10
Supplementary_files_format_and_content: gct files include normalized expression values for each sample

source_name: liver

extract_protocol:
RNA was extracted from liver tissue using ISOGEN with Spin Column (Nippon Gene).
Illumina TruSeq Library Prep Kit v2 was used with 500ng of total RNA for the construction of sequencing libraries. RNA-Seq libraries were prepared for sequencing using standard Illumina protocols.

tag: genetic modification


title: Liver tissue of wild-type mouse 2


title: Liver tissue of wild-type mouse 1


title: P190604_Blood_1


title: P190604_Blood_2


title: Mouse Median Preoptic Nucleus (MnPO)

source_name: Dissociated single cell suspension from mouse MnPO

value: Median preoptic nucleus (MnPO)


title: Liver tissue of mouse with liver-specific  knockout of Scap 3

value: Scap knockdown


title: Liver tissue of mouse with liver-specific  knockout of Scap 2


title: P190716_Blood_2


title: WT Raw264.7-0h-input

city: Weifang

first: Panpan

address: No.7166 Baotong West Street

institute: Shandong Second Medical University

description:
wild-type Raw264.7 macrophages
total RNA removing rRNAs

data_processing:
Raw data were harvested from Illumina HiSeq4000 sequencer, and were quality controlled by Q30
adaptor-trimming and low quality reads removing by cutadapt (v1.9.1) software
clean reads were aligned to reference genome (mm10) using bowtie2 (v2.2.4) software with end-to-end mode
2'-O-methylation sites were annotated with gene information by bedtools software(v2.24) .
Genome_build: mm10
Supplementary_files_format_and_content: excel format
Supplementary_files_format_and_content: the count，coverage, ratio and fc of the methylated sites

source_name: mononuclear macrophages

extract_protocol:
Total RNA was harvested using Trizol reagent. Then total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (NEB) following the manufacturer's instructions.
RNA libraries were constructed by using a protocol from Dai Q et al., Nat Methods, 2017. with slight modification.
Nm-Seq

value: leukemia cells in mouse macrophage

value: wild type


title: Fbl+/- Raw264.7-0h-input

description:
Fbl+/- Raw264.7 macrophages
total RNA removing rRNAs

value: Heterozygous genotype


title: WT Raw264.7-0h-enriched


title: Fbl+/- Raw264.7-0h-enriched


title: Fbl+/- Raw264.7 rep3

description: total RNA removing rRNAs

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the mouse reference genome (UCSC mm10) with hisat2 software (v2.0.4).
Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified.
Genome_build: mm10
Supplementary_files_format_and_content: excel format
Supplementary_files_format_and_content: FPKM

extract_protocol:
Total RNA was harvested using Trizol reagent. Then total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (NEB) following the manufacturer's instructions.
RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB) according to the manufacturer's instructions.

value: leukemia cellsin mouse macrophage

value: Fbl+/-


title: Liver tissue of mouse with liver-specific  knockout of Scap 1


title: Liver tissue of mouse with liver-specific  knockout of Pten 2

value: Pten knockdown


title: Liver tissue of mouse with liver-specific  knockout of Pten 3


title: P190716_Blood_1


title: Liver tissue of mouse with liver-specific  knockout of Pten 1


title: WT Raw264.7 rep3

description: total RNA removing rRNAs


title: P190604_Liver_1


title: Liver tissue of mouse with liver-specific double knockout of Pten and Scap 3

value: Pten-Scap double knockdown


title: Liver tissue of mouse with liver-specific double knockout of Pten and Scap 2


title: ADSC, Donor 67, FBS culture condition

city: Seoul

first: Min Hee

last: Kang

state: Gangnam-gu

address: Dong won Building, 333

country: South Korea

institute: Xcell Therapeutics

description: RNA seq sample

data_processing:
Sequenced on an Ion Torrent S5xl machine (Thermo Fisher). Normalized method using ampliSeq RNA Plug in (ver 5.6.0.3) by Torrent Suite Software (Thermo Fisher).
Data mining and graphic visualization were performed using ExDEGA (Ebiogen Inc., Korea)
Assembly: hg19_ampliseq_transcriptome_ercc_v1
Supplementary files format and content: tab-delimited text files include expression values for each Sample

source_name: adipose derived

growth_protocol: Human adipose tissue was obtained from plastic surgeries from Dr. Jung (Dacapo Dental Hospital, Seoul, Korea). ADSCs were isolated by mechanical and enzymatical treatment of the tissue as described previously [24]. In brief, adipose tissue was minced manually into small fragments and digested with 0.075% collagenase type I (Gibco, Thermo Fisher Scientific, MA, USA) in a water bath at 37C. The digested tissue was centrifuged and filtered in sequential steps to separate the ADSCs from the surrounding tissue. The isolated ADSCs were expanded in low glucose DMEM supplemented with 10% FBS and 1% penicillin/streptomycin (P/S; HyClone, Cytiva, Marlborough, MA, USA), or in serum free establishment media (CellCor establishment media, Xcell Therapeutics, Seoul, Korea). After reaching 85% confluency, cells were digested with Accutase (Gibco) and seeded (3 x 105 cells) in a T75 culture flask (Corning, Oneonta, NY, USA).

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen). RNA quality was assessed using Agilent 2100 bioanalyzer with the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, Netherlands). RNA was quantified using ND-2000 spectrophotometer (Thermo Fisher Scientific).
AmpliSeq libraries were constructed and sequenced on the Ion Torrent S5xl platform (Thermo Fisher) according to the manufacturer’s instructions.
For human gene analysis in cell lines, the Ion AmpliSeq Transcriptome Human Gene Expression Kit is designed for targeted amplification of over 20,000 human RefSeq genes simultaneously in a single primer pool.
A short amplicon (~ 110 base pairs (bp)) is amplified for targeted gene. For each sample, 30 ng of total RNA was used for cDNA library preparation.
Multiple libraries were multiplexed and clonally amplified using the Ion Chef System (Thermo Fisher).

treatment_protocol: Not applicable

value: adipose derived

value: MSC

value: ADSC

value: WT


title: MT RNAseq rep 1 [G5_1E_RNA_seq]

city: Blacksburg

first: Zachary

last: Johnson

state: VA

address: 1015 Life Science Cir

department: FLSI

institute: Virginia Tech

data_processing:
Fastp v0.20 was used to remove adapter sequences, identify and remove low-quality reads and called bases
meRanGh v1.2.1 was used to map reads to C2T and G2A converted reference genomes
umi-Tools was used to identify and remove PCR duplicates
meRanCall was used to call m5C sites from mapped read files
In-house scripts using Python 3.9 and R 4.1.1 were used to further filter and process methylation calling files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited transcript abundance counts for all mitochondrial samples and all RNAseq samples
Supplementary_files_format_and_content: tab-delimited files containing methylation calling information for each called methylated site

source_name: Neural stem cells

extract_protocol:
Mitochondria were isolated from NSCs cultured in medium containing 10 μmol/L folic acid using the mitochondrial isolation kit for culture cells (Abcam, ab110171) following the manufacturer's instructions. The isolated mitochondria were used for RNA extraction with DNase digestion. One round of poly(A) selection was performed to enrich mitochondrial mRNA molecules
RNA bisulfite conversion was performed as described previously with minor modifications. Briefly, poly(A) RNA was first mixed with spiked-in Xef1 unmethylated RNA at a ratio of 0.5%. The spiked-in unmethylated mRNA was transcribed from the pTRI-Xef plasmid supplied by the MEGAscript™ T7 Transcription Kit (Invitorgen), which encodes 1.85 kb Xenopus elongation factor 1α mRNA according to the manufacturer’s manual. Briefly, the linearized pTRI-Xef plasmid was in vitro transcribed in a reaction with MEGAscript T7 RNA polymerase (Ambion) at 37 °C for 4 h, followed by DNase treatment at 37 °C for 15min to remove DNA template and then purified by RNeasy Mini Kit (QIAGEN).  RNA bisulfite conversion was performed with an initial denaturation at 95°C for 1min, followed by three cycles of 70°C for 10min and 64°C for 45min using the EZ RNA methylation Kit (Zymo Research). The bisulfite converted RNA was subjected to stranded RNA-seq library construction procedure using the TruSeq Stranded mRNA Library Preparation Kit (Illumina).

value: Neural stem cells

tag: fraction

value: Mitochondrial fraction

tag: conversion status

value: RNAseq


title: ADSC, Donor 67, SFD culture condition

description: RNA seq sample

tag: tissue


title: MT-D rep 2 [G4_2D]

data_processing:
library strategy: RNA bisulfite sequencing
Fastp v0.20 was used to remove adapter sequences, identify and remove low-quality reads and called bases
meRanGh v1.2.1 was used to map reads to C2T and G2A converted reference genomes
umi-Tools was used to identify and remove PCR duplicates
meRanCall was used to call m5C sites from mapped read files
In-house scripts using Python 3.9 and R 4.1.1 were used to further filter and process methylation calling files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited transcript abundance counts for all mitochondrial samples and all RNAseq samples
Supplementary_files_format_and_content: tab-delimited files containing methylation calling information for each called methylated site

value: RNA BS-seq

tag: preparation condition

value: Preparation condition D:RNA fragmentation was performed first, then bisulfite conversion was performed using three cycles of 95°C for 1min, 70°C for 10min and 64°C for 45min, ACT random hexamer primers were used for 1st strand cDNA synthesis.


title: ADSC, Donor 66, SFD culture condition

description: RNA seq sample


title: ADSC, Donor 61, FBS culture condition

description: RNA seq sample


title: ADSC, Donor 61, SFD culture condition

description: RNA seq sample


title: Liver tissue of mouse with liver-specific double knockout of Pten and Scap 1


title: MT-D rep 1 [G4_1D]


title: ADSC, Donor 55, FBS culture condition

description: RNA seq sample